diff --git a/README.md b/README.md
index ea792b546e71aba9c5844a03a031fa6fa94ad3be..2e112b1059fa8c2e6a5e24fe1423dbd05cfcb694 100644
--- a/README.md
+++ b/README.md
@@ -1,8 +1,9 @@
-#prevod html do md
+# Převod html dokumentace do md formátu
-* adresarova struktura je ulozena ve slozce info, soubor strukture
-* skript html_md.sh je ulozen v korenovem adresari a odtud je ho treba spoustet
-* v korenovem adresari se nachazi i filtracni soubor s prvky, ktere se maji odstranovat (filter.txt)
+html_md.sh ... převede html do md, vytvořà složku info, kde se evidujà odkazy na soubory ve složkách
+html_md.sh -d -html ... odstranà všechny html soubory
---v1.0--
+html_md.sh -d -md ... odstranà všechny md souborz
+
+filter.txt ... filtrovanĂ˝ text
diff --git a/anselm-cluster-documentation.md b/anselm-cluster-documentation.md
deleted file mode 100644
index 9e880b0403d675ec3c21ce38b53b7da42bcaa74b..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation.md
+++ /dev/null
@@ -1,43 +0,0 @@
-over 94 Tflop/s theoretical peak performance. Each node is a
-class="WYSIWYG_LINK">powerful x86-64 computer, equipped with 16
-cores, at least 64GB RAM, and 500GB harddrive. Nodes are interconnected
-by fully non-blocking fat-tree Infiniband network and equipped with
-Intel Sandy Bridge processors. A few nodes are also equipped with NVIDIA
-Kepler GPU or Intel Xeon Phi MIC accelerators. Read more in [Hardware
-Overview](anselm-cluster-documentation/hardware-overview.html).
-The cluster runs bullx Linux [
-class="WYSIWYG_LINK">](http//www.bull.com/bullx-logiciels/systeme-exploitation.html)[operating
-system](anselm-cluster-documentation/software/operating-system.html),
-which is compatible with the RedHat
-[Linux
-family.](http//upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
-We have installed a wide range of
-[software](anselm-cluster-documentation/software.html)
-packages targeted at different scientific domains. These packages are
-accessible via the [modules
-environment](anselm-cluster-documentation/environment-and-modules.html).
-User data shared file-system (HOME, 320TB) and job data shared
-file-system (SCRATCH, 146TB) are available to users.
-The PBS Professional workload manager provides [computing resources
-allocations and job
-execution](anselm-cluster-documentation/resource-allocation-and-job-execution.html).
-Read more on how to [apply for
-resources](get-started-with-it4innovations/applying-for-resources.html),
-[obtain login
-credentials,](get-started-with-it4innovations/obtaining-login-credentials.html)
-and [access the
-cluster](anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access.html).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](sitemap.html)
- - [What's New](whats-new.html)
-
- - [Get Started with
- IT4Innovations](get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](salomon.html)
diff --git a/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md b/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
deleted file mode 100644
index c25dee233f6faf0f9c95958bcf95a1be747d4fef..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
+++ /dev/null
@@ -1,108 +0,0 @@
-
-
-Accessing IT4Innovations internal resources via VPN
----------------------------------------------------
-**Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS
-patch**
-Workaround can be found at
-[https//docs.it4i.cz/vpn-connection-fail-in-win-8.1](../../vpn-connection-fail-in-win-8.html)
-Â
-For using resources and licenses which are located at IT4Innovations
-local network, it is necessary to VPN connect to this network.
-We use Cisco AnyConnect Secure Mobility Client, which is supported on
-the following operating systems
-- Windows XP
-- Windows Vista
-- Windows 7
-- Windows 8
-- Linux
-- MacOS
-It is impossible to connect to VPN from other operating systems.
-VPN client installation
-------------------------------------
-You can install VPN client from web interface after successful login
-with LDAP credentials on address
-
-According to the Java settings after login, the client either
-automatically installs, or downloads installation file for your
-operating system. It is necessary to allow start of installation tool
-for automatic installation.
-
-
-After successful installation, VPN connection will be established and
-you can use available resources from IT4I network.
-
-If your Java setting doesn't allow automatic installation, you can
-download installation file and install VPN client manually.
-
-After you click on the link, download of installation file will start.
-
-After successful download of installation file, you have to execute this
-tool with administrator's rights and install VPN client manually.
-Working with VPN client
------------------------
-You can use graphical user interface or command line interface to run
-VPN client on all supported operating systems. We suggest using GUI.
-
-Before the first login to VPN, you have to fill
-URLÂ **https//vpn1.it4i.cz/anselm** into the text field.
-
-After you click on the Connect button, you must fill your login
-credentials.
-
-After a successful login, the client will minimize to the system tray.
-If everything works, you can see a lock in the Cisco tray icon.
-
-If you right-click on this icon, you will see a context menu in which
-you can control the VPN connection.
-
-When you connect to the VPN for the first time, the client downloads the
-profile and creates a new item "ANSELM" in the connection list. For
-subsequent connections, it is not necessary to re-enter the URL address,
-but just select the corresponding item.
-
-Then AnyConnect automatically proceeds like in the case of first logon.
-
-After a successful logon, you can see a green circle with a tick mark on
-the lock icon.
-
-For disconnecting, right-click on the AnyConnect client icon in the
-system tray and select **VPN Disconnect**.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](shell-and-data-access.html)
-
- - [Shell access and data
- transfer](shell-and-data-access.html)
diff --git a/anselm-cluster-documentation/anyconnectcontextmenu.jpg/@@images/9655f6a6-cd7b-4462-90d6-480d43c8cc0c.jpg b/anselm-cluster-documentation/anyconnectcontextmenu.jpg/@@images/9655f6a6-cd7b-4462-90d6-480d43c8cc0c.jpg
deleted file mode 100755
index e39c3652e616b8c1102af90746c5a1be382f3a73..0000000000000000000000000000000000000000
Binary files a/anselm-cluster-documentation/anyconnectcontextmenu.jpg/@@images/9655f6a6-cd7b-4462-90d6-480d43c8cc0c.jpg and /dev/null differ
diff --git a/anselm-cluster-documentation/anyconnecticon.jpg/@@images/ebdd0e41-e839-497e-ab33-45162d00b03b.jpg b/anselm-cluster-documentation/anyconnecticon.jpg/@@images/ebdd0e41-e839-497e-ab33-45162d00b03b.jpg
deleted file mode 100755
index 6d70fc5441cef9e2fe1f47c34bfa1a69e4275b44..0000000000000000000000000000000000000000
Binary files a/anselm-cluster-documentation/anyconnecticon.jpg/@@images/ebdd0e41-e839-497e-ab33-45162d00b03b.jpg and /dev/null differ
diff --git a/anselm-cluster-documentation/introduction.md b/anselm-cluster-documentation/introduction.md
deleted file mode 100644
index e478abbc8eaab412fee009b8bf4bf7debc44ef46..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/introduction.md
+++ /dev/null
@@ -1,42 +0,0 @@
-over 94 Tflop/s theoretical peak performance. Each node is a
-class="WYSIWYG_LINK">powerful x86-64 computer, equipped with 16
-cores, at least 64GB RAM, and 500GB harddrive. Nodes are interconnected
-by fully non-blocking fat-tree Infiniband network and equipped with
-Intel Sandy Bridge processors. A few nodes are also equipped with NVIDIA
-Kepler GPU or Intel Xeon Phi MIC accelerators. Read more in [Hardware
-Overview](hardware-overview.html).
-The cluster runs bullx Linux [
-class="WYSIWYG_LINK">](http//www.bull.com/bullx-logiciels/systeme-exploitation.html)[operating
-system](software/operating-system.html), which is
-compatible with the RedHat [
-class="WYSIWYG_LINK">Linux
-family.](http//upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
-We have installed a wide range of
-[software](software.html) packages targeted at different
-scientific domains. These packages are accessible via the [modules
-environment](environment-and-modules.html).
-User data shared file-system (HOME, 320TB) and job data shared
-file-system (SCRATCH, 146TB) are available to users.
-The PBS Professional workload manager provides [computing resources
-allocations and job
-execution](resource-allocation-and-job-execution.html).
-Read more on how to [apply for
-resources](../get-started-with-it4innovations/applying-for-resources.html),
-[obtain login
-credentials,](../get-started-with-it4innovations/obtaining-login-credentials.html)
-and [access the
-cluster](accessing-the-cluster/shell-and-data-access.html).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
diff --git a/anselm-cluster-documentation/resource-allocation-and-job-execution.md b/anselm-cluster-documentation/resource-allocation-and-job-execution.md
deleted file mode 100644
index b890c5491d3ea9c860fcd4d183abbd762548049d..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/resource-allocation-and-job-execution.md
+++ /dev/null
@@ -1,84 +0,0 @@
-
-
-To run a [job](introduction.html), [computational
-resources](introduction.html) for this particular job
-must be allocated. This is done via the PBS Pro job workload manager
-software, which efficiently distributes workloads across the
-supercomputer. Extensive informations about PBS Pro can be found in the
-[official documentation
-here](../pbspro-documentation.html), especially in the
-[PBS Pro User's
-Guide](../pbspro-documentation/PBSProUserGuide12.pdf).
-Resources Allocation Policy
----------------------------
-The resources are allocated to the job in a fairshare fashion, subject
-to constraints set by the queue and resources available to the Project.
-[The
-Fairshare](resource-allocation-and-job-execution/job-priority.html)
-at Anselm ensures that individual users may consume approximately equal
-amount of resources per week. The resources are accessible via several
-queues for queueing the jobs. The queues provide prioritized and
-exclusive access to the computational resources. Following queues are
-available to Anselm users
-- **qexp**, the Express queue
-- **qprod**, the Production queue****
-- **qlong**, the Long queue, regula
-- **qnvidia, qmic, qfat**, the Dedicated queues
-- **qfree,** the Free resource utilization queue
-Check the queue status at
-Read more on the [Resource Allocation
-Policy](resource-allocation-and-job-execution/resources-allocation-policy.html)
-page.
-Job submission and execution
-----------------------------
-Use the **qsub** command to submit your jobs.
-The qsub submits the job into the queue. The qsub command creates a
-request to the PBS Job manager for allocation of specified resources.Â
-The **smallest allocation unit is entire node, 16 cores**, with
-exception of the qexp queue. The resources will be allocated when
-available, subject to allocation policies and constraints. **After the
-resources are allocated the jobscript or interactive shell is executed
-on first of the allocated nodes.**
-Read more on the [Job submission and
-execution](resource-allocation-and-job-execution/job-submission-and-execution.html)
-page.
-Capacity computing
-------------------
-Use Job arrays when running huge number of jobs.
-Use GNU Parallel and/or Job arrays when running (many) single core jobs.
-In many cases, it is useful to submit huge (100+) number of
-computational jobs into the PBS queue system. Huge number of (small)
-jobs is one of the most effective ways to execute embarrassingly
-parallel calculations, achieving best runtime, throughput and computer
-utilization. In this chapter, we discuss the the recommended way to run
-huge number of jobs, including **ways to run huge number of single core
-jobs**.
-Read more on [Capacity
-computing](resource-allocation-and-job-execution/capacity-computing.html)
-page.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
-
- - [Anselm Cluster
- Documentation](../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](hardware-overview.html)
-
- - [Accessing the
- Cluster](accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](environment-and-modules.html)
diff --git a/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md b/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md
deleted file mode 100644
index b99bf5742b753828edd60106b60b2b9aa2a847e9..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md
+++ /dev/null
@@ -1,79 +0,0 @@
-
-To run a [job](../introduction.html), [computational
-resources](../introduction.html) for this particular job
-must be allocated. This is done via the PBS Pro job workload manager
-software, which efficiently distributes workloads across the
-supercomputer. Extensive informations about PBS Pro can be found in the
-[official documentation
-here](../../pbspro-documentation.html), especially in
-the [PBS Pro User's
-Guide](../../pbspro-documentation/PBSProUserGuide12.pdf).
-Resources Allocation Policy
----------------------------
-The resources are allocated to the job in a fairshare fashion, subject
-to constraints set by the queue and resources available to the Project.
-[The Fairshare](job-priority.html) at Anselm ensures
-that individual users may consume approximately equal amount of
-resources per week. The resources are accessible via several queues for
-queueing the jobs. The queues provide prioritized and exclusive access
-to the computational resources. Following queues are available to Anselm
-users
-- **qexp**, the Express queue
-- **qprod**, the Production queue****
-- **qlong**, the Long queue, regula
-- **qnvidia, qmic, qfat**, the Dedicated queues
-- **qfree,** the Free resource utilization queue
-Check the queue status at
-Read more on the [Resource Allocation
-Policy](resources-allocation-policy.html) page.
-Job submission and execution
-----------------------------
-Use the **qsub** command to submit your jobs.
-The qsub submits the job into the queue. The qsub command creates a
-request to the PBS Job manager for allocation of specified resources.Â
-The **smallest allocation unit is entire node, 16 cores**, with
-exception of the qexp queue. The resources will be allocated when
-available, subject to allocation policies and constraints. **After the
-resources are allocated the jobscript or interactive shell is executed
-on first of the allocated nodes.**
-Read more on the [Job submission and
-execution](job-submission-and-execution.html) page.
-Capacity computing
-------------------
-Use Job arrays when running huge number of jobs.
-Use GNU Parallel and/or Job arrays when running (many) single core jobs.
-In many cases, it is useful to submit huge (100+) number of
-computational jobs into the PBS queue system. Huge number of (small)
-jobs is one of the most effective ways to execute embarrassingly
-parallel calculations, achieving best runtime, throughput and computer
-utilization. In this chapter, we discuss the the recommended way to run
-huge number of jobs, including **ways to run huge number of single core
-jobs**.
-Read more on [Capacity
-computing](capacity-computing.html) page.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
diff --git a/anselm-cluster-documentation/software.md b/anselm-cluster-documentation/software.md
deleted file mode 100644
index 0a34252f240fa3999c103f90d1898aa20b1735c6..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software.md
+++ /dev/null
@@ -1,108 +0,0 @@
- An engineering simulation software
- [COMSOL](software/comsol.html){.contenttype-folder .state-published .url}
- A finite element analysis, solver and
- Simulation software
- [Debuggers and profilers](software/debuggers.html){.contenttype-folder .state-published .url}
- A collection of development tools
- [Chemistry and Materials science](software/chemistry.html){.contenttype-folder .state-published .url}
- Tools for computational chemistry.
- [Intel Parallel studio](software/intel-suite.html){.contenttype-folder .state-published .url}
- The Intel Parallel Studio XE
- [MPI](software/mpi-1.html){.contenttype-folder .state-published .url}
- Message Passing Interface libraries on
- ANSELM
- [Numerical Libraries](software/numerical-libraries.html){.contenttype-folder .state-published .url}
- Libraries for numerical
- computations
- [Numerical languages](software/numerical-languages.html){.contenttype-folder .state-published .url}
- Interpreted languages for numerical
- computations
- [Virtualization](software/virtualization.html){.contenttype-folder .state-published .url}
-
- [Compilers](software/compilers.html){.contenttype-document .state-published .url}
- Available compilers, including GNU, INTEL
- and UPC compilers
- [Intel Xeon Phi](software/intel-xeon-phi.html){.contenttype-document .state-published .url}
- A guide to Intel Xeon Phi usage
- [ISV Licenses](software/isv_licenses.html){.contenttype-document .state-published .url}
- A guide to managing Independent Software
- Vendor licences
- [Java](software/java.html){.contenttype-document .state-published .url}
- Java on ANSELM
- [nVidia CUDA](software/nvidia-cuda.html){.contenttype-document .state-published .url}
- A guide to nVidia CUDA programming and GPU
- usage
- [OMICS Master](software/omics-master-1.html){.contenttype-folder .state-published .url}
-
- [OpenFOAM](software/openfoam.html){.contenttype-document .state-published .url}
- A free, open source CFD software
- package
- [Operating System](software/operating-system.html){.contenttype-document .state-published .url}
- The operating system, deployed on
- ANSELM
- [ParaView](software/paraview.html){.contenttype-document .state-published .url}
- An open-source, multi-platform data
- analysis and visualization application
- [GPI-2](software/gpi2.html){.contenttype-document .state-published .url}
- A library that implements the GASPI
- specification
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
-
- - [Anselm Cluster
- Documentation](../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](hardware-overview.html)
-
- - [Accessing the
- Cluster](accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](compute-nodes.html)
-
- - [Storage](storage-1.html)
-
- - [Network](network.html)
-
- - [Software](software.html "In this section we provide overview of installed software and its usage.
- ")
-
- - [ANSYS](software/ansys.html "An engineering simulation software ")
-
- - [COMSOL](software/comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](software/debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](software/chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](software/intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](software/mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](software/numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](software/numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](software/virtualization.html)
diff --git a/anselm-cluster-documentation/software/ansys.md b/anselm-cluster-documentation/software/ansys.md
deleted file mode 100644
index 5d9c8ade43d24294194d3d315d4231f40ccbcc6b..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/ansys.md
+++ /dev/null
@@ -1,121 +0,0 @@
-**[SVS FEM](http//www.svsfem.cz/)** as ***[ANSYS
-Channel partner](http//www.ansys.com/)***Â for Czech
-Republic provided all ANSYS licenses for ANSELM cluster and supports of
-all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent,
-Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging
-to problem of ANSYS functionality contact
-please [hotline@svsfem.cz](mailtohotline@svsfem.cz?subject=Ostrava%20-%20ANSELM){.email-link}
-Anselm provides as commercial as academic variants. Academic variants
-are distinguished by "**Academic...**" word in the name of  license or
-by two letter preposition "**aa_**" in the license feature name. Change
-of license is realized on command line respectively directly in user's
-pbs file (see individual products). [ id="result_box"
-class="short_text">More about
-licensing
-class="hps">here](../../acl_users/credentials_cookie_auth/require_login888f.html)
-To load the latest version of any ANSYS product (Mechanical, Fluent,
-CFX, MAPDL,...) load the module
- $ module load ansys
-ANSYS supports interactive regime, but due to assumed solution of
-extremely difficult tasks it is not recommended.
-If user needs to work in interactive regime we recommend to configure
-the RSM service on the client machine which allows to forward the
-solution to the Anselm directly from the client's Workbench project
-(see ANSYS RSM service).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage-1.html)
-
- - [Network](../network.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
-
- - [ANSYS
- MAPDL](ansys/ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](ansys/ansys-cfx.html)
-
- - [ANSYS
- Fluent](ansys/ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](ansys/ansys-ls-dyna.html)
-
- - [LS-DYNA](ansys/ls-dyna.html)
-
- - [{width="16" height="16"}
- ANSYS MAPDL PBS
- file](ansys/ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS CFX PBS
- file](ansys/ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS Fluent PBS
- file](ansys/ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS LS-DYNA PBS
- file](ansys/ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- LS-DYNA PBS
- file](ansys/ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](virtualization.html)
diff --git a/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view.md b/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view.md
deleted file mode 100644
index bd181edb45a62ef3e83893f0c6e998e8e43608cf..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view.md
+++ /dev/null
@@ -1,102 +0,0 @@
-ANSYS CFX PBS file
-==================
- [
-cfx.pbs](at_download/cfx.pbs) — shell script, 1
-KB (1026 bytes)
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../sitemap.html)
- - [What's
- New](../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../compute-nodes.html)
-
- - [Storage](../../../storage-1.html)
-
- - [Network](../../../network.html)
-
- - [Software](../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](../ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](../ansys-cfx.html)
-
- - [ANSYS
- Fluent](../ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](../ansys-ls-dyna.html)
-
- - [LS-DYNA](../ls-dyna.html)
-
- - [{width="16"
- height="16"} ANSYS MAPDL PBS
- file](../ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS CFX PBS
- file](view.html){.state-missing-value
-
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS Fluent PBS
- file](../ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS LS-DYNA PBS
- file](../ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} LS-DYNA PBS
- file](../ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [COMSOL](../../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../../virtualization.html)
diff --git a/anselm-cluster-documentation/software/ansys/ansys-cfx.md b/anselm-cluster-documentation/software/ansys/ansys-cfx.md
deleted file mode 100644
index 2a08b9dcd749598c6e09ab4f3565e4deea24eb0f..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/ansys/ansys-cfx.md
+++ /dev/null
@@ -1,171 +0,0 @@
-ANSYS CFX
-=========
-[ANSYS
-CFX](http//www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+CFX)
-software is a high-performance, general purpose fluid dynamics program
-that has been applied to solve wide-ranging fluid flow problems for over
-20 years. At the heart of ANSYS CFX is its advanced solver technology,
-the key to achieving reliable and accurate solutions quickly and
-robustly. The modern, highly parallelized solver is the foundation for
-an abundant choice of physical models to capture virtually any type of
-phenomena related to fluid flow. The solver and its many physical models
-are wrapped in a modern, intuitive, and flexible GUI and user
-environment, with extensive capabilities for customization and
-automation using session files, scripting and a powerful expression
-language.
-To run ANSYS CFX in batch mode you can utilize/modify the default
-cfx.pbs script and execute it via the qsub command.
-``` {.prettyprint .lang-sh}
-#!/bin/bash
-#PBS -l nodes=2ppn=16
-#PBS -q qprod
-#PBS -N $USER-CFX-Project
-#PBS -A XX-YY-ZZ
-#! Mail to user when job terminate or abort
-#PBS -m ae
-#!change the working directory (default is home directory)
-#cd (working directory must exists)
-WORK_DIR="/scratch/$USER/work"
-cd $WORK_DIR
-echo Running on host `hostname`
-echo Time is `date`
-echo Directory is `pwd`
-echo This jobs runs on the following processors
-echo `cat $PBS_NODEFILE`
-module load ansys
-#### Set number of processors per host listing
-#### (set to 1 as $PBS_NODEFILE lists each node twice if ppn=2)
-procs_per_host=1
-#### Create host list
-hl=""
-for host in `cat $PBS_NODEFILE`
-do
- if [ "$hl" = "" ]
- then hl="$host$procs_per_host"
- else hl="${hl}$host$procs_per_host"
- fi
-done
-echo Machines $hl
-#-dev input.def includes the input of CFX analysis in DEF format
-#-P the name of prefered license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial))
-/ansys_inc/v145/CFX/bin/cfx5solve -def input.def -size 4 -size-ni 4x -part-large -start-method "Platform MPI Distributed Parallel" -par-dist $hl -P aa_r
-```
-Header of the pbs file (above) is common and description can be find
-on [this
-site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
-SVS FEM recommends to utilize sources by keywords nodes, ppn. These
-keywords allows to address directly the number of nodes (computers) and
-cores (ppn) which will be utilized in the job. Also the rest of code
-assumes such structure of allocated resources.
-Working directory has to be created before sending pbs job into the
-queue. Input file should be in working directory or full path to input
-file has to be specified. Input file has to be defined by common
-CFX def file which is attached to the cfx solver via parameter
--def
-**License**Â should be selected by parameter -P (Big letter **P**).
-Licensed products are the following aa_r
-(ANSYSÂ **Academic**Â Research), ane3fl (ANSYS
-Multiphysics)-**Commercial.**
-[More
-about licensing
-class="hps">here](../../../acl_users/credentials_cookie_auth/require_login888f.html)
-Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](ansys-cfx.html)
-
-
- - [ANSYS
- Fluent](ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](ansys-ls-dyna.html)
-
- - [LS-DYNA](ls-dyna.html)
-
- - [{width="16" height="16"}
- ANSYS MAPDL PBS
- file](ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS CFX PBS
- file](ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS Fluent PBS
- file](ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS LS-DYNA PBS
- file](ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- LS-DYNA PBS
- file](ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view.md b/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view.md
deleted file mode 100644
index bf354b8e95cca2c95f2b10f511be465e16b29115..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view.md
+++ /dev/null
@@ -1,102 +0,0 @@
-ANSYS Fluent PBS file
-=====================
- [
-fluent.pbs](at_download/fluent.pbs) — shell
-script, 1 KB
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../sitemap.html)
- - [What's
- New](../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../compute-nodes.html)
-
- - [Storage](../../../storage-1.html)
-
- - [Network](../../../network.html)
-
- - [Software](../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](../ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](../ansys-cfx.html)
-
- - [ANSYS
- Fluent](../ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](../ansys-ls-dyna.html)
-
- - [LS-DYNA](../ls-dyna.html)
-
- - [{width="16"
- height="16"} ANSYS MAPDL PBS
- file](../ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS CFX PBS
- file](../ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS Fluent PBS
- file](view.html){.state-missing-value
-
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS LS-DYNA PBS
- file](../ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} LS-DYNA PBS
- file](../ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [COMSOL](../../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../../virtualization.html)
diff --git a/anselm-cluster-documentation/software/ansys/ansys-fluent.md b/anselm-cluster-documentation/software/ansys/ansys-fluent.md
deleted file mode 100644
index a288e0e039d9d2378d705adbaa79b569361ca30d..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/ansys/ansys-fluent.md
+++ /dev/null
@@ -1,282 +0,0 @@
-ANSYS Fluent
-============
-[ANSYS
-Fluent](http//www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent)
-software contains the broad physical modeling capabilities needed to
-model flow, turbulence, heat transfer, and reactions for industrial
-applications ranging from air flow over an aircraft wing to combustion
-in a furnace, from bubble columns to oil platforms, from blood flow to
-semiconductor manufacturing, and from clean room design to wastewater
-treatment plants. Special models that give the software the ability to
-model in-cylinder combustion, aeroacoustics, turbomachinery, and
-multiphase systems have served to broaden its reach.
-1. Common way to run Fluent over pbs file
-------------------------------------------------------
-To run ANSYS Fluent in batch mode you can utilize/modify the
-default fluent.pbs script and execute it via the qsub command.
-``` {.prettyprint .lang-sh}
-#!/bin/bash
-#PBS -S /bin/bash
-#PBS -l nodes=2ppn=16
-#PBS -q qprod
-#PBS -N $USER-Fluent-Project
-#PBS -A XX-YY-ZZ
-#! Mail to user when job terminate or abort
-#PBS -m ae
-#!change the working directory (default is home directory)
-#cd (working directory must exists)
-WORK_DIR="/scratch/$USER/work"
-cd $WORK_DIR
-echo Running on host `hostname`
-echo Time is `date`
-echo Directory is `pwd`
-echo This jobs runs on the following processors
-echo `cat $PBS_NODEFILE`
-#### Load ansys module so that we find the cfx5solve command
-module load ansys
-# Use following line to specify MPI for message-passing instead
-NCORES=`wc -l $PBS_NODEFILE |awk '{print $1}'`
-/ansys_inc/v145/fluent/bin/fluent 3d -t$NCORES -cnf=$PBS_NODEFILE -g -i fluent.jou
-```
-Header of the pbs file (above) is common and description can be find
-on [this
-site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
-[SVS FEM](http//www.svsfem.cz/) recommends to utilize
-sources by keywords nodes, ppn. These keywords allows to address
-directly the number of nodes (computers) and cores (ppn) which will be
-utilized in the job. Also the rest of code assumes such structure of
-allocated resources.
-Working directory has to be created before sending pbs job into the
-queue. Input file should be in working directory or full path to input
-file has to be specified. Input file has to be defined by common Fluent
-journal file which is attached to the Fluent solver via parameter -i
-fluent.jou
-Journal file with definition of the input geometry and boundary
-conditions and defined process of solution has e.g. the following
-structure
- /file/read-case aircraft_2m.cas.gz
- /solve/init
- init
- /solve/iterate
- 10
- /file/write-case-dat aircraft_2m-solution
- /exit yes
-The appropriate dimension of the problem has to be set by
-parameter (2d/3d).Â
-2. Fast way to run Fluent from command line
---------------------------------------------------------
-``` {.prettyprint .lang-sh}
-fluent solver_version [FLUENT_options] -i journal_file -pbs
-```
-This syntax will start the ANSYS FLUENT job under PBS Professional using
-the qsub command in a batch manner. When
-resources are available, PBS Professional will start the job and return
-a job ID, usually in the form of
-class="emphasis">*job_ID.hostname*. This job ID can then be used
-to query, control, or stop the job using standard PBS Professional
-commands, such as qstat or
-class="monospace">qdel. The job will be run out of the current
-working directory, and all output will be written to the file
-class="monospace">fluent.oÂ
-class="emphasis">*job_ID*. Â Â Â Â
-3. Running Fluent via user's config file
-----------------------------------------
-The sample script uses a configuration file called
-class="monospace">pbs_fluent.conf  if no command line arguments
-are present. This configuration file should be present in the directory
-from which the jobs are submitted (which is also the directory in which
-the jobs are executed). The following is an example of what the content
-of pbs_fluent.conf can be
-``` {.screen}
-input="example_small.flin"
-case="Small-1.65m.cas"
-fluent_args="3d -pmyrinet"
-outfile="fluent_test.out"
-mpp="true"
-```
-The following is an explanation of the parameters
-input is the name of the input
-file.
-case is the name of the
-class="monospace">.cas file that the input file will utilize.
-fluent_args are extra ANSYS FLUENT
-arguments. As shown in the previous example, you can specify the
-interconnect by using the -p interconnect
-command. The available interconnects include
-class="monospace">ethernet (the default),
-class="monospace">myrinet,
-infiniband, vendor,
-class="monospace">altix, and
-class="monospace">crayx. The MPI is selected automatically, based
-on the specified interconnect.
-outfile is the name of the file to which
-the standard output will be sent.
-mpp="true" will tell the job script to
-execute the job across multiple processors. Â Â Â Â Â Â Â Â
-To run ANSYS Fluent in batch mode with user's config file you can
-utilize/modify the following script and execute it via the qsub
-command.
-``` {.prettyprint .lang-sh}
-#!/bin/sh
-#PBS -l nodes=2ppn=4
-#PBS -1 qprod
-#PBS -N $USE-Fluent-Project
-#PBS -A XX-YY-ZZ
- cd $PBS_O_WORKDIR
-
- #We assume that if they didn’t specify arguments then they should use the
- #config file if [ "xx${input}${case}${mpp}${fluent_args}zz" = "xxzz" ]; then
- if [ -f pbs_fluent.conf ]; then
- . pbs_fluent.conf
- else
- printf "No command line arguments specified, "
- printf "and no configuration file found. Exiting n"
- fi
- fi
-
- #Augment the ANSYS FLUENT command line arguments case "$mpp" in
- true)
- #MPI job execution scenario
- num_nodes=â€cat $PBS_NODEFILE | sort -u | wc -lâ€
- cpus=â€expr $num_nodes * $NCPUSâ€
- #Default arguments for mpp jobs, these should be changed to suit your
- #needs.
- fluent_args="-t${cpus} $fluent_args -cnf=$PBS_NODEFILE"
- ;;
- *)
- #SMP case
- #Default arguments for smp jobs, should be adjusted to suit your
- #needs.
- fluent_args="-t$NCPUS $fluent_args"
- ;;
- esac
- #Default arguments for all jobs
- fluent_args="-ssh -g -i $input $fluent_args"
- echo "---------- Going to start a fluent job with the following settings
- Input $input
- Case $case
- Output $outfile
- Fluent arguments $fluent_args"
-
- #run the solver
- /ansys_inc/v145/fluent/bin/fluent $fluent_args > $outfile
-```
-It runs the jobs out of the directory from which they are
-submitted (PBS_O_WORKDIR).
-4. Running Fluent in parralel
------------------------------
-Fluent could be run in parallel only under Academic Research license. To
-do so this ANSYS Academic Research license must be placed before ANSYS
-CFD license in user preferences. To make this change anslic_admin
-utility should be run
-``` {.prettyprint .lang-sh}
-/ansys_inc/shared_ les/licensing/lic_admin/anslic_admin
-```
-ANSLIC_ADMIN Utility will be run
-
-
-
-Â
-ANSYS Academic Research license should be moved up to the top of the
-list.
-Â
-
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](ansys-cfx.html)
-
- - [ANSYS
- Fluent](ansys-fluent.html)
-
-
- - [ANSYS
- LS-DYNA](ansys-ls-dyna.html)
-
- - [LS-DYNA](ls-dyna.html)
-
- - [{width="16" height="16"}
- ANSYS MAPDL PBS
- file](ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS CFX PBS
- file](ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS Fluent PBS
- file](ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS LS-DYNA PBS
- file](ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- LS-DYNA PBS
- file](ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view.md b/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view.md
deleted file mode 100644
index ffa00b274c30dccb64e774d883114c621e8de401..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view.md
+++ /dev/null
@@ -1,102 +0,0 @@
-ANSYS LS-DYNA PBS file
-======================
- [
-ansysdyna.pbs](at_download/ansysdyna.pbs) —
-shell script, 1 KB
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../sitemap.html)
- - [What's
- New](../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../compute-nodes.html)
-
- - [Storage](../../../storage-1.html)
-
- - [Network](../../../network.html)
-
- - [Software](../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](../ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](../ansys-cfx.html)
-
- - [ANSYS
- Fluent](../ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](../ansys-ls-dyna.html)
-
- - [LS-DYNA](../ls-dyna.html)
-
- - [{width="16"
- height="16"} ANSYS MAPDL PBS
- file](../ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS CFX PBS
- file](../ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS Fluent PBS
- file](../ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS LS-DYNA PBS
- file](view.html){.state-missing-value
-
- .contenttype-file}
- - [{width="16"
- height="16"} LS-DYNA PBS
- file](../ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [COMSOL](../../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../../virtualization.html)
diff --git a/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md b/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
deleted file mode 100644
index a8f4154d413bf76a000e1a18d565969cda0781f8..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
+++ /dev/null
@@ -1,169 +0,0 @@
-ANSYS LS-DYNA
-=============
-[ANSYS
-LS-DYNA](http//www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/Explicit+Dynamics/ANSYS+LS-DYNA)
-software provides convenient and easy-to-use access to the
-technology-rich, time-tested explicit solver without the need to contend
-with the complex input requirements of this sophisticated program.
-Introduced in 1996, ANSYS LS-DYNA capabilities have helped customers in
-numerous industries to resolve highly intricate design
-issues. ANSYS Mechanical users have been able take advantage of
-complex explicit solutions for a long time utilizing the traditional
-ANSYS Parametric Design Language (APDL) environment. These
-explicit capabilities are available to ANSYS Workbench users as well.
-The Workbench platform is a powerful, comprehensive, easy-to-use
-environment for engineering simulation. CAD import from all sources,
-geometry cleanup, automatic meshing, solution, parametric optimization,
-result visualization and comprehensive report generation are all
-available within a single fully interactive modern graphical user
-environment.
-To run ANSYS LS-DYNA in batch mode you can utilize/modify the
-default ansysdyna.pbs script and execute it via the qsub command.
-``` {.prettyprint .lang-sh}
-#!/bin/bash
-#PBS -l nodes=2ppn=16
-#PBS -q qprod
-#PBS -N $USER-DYNA-Project
-#PBS -A XX-YY-ZZ
-#! Mail to user when job terminate or abort
-#PBS -m ae
-#!change the working directory (default is home directory)
-#cd
-WORK_DIR="/scratch/$USER/work"
-cd $WORK_DIR
-echo Running on host `hostname`
-echo Time is `date`
-echo Directory is `pwd`
-echo This jobs runs on the following processors
-echo `cat $PBS_NODEFILE`
-#! Counts the number of processors
-NPROCS=`wc -l < $PBS_NODEFILE`
-echo This job has allocated $NPROCS nodes
-module load ansys
-#### Set number of processors per host listing
-#### (set to 1 as $PBS_NODEFILE lists each node twice if ppn=2)
-procs_per_host=1
-#### Create host list
-hl=""
-for host in `cat $PBS_NODEFILE`
-do
- if [ "$hl" = "" ]
- then hl="$host$procs_per_host"
- else hl="${hl}$host$procs_per_host"
- fi
-done
-echo Machines $hl
-/ansys_inc/v145/ansys/bin/ansys145 -dis -lsdynampp i=input.k -machines $hl
-```
-Header of the pbs file (above) is common and description can be
-find on [this
-site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
-[SVS FEM](http//www.svsfem.cz/) recommends to utilize
-sources by keywords nodes, ppn. These keywords allows to address
-directly the number of nodes (computers) and cores (ppn) which will be
-utilized in the job. Also the rest of code assumes such structure of
-allocated resources.
-Working directory has to be created before sending pbs job into the
-queue. Input file should be in working directory or full path to input
-file has to be specified. Input file has to be defined by common LS-DYNA
-.**k** file which is attached to the ansys solver via parameter i=
-Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](ansys-cfx.html)
-
- - [ANSYS
- Fluent](ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](ansys-ls-dyna.html)
-
-
- - [LS-DYNA](ls-dyna.html)
-
- - [{width="16" height="16"}
- ANSYS MAPDL PBS
- file](ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS CFX PBS
- file](ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS Fluent PBS
- file](ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS LS-DYNA PBS
- file](ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- LS-DYNA PBS
- file](ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view.md b/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view.md
deleted file mode 100644
index 7913d3b606d344443c965c3188e24136c2004a60..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view.md
+++ /dev/null
@@ -1,102 +0,0 @@
-ANSYS MAPDL PBS file
-====================
- [
-mapdl.pbs](at_download/mapdl.pbs) — shell
-script, 1 KB (1201 bytes)
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../sitemap.html)
- - [What's
- New](../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../compute-nodes.html)
-
- - [Storage](../../../storage-1.html)
-
- - [Network](../../../network.html)
-
- - [Software](../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](../ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](../ansys-cfx.html)
-
- - [ANSYS
- Fluent](../ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](../ansys-ls-dyna.html)
-
- - [LS-DYNA](../ls-dyna.html)
-
- - [{width="16"
- height="16"} ANSYS MAPDL PBS
- file](view.html){.state-missing-value
-
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS CFX PBS
- file](../ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS Fluent PBS
- file](../ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS LS-DYNA PBS
- file](../ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} LS-DYNA PBS
- file](../ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [COMSOL](../../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../../virtualization.html)
diff --git a/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md b/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
deleted file mode 100644
index e8ea26848c2695639caa3691684042dc0333b0fb..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
+++ /dev/null
@@ -1,166 +0,0 @@
-ANSYS MAPDL
-===========
-**[ANSYS
-Multiphysics](http//www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics)**
-software offers a comprehensive product solution for both multiphysics
-and single-physics analysis. The product includes structural, thermal,
-fluid and both high- and low-frequency electromagnetic analysis. The
-product also contains solutions for both direct and sequentially coupled
-physics problems including direct coupled-field elements and the ANSYS
-multi-field solver.
-To run ANSYS MAPDL in batch mode you can utilize/modify the
-default mapdl.pbs script and execute it via the qsub command.
-``` {.prettyprint .lang-sh}
-#!/bin/bash
-#PBS -l nodes=2ppn=16
-#PBS -q qprod
-#PBS -N $USER-ANSYS-Project
-#PBS -A XX-YY-ZZ
-#! Mail to user when job terminate or abort
-#PBS -m ae
-#!change the working directory (default is home directory)
-#cd (working directory must exists)
-WORK_DIR="/scratch/$USER/work"
-cd $WORK_DIR
-echo Running on host `hostname`
-echo Time is `date`
-echo Directory is `pwd`
-echo This jobs runs on the following processors
-echo `cat $PBS_NODEFILE`
-module load ansys
-#### Set number of processors per host listing
-#### (set to 1 as $PBS_NODEFILE lists each node twice if ppn=2)
-procs_per_host=1
-#### Create host list
-hl=""
-for host in `cat $PBS_NODEFILE`
-do
- if [ "$hl" = "" ]
- then hl="$host$procs_per_host"
- else hl="${hl}$host$procs_per_host"
- fi
-done
-echo Machines $hl
-#-i input.dat includes the input of analysis in APDL format
-#-o file.out is output file from ansys where all text outputs will be redirected
-#-p the name of license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial), aa_r_dy=Academic AUTODYN)
-/ansys_inc/v145/ansys/bin/ansys145 -b -dis -p aa_r -i input.dat -o file.out -machines $hl -dir $WORK_DIR
-```
-Header of the pbs file (above) is common and description can be find on
-[this
-site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
-[SVS FEM](http//www.svsfem.cz/) recommends to utilize
-sources by keywords nodes, ppn. These keywords allows to address
-directly the number of nodes (computers) and cores (ppn) which will be
-utilized in the job. Also the rest of code assumes such structure of
-allocated resources.
-Working directory has to be created before sending pbs job into the
-queue. Input file should be in working directory or full path to input
-file has to be specified. Input file has to be defined by common APDL
-file which is attached to the ansys solver via parameter -i
-**License** should be selected by parameter -p. Licensed products are
-the following aa_r (ANSYS **Academic** Research), ane3fl (ANSYS
-Multiphysics)-**Commercial**, aa_r_dy (ANSYS **Academic**
-AUTODYN)
-[More
-about licensing
-class="hps">here](../../../acl_users/credentials_cookie_auth/require_login888f.html)
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](ansys-mechanical-apdl.html)
-
-
- - [ANSYS
- CFX](ansys-cfx.html)
-
- - [ANSYS
- Fluent](ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](ansys-ls-dyna.html)
-
- - [LS-DYNA](ls-dyna.html)
-
- - [{width="16" height="16"}
- ANSYS MAPDL PBS
- file](ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS CFX PBS
- file](ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS Fluent PBS
- file](ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS LS-DYNA PBS
- file](ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- LS-DYNA PBS
- file](ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view.md b/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view.md
deleted file mode 100644
index 328f048fe07fe0363ccb85adca93a1eda56016ec..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view.md
+++ /dev/null
@@ -1,102 +0,0 @@
-LS-DYNA PBS file
-================
- [
-lsdyna.pbs](at_download/lsdyna.pbs) — shell
-script, 1 KB
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../sitemap.html)
- - [What's
- New](../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../compute-nodes.html)
-
- - [Storage](../../../storage-1.html)
-
- - [Network](../../../network.html)
-
- - [Software](../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](../ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](../ansys-cfx.html)
-
- - [ANSYS
- Fluent](../ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](../ansys-ls-dyna.html)
-
- - [LS-DYNA](../ls-dyna.html)
-
- - [{width="16"
- height="16"} ANSYS MAPDL PBS
- file](../ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS CFX PBS
- file](../ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS Fluent PBS
- file](../ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS LS-DYNA PBS
- file](../ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} LS-DYNA PBS
- file](view.html){.state-missing-value
-
- .contenttype-file}
- - [COMSOL](../../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../../virtualization.html)
diff --git a/anselm-cluster-documentation/software/ansys/ls-dyna.md b/anselm-cluster-documentation/software/ansys/ls-dyna.md
deleted file mode 100644
index c7b8dbc91fa44e8f5859269e8ee6c3aa3d8a5218..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/ansys/ls-dyna.md
+++ /dev/null
@@ -1,152 +0,0 @@
-LS-DYNA
-=======
-[LS-DYNA](http//www.lstc.com/) is a multi-purpose,
-explicit and implicit finite element program used to analyze the
-nonlinear dynamic response of structures. Its fully automated contact
-analysis capability, a wide range of constitutive models to simulate a
-whole range of engineering materials (steels, composites, foams,
-concrete, etc.), error-checking features and the high scalability have
-enabled users worldwide to solve successfully many complex
-problems. Additionally LS-DYNA is extensively used to simulate
-impacts on structures from drop tests, underwater shock, explosions or
-high-velocity impacts. Explosive forming, process engineering, accident
-reconstruction, vehicle dynamics, thermal brake disc analysis or nuclear
-safety are further areas in the broad range of possible applications. In
-leading-edge research LS-DYNA is used to investigate the behaviour of
-materials like composites, ceramics, concrete, or wood. Moreover, it is
-used in biomechanics, human modelling, molecular structures, casting,
-forging, or virtual testing.
-Anselm provides **1 commercial license of LS-DYNA without HPC**
-support now.Â
-To run LS-DYNA in batch mode you can utilize/modify the
-default lsdyna.pbs script and execute it via the qsub
-command.
-``` {.prettyprint .lang-sh}
-#!/bin/bash
-#PBS -l nodes=1ppn=16
-#PBS -q qprod
-#PBS -N $USER-LSDYNA-Project
-#PBS -A XX-YY-ZZ
-#! Mail to user when job terminate or abort
-#PBS -m ae
-#!change the working directory (default is home directory)
-#cd (working directory must exists)
-WORK_DIR="/scratch/$USER/work"
-cd $WORK_DIR
-echo Running on host `hostname`
-echo Time is `date`
-echo Directory is `pwd`
-module load lsdyna
-/apps/engineering/lsdyna/lsdyna700s i=input.k
-```
-Header of the pbs file (above) is common and description can be find
-on [this
-site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
-[SVS FEM](http//www.svsfem.cz/) recommends to utilize
-sources by keywords nodes, ppn. These keywords allows to address
-directly the number of nodes (computers) and cores (ppn) which will be
-utilized in the job. Also the rest of code assumes such structure of
-allocated resources.
-Working directory has to be created before sending pbs job into the
-queue. Input file should be in working directory or full path to input
-file has to be specified. Input file has to be defined by common LS-DYNA
-**.k** file which is attached to the LS-DYNA solver via parameter i=
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](ansys-cfx.html)
-
- - [ANSYS
- Fluent](ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](ansys-ls-dyna.html)
-
- - [LS-DYNA](ls-dyna.html)
-
-
- - [{width="16" height="16"}
- ANSYS MAPDL PBS
- file](ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS CFX PBS
- file](ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS Fluent PBS
- file](ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS LS-DYNA PBS
- file](ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- LS-DYNA PBS
- file](ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/chemistry.md b/anselm-cluster-documentation/software/chemistry.md
deleted file mode 100644
index b99d8c3a4cb290d57e18984b4f7938c20dbee971..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/chemistry.md
+++ /dev/null
@@ -1,73 +0,0 @@
-===============================
-Tools for computational chemistry.
- [Molpro](chemistry/molpro.html){.contenttype-document .state-published .url}
- Molpro is a complete system of ab initio
- programs for molecular electronic structure calculations.
- [NWChem](chemistry/nwchem.html){.contenttype-document .state-published .url}
- High-Performance Computational
- Chemistry
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage-1.html)
-
- - [Network](../network.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](chemistry.html "Tools for computational chemistry.")
-
-
- - [Molpro](chemistry/molpro.html "Molpro is a complete system of ab initio programs for molecular electronic structure calculations.")
-
- - [NWChem](chemistry/nwchem.html "High-Performance Computational Chemistry")
-
- - [Intel Parallel
- studio](intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](virtualization.html)
diff --git a/anselm-cluster-documentation/software/chemistry/molpro.md b/anselm-cluster-documentation/software/chemistry/molpro.md
deleted file mode 100644
index 66ca5501e21332daeefddc16d4a471c79bc99153..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/chemistry/molpro.md
+++ /dev/null
@@ -1,136 +0,0 @@
-Molpro
-======
-Molpro is a complete system of ab initio programs for molecular
-electronic structure calculations.
-About Molpro
-------------
-Molpro is a software package used for accurate ab-initio quantum
-chemistry calculations. More information can be found at the [official
-webpage](http//www.molpro.net/).
-License
--------
-Molpro software package is available only to users that have a valid
-license. Please contact support to enable access to Molpro if you have a
-valid license appropriate for running on our cluster (eg. academic
-research group licence, parallel execution).
-To run Molpro, you need to have a valid license token present in
-"$HOME/.molpro/token". You can
-download the token from [Molpro
-website](https//www.molpro.net/licensee/?portal=licensee).
-Installed version
------------------
-Currently on Anselm is installed version 2010.1, patch level 45,
-parallel version compiled with Intel compilers and Intel MPI.
-Compilation parameters are default
- Parameter Value
- ------------------------------------------------- -----------------------------
- max number of atoms 200
- max number of valence orbitals 300
- max number of basis functions 4095
- max number of states per symmmetry 20
- max number of state symmetries 16
- max number of records 200
- max number of primitives maxbfn x [2]
-Â
-Running
--------
-Molpro is compiled for parallel execution using MPI and OpenMP. By
-default, Molpro reads the number of allocated nodes from PBS and
-launches a data server on one node. On the remaining allocated nodes,
-compute processes are launched, one process per node, each with 16
-threads. You can modify this behavior by using -n, -t and helper-server
-options. Please refer to the [Molpro
-documentation](http//www.molpro.net/info/2010.1/doc/manual/node9.html)
-for more details.Â
-The OpenMP parallelization in Molpro is limited and has been observed to
-produce limited scaling. We therefore recommend to use MPI
-parallelization only. This can be achieved by passing option
-class="monospace">mpiprocs=16ompthreads=1 to PBS.
-You are advised to use the -d option to point to a directory in [SCRATCH
-filesystem](../../storage-1/storage.html). Molpro can
-produce a large amount of temporary data during its run, and it is
-important that these are placed in the fast scratch filesystem.
-### Example jobscript
- #PBS -A IT4I-0-0
- #PBS -q qprod
- #PBS -l select=1ncpus=16mpiprocs=16ompthreads=1
- cd $PBS_O_WORKDIR
- # load Molpro module
- module add molpro
- # create a directory in the SCRATCH filesystem
- mkdir -p /scratch/$USER/$PBS_JOBID
- # copy an example input
- cp /apps/chem/molpro/2010.1/molprop_2010_1_Linux_x86_64_i8/examples/caffeine_opt_diis.com .
- # run Molpro with default options
- molpro -d /scratch/$USER/$PBS_JOBID caffeine_opt_diis.com
- # delete scratch directory
- rm -rf /scratch/$USER/$PBS_JOBIDÂ
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
- .navTreeFolderish
- .contenttype-folder}
- - [Molpro](molpro.html "Molpro is a complete system of ab initio programs for molecular electronic structure calculations.")
-
-
- - [NWChem](nwchem.html "High-Performance Computational Chemistry")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/chemistry/nwchem.md b/anselm-cluster-documentation/software/chemistry/nwchem.md
deleted file mode 100644
index 50d598516152c87a075edf09b3a916c53fbec1c6..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/chemistry/nwchem.md
+++ /dev/null
@@ -1,115 +0,0 @@
-NWChem
-======
-High-Performance Computational Chemistry
-Introduction
--------------------------
-NWChem aims to provide its users with computational chemistry
-tools that are scalable both in their ability to treat large scientific
-computational chemistry problems efficiently, and in their use of
-available parallel computing resources from high-performance parallel
-supercomputers to conventional workstation clusters.
-[Homepage](http//www.nwchem-sw.org/index.php/Main_Page)
-Installed versions
-------------------
-The following versions are currently installed Â
-- 6.1.1, not recommended, problems have been observed with this
- version
-- 6.3-rev2-patch1, current release with QMD patch applied. Compiled
- with Intel compilers, MKL and Intel MPI
-- 6.3-rev2-patch1-openmpi, same as above, but compiled with OpenMPI
- and NWChem provided BLAS instead of MKL. This version is expected to
- be slower
-- 6.3-rev2-patch1-venus, this version contains only libraries for
- VENUS interface linking. Does not provide standalone NWChem
- executable
-For a current list of installed versions, execute Â
- module avail nwchem
-Running
--------
-NWChem is compiled for parallel MPI execution. Normal procedure for MPI
-jobs applies. Sample jobscript
- #PBS -A IT4I-0-0
- #PBS -q qprod
- #PBS -l select=1ncpus=16
- module add nwchem/6.3-rev2-patch1
- mpirun -np 16 nwchem h2o.nw
-Options
---------------------
-Please refer to [the
-documentation](http//www.nwchem-sw.org/index.php/Release62Top-level)Â and
-in the input file set the following directives
-- MEMORY controls the amount of memory NWChem will use
-- SCRATCH_DIR set this to a directory in [SCRATCH
- filesystem](../../storage-1/storage.html#scratch)Â (or
- run the calculation completely in a scratch directory). For certain
- calculations, it might be advisable to reduce I/O by forcing
- "direct" mode, eg. "scf direct"
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
- .navTreeFolderish
- .contenttype-folder}
- - [Molpro](molpro.html "Molpro is a complete system of ab initio programs for molecular electronic structure calculations.")
-
- - [NWChem](nwchem.html "High-Performance Computational Chemistry")
-
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/comsol.md b/anselm-cluster-documentation/software/comsol.md
deleted file mode 100644
index f96cef6bfe77661560288847e3bd7f317cd52522..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/comsol.md
+++ /dev/null
@@ -1,222 +0,0 @@
-
-
-Introduction
--------------------------
-[COMSOL](http//www.comsol.com/)
-is a powerful environment for modelling and solving various engineering
-and scientific problems based on partial differential equations. COMSOL
-is designed to solve coupled or multiphysics phenomena. For many
-standard engineering problems COMSOL provides add-on products such as
-electrical, mechanical, fluid flow, and chemical
-applications.
-- [Structural Mechanics
- Module](http//www.comsol.com/structural-mechanics-module),
-
-- [Heat Transfer
- Module](http//www.comsol.com/heat-transfer-module),
-
-- [CFD
- Module](http//www.comsol.com/cfd-module),
-
-- [Acoustics
- Module](http//www.comsol.com/acoustics-module),
-
-- and [many
- others](http//www.comsol.com/products)
-COMSOL also allows an
-interface support for
-equation-based modelling of
-partial differential
-equations.
-Execution
-----------------------
-On the Anselm cluster COMSOL is available in the latest
-stable version. There are two variants of the release
-- **Non commercial** or so
- called **EDU
- variant**, which can be used for research
- and educational purposes.
-- **Commercial** or so called
- **COM variant**,
- which can used also for commercial activities.
- **COM variant**
- has only subset of features compared to the
- **EDU
- variant** available.
- class="internal-link">
- class="hps">More about
- licensing will be posted here
- soon.
-
-To load the of COMSOL load the module
-``` {.prettyprint .lang-sh}
-$ module load comsol
-```
-By default the **EDU
-variant** will be loaded. If user needs other
-version or variant, load the particular version. To obtain the list of
-available versions use
-``` {.prettyprint .lang-sh}
-$ module avail comsol
-```
-If user needs to prepare COMSOL jobs in the interactive mode
-it is recommend to use COMSOL on the compute nodes via PBS Pro
-scheduler. In order run the COMSOL Desktop GUI on Windows is recommended
-to use the [Virtual Network Computing
-(VNC)](comsol/resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html).
-``` {.prettyprint .lang-sh}
-$ xhost +
-$ qsub -I -X -A PROJECT_ID -q qprod -l select=1ncpus=16
-$ module load comsol
-$ comsol
-```
-To run COMSOL in batch mode, without the COMSOL Desktop GUI
-environment, user can utilized the default (comsol.pbs) job script and
-execute it via the qsub command.
-``` {.prettyprint .lang-sh}
-#!/bin/bash
-#PBS -l select=3ncpus=16
-#PBS -q qprod
-#PBS -N JOB_NAME
-#PBS -AÂ PROJECT_ID
-cd /scratch/$USER/ || exit
-echo Time is `date`
-echo Directory is `pwd`
-echo '***PBS_NODEFILE***START*******'
-cat $PBS_NODEFILE
-echo '***PBS_NODEFILE***END*********'
-text_nodes < cat $PBS_NODEFILE
-module load comsol
-# module load comsol/43b-COM
-ntask=$(wc -l $PBS_NODEFILE)
-comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log
-```
-Working directory has to be created before sending the
-(comsol.pbs) job script into the queue. Input file (name_input_f.mph)
-has to be in working directory or full path to input file has to be
-specified. The appropriate path to the temp directory of the job has to
-be set by command option (-tmpdir).
-LiveLink™* *for MATLAB^®^
--------------------------
-COMSOL is the software package for the numerical solution of
-the partial differential equations. LiveLink for MATLAB allows
-connection to the
-COMSOL^**®**^
-API (Application Programming Interface) with the benefits of the
-programming language and computing environment of the MATLAB.
-LiveLink for MATLAB is available in both
-**EDU** and
-**COM**
-**variant** of the
-COMSOL release. On Anselm 1 commercial
-(**COM**) license
-and the 5 educational
-(**EDU**) licenses
-of LiveLink for MATLAB (please see the [ISV
-Licenses](isv_licenses.html)) are available. Following
-example shows how to start COMSOL model from MATLAB via LiveLink in the
-interactive mode.
-``` {.prettyprint .lang-sh}
-$ xhost +
-$ qsub -I -X -A PROJECT_ID -q qexp -l select=1ncpus=16
-$ module load matlab
-$ module load comsol
-$ comsol server matlab
-```
-At the first time to launch the LiveLink for MATLAB
-(client-MATLAB/server-COMSOL connection) the login and password is
-requested and this information is not requested again.
-To run LiveLink for MATLAB in batch mode with
-(comsol_matlab.pbs) job script you can utilize/modify the following
-script and execute it via the qsub command.
-``` {.prettyprint .lang-sh}
-#!/bin/bash
-#PBS -l select=3ncpus=16
-#PBS -q qprod
-#PBS -N JOB_NAME
-#PBS -AÂ PROJECT_ID
-cd /scratch/$USER || exit
-echo Time is `date`
-echo Directory is `pwd`
-echo '***PBS_NODEFILE***START*******'
-cat $PBS_NODEFILE
-echo '***PBS_NODEFILE***END*********'
-text_nodes < cat $PBS_NODEFILE
-module load matlab
-module load comsol/43b-EDU
-ntask=$(wc -l $PBS_NODEFILE)
-comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/$USER &
-cd /apps/engineering/comsol/comsol43b/mli
-matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/$USER; test_job"
-```
-This example shows how to run Livelink for MATLAB with following
-configuration 3 nodes and 16 cores per node. Working directory has to
-be created before submitting (comsol_matlab.pbs) job script into the
-queue. Input file (test_job.m) has to be in working directory or full
-path to input file has to be specified. The Matlab command option (-r
-”mphstart”) created a connection with a COMSOL server using the default
-port number.
-
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage-1.html)
-
- - [Network](../network.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](virtualization.html)
diff --git a/anselm-cluster-documentation/software/debuggers.md b/anselm-cluster-documentation/software/debuggers.md
deleted file mode 100644
index 0684cb457d85e990319ef41839e9cf2407ce0609..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/debuggers.md
+++ /dev/null
@@ -1,154 +0,0 @@
-
-
-Introduction
-------------
-We provide state of the art programms and tools to develop, profile and
-debug HPC codes at IT4Innovations.
-On these pages, we provide an overview of the profiling and debugging
-tools available on Anslem at IT4I.
-Intel debugger
---------------
-The intel debugger version 13.0 is available, via module intel. The
-debugger works for applications compiled with C and C++ compiler and the
-ifort fortran 77/90/95 compiler. The debugger provides java GUI
-environment. Use [X
-display](debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html)
-for running the GUI.
- $ module load intel
- $ idb
-Read more at the [Intel
-Debugger](intel-suite/intel-debugger.html) page.
-Allinea Forge (DDT/MAP)
------------------------
-Allinea DDT, is a commercial debugger primarily for debugging parallel
-MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel
-Xeon Phi accelerators. DDT provides all the standard debugging features
-(stack trace, breakpoints, watches, view variables, threads etc.) for
-every thread running as part of your program, or for every process -
-even if these processes are distributed across a cluster using an MPI
-implementation.
- $ module load Forge
- $ forge
-Read more at the [Allinea
-DDT](debuggers/allinea-ddt.html) page.
-Allinea Performance Reports
----------------------------
-Allinea Performance Reports characterize the performance of HPC
-application runs. After executing your application through the tool, a
-synthetic HTML report is generated automatically, containing information
-about several metrics along with clear behavior statements and hints to
-help you improve the efficiency of your runs. Our license is limited to
-64 MPI processes.
- $ module load PerformanceReports/6.0
- $ perf-report mpirun -n 64 ./my_application argument01 argument02
-Read more at the [Allinea Performance
-Reports](debuggers/allinea-performance-reports.html)
-page.
-RougeWave Totalview
--------------------
-TotalView is a source- and machine-level debugger for multi-process,
-multi-threaded programs. Its wide range of tools provides ways to
-analyze, organize, and test programs, making it easy to isolate and
-identify problems in individual threads and processes in programs of
-great complexity.
- $ module load totalview
- $ totalview
-Read more at the [Totalview](debuggers/total-view.html)
-page.
-Vampir trace analyzer
----------------------
-Vampir is a GUI trace analyzer for traces in OTF format.
- $ module load Vampir/8.5.0
- $ vampir
-Read more at
-the [Vampir](../../salomon/software/debuggers/vampir.html) page.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage-1.html)
-
- - [Network](../network.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
-
- - [Allinea
- Forge (DDT,MAP)](debuggers/allinea-ddt.html)
-
- - [Allinea Performance
- Reports](debuggers/allinea-performance-reports.html "quick application profiling")
-
- - [CUBE](debuggers/cube.html)
-
- - [Intel Performance Counter
- Monitor](debuggers/intel-performance-counter-monitor.html)
-
- - [Intel VTune
- Amplifier](debuggers/intel-vtune-amplifier.html)
-
- - [PAPI](debuggers/papi.html)
-
- - [Scalasca](debuggers/scalasca.html)
-
- - [Score-P](debuggers/score-p.html)
-
- - [Total
- View](debuggers/total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
-
- - [Valgrind](debuggers/valgrind.html "Valgrind is a tool for memory debugging and profiling.")
-
- - [Vampir](debuggers/vampir.html)
-
- - [Chemistry and Materials
- science](chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](virtualization.html)
diff --git a/anselm-cluster-documentation/software/debuggers/allinea-ddt.md b/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
deleted file mode 100644
index b73ffecd1c74e010f183c2f19e7fa59cdb4d9ffd..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
+++ /dev/null
@@ -1,178 +0,0 @@
-Allinea Forge (DDT,MAP)
-=======================
-
-
-Allinea Forge consist of two tools - debugger DDT and profiler MAP.
-Allinea DDT, is a commercial debugger primarily for debugging parallel
-MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel
-Xeon Phi accelerators. DDT provides all the standard debugging features
-(stack trace, breakpoints, watches, view variables, threads etc.) for
-every thread running as part of your program, or for every process -
-even if these processes are distributed across a cluster using an MPI
-implementation.
-Allinea MAP is a profiler for C/C++/Fortran HPC codes. It is designed
-for profiling parallel code, which uses pthreads, OpenMP or MPI.
-License and Limitations for Anselm Users
-----------------------------------------
-On Anselm users can debug OpenMP or MPI code that runs up to 64 parallel
-processes. In case of debugging GPU or Xeon Phi accelerated codes the
-limit is 8 accelerators. These limitation means that
-- 1 user can debug up 64 processes, or
-- 32 users can debug 2 processes, etc.
-In case of debugging on accelerators
-- 1 user can debug on up to 8 accelerators, orÂ
-- 8 users can debug on single accelerator.Â
-Compiling Code to run with DDT
-------------------------------
-### Modules
-Load all necessary modules to compile the code. For exampleÂ
- $ module load intel
- $ module load impi ... or ... module load openmpi/X.X.X-icc
-Load the Allinea DDT module
- $ module load Forge
-Compile the code
-``` {.code-basic style="text-align start; "}
-$ mpicc -g -O0 -o test_debug test.c
-$ mpif90 -g -O0 -o test_debug test.f
-```
-Â
-### Compiler flags
-Before debugging, you need to compile your code with theses flags
-**-g** Generates extra debugging information usable by GDB. -g3
-includes even more debugging information. This option is available for
-GNU and INTEL C/C++ and Fortran compilers.
-
-**-O0** Suppress all optimizations.
-Â
-Starting a Job with DDT
------------------------
-Be sure to log in with an X window
-forwarding enabled. This could mean using the -X in the ssh Â
- $ ssh -X username@anselm.it4i.cz
-Other options is to access login node using VNC. Please see the detailed
-information on how to [use graphic user interface on
-Anselm](resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html)
-class="internal-link">.
-From the login node an interactive session **with X windows forwarding**
-(-X option) can be started by following commandÂ
- $ qsub -I -X -A NONE-0-0 -q qexp -lselect=1ncpus=16mpiprocs=16,walltime=010000Â
-Then launch the debugger with the ddt command followed by the name of
-the executable to debug
- $ ddt test_debug
-A submission window that appears have
-a prefilled path to the executable to debug. You can select the number
-of MPI processors and/or OpenMP threads on which to run and press run.
-Command line arguments to a program can be entered to the
-"Arguments"
-style="text-align start; ">box.
-{.image-inline width="451" height="513"}Â
-To start the debugging directly without the submission window, user can
-specify the debugging and execution parameters from the command line.
-For example the number of MPI processes is set by option "-np 4".
-Skipping the dialog is done by "-start" option. To see the list of the
-"ddt" command line parameters, run "ddt --help". Â
- ddt -start -np 4 ./hello_debug_impi
-Â
-Documentation
--------------
-Users can find original User Guide after loading the DDT moduleÂ
- $DDTPATH/doc/userguide.pdf
-Â
-Â
-Â [1] Discipline, Magic, Inspiration and Science Best Practice
-Debugging with Allinea DDT, Workshop conducted at LLNL by Allinea on May
-10, 2013,
-[link](https//computing.llnl.gov/tutorials/allineaDDT/index.html)
-Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
- .navTreeFolderish
- .contenttype-folder}
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
- - [CUBE](cube.html)
-
- - [Intel Performance Counter
- Monitor](intel-performance-counter-monitor.html)
-
- - [Intel VTune
- Amplifier](intel-vtune-amplifier.html)
-
- - [PAPI](papi.html)
-
- - [Scalasca](scalasca.html)
-
- - [Score-P](score-p.html)
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
-
- - [Valgrind](valgrind.html "Valgrind is a tool for memory debugging and profiling.")
-
- - [Vampir](vampir.html)
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md b/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
deleted file mode 100644
index 84f199999ea24df87968404436b8c837b32fad38..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
+++ /dev/null
@@ -1,146 +0,0 @@
-
-Allinea Performance Reports
-===========================
-quick application profiling
-
-
-Introduction
-------------
-Allinea Performance Reports characterize the performance of HPC
-application runs. After executing your application through the tool, a
-synthetic HTML report is generated automatically, containing information
-about several metrics along with clear behavior statements and hints to
-help you improve the efficiency of your runs.
-The Allinea Performance Reports is most useful in profiling MPI
-programs.
-Our license is limited to 64 MPI processes.
-Modules
--------
-Allinea Performance Reports version 6.0 is available
- $ module load PerformanceReports/6.0
-The module sets up environment variables, required for using the Allinea
-Performance Reports. This particular command loads the default module,
-which is performance reports version 4.2.
-Usage
------
-Use the the perf-report wrapper on your (MPI) program.
-Instead of [running your MPI program the usual
-way](../mpi-1.html), use the the perf report wrapper
- $ perf-report mpirun ./mympiprog.x
-The mpi program will run as usual. The perf-report creates two
-additional files, in *.txt and *.html format, containing the
-performance report. Note that [demanding MPI codes should be run within
-the queue
-system](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
-Example
--------
-In this example, we will be profiling the mympiprog.x MPI program, using
-Allinea performance reports. Assume that the code is compiled with intel
-compilers and linked against intel MPI library
-First, we allocate some nodes via the express queue
- $ qsub -q qexp -l select=2ncpus=16mpiprocs=16ompthreads=1 -I
- qsub waiting for job 262197.dm2 to start
- qsub job 262197.dm2 ready
-Then we load the modules and run the program the usual way
- $ module load intel impi allinea-perf-report/4.2
- $ mpirun ./mympiprog.x
-Now lets profile the code
- $ perf-report mpirun ./mympiprog.x
-Performance report files
-[mympiprog_32p*.txt](mympiprog_32p_2014-10-15_16-56.txt)
-and
-[mympiprog_32p*.html](mympiprog_32p_2014-10-15_16-56.html)
-were created. We can see that the code is very efficient on MPI and is
-CPU bounded.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
- .navTreeFolderish
- .contenttype-folder}
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
-
- - [CUBE](cube.html)
-
- - [Intel Performance Counter
- Monitor](intel-performance-counter-monitor.html)
-
- - [Intel VTune
- Amplifier](intel-vtune-amplifier.html)
-
- - [PAPI](papi.html)
-
- - [Scalasca](scalasca.html)
-
- - [Score-P](score-p.html)
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
-
- - [Valgrind](valgrind.html "Valgrind is a tool for memory debugging and profiling.")
-
- - [Vampir](vampir.html)
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/debuggers/cube.md b/anselm-cluster-documentation/software/debuggers/cube.md
deleted file mode 100644
index 16c33e19fead704f78f518e881314d2ab0666b0b..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/debuggers/cube.md
+++ /dev/null
@@ -1,140 +0,0 @@
-CUBE
-====
-Introduction
-------------
-CUBE is a graphical performance report explorer for displaying data from
-Score-P and Scalasca (and other compatible tools). The name comes from
-the fact that it displays performance data in a three-dimensions
-- **performance metric**, where a number of metrics are available,
- such as communication time or cache misses,
-- **call path**, which contains the call tree of your program
-- s**ystem resource**, which contains system's nodes, processes and
- threads, depending on the parallel programming model.
-Each dimension is organized in a tree, for example the time performance
-metric is divided into Execution time and Overhead time, call path
-dimension is organized by files and routines in your source code etc.
-
-*Figure 1. Screenshot of CUBE displaying data from Scalasca.*
-*
-*Each node in the tree is colored by severity (the color scheme is
-displayed at the bottom of the window, ranging from the least severe
-blue to the most severe being red). For example in Figure 1, we can see
-that most of the point-to-point MPI communication happens in routine
-exch_qbc, colored red.
-Installed versions
-------------------
-Currently, there are two versions of CUBE 4.2.3 available as
-[modules](../../environment-and-modules.html)
-- cube/4.2.3-gcc,
- compiled with GCC
-- cube/4.2.3-icc,
- compiled with Intel compiler
-Usage
------
-CUBE is a graphical application. Refer to [Graphical User Interface
-documentation](resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html)
-for a list of methods to launch graphical applications on Anselm.
-Analyzing large data sets can consume large amount of CPU and RAM. Do
-not perform large analysis on login nodes.
-After loading the apropriate module, simply launch
-class="monospace">cube command, or alternatively you can use
-scalasca -examine command to launch the
-GUI. Note that for Scalasca datasets, if you do not analyze the data
-with scalasca
--examine before to opening them with CUBE, not all
-performance data will be available.
-Â References
-1.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
- .navTreeFolderish
- .contenttype-folder}
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
- - [CUBE](cube.html)
-
-
- - [Intel Performance Counter
- Monitor](intel-performance-counter-monitor.html)
-
- - [Intel VTune
- Amplifier](intel-vtune-amplifier.html)
-
- - [PAPI](papi.html)
-
- - [Scalasca](scalasca.html)
-
- - [Score-P](score-p.html)
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
-
- - [Valgrind](valgrind.html "Valgrind is a tool for memory debugging and profiling.")
-
- - [Vampir](vampir.html)
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md b/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
deleted file mode 100644
index 49161745acf2bbc178a3ca554b4a32d1fed4e916..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
+++ /dev/null
@@ -1,323 +0,0 @@
-Info
-
-Intel Performance Counter Monitor
-=================================
-Introduction
-------------
-Intel PCM (Performance Counter Monitor) is a tool to monitor performance
-hardware counters on Intel® processors, similar to
-[PAPI](papi.html). The difference between PCM and PAPI
-is that PCM supports only Intel hardware, but PCM can monitor also
-uncore metrics, like memory controllers and QuickPath Interconnect
-links.
-Installed version
-------------------------------
-Currently installed version 2.6. To load the
-[module](../../environment-and-modules.html), issue
- $ module load intelpcm
-Command line tools
-------------------
-PCM provides a set of tools to monitor system/or application.Â
-### pcm-memory
-Measures memory bandwidth of your application or the whole system.
-Usage
- $ pcm-memory.x |[external_program parameters]
-Specify either a delay of updates in seconds or an external program to
-monitor. If you get an error about PMU in use, respond "y" and relaunch
-the program.
-Sample output
- ---------------------------------------||---------------------------------------
- -- Socket 0 --||-- Socket 1 --
- ---------------------------------------||---------------------------------------
- ---------------------------------------||---------------------------------------
- ---------------------------------------||---------------------------------------
- -- Memory Performance Monitoring --||-- Memory Performance Monitoring --
- ---------------------------------------||---------------------------------------
- -- Mem Ch 0 Reads (MB/s) 2.44 --||-- Mem Ch 0 Reads (MB/s) 0.26 --
- -- Writes(MB/s) 2.16 --||-- Writes(MB/s) 0.08 --
- -- Mem Ch 1 Reads (MB/s) 0.35 --||-- Mem Ch 1 Reads (MB/s) 0.78 --
- -- Writes(MB/s) 0.13 --||-- Writes(MB/s) 0.65 --
- -- Mem Ch 2 Reads (MB/s) 0.32 --||-- Mem Ch 2 Reads (MB/s) 0.21 --
- -- Writes(MB/s) 0.12 --||-- Writes(MB/s) 0.07 --
- -- Mem Ch 3 Reads (MB/s) 0.36 --||-- Mem Ch 3 Reads (MB/s) 0.20 --
- -- Writes(MB/s) 0.13 --||-- Writes(MB/s) 0.07 --
- -- NODE0 Mem Read (MB/s) 3.47 --||-- NODE1 Mem Read (MB/s) 1.45 --
- -- NODE0 Mem Write (MB/s) 2.55 --||-- NODE1 Mem Write (MB/s) 0.88 --
- -- NODE0 P. Write (T/s) 31506 --||-- NODE1 P. Write (T/s) 9099 --
- -- NODE0 Memory (MB/s) 6.02 --||-- NODE1 Memory (MB/s) 2.33 --
- ---------------------------------------||---------------------------------------
- -- System Read Throughput(MB/s) 4.93 --
- -- System Write Throughput(MB/s) 3.43 --
- -- System Memory Throughput(MB/s) 8.35 --
- ---------------------------------------||---------------------------------------Â
-### pcm-msr
-Command pcm-msr.x can be used to
-read/write model specific registers of the CPU.
-### pcm-numa
-NUMA monitoring utility does not work on Anselm.
-### pcm-pcie
-Can be used to monitor PCI Express bandwith. Usage
-class="monospace">pcm-pcie.x <delay>
-### pcm-power
-Displays energy usage and thermal headroom for CPU and DRAM sockets.
-Usage  pcm-power.x <delay> |
-<external program>
-### pcm
-This command provides an overview of performance counters and memory
-usage. Usage  pcm.x
-<delay> | <external program>
-Sample output
- $ pcm.x ./matrix
- Intel(r) Performance Counter Monitor V2.6 (2013-11-04 134331 +0100 ID=db05e43)
- Copyright (c) 2009-2013 Intel Corporation
- Number of physical cores 16
- Number of logical cores 16
- Threads (logical cores) per physical core 1
- Num sockets 2
- Core PMU (perfmon) version 3
- Number of core PMU generic (programmable) counters 8
- Width of generic (programmable) counters 48 bits
- Number of core PMU fixed counters 3
- Width of fixed counters 48 bits
- Nominal core frequency 2400000000 Hz
- Package thermal spec power 115 Watt; Package minimum power 51 Watt; Package maximum power 180 Watt;
- Socket 0 1 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
- Socket 1 1 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
- Number of PCM instances 2
- Max QPI link speed 16.0 GBytes/second (8.0 GT/second)
- Detected Intel(R) Xeon(R) CPU E5-2665 0 @ 2.40GHz "Intel(r) microarchitecture codename Sandy Bridge-EP/Jaketown"
- Executing "./matrix" command
- Exit code 0
- EXEC instructions per nominal CPU cycle
- IPC instructions per CPU cycle
- FREQ relation to nominal CPU frequency='unhalted clock ticks'/'invariant timer ticks' (includes Intel Turbo Boost)
- AFREQ relation to nominal CPU frequency while in active state (not in power-saving C state)='unhalted clock ticks'/'invariant timer ticks while in C0-state' (includes Intel Turbo Boost)
- L3MISS L3 cache misses
- L2MISS L2 cache misses (including other core's L2 cache *hits*)
- L3HIT L3 cache hit ratio (0.00-1.00)
- L2HIT L2 cache hit ratio (0.00-1.00)
- L3CLK ratio of CPU cycles lost due to L3 cache misses (0.00-1.00), in some cases could be >1.0 due to a higher memory latency
- L2CLK ratio of CPU cycles lost due to missing L2 cache but still hitting L3 cache (0.00-1.00)
- READ bytes read from memory controller (in GBytes)
- WRITE bytes written to memory controller (in GBytes)
- TEMP Temperature reading in 1 degree Celsius relative to the TjMax temperature (thermal headroom) 0 corresponds to the max temperature
- Core (SKT) | EXEC | IPC | FREQ | AFREQ | L3MISS | L2MISS | L3HIT | L2HIT | L3CLK | L2CLK | READ | WRITE | TEMP
- 0 0 0.00 0.64 0.01 0.80 5592 11 K 0.49 0.13 0.32 0.06 N/A N/A 67
- 1 0 0.00 0.18 0.00 0.69 3086 5552 0.44 0.07 0.48 0.08 N/A N/A 68
- 2 0 0.00 0.23 0.00 0.81 300 562 0.47 0.06 0.43 0.08 N/A N/A 67
- 3 0 0.00 0.21 0.00 0.99 437 862 0.49 0.06 0.44 0.09 N/A N/A 73
- 4 0 0.00 0.23 0.00 0.93 293 559 0.48 0.07 0.42 0.09 N/A N/A 73
- 5 0 0.00 0.21 0.00 1.00 423 849 0.50 0.06 0.43 0.10 N/A N/A 69
- 6 0 0.00 0.23 0.00 0.94 285 558 0.49 0.06 0.41 0.09 N/A N/A 71
- 7 0 0.00 0.18 0.00 0.81 674 1130 0.40 0.05 0.53 0.08 N/A N/A 65
- 8 1 0.00 0.47 0.01 1.26 6371 13 K 0.51 0.35 0.31 0.07 N/A N/A 64
- 9 1 2.30 1.80 1.28 1.29 179 K 15 M 0.99 0.59 0.04 0.71 N/A N/A 60
- 10 1 0.00 0.22 0.00 1.26 315 570 0.45 0.06 0.43 0.08 N/A N/A 67
- 11 1 0.00 0.23 0.00 0.74 321 579 0.45 0.05 0.45 0.07 N/A N/A 66
- 12 1 0.00 0.22 0.00 1.25 305 570 0.46 0.05 0.42 0.07 N/A N/A 68
- 13 1 0.00 0.22 0.00 1.26 336 581 0.42 0.04 0.44 0.06 N/A N/A 69
- 14 1 0.00 0.22 0.00 1.25 314 565 0.44 0.06 0.43 0.07 N/A N/A 69
- 15 1 0.00 0.29 0.00 1.19 2815 6926 0.59 0.39 0.29 0.08 N/A N/A 69
- -------------------------------------------------------------------------------------------------------------------
- SKT 0 0.00 0.46 0.00 0.79 11 K 21 K 0.47 0.10 0.38 0.07 0.00 0.00 65
- SKT 1 0.29 1.79 0.16 1.29 190 K 15 M 0.99 0.59 0.05 0.70 0.01 0.01 61
- -------------------------------------------------------------------------------------------------------------------
- TOTAL * 0.14 1.78 0.08 1.28 201 K 15 M 0.99 0.59 0.05 0.70 0.01 0.01 N/A
- Instructions retired 1345 M ; Active cycles 755 M ; Time (TSC) 582 Mticks ; C0 (active,non-halted) core residency 6.30 %
- C1 core residency 0.14 %; C3 core residency 0.20 %; C6 core residency 0.00 %; C7 core residency 93.36 %;
- C2 package residency 48.81 %; C3 package residency 0.00 %; C6 package residency 0.00 %; C7 package residency 0.00 %;
- PHYSICAL CORE IPC 1.78 => corresponds to 44.50 % utilization for cores in active state
- Instructions per nominal CPU cycle 0.14 => corresponds to 3.60 % core utilization over time interval
- Intel(r) QPI data traffic estimation in bytes (data traffic coming to CPU/socket through QPI links)
- QPI0 QPI1 | QPI0 QPI1
- ----------------------------------------------------------------------------------------------
- SKT 0 0 0 | 0% 0%
- SKT 1 0 0 | 0% 0%
- ----------------------------------------------------------------------------------------------
- Total QPI incoming data traffic 0 QPI data traffic/Memory controller traffic 0.00
- Intel(r) QPI traffic estimation in bytes (data and non-data traffic outgoing from CPU/socket through QPI links)
- QPI0 QPI1 | QPI0 QPI1
- ----------------------------------------------------------------------------------------------
- SKT 0 0 0 | 0% 0%
- SKT 1 0 0 | 0% 0%
- ----------------------------------------------------------------------------------------------
- Total QPI outgoing data and non-data traffic 0
- ----------------------------------------------------------------------------------------------
- SKT 0 package consumed 4.06 Joules
- SKT 1 package consumed 9.40 Joules
- ----------------------------------------------------------------------------------------------
- TOTAL 13.46 Joules
- ----------------------------------------------------------------------------------------------
- SKT 0 DIMMs consumed 4.18 Joules
- SKT 1 DIMMs consumed 4.28 Joules
- ----------------------------------------------------------------------------------------------
- TOTAL 8.47 Joules
- Cleaning up
-Â
-### pcm-sensor
-Can be used as a sensor for ksysguard GUI, which is currently not
-installed on Anselm.Â
-API
----
-In a similar fashion to PAPI, PCM provides a C++ API to access the
-performance counter from within your application. Refer to the [doxygen
-documentation](http//intel-pcm-api-documentation.github.io/classPCM.html)
-for details of the API.
-Due to security limitations, using PCM API to monitor your applications
-is currently not possible on Anselm. (The application must be run as
-root user)
-Sample program using the API
- #include
- #include
- #include "cpucounters.h"
- #define SIZE 1000
- using namespace std;
- int main(int argc, char **argv) {
- float matrixa[SIZE][SIZE], matrixb[SIZE][SIZE], mresult[SIZE][SIZE];
- float real_time, proc_time, mflops;
- long long flpins;
- int retval;
- int i,j,k;
- PCM * m = PCMgetInstance();
- if (m->program() != PCMSuccess) return 1;
- SystemCounterState before_sstate = getSystemCounterState();
- /* Initialize the Matrix arrays */
- for ( i=0; i<SIZE*SIZE; i++ ){
- mresult[0][i] = 0.0;
- matrixa[0][i] = matrixb[0][i] = rand()*(float)1.1; }
- /* A naive Matrix-Matrix multiplication */
- for (i=0;i<SIZE;i++)
- for(j=0;j<SIZE;j++)
- for(k=0;k<SIZE;k++)
- mresult[i][j]=mresult[i][j] + matrixa[i][k]*matrixb[k][j];
- SystemCounterState after_sstate = getSystemCounterState();
- cout << "Instructions per clock" << getIPC(before_sstate,after_sstate)
- << "L3 cache hit ratio" << getL3CacheHitRatio(before_sstate,after_sstate)
- << "Bytes read" << getBytesReadFromMC(before_sstate,after_sstate);
- for (i=0; i<SIZE;i++)
- for (j=0; j<SIZE; j++)
- if (mresult[i][j] == -1) printf("x");
- return 0;
- }
-Compile it with
- $ icc matrix.cpp -o matrix -lpthread -lpcm
-Sample output Â
- $ ./matrix
- Number of physical cores 16
- Number of logical cores 16
- Threads (logical cores) per physical core 1
- Num sockets 2
- Core PMU (perfmon) version 3
- Number of core PMU generic (programmable) counters 8
- Width of generic (programmable) counters 48 bits
- Number of core PMU fixed counters 3
- Width of fixed counters 48 bits
- Nominal core frequency 2400000000 Hz
- Package thermal spec power 115 Watt; Package minimum power 51 Watt; Package maximum power 180 Watt;
- Socket 0 1 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
- Socket 1 1 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
- Number of PCM instances 2
- Max QPI link speed 16.0 GBytes/second (8.0 GT/second)
- Instructions per clock1.7
- L3 cache hit ratio1.0
- Bytes read12513408
-References
-----------
-1.
-2.  Intel®
- Xeon® Processor E5-2600 Product Family Uncore Performance
- Monitoring Guide.
-3. Â API
- Documentation
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
- .navTreeFolderish
- .contenttype-folder}
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
- - [CUBE](cube.html)
-
- - [Intel Performance Counter
- Monitor](intel-performance-counter-monitor.html)
-
-
- - [Intel VTune
- Amplifier](intel-vtune-amplifier.html)
-
- - [PAPI](papi.html)
-
- - [Scalasca](scalasca.html)
-
- - [Score-P](score-p.html)
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
-
- - [Valgrind](valgrind.html "Valgrind is a tool for memory debugging and profiling.")
-
- - [Vampir](vampir.html)
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md b/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
deleted file mode 100644
index 77d6c93e1c1e243f44358b48eceb3eb1c8575b35..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
+++ /dev/null
@@ -1,172 +0,0 @@
-Intel VTune Amplifier
-=====================
-
-
-Introduction
-------------
-Intel*® *VTune™ Amplifier, part of Intel Parallel studio, is a GUI
-profiling tool designed for Intel processors. It offers a graphical
-performance analysis of single core and multithreaded applications. A
-highlight of the features
-- Hotspot analysis
-- Locks and waits analysis
-- Low level specific counters, such as branch analysis and memory
- bandwidth
-- Power usage analysis - frequency and sleep states.
-
-Usage
------
-To launch the GUI, first load the module
- $ module add VTune/2016_update1
-and launch the GUI
- $Â amplxe-gui
-To profile an application with VTune Amplifier, special kernel
-modules need to be loaded. The modules are not loaded on Anselm login
-nodes, thus direct profiling on login nodes is not possible. Use VTune
-on compute nodes and refer to the documentation on [using GUI
-applications](resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html).
-The GUI will open in new window. Click on "*New Project...*" to
-create a new project. After clicking *OK*, a new window with project
-properties will appear. Â At "*Application*", select the bath to your
-binary you want to profile (the binary should be compiled with -g flag).
-Some additional options such as command line arguments can be selected.
-At "*Managed code profiling mode*" select "*Native*" (unless you want
-to profile managed mode .NET/Mono applications). After clicking *OK*,
-your project is created.
-To run a new analysis, click "*New analysis...*". You will see a list of
-possible analysis. Some of them will not be possible on the current CPU
-(eg. Intel Atom analysis is not possible on Sandy Bridge CPU), the GUI
-will show an error box if you select the wrong analysis. For example,
-select "*Advanced Hotspots*". Clicking on *Start *will start profiling
-of the application.
-Remote Analysis
----------------
-VTune Amplifier also allows a form of remote analysis. In this mode,
-data for analysis is collected from the command line without GUI, and
-the results are then loaded to GUI on another machine. This allows
-profiling without interactive graphical jobs. To perform a remote
-analysis, launch a GUI somewhere, open the new analysis window and then
-click the button "*Command line*" in bottom right corner. It will show
-the command line needed to perform the selected analysis.
-The command line will look like this
- /apps/all/VTune/2016_update1/vtune_amplifier_xe_2016.1.1.434111/bin64/amplxe-cl -collect advanced-hotspots -knob collection-detail=stack-and-callcount -mrte-mode=native -target-duration-type=veryshort -app-working-dir /home/sta545/test -- /home/sta545/test_pgsesv
-Copy the line to clipboard and then you can paste it in your jobscript
-or in command line. After the collection is run, open the GUI once
-again, click the menu button in the upper right corner, and select
-"*Open > Result...*". The GUI will load the results from the run.
-Xeon Phi
---------
-This section is outdated. It will be updated with new information soon.
-It is possible to analyze both native and offload Xeon Phi applications.
-For offload mode, just specify the path to the binary. For native mode,
-you need to specify in project properties
-Application ssh
-Application parameters mic0 source ~/.profile
-&& /path/to/your/bin
-Note that we include source ~/.profile
-in the command to setup environment paths [as described
-here](../intel-xeon-phi.html).Â
-If the analysis is interrupted or aborted, further analysis on the card
-might be impossible and you will get errors like "ERROR connecting to
-MIC card". In this case please contact our support to reboot the MIC
-card.
-You may also use remote analysis to collect data from the MIC and then
-analyze it in the GUI later
- $ amplxe-cl -collect knc-hotspots -no-auto-finalize -- ssh mic0
- "export LD_LIBRARY_PATH=/apps/intel/composer_xe_2015.2.164/compiler/lib/mic//apps/intel/composer_xe_2015.2.164/mkl/lib/mic/; export KMP_AFFINITY=compact; /tmp/app.mic"
-References
-----------
-1. Â Performance
- Tuning for Intel® Xeon Phi™ Coprocessors
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
- .navTreeFolderish
- .contenttype-folder}
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
- - [CUBE](cube.html)
-
- - [Intel Performance Counter
- Monitor](intel-performance-counter-monitor.html)
-
- - [Intel VTune
- Amplifier](intel-vtune-amplifier.html)
-
-
- - [PAPI](papi.html)
-
- - [Scalasca](scalasca.html)
-
- - [Score-P](score-p.html)
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
-
- - [Valgrind](valgrind.html "Valgrind is a tool for memory debugging and profiling.")
-
- - [Vampir](vampir.html)
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/debuggers/mympiprog_32p_2014-10-15_16-56.md b/anselm-cluster-documentation/software/debuggers/mympiprog_32p_2014-10-15_16-56.md
deleted file mode 100644
index 382bda93cf7877a8ac1fdab620de66bc2741fc57..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/debuggers/mympiprog_32p_2014-10-15_16-56.md
+++ /dev/null
@@ -1,10 +0,0 @@
-88.6%
-Time spent running application code. High values are usually good.
-This is high; check the CPU performance section for optimization advice.
-MPI
-11.4%
-Time spent in MPI calls. High values are usually bad.
-This is very low; this code may benefit from increasing the process count.
-I/O
-0.0%
-Time spent in filesystem I/O. High values are usually bad.
diff --git a/anselm-cluster-documentation/software/debuggers/papi.md b/anselm-cluster-documentation/software/debuggers/papi.md
deleted file mode 100644
index 1c350c4c6e6ae752e11db58adecd5e427c7057c5..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/debuggers/papi.md
+++ /dev/null
@@ -1,295 +0,0 @@
-PAPI
-====
-
-
-Introduction
-------------
-Performance Application Programming
-Interface (PAPI)  is a portable interface to access
-hardware performance counters (such as instruction counts and cache
-misses) found in most modern architectures. With the new component
-framework, PAPI is not limited only to CPU counters, but offers also
-components for CUDA, network, Infiniband etc.
-PAPI provides two levels of interface - a simpler, high level
-interface and more detailed low level interface.
-PAPI can be used with parallel as well as serial programs.
-Usage
------
-To use PAPI, load
-[module](../../environment-and-modules.html)
-class="monospace">papi
- $ module load papi
-This will load the default version. Execute
-class="monospace">module avail papi for a list of installed
-versions.
-Utilites
---------
-The bin directory of PAPI (which is
-automatically added to $PATH upon
-loading the module) contains various utilites.
-### papi_avail
-Prints which preset events are available on the current CPU. The third
-column indicated whether the preset event is available on the current
-CPU.
- $ papi_avail
- Available events and hardware information.
- --------------------------------------------------------------------------------
- PAPI Version 5.3.2.0
- Vendor string and code GenuineIntel (1)
- Model string and code Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz (45)
- CPU Revision 7.000000
- CPUID Info Family 6 Model 45 Stepping 7
- CPU Max Megahertz 2601
- CPU Min Megahertz 1200
- Hdw Threads per core 1
- Cores per Socket 8
- Sockets 2
- NUMA Nodes 2
- CPUs per Node 8
- Total CPUs 16
- Running in a VM no
- Number Hardware Counters 11
- Max Multiplex Counters 32
- --------------------------------------------------------------------------------
- Name Code Avail Deriv Description (Note)
- PAPI_L1_DCM 0x80000000 Yes No Level 1 data cache misses
- PAPI_L1_ICM 0x80000001 Yes No Level 1 instruction cache misses
- PAPI_L2_DCM 0x80000002 Yes Yes Level 2 data cache misses
- PAPI_L2_ICM 0x80000003 Yes No Level 2 instruction cache misses
- PAPI_L3_DCM 0x80000004 No No Level 3 data cache misses
- PAPI_L3_ICM 0x80000005 No No Level 3 instruction cache misses
- PAPI_L1_TCM 0x80000006 Yes Yes Level 1 cache misses
- PAPI_L2_TCM 0x80000007 Yes No Level 2 cache misses
- PAPI_L3_TCM 0x80000008 Yes No Level 3 cache misses
- ....Â
-### papi_native_avail
-Prints which native events are available on the current
-CPU.
-### papi_cost
-Measures the cost (in cycles) of basic PAPI operations.
-### papi_mem_info
-Prints information about the memory architecture of the current
-CPU.
-PAPI API
---------
-PAPI provides two kinds of eventsÂ
-- **Preset events** is a set of predefined common CPU events,
- standardized across platforms.
-- **Native events **is a set of all events supported by the
- current hardware. This is a larger set of features than preset. For
- other components than CPU, only native events are usually available.
-To use PAPI in your application, you need to link the appropriate
-include file.
-- papi.h for C
-- f77papi.h for Fortran 77
-- f90papi.h for Fortran 90
-- fpapi.h for Fortran with preprocessor
-The include path is automatically added by papi module to
-class="monospace">$INCLUDE.
-### High level API
-Please refer
-to  for a
-description of the High level API.
-### Low level API
-Please refer
-to  for a
-description of the Low level API.
-### Timers
-PAPI provides the most accurate timers the platform can support.
-SeeÂ
-### System information
-PAPI can be used to query some system infromation, such as CPU name and
-MHz.
-SeeÂ
-Example
--------
-The following example prints MFLOPS rate of a naive matrix-matrix
-multiplication
- #include
- #include
- #include "papi.h"
- #define SIZE 1000
- int main(int argc, char **argv) {
- float matrixa[SIZE][SIZE], matrixb[SIZE][SIZE], mresult[SIZE][SIZE];
- float real_time, proc_time, mflops;
- long long flpins;
- int retval;
- int i,j,k;
- /* Initialize the Matrix arrays */
- for ( i=0; i<SIZE*SIZE; i++ ){
- mresult[0][i] = 0.0;
- matrixa[0][i] = matrixb[0][i] = rand()*(float)1.1;Â
- }
- Â
- /* Setup PAPI library and begin collecting data from the counters */
- if((retval=PAPI_flops( &real_time, &proc_time, &flpins, &mflops))<PAPI_OK)
- printf("Error!");
- /* A naive Matrix-Matrix multiplication */
- for (i=0;i<SIZE;i++)
- for(j=0;j<SIZE;j++)
- for(k=0;k<SIZE;k++)
- mresult[i][j]=mresult[i][j] + matrixa[i][k]*matrixb[k][j];
- /* Collect the data into the variables passed in */
- if((retval=PAPI_flops( &real_time, &proc_time, &flpins, &mflops))<PAPI_OK)
- printf("Error!");
-
- printf("Real_timet%fnProc_timet%fnTotal flpinst%lldnMFLOPStt%fn", real_time, proc_time, flpins, mflops);
- PAPI_shutdown();
- return 0;
- }
-Â Now compile and run the example
- $ gcc matrix.c -o matrix -lpapi
- $ ./matrix
- Real_time 8.852785
- Proc_time 8.850000
- Total flpins 6012390908
- MFLOPS 679.366211Â
-Let's try with optimizations enabled
- $ gcc -O3 matrix.c -o matrix -lpapi
- $ ./matrix
- Real_time 0.000020
- Proc_time 0.000000
- Total flpins 6
- MFLOPS inf
-Now we see a seemingly strange result - the multiplication took no time
-and only 6 floating point instructions were issued. This is because the
-compiler optimizations have completely removed the multiplication loop,
-as the result is actually not used anywhere in the program. We can fix
-this by adding some "dummy" code at the end of the Matrix-Matrix
-multiplication routine
- for (i=0; i<SIZE;i++)
- for (j=0; j<SIZE; j++)
- if (mresult[i][j] == -1.0) printf("x");
-Now the compiler won't remove the multiplication loop. (However it is
-still not that smart to see that the result won't ever be negative). Now
-run the code again
- $ gcc -O3 matrix.c -o matrix -lpapi
- $ ./matrix
- Real_time 8.795956
- Proc_time 8.790000
- Total flpins 18700983160
- MFLOPS 2127.529297Â
-### Intel Xeon Phi
-PAPI currently supports only a subset of counters on the Intel Xeon Phi
-processor compared to Intel Xeon, for example the floating point
-operations counter is missing.
-To use PAPI in [Intel Xeon
-Phi](../intel-xeon-phi.html)Â native applications, you
-need to load module with "-mic" suffix,
-for example "papi/5.3.2-mic"
- $ module load papi/5.3.2-mic
-Then, compile your application in the following way
- $ module load intel
- $ icc -mmic -Wl,-rpath,/apps/intel/composer_xe_2013.5.192/compiler/lib/mic matrix-mic.c -o matrix-mic -lpapi -lpfm
-To execute the application on MIC, you need to manually setÂ
-class="monospace">LD_LIBRARY_PATH
- $Â qsub -q qmic -A NONE-0-0 -I
- $ ssh mic0
- $ export LD_LIBRARY_PATH=/apps/tools/papi/5.4.0-mic/lib/Â
- $ ./matrix-micÂ
-Alternatively, you can link PAPI statically (
-class="monospace">-static flag), then
-class="monospace">LD_LIBRARY_PATH does not need to be set.
-You can also execute the PAPI tools on MIC
- $ /apps/tools/papi/5.4.0-mic/bin/papi_native_avail
-To use PAPI in offload mode, you need to provide both host and MIC
-versions of PAPI
- $ module load papi/5.4.0
- $ icc matrix-offload.c -o matrix-offload -offload-option,mic,compiler,"-L$PAPI_HOME-mic/lib -lpapi" -lpapi
-References
-----------
-1. Â Main project page
-2. Â Wiki
-3. API Documentation
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
- .navTreeFolderish
- .contenttype-folder}
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
- - [CUBE](cube.html)
-
- - [Intel Performance Counter
- Monitor](intel-performance-counter-monitor.html)
-
- - [Intel VTune
- Amplifier](intel-vtune-amplifier.html)
-
- - [PAPI](papi.html)
-
-
- - [Scalasca](scalasca.html)
-
- - [Score-P](score-p.html)
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
-
- - [Valgrind](valgrind.html "Valgrind is a tool for memory debugging and profiling.")
-
- - [Vampir](vampir.html)
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/debuggers/scalasca.md b/anselm-cluster-documentation/software/debuggers/scalasca.md
deleted file mode 100644
index ce4ed7bcc8fc37277288acb17d3cdb226e8b9afc..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/debuggers/scalasca.md
+++ /dev/null
@@ -1,169 +0,0 @@
-Scalasca
-========
-Introduction
--------------------------
-[Scalasca](http//www.scalasca.org/) is a software tool
-that supports the performance optimization of parallel programs by
-measuring and analyzing their runtime behavior. The analysis identifies
-potential performance bottlenecks – in particular those concerning
-communication and synchronization – and offers guidance in exploring
-their causes.
-Scalasca supports profiling of MPI, OpenMP and hybrid MPI+OpenMP
-applications.
-Installed versions
-------------------
-There are currently two versions of Scalasca 2.0
-[modules](../../environment-and-modules.html) installed
-on Anselm
--
- class="monospace">scalasca2/2.0-gcc-openmpi, for usage with
- [GNU Compiler](../compilers.html) and
- [OpenMPI](../mpi-1/Running_OpenMPI.html),
--
- class="monospace">scalasca2/2.0-icc-impi, for usage with
- [Intel Compiler](../compilers.html) and [Intel
- MPI](../mpi-1/running-mpich2.html).
-Usage
------
-Profiling a parallel application with Scalasca consists of three steps
-1. Instrumentation, compiling the application such way, that the
- profiling data can be generated.
-2. Runtime measurement, running the application with the Scalasca
- profiler to collect performance data.
-3. Analysis of reports
-### Instrumentation
-Instrumentation via "scalasca
--instrument" is discouraged. Use [Score-P
-instrumentation](score-p.html).
-### Runtime measurement
-After the application is instrumented, runtime measurement can be
-performed with the "scalasca -analyze"
-command. The syntax is
-scalasca -analyze [scalasca options]
-[launcher] [launcher options] [program] [program options]
-An example
- $ scalasca -analyze mpirun -np 4 ./mympiprogram
-Some notable Scalsca options are
--t Enable trace data collection. By default, only summary data are
-collected.
--e <directory> Specify a directory to save the collected data to.
-By default, Scalasca saves the data to a directory with
-prefix scorep_, followed by name of the executable and launch
-configuration.
-
-Scalasca can generate a huge amount of data, especially if tracing is
-enabled. Please consider saving the data to a [scratch
-directory](../../storage-1/storage.html).
-### Analysis of reports
-For the analysis, you must have [Score-P](score-p.html)
-and [CUBE](cube.html) modules loaded. The analysis is
-done in two steps, first, the data is preprocessed and then CUBE GUI
-tool is launched.
-To launch the analysis, run
-``` {.fragment}
-scalasca -examine [options]
-```
-If you do not wish to launch the GUI tool, use the "-s" option
-``` {.fragment}
-scalasca -examine -s
-```
-Alternatively you can open CUBE and load the data directly from here.
-Keep in mind that in that case the preprocessing is not done and not all
-metrics will be shown in the viewer.
-Refer to [CUBE documentation](cube.html)Â on usage of the
-GUI viewer.
-References
-----------
-1.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
- .navTreeFolderish
- .contenttype-folder}
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
- - [CUBE](cube.html)
-
- - [Intel Performance Counter
- Monitor](intel-performance-counter-monitor.html)
-
- - [Intel VTune
- Amplifier](intel-vtune-amplifier.html)
-
- - [PAPI](papi.html)
-
- - [Scalasca](scalasca.html)
-
-
- - [Score-P](score-p.html)
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
-
- - [Valgrind](valgrind.html "Valgrind is a tool for memory debugging and profiling.")
-
- - [Vampir](vampir.html)
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/debuggers/score-p.md b/anselm-cluster-documentation/software/debuggers/score-p.md
deleted file mode 100644
index fe0c00cd310a12542e3dbcc410460094715815bf..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/debuggers/score-p.md
+++ /dev/null
@@ -1,208 +0,0 @@
-Score-P
-=======
-Introduction
-------------
-The [Score-P measurement
-infrastructure](http//www.vi-hps.org/projects/score-p/)
-is a highly scalable and easy-to-use tool suite for profiling, event
-tracing, and online analysis of HPC applications.Â
-Score-P can be used as an instrumentation tool for
-[Scalasca](scalasca.html).
-Installed versions
-------------------
-There are currently two versions of Score-P version 1.2.6
-[modules](../../environment-and-modules.html)Â installed
-on Anselm
-- scorep/1.2.3-gcc-openmpi, for usage
- with [GNU
- Compiler](../compilers.html) and [OpenMPI](../mpi-1/Running_OpenMPI.html),
-- scorep/1.2.3-icc-impi, for usage
- with [Intel
- Compiler](../compilers.html) and [Intel
- MPI](../mpi-1/running-mpich2.html).
-Instrumentation
----------------
-There are three ways to instrument your parallel applications in
-order to enable performance data collection
-1. Automated instrumentation using compiler
-2. Manual instrumentation using API calls
-3. Manual instrumentation using directives
-### Automated instrumentation
-is the easiest method. Score-P will automatically add instrumentation to
-every routine entry and exit using compiler hooks, and will intercept
-MPI calls and OpenMP regions. This method might, however, produce a
-large number of data. If you want to focus on profiler a specific
-regions of your code, consider using the manual instrumentation methods.
-To use automated instrumentation, simply prepend
-class="monospace">scorep to your compilation command. For
-example, replace Â
-``` {.fragment}
-$ mpif90 -c foo.f90
-$ mpif90 -c bar.f90
-$ mpif90 -o myapp foo.o bar.o
-```
-with
-``` {.fragment}
-$ scorep mpif90 -c foo.f90
-$ scorep mpif90 -c bar.f90
-$ scorep mpif90 -o myapp foo.o bar.o
-```
-Usually your program is compiled using a Makefile or similar script, so
-it advisable to add the scorep command to
-your definition of variables CC,
-class="monospace">CXX, FCC etc.
-It is important that scorep is prepended
-also to the linking command, in order to link with Score-P
-instrumentation libraries.
-### Manual instrumentation using API calls
-To use this kind of instrumentation, use
-class="monospace">scorep with switch
-class="monospace">--user. You will then mark regions to be
-instrumented by inserting API calls.
-An example in C/C++
- #include
- void foo()
- {
- SCOREP_USER_REGION_DEFINE( my_region_handle )
- // more declarations
- SCOREP_USER_REGION_BEGIN( my_region_handle, "foo", SCOREP_USER_REGION_TYPE_COMMON )
- // do something
- SCOREP_USER_REGION_END( my_region_handle )
- }
-Â and Fortran
- #include "scorep/SCOREP_User.inc"
- subroutine foo
- SCOREP_USER_REGION_DEFINE( my_region_handle )
- ! more declarations
- SCOREP_USER_REGION_BEGIN( my_region_handle, "foo", SCOREP_USER_REGION_TYPE_COMMON )
- ! do something
- SCOREP_USER_REGION_END( my_region_handle )
- end subroutine foo
-Please refer to the [documentation for description of the
-API](https//silc.zih.tu-dresden.de/scorep-current/pdf/scorep.pdf).
-### Manual instrumentation using directives
-This method uses POMP2 directives to mark regions to be instrumented. To
-use this method, use command scorep
---pomp.
-Example directives in C/C++
- void foo(...)
- {
- /* declarations */
- #pragma pomp inst begin(foo)
- ...
- if ()
- {
- #pragma pomp inst altend(foo)
- return;
- }
- ...
- #pragma pomp inst end(foo)
- }
-and in Fortran
- subroutine foo(...)
- !declarations
- !POMP$ INST BEGIN(foo)
- ...
- if () then
- !POMP$ INST ALTEND(foo)
- return
- end if
- ...
- !POMP$ INST END(foo)
- end subroutine foo
-The directives are ignored if the program is compiled without Score-P.
-Again, please refer to the
-[documentation](https//silc.zih.tu-dresden.de/scorep-current/pdf/scorep.pdf)
-for a more elaborate description.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
- .navTreeFolderish
- .contenttype-folder}
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
- - [CUBE](cube.html)
-
- - [Intel Performance Counter
- Monitor](intel-performance-counter-monitor.html)
-
- - [Intel VTune
- Amplifier](intel-vtune-amplifier.html)
-
- - [PAPI](papi.html)
-
- - [Scalasca](scalasca.html)
-
- - [Score-P](score-p.html)
-
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
-
- - [Valgrind](valgrind.html "Valgrind is a tool for memory debugging and profiling.")
-
- - [Vampir](vampir.html)
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/debuggers/summary.md b/anselm-cluster-documentation/software/debuggers/summary.md
deleted file mode 100644
index b989d14d827e999a1538eb8f2e9245990bb33f26..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/debuggers/summary.md
+++ /dev/null
@@ -1,152 +0,0 @@
-
-
-Introduction
-------------
-We provide state of the art programms and tools to develop, profile and
-debug HPC codes at IT4Innovations.
-On these pages, we provide an overview of the profiling and debugging
-tools available on Anslem at IT4I.
-Intel debugger
---------------
-The intel debugger version 13.0 is available, via module intel. The
-debugger works for applications compiled with C and C++ compiler and the
-ifort fortran 77/90/95 compiler. The debugger provides java GUI
-environment. Use [X
-display](resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html)
-for running the GUI.
- $ module load intel
- $ idb
-Read more at the [Intel
-Debugger](../intel-suite/intel-debugger.html) page.
-Allinea Forge (DDT/MAP)
------------------------
-Allinea DDT, is a commercial debugger primarily for debugging parallel
-MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel
-Xeon Phi accelerators. DDT provides all the standard debugging features
-(stack trace, breakpoints, watches, view variables, threads etc.) for
-every thread running as part of your program, or for every process -
-even if these processes are distributed across a cluster using an MPI
-implementation.
- $ module load Forge
- $ forge
-Read more at the [Allinea DDT](allinea-ddt.html) page.
-Allinea Performance Reports
----------------------------
-Allinea Performance Reports characterize the performance of HPC
-application runs. After executing your application through the tool, a
-synthetic HTML report is generated automatically, containing information
-about several metrics along with clear behavior statements and hints to
-help you improve the efficiency of your runs. Our license is limited to
-64 MPI processes.
- $ module load PerformanceReports/6.0
- $ perf-report mpirun -n 64 ./my_application argument01 argument02
-Read more at the [Allinea Performance
-Reports](allinea-performance-reports.html) page.
-RougeWave Totalview
--------------------
-TotalView is a source- and machine-level debugger for multi-process,
-multi-threaded programs. Its wide range of tools provides ways to
-analyze, organize, and test programs, making it easy to isolate and
-identify problems in individual threads and processes in programs of
-great complexity.
- $ module load totalview
- $ totalview
-Read more at the [Totalview](total-view.html) page.
-Vampir trace analyzer
----------------------
-Vampir is a GUI trace analyzer for traces in OTF format.
- $ module load Vampir/8.5.0
- $ vampir
-Read more at
-the [Vampir](../../../salomon/software/debuggers/vampir.html) page.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
-
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
- - [CUBE](cube.html)
-
- - [Intel Performance Counter
- Monitor](intel-performance-counter-monitor.html)
-
- - [Intel VTune
- Amplifier](intel-vtune-amplifier.html)
-
- - [PAPI](papi.html)
-
- - [Scalasca](scalasca.html)
-
- - [Score-P](score-p.html)
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
-
- - [Valgrind](valgrind.html "Valgrind is a tool for memory debugging and profiling.")
-
- - [Vampir](vampir.html)
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/debuggers/total-view.md b/anselm-cluster-documentation/software/debuggers/total-view.md
deleted file mode 100644
index e9ffe43332a0b0e7d22568d156fac531618574f7..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/debuggers/total-view.md
+++ /dev/null
@@ -1,201 +0,0 @@
-Total View
-==========
-TotalView is a GUI-based source code multi-process, multi-thread
-debugger.
-License and Limitations for Anselm Users
-----------------------------------------
-On Anselm users can debug OpenMP or MPI code that runs up to 64 parallel
-processes. These limitation means that
-
-Â Â Â 1 user can debug up 64 processes, or
-Â Â Â 32 users can debug 2 processes, etc.
-
-Debugging of GPU accelerated codes is also supported.
-You can check the status of the licenses here
- cat /apps/user/licenses/totalview_features_state.txt
- # totalview
- # -------------------------------------------------
- # FEATUREÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â TOTALÂ Â USEDÂ AVAIL
- # -------------------------------------------------
- TotalView_Team                    64     0    64
- Replay                            64     0    64
- CUDAÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â 64Â Â Â Â Â 0Â Â Â Â 64
-Compiling Code to run with TotalView
-------------------------------------
-### Modules
-Load all necessary modules to compile the code. For example
- module load intel
- module load impi  ... or ... module load openmpi/X.X.X-icc
-Load the TotalView module
- module load totalview/8.12
-Compile the code
- mpicc -g -O0 -o test_debug test.c
- mpif90 -g -O0 -o test_debug test.f
-### Compiler flags
-Before debugging, you need to compile your code with theses flags
-**-g** Generates extra debugging information usable by GDB. -g3
-includes even more debugging information. This option is available for
-GNU and INTEL C/C++ and Fortran compilers.
-
-**-O0** Suppress all optimizations.
-Starting a Job with TotalView
------------------------------
-Be sure to log in with an X window forwarding enabled. This could mean
-using the -X in the sshÂ
- ssh -X username@anselm.it4i.cz
-Other options is to access login node using VNC. Please see the detailed
-information on how to use graphic user interface on Anselm
-[here](resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html#VNC).
-From the login node an interactive session with X windows forwarding (-X
-option) can be started by following command
- qsub -I -X -A NONE-0-0 -q qexp -lselect=1ncpus=16mpiprocs=16,walltime=010000
-Then launch the debugger with the totalview command followed by the name
-of the executable to debug.
-### Debugging a serial code
-To debug a serial code use
- totalview test_debug
-### Debugging a parallel code - option 1
-To debug a parallel code compiled with **OpenMPI** you need
-to setup your TotalView environmentÂ
-**Please note** To be able to run parallel debugging procedure from the
-command line without stopping the debugger in the mpiexec source code
-you have to add the following function to your **~/.tvdrc** file
- proc mpi_auto_run_starter {loaded_id} {
- Â Â Â set starter_programs {mpirun mpiexec orterun}
- Â Â Â set executable_name [TVsymbol get $loaded_id full_pathname]
- Â Â Â set file_component [file tail $executable_name]
- Â Â Â if {[lsearch -exact $starter_programs $file_component] != -1} {
- Â Â Â Â Â Â Â puts "**************************************"
- Â Â Â Â Â Â Â puts "Automatically starting $file_component"
- Â Â Â Â Â Â Â puts "**************************************"
- Â Â Â Â Â Â Â dgo
- Â Â Â }
- }
- # Append this function to TotalView's image load callbacks so that
- # TotalView run this program automatically.
- dlappend TVimage_load_callbacks mpi_auto_run_starter
-The source code of this function can be also found in
- /apps/mpi/openmpi/intel/1.6.5/etc/openmpi-totalview.tcl
-You can also add only following line to you ~/.tvdrc file instead of
-the entire function
-
-**source /apps/mpi/openmpi/intel/1.6.5/etc/openmpi-totalview.tcl**
-You need to do this step only once.
-Now you can run the parallel debugger using
- mpirun -tv -n 5 ./test_debug
-When following dialog appears click on "Yes"
-
-At this point the main TotalView GUI window will appear and you can
-insert the breakpoints and start debugging
-
-### Debugging a parallel code - option 2
-Other option to start new parallel debugging session from a command line
-is to let TotalView to execute mpirun by itself. In this case user has
-to specify a MPI implementation used to compile the source code.Â
-The following example shows how to start debugging session with Intel
-MPI
- module load intel/13.5.192 impi/4.1.1.036 totalview/8/13
- totalview -mpi "Intel MPI-Hydra" -np 8 ./hello_debug_impi
-After running previous command you will see the same window as shown in
-the screenshot above.
-More information regarding the command line parameters of the TotalView
-can be found TotalView Reference Guide, Chapter 7 TotalView Command
-Syntax. Â
-Documentation
--------------
-[1] The [TotalView
-documentation](http//www.roguewave.com/support/product-documentation/totalview-family.aspx#totalview)
-web page is a good resource for learning more about some of the advanced
-TotalView features.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
- .navTreeFolderish
- .contenttype-folder}
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
- - [CUBE](cube.html)
-
- - [Intel Performance Counter
- Monitor](intel-performance-counter-monitor.html)
-
- - [Intel VTune
- Amplifier](intel-vtune-amplifier.html)
-
- - [PAPI](papi.html)
-
- - [Scalasca](scalasca.html)
-
- - [Score-P](score-p.html)
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
-
-
- - [Valgrind](valgrind.html "Valgrind is a tool for memory debugging and profiling.")
-
- - [Vampir](vampir.html)
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/debuggers/valgrind.md b/anselm-cluster-documentation/software/debuggers/valgrind.md
deleted file mode 100644
index 6f3912de28fc80579bf484487308d454daa60deb..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/debuggers/valgrind.md
+++ /dev/null
@@ -1,343 +0,0 @@
-Valgrind
-========
-Valgrind is a tool for memory debugging and profiling.
-About Valgrind
---------------
-Valgrind is an open-source tool, used mainly for debuggig memory-related
-problems, such as memory leaks, use of uninitalized memory etc. in C/C++
-applications. The toolchain was however extended over time with more
-functionality, such as debugging of threaded applications, cache
-profiling, not limited only to C/C++.
-Valgind is an extremely useful tool for debugging memory errors such as
-[off-by-one](http//en.wikipedia.org/wiki/Off-by-one_error).
-Valgrind uses a virtual machine and dynamic recompilation of binary
-code, because of that, you can expect that programs being debugged by
-Valgrind run 5-100 times slower.
-The main tools available in Valgrind are
-- **Memcheck**, the original, must used and default tool. Verifies
- memory access in you program and can detect use of unitialized
- memory, out of bounds memory access, memory leaks, double free, etc.
-- **Massif**, a heap profiler.
-- **Hellgrind** and **DRD** can detect race conditions in
- multi-threaded applications.
-- **Cachegrind**, a cache profiler.
-- **Callgrind**, a callgraph analyzer.
-- For a full list and detailed documentation, please refer to the
- [official Valgrind
- documentation](http//valgrind.org/docs/).
-Installed versions
-------------------
-There are two versions of Valgrind available on Anselm.
-- Version 3.6.0, installed by operating system vendor
- in /usr/bin/valgrind.
- This version is available by default, without the need
- to load any module. This version however does not provide additional
- MPI support.
-- Version 3.9.0 with support for Intel MPI, available in
- [module](../../environment-and-modules.html)Â
- class="monospace">valgrind/3.9.0-impi. After loading the
- module, this version replaces the default valgrind.
-Usage
------
-Compile the application which you want to debug as usual. It is
-advisable to add compilation flags -g (to
-add debugging information to the binary so that you will see original
-source code lines in the output) and -O0
-(to disable compiler optimizations).Â
-For example, lets look at this C code, which has two problems
- #include
- void f(void)
- {
- int* x = malloc(10 * sizeof(int));
- x[10] = 0; // problem 1 heap block overrun
- } // problem 2 memory leak -- x not freed
- int main(void)
- {
- f();
- return 0;
- }
-Now, compile it with Intel compiler
- $ module add intel
- $ icc -g valgrind-example.c -o valgrind-exampleÂ
-Now, lets run it with Valgrind. The syntax is
-valgrind [valgrind options] <your program
-binary> [your program options]
-If no Valgrind options are specified, Valgrind defaults to running
-Memcheck tool. Please refer to the Valgrind documentation for a full
-description of command line options.
- $ valgrind ./valgrind-example
- ==12652== Memcheck, a memory error detector
- ==12652== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
- ==12652== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info
- ==12652== Command ./valgrind-example
- ==12652==
- ==12652== Invalid write of size 4
- ==12652== at 0x40053E f (valgrind-example.c6)
- ==12652== by 0x40054E main (valgrind-example.c11)
- ==12652== Address 0x5861068 is 0 bytes after a block of size 40 alloc'd
- ==12652== at 0x4C27AAA malloc (vg_replace_malloc.c291)
- ==12652== by 0x400528 f (valgrind-example.c5)
- ==12652== by 0x40054E main (valgrind-example.c11)
- ==12652==
- ==12652==
- ==12652== HEAP SUMMARY
- ==12652== in use at exit 40 bytes in 1 blocks
- ==12652== total heap usage 1 allocs, 0 frees, 40 bytes allocated
- ==12652==
- ==12652== LEAK SUMMARY
- ==12652== definitely lost 40 bytes in 1 blocks
- ==12652== indirectly lost 0 bytes in 0 blocks
- ==12652== possibly lost 0 bytes in 0 blocks
- ==12652== still reachable 0 bytes in 0 blocks
- ==12652== suppressed 0 bytes in 0 blocks
- ==12652== Rerun with --leak-check=full to see details of leaked memory
- ==12652==
- ==12652== For counts of detected and suppressed errors, rerun with -v
- ==12652== ERROR SUMMARY 1 errors from 1 contexts (suppressed 6 from 6)
-In the output we can see that Valgrind has detected both errors - the
-off-by-one memory access at line 5 and a memory leak of 40 bytes. If we
-want a detailed analysis of the memory leak, we need to run Valgrind
-with --leak-check=full option
- $ valgrind --leak-check=full ./valgrind-example
- ==23856== Memcheck, a memory error detector
- ==23856== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.
- ==23856== Using Valgrind-3.6.0 and LibVEX; rerun with -h for copyright info
- ==23856== Command ./valgrind-example
- ==23856==
- ==23856== Invalid write of size 4
- ==23856== at 0x40067E f (valgrind-example.c6)
- ==23856== by 0x40068E main (valgrind-example.c11)
- ==23856== Address 0x66e7068 is 0 bytes after a block of size 40 alloc'd
- ==23856== at 0x4C26FDE malloc (vg_replace_malloc.c236)
- ==23856== by 0x400668 f (valgrind-example.c5)
- ==23856== by 0x40068E main (valgrind-example.c11)
- ==23856==
- ==23856==
- ==23856== HEAP SUMMARY
- ==23856== in use at exit 40 bytes in 1 blocks
- ==23856== total heap usage 1 allocs, 0 frees, 40 bytes allocated
- ==23856==
- ==23856== 40 bytes in 1 blocks are definitely lost in loss record 1 of 1
- ==23856== at 0x4C26FDE malloc (vg_replace_malloc.c236)
- ==23856== by 0x400668 f (valgrind-example.c5)
- ==23856== by 0x40068E main (valgrind-example.c11)
- ==23856==
- ==23856== LEAK SUMMARY
- ==23856== definitely lost 40 bytes in 1 blocks
- ==23856== indirectly lost 0 bytes in 0 blocks
- ==23856== possibly lost 0 bytes in 0 blocks
- ==23856== still reachable 0 bytes in 0 blocks
- ==23856== suppressed 0 bytes in 0 blocks
- ==23856==
- ==23856== For counts of detected and suppressed errors, rerun with -v
- ==23856== ERROR SUMMARY 2 errors from 2 contexts (suppressed 6 from 6)
-Now we can see that the memory leak is due to the
-class="monospace">malloc() at line 6.
-Usage with MPI
----------------------------
-Although Valgrind is not primarily a parallel debugger, it can be used
-to debug parallel applications as well. When launching your parallel
-applications, prepend the valgrind command. For example
- $ mpirun -np 4 valgrind myapplication
-The default version without MPI support will however report a large
-number of false errors in the MPI library, such as
- ==30166== Conditional jump or move depends on uninitialised value(s)
- ==30166== at 0x4C287E8 strlen (mc_replace_strmem.c282)
- ==30166== by 0x55443BD I_MPI_Processor_model_number (init_interface.c427)
- ==30166== by 0x55439E0 I_MPI_Processor_arch_code (init_interface.c171)
- ==30166== by 0x558D5AE MPID_nem_impi_init_shm_configuration (mpid_nem_impi_extensions.c1091)
- ==30166== by 0x5598F4C MPID_nem_init_ckpt (mpid_nem_init.c566)
- ==30166== by 0x5598B65 MPID_nem_init (mpid_nem_init.c489)
- ==30166== by 0x539BD75 MPIDI_CH3_Init (ch3_init.c64)
- ==30166== by 0x5578743 MPID_Init (mpid_init.c193)
- ==30166== by 0x554650A MPIR_Init_thread (initthread.c539)
- ==30166== by 0x553369F PMPI_Init (init.c195)
- ==30166== by 0x4008BD main (valgrind-example-mpi.c18)
-so it is better to use the MPI-enabled valgrind from module. The MPI
-version requires libraryÂ
-class="monospace">/apps/tools/valgrind/3.9.0/impi/lib/valgrind/libmpiwrap-amd64-linux.so,
-which must be included in the LD_PRELOAD
-environment variable.
-Lets look at this MPI example
- #include
- #include Â
- int main(int argc, char *argv[])
- {
- Â Â Â Â Â int *data = malloc(sizeof(int)*99);
- Â Â Â Â Â MPI_Init(&argc, &argv);
- Â Â Â Â MPI_Bcast(data, 100, MPI_INT, 0, MPI_COMM_WORLD);
- Â Â Â Â Â MPI_Finalize();Â
- Â Â Â Â Â Â Â return 0;
- }
-There are two errors - use of uninitialized memory and invalid length of
-the buffer. Lets debug it with valgrind
- $ module add intel impi
- $ mpicc -g valgrind-example-mpi.c -o valgrind-example-mpi
- $ module add valgrind/3.9.0-impi
- $ mpirun -np 2 -env LD_PRELOAD /apps/tools/valgrind/3.9.0/impi/lib/valgrind/libmpiwrap-amd64-linux.so valgrind ./valgrind-example-mpi
-Prints this output (note that there is output printed for every
-launched MPI process)
- ==31318== Memcheck, a memory error detector
- ==31318== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
- ==31318== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info
- ==31318== Command ./valgrind-example-mpi
- ==31318==
- ==31319== Memcheck, a memory error detector
- ==31319== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
- ==31319== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info
- ==31319== Command ./valgrind-example-mpi
- ==31319==
- valgrind MPI wrappers 31319 Active for pid 31319
- valgrind MPI wrappers 31319 Try MPIWRAP_DEBUG=help for possible options
- valgrind MPI wrappers 31318 Active for pid 31318
- valgrind MPI wrappers 31318 Try MPIWRAP_DEBUG=help for possible options
- ==31319== Unaddressable byte(s) found during client check request
- ==31319== at 0x4E35974 check_mem_is_addressable_untyped (libmpiwrap.c960)
- ==31319== by 0x4E5D0FE PMPI_Bcast (libmpiwrap.c908)
- ==31319== by 0x400911 main (valgrind-example-mpi.c20)
- ==31319== Address 0x69291cc is 0 bytes after a block of size 396 alloc'd
- ==31319== at 0x4C27AAA malloc (vg_replace_malloc.c291)
- ==31319== by 0x4007BC main (valgrind-example-mpi.c8)
- ==31319==
- ==31318== Uninitialised byte(s) found during client check request
- ==31318== at 0x4E3591D check_mem_is_defined_untyped (libmpiwrap.c952)
- ==31318== by 0x4E5D06D PMPI_Bcast (libmpiwrap.c908)
- ==31318== by 0x400911 main (valgrind-example-mpi.c20)
- ==31318== Address 0x6929040 is 0 bytes inside a block of size 396 alloc'd
- ==31318== at 0x4C27AAA malloc (vg_replace_malloc.c291)
- ==31318== by 0x4007BC main (valgrind-example-mpi.c8)
- ==31318==
- ==31318== Unaddressable byte(s) found during client check request
- ==31318== at 0x4E3591D check_mem_is_defined_untyped (libmpiwrap.c952)
- ==31318== by 0x4E5D06D PMPI_Bcast (libmpiwrap.c908)
- ==31318== by 0x400911 main (valgrind-example-mpi.c20)
- ==31318== Address 0x69291cc is 0 bytes after a block of size 396 alloc'd
- ==31318== at 0x4C27AAA malloc (vg_replace_malloc.c291)
- ==31318== by 0x4007BC main (valgrind-example-mpi.c8)
- ==31318==
- ==31318==
- ==31318== HEAP SUMMARY
- ==31318== in use at exit 3,172 bytes in 67 blocks
- ==31318== total heap usage 191 allocs, 124 frees, 81,203 bytes allocated
- ==31318==
- ==31319==
- ==31319== HEAP SUMMARY
- ==31319== in use at exit 3,172 bytes in 67 blocks
- ==31319== total heap usage 175 allocs, 108 frees, 48,435 bytes allocated
- ==31319==
- ==31318== LEAK SUMMARY
- ==31318== definitely lost 408 bytes in 3 blocks
- ==31318== indirectly lost 256 bytes in 1 blocks
- ==31318== possibly lost 0 bytes in 0 blocks
- ==31318== still reachable 2,508 bytes in 63 blocks
- ==31318== suppressed 0 bytes in 0 blocks
- ==31318== Rerun with --leak-check=full to see details of leaked memory
- ==31318==
- ==31318== For counts of detected and suppressed errors, rerun with -v
- ==31318== Use --track-origins=yes to see where uninitialised values come from
- ==31318== ERROR SUMMARY 2 errors from 2 contexts (suppressed 4 from 4)
- ==31319== LEAK SUMMARY
- ==31319== definitely lost 408 bytes in 3 blocks
- ==31319== indirectly lost 256 bytes in 1 blocks
- ==31319== possibly lost 0 bytes in 0 blocks
- ==31319== still reachable 2,508 bytes in 63 blocks
- ==31319== suppressed 0 bytes in 0 blocks
- ==31319== Rerun with --leak-check=full to see details of leaked memory
- ==31319==
- ==31319== For counts of detected and suppressed errors, rerun with -v
- ==31319== ERROR SUMMARY 1 errors from 1 contexts (suppressed 4 from 4)
-We can see that Valgrind has reported use of unitialised memory on the
-master process (which reads the array to be broadcasted) and use of
-unaddresable memory on both processes.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
- .navTreeFolderish
- .contenttype-folder}
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
- - [CUBE](cube.html)
-
- - [Intel Performance Counter
- Monitor](intel-performance-counter-monitor.html)
-
- - [Intel VTune
- Amplifier](intel-vtune-amplifier.html)
-
- - [PAPI](papi.html)
-
- - [Scalasca](scalasca.html)
-
- - [Score-P](score-p.html)
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
-
- - [Valgrind](valgrind.html "Valgrind is a tool for memory debugging and profiling.")
-
-
- - [Vampir](vampir.html)
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/debuggers/vampir.md b/anselm-cluster-documentation/software/debuggers/vampir.md
deleted file mode 100644
index 2fdd2e8a389dfe43269c38cbcf1139226e3c3b06..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/debuggers/vampir.md
+++ /dev/null
@@ -1,115 +0,0 @@
-Vampir
-======
-Vampir is a commercial trace analysis and visualisation tool. It can
-work with traces in OTF and OTF2 formats. It does not have the
-functionality to collect traces, you need to use a trace collection tool
-(such
-as [Score-P](../../../acl_users/credentials_cookie_auth/require_loginc71d.html))
-first to collect the traces.
-
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Installed versions
-------------------
-Version 8.5.0 is currently installed as moduleÂ
-class="monospace">Vampir/8.5.0Â
- $ module load Vampir/8.5.0
- $ vampir &
-User manual
------------
-You can find the detailed user manual in PDF format inÂ
-class="monospace">$EBROOTVAMPIR/doc/vampir-manual.pdf
-References
-----------
-1. [https//www.vampir.eu](https//www.vampir.eu/)
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
- .navTreeFolderish
- .contenttype-folder}
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
- - [CUBE](cube.html)
-
- - [Intel Performance Counter
- Monitor](intel-performance-counter-monitor.html)
-
- - [Intel VTune
- Amplifier](intel-vtune-amplifier.html)
-
- - [PAPI](papi.html)
-
- - [Scalasca](scalasca.html)
-
- - [Score-P](score-p.html)
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
-
- - [Valgrind](valgrind.html "Valgrind is a tool for memory debugging and profiling.")
-
- - [Vampir](vampir.html)
-
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/intel-suite.md b/anselm-cluster-documentation/software/intel-suite.md
deleted file mode 100644
index 546cd07858e8429aa2883da9b022500d48327a45..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/intel-suite.md
+++ /dev/null
@@ -1,146 +0,0 @@
-
-
-The Anselm cluster provides following elements of the Intel Parallel
-Studio XE
- Intel Parallel Studio XE
- -------------------------------------------------
- Intel Compilers
- Intel Debugger
- Intel MKL Library
- Intel Integrated Performance Primitives Library
- Intel Threading Building Blocks Library
-Intel compilers
----------------
-The Intel compilers version 13.1.3 are available, via module intel. The
-compilers include the icc C and C++ compiler and the ifort fortran
-77/90/95 compiler.
- $ module load intel
- $ icc -v
- $ ifort -v
-Read more at the [Intel
-Compilers](intel-suite/intel-compilers.html) page.
-Intel debugger
---------------
-Â The intel debugger version 13.0 is available, via module intel. The
-debugger works for applications compiled with C and C++ compiler and the
-ifort fortran 77/90/95 compiler. The debugger provides java GUI
-environment. Use [X
-display](intel-suite/resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html)
-for running the GUI.
- $ module load intel
- $ idb
-Read more at the [Intel
-Debugger](intel-suite/intel-debugger.html) page.
-Intel Math Kernel Library
--------------------------
-Intel Math Kernel Library (Intel MKL) is a library of math kernel
-subroutines, extensively threaded and optimized for maximum performance.
-Intel MKL unites and provides these basic components BLAS, LAPACK,
-ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and
-many more.
- $ module load mkl
-Read more at the [Intel MKL](intel-suite/intel-mkl.html)
-page.
-Intel Integrated Performance Primitives
----------------------------------------
-Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX
-is available, via module ipp. The IPP is a library of highly optimized
-algorithmic building blocks for media and data applications. This
-includes signal, image and frame processing algorithms, such as FFT,
-FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many
-more.
- $ module load ipp
-Read more at the [Intel
-IPP](intel-suite/intel-integrated-performance-primitives.html)
-page.
-Intel Threading Building Blocks
--------------------------------
-Intel Threading Building Blocks (Intel TBB) is a library that supports
-scalable parallel programming using standard ISO C++ code. It does not
-require special languages or compilers. It is designed to promote
-scalable data parallel programming. Additionally, it fully supports
-nested parallelism, so you can build larger parallel components from
-smaller parallel components. To use the library, you specify tasks, not
-threads, and let the library map tasks onto threads in an efficient
-manner.
- $ module load tbb
-Read more at the [Intel TBB](intel-suite/intel-tbb.html)
-page.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage-1.html)
-
- - [Network](../network.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](intel-suite.html "The Intel Parallel Studio XE")
-
-
- - [Intel
- Compilers](intel-suite/intel-compilers.html)
-
- - [Intel
- Debugger](intel-suite/intel-debugger.html)
-
- - [Intel
- MKL](intel-suite/intel-mkl.html)
-
- - [Intel
- IPP](intel-suite/intel-integrated-performance-primitives.html)
-
- - [Intel
- TBB](intel-suite/intel-tbb.html)
-
- - [MPI](mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](virtualization.html)
diff --git a/anselm-cluster-documentation/software/intel-suite/intel-compilers.md b/anselm-cluster-documentation/software/intel-suite/intel-compilers.md
deleted file mode 100644
index c8893af9ac9b3da63c0001cb647bd5cac1f198a4..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/intel-suite/intel-compilers.md
+++ /dev/null
@@ -1,132 +0,0 @@
-Intel Compilers
-===============
-
-
-The Intel compilers version 13.1.1 are available, via module intel. The
-compilers include the icc C and C++ compiler and the ifort fortran
-77/90/95 compiler.
- $ module load intel
- $ icc -v
- $ ifort -v
-The intel compilers provide for vectorization of the code, via the AVX
-instructions and support threading parallelization via OpenMP
-For maximum performance on the Anselm cluster, compile your programs
-using the AVX instructions, with reporting where the vectorization was
-used. We recommend following compilation options for high performance
- $ icc -ipo -O3 -vec -xAVX -vec-report1 myprog.c mysubroutines.c -o myprog.x
- $ ifort -ipo -O3 -vec -xAVX -vec-report1 myprog.f mysubroutines.f -o myprog.x
-In this example, we compile the program enabling interprocedural
-optimizations between source files (-ipo), aggresive loop optimizations
-(-O3) and vectorization (-vec -xAVX)
-The compiler recognizes the omp, simd, vector and ivdep pragmas for
-OpenMP parallelization and AVX vectorization. Enable the OpenMP
-parallelization by the **-openmp** compiler switch.
- $ icc -ipo -O3 -vec -xAVX -vec-report1 -openmp myprog.c mysubroutines.c -o myprog.x
- $ ifort -ipo -O3 -vec -xAVX -vec-report1 -openmp myprog.f mysubroutines.f -o myprog.x
-Read more at
-Sandy Bridge/Haswell binary compatibility
------------------------------------------
-Anselm nodes are currently equipped with Sandy Bridge CPUs, while
-Salomon will use Haswell architecture. The new processors are
-backward compatible with the Sandy Bridge nodes, so all programs that
-ran on the Sandy Bridge processors, should also run on the new Haswell
-nodes. To get optimal performance out of the Haswell
-processors a program should make use of the special AVX2
-instructions for this processor. One can do this by recompiling codes
-with the compiler flags designated to invoke these
-instructions. For the Intel compiler suite, there are two ways of
-doing this
-- Using compiler flag (both for Fortran and C)
- class="monospace">-xCORE-AVX2. This will create a
- binary with AVX2 instructions, specifically
- for the Haswell processors. Note that the
- executable will not run on Sandy Bridge nodes.
-- Using compiler flags (both for Fortran and C)
- class="monospace">-xAVX -axCORE-AVX2. This
- will generate multiple, feature specific auto-dispatch
- code paths for Intel® processors, if there is a
- performance benefit. So this binary will run both on Sandy Bridge
- and Haswell processors. During runtime it will be
- decided which path to follow, dependent on
- which processor you are running on. In general this
- will result in larger binaries.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
- .navTreeFolderish
- .contenttype-folder}
- - [Intel
- Compilers](intel-compilers.html)
-
-
- - [Intel
- Debugger](intel-debugger.html)
-
- - [Intel
- MKL](intel-mkl.html)
-
- - [Intel
- IPP](intel-integrated-performance-primitives.html)
-
- - [Intel
- TBB](intel-tbb.html)
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/intel-suite/intel-debugger.md b/anselm-cluster-documentation/software/intel-suite/intel-debugger.md
deleted file mode 100644
index e0609a630a3ffaa106363b40c87dc00cb861eac1..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/intel-suite/intel-debugger.md
+++ /dev/null
@@ -1,150 +0,0 @@
-Intel Debugger
-==============
-
-
-Debugging serial applications
------------------------------
-Â The intel debugger version 13.0 is available, via module intel. The
-debugger works for applications compiled with C and C++ compiler and the
-ifort fortran 77/90/95 compiler. The debugger provides java GUI
-environment. Use [X
-display](resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html)
-for running the GUI.
- $ module load intel
- $ idb
-The debugger may run in text mode. To debug in text mode, use
- $ idbc
-To debug on the compute nodes, module intel must be loaded.
-The GUI on compute nodes may be accessed using the same way as in [the
-GUI
-section](resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html)
-Example
- $ qsub -q qexp -l select=1ncpus=16 -X -I
- qsub waiting for job 19654.srv11 to start
- qsub job 19654.srv11 ready
- $ module load intel
- $ module load java
- $ icc -O0 -g myprog.c -o myprog.x
- $ idb ./myprog.x
-In this example, we allocate 1 full compute node, compile program
-myprog.c with debugging options -O0 -g and run the idb debugger
-interactively on the myprog.x executable. The GUI access is via X11 port
-forwarding provided by the PBS workload manager.
-Debugging parallel applications
--------------------------------
-Intel debugger is capable of debugging multithreaded and MPI parallel
-programs as well.
-### Small number of MPI ranks
-For debugging small number of MPI ranks, you may execute and debug each
-rank in separate xterm terminal (do not forget the [X
-display](resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html)).
-Using Intel MPI, this may be done in following way
- $ qsub -q qexp -l select=2ncpus=16 -X -I
- qsub waiting for job 19654.srv11 to start
- qsub job 19655.srv11 ready
- $ module load intel impi
- $ mpirun -ppn 1 -hostfile $PBS_NODEFILE --enable-x xterm -e idbc ./mympiprog.x
-In this example, we allocate 2 full compute node, run xterm on each node
-and start idb debugger in command line mode, debugging two ranks of
-mympiprog.x application. The xterm will pop up for each rank, with idb
-prompt ready. The example is not limited to use of Intel MPI
-### Large number of MPI ranks
-Run the idb debugger from within the MPI debug option. This will cause
-the debugger to bind to all ranks and provide aggregated outputs across
-the ranks, pausing execution automatically just after startup. You may
-then set break points and step the execution manually. Using Intel MPI
- $ qsub -q qexp -l select=2ncpus=16 -X -I
- qsub waiting for job 19654.srv11 to start
- qsub job 19655.srv11 ready
- $ module load intel impi
- $ mpirun -n 32 -idb ./mympiprog.x
-### Debugging multithreaded application
-Run the idb debugger in GUI mode. The menu Parallel contains number of
-tools for debugging multiple threads. One of the most useful tools is
-the **Serialize Execution** tool, which serializes execution of
-concurrent threads for easy orientation and identification of
-concurrency related bugs.
-Further information
--------------------
-Exhaustive manual on idb features and usage is published at Intel
-website,
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
- .navTreeFolderish
- .contenttype-folder}
- - [Intel
- Compilers](intel-compilers.html)
-
- - [Intel
- Debugger](intel-debugger.html)
-
-
- - [Intel
- MKL](intel-mkl.html)
-
- - [Intel
- IPP](intel-integrated-performance-primitives.html)
-
- - [Intel
- TBB](intel-tbb.html)
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md b/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
deleted file mode 100644
index b182375df3fe3f0e68eb8da21157e64a20a4554d..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
+++ /dev/null
@@ -1,154 +0,0 @@
-
-Intel IPP
-=========
-
-
-Intel Integrated Performance Primitives
----------------------------------------
-Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX
-vector instructions is available, via module ipp. The IPP is a very rich
-library of highly optimized algorithmic building blocks for media and
-data applications. This includes signal, image and frame processing
-algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough
-transform, Sum, MinMax, as well as cryptographic functions, linear
-algebra functions and many more.
-Check out IPP before implementing own math functions for data
-processing, it is likely already there.
- $ module load ipp
-The module sets up environment variables, required for linking and
-running ipp enabled applications.
-IPP example
------------
- #include "ipp.h"
- #include
- int main(int argc, char* argv[])
- {
- const IppLibraryVersion *lib;
- Ipp64u fm;
- IppStatus status;
- status= ippInit(); //IPP initialization with the best optimization layer
- if( status != ippStsNoErr ) {
- printf("IppInit() Errorn");
- printf("%sn", ippGetStatusString(status) );
- return -1;
- }
- //Get version info
- lib = ippiGetLibVersion();
- printf("%s %sn", lib->Name, lib->Version);
- //Get CPU features enabled with selected library level
- fm=ippGetEnabledCpuFeatures();
- printf("SSE %cn",(fm>>1)&1?'Y''N');
- printf("SSE2 %cn",(fm>>2)&1?'Y''N');
- printf("SSE3 %cn",(fm>>3)&1?'Y''N');
- printf("SSSE3 %cn",(fm>>4)&1?'Y''N');
- printf("SSE41 %cn",(fm>>6)&1?'Y''N');
- printf("SSE42 %cn",(fm>>7)&1?'Y''N');
- printf("AVX %cn",(fm>>8)&1 ?'Y''N');
- printf("AVX2 %cn", (fm>>15)&1 ?'Y''N' );
- printf("----------n");
- printf("OS Enabled AVX %cn", (fm>>9)&1 ?'Y''N');
- printf("AES %cn", (fm>>10)&1?'Y''N');
- printf("CLMUL %cn", (fm>>11)&1?'Y''N');
- printf("RDRAND %cn", (fm>>13)&1?'Y''N');
- printf("F16C %cn", (fm>>14)&1?'Y''N');
- return 0;
- }
-Â Compile above example, using any compiler and the ipp module.
- $ module load intel
- $ module load ipp
- $ icc testipp.c -o testipp.x -lippi -lipps -lippcore
-You will need the ipp module loaded to run the ipp enabled executable.
-This may be avoided, by compiling library search paths into the
-executable
- $ module load intel
- $ module load ipp
- $ icc testipp.c -o testipp.x -Wl,-rpath=$LIBRARY_PATH -lippi -lipps -lippcore
-Code samples and documentation
-------------------------------
-Intel provides number of [Code Samples for
-IPP](https//software.intel.com/en-us/articles/code-samples-for-intel-integrated-performance-primitives-library),
-illustrating use of IPP.
-Read full documentation on IPP [on Intel
-website,](http//software.intel.com/sites/products/search/search.php?q=&x=15&y=6&product=ipp&version=7.1&docos=lin)
-in particular the [IPP Reference
-manual.](http//software.intel.com/sites/products/documentation/doclib/ipp_sa/71/ipp_manual/index.htm)
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
- .navTreeFolderish
- .contenttype-folder}
- - [Intel
- Compilers](intel-compilers.html)
-
- - [Intel
- Debugger](intel-debugger.html)
-
- - [Intel
- MKL](intel-mkl.html)
-
- - [Intel
- IPP](intel-integrated-performance-primitives.html)
-
-
- - [Intel
- TBB](intel-tbb.html)
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/intel-suite/intel-tbb.md b/anselm-cluster-documentation/software/intel-suite/intel-tbb.md
deleted file mode 100644
index 45b68aff326f1b9d204605bef4ca07997f99eb44..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/intel-suite/intel-tbb.md
+++ /dev/null
@@ -1,118 +0,0 @@
-Intel TBB
-=========
-
-
-Intel Threading Building Blocks
--------------------------------
-Intel Threading Building Blocks (Intel TBB) is a library that supports
-scalable parallel programming using standard ISO C++ code. It does not
-require special languages or compilers. To use the library, you specify
-tasks, not threads, and let the library map tasks onto threads in an
-efficient manner. The tasks are executed by a runtime scheduler and may
-be offloaded to [MIC
-accelerator](../intel-xeon-phi.html).
-Intel TBB version 4.1 is available on Anselm
- $ module load tbb
-The module sets up environment variables, required for linking and
-running tbb enabled applications.
-Link the tbb library, using -ltbb
-Examples
---------
-Number of examples, demonstrating use of TBB and its built-in schedulerÂ
-is available on Anselm, in the $TBB_EXAMPLES directory.
- $ module load intel
- $ module load tbb
- $ cp -a $TBB_EXAMPLES/common $TBB_EXAMPLES/parallel_reduce /tmp/
- $ cd /tmp/parallel_reduce/primes
- $ icc -O2 -DNDEBUG -o primes.x main.cpp primes.cpp -ltbb
- $ ./primes.x
-In this example, we compile, link and run the primes example,
-demonstrating use of parallel task-based reduce in computation of prime
-numbers.
-You will need the tbb module loaded to run the tbb enabled executable.
-This may be avoided, by compiling library search paths into the
-executable.
- $ icc -O2 -o primes.x main.cpp primes.cpp -Wl,-rpath=$LIBRARY_PATH -ltbb
-Further reading
----------------
-Read more on Intel website,
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
- .navTreeFolderish
- .contenttype-folder}
- - [Intel
- Compilers](intel-compilers.html)
-
- - [Intel
- Debugger](intel-debugger.html)
-
- - [Intel
- MKL](intel-mkl.html)
-
- - [Intel
- IPP](intel-integrated-performance-primitives.html)
-
- - [Intel
- TBB](intel-tbb.html)
-
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/isv_licenses.md b/anselm-cluster-documentation/software/isv_licenses.md
deleted file mode 100644
index 4e51cef7270c1bcd39b0622da7b49190093c24a9..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/isv_licenses.md
+++ /dev/null
@@ -1,197 +0,0 @@
-A guide to managing Independent Software Vendor licences
-
-
-On Anselm cluster there are also installed commercial software
-applications, also known as ISV (Independent Software Vendor), which are
-subjects to licensing. The licenses are limited and their usage may be
-restricted only to some users or user groups.
-Currently Flex License Manager based licensing is supported on the
-cluster for products Ansys, Comsol and Matlab. More information about
-the applications can be found in the general
-[Software](../software.html) section.
-If an ISV application was purchased for educational (research) purposes
-and also for commercial purposes, then there are always two separate
-versions maintained and suffix "edu" is used in the name of the
-non-commercial version.
-Overview of the licenses usage
-------------------------------
-The overview is generated every minute and is accessible from web or
-command line interface.
-### Web interface
-For each license there is a table, which provides the information about
-the name, number of available (purchased/licensed), number of used and
-number of free license features
-### Text interface
-For each license there is a unique text file, which provides the
-information about the name, number of available (purchased/licensed),
-number of used and number of free license features. The text files are
-accessible from the Anselm command prompt.[]()
- Product File with license state Note
- ------------ ----------------------------------------------------- ---------------------
- ansys /apps/user/licenses/ansys_features_state.txt Commercial
- comsol /apps/user/licenses/comsol_features_state.txt Commercial
- comsol-edu /apps/user/licenses/comsol-edu_features_state.txt Non-commercial only
- matlab /apps/user/licenses/matlab_features_state.txt Commercial
- matlab-edu /apps/user/licenses/matlab-edu_features_state.txt Non-commercial only
-The file has a header which serves as a legend. All the info in the
-legend starts with a hash (#) so it can be easily filtered when parsing
-the file via a script.
-Example of the Commercial Matlab license state
- $ cat /apps/user/licenses/matlab_features_state.txt
- # matlab
- # -------------------------------------------------
- # FEATURE TOTAL USED AVAIL
- # -------------------------------------------------
- MATLAB 1 1 0
- SIMULINK 1 0 1
- Curve_Fitting_Toolbox 1 0 1
- Signal_Blocks 1 0 1
- GADS_Toolbox 1 0 1
- Image_Toolbox 1 0 1
- Compiler 1 0 1
- Neural_Network_Toolbox 1 0 1
- Optimization_Toolbox 1 0 1
- Signal_Toolbox 1 0 1
- Statistics_Toolbox 1 0 1
-License tracking in PBS Pro scheduler and users usage
------------------------------------------------------
-Each feature of each license is accounted and checked by the scheduler
-of PBS Pro. If you ask for certain licences, the scheduler won't start
-the job until the asked licenses are free (available). This prevents to
-crash batch jobs, just because of id="result_box"
-class="short_text">unavailability of the
-needed licenses.
-The general format of the name is
-**feature__APP__FEATURE**
-Names of applications (APP)
-- ansys
-- comsol
-- comsol-edu
-- matlab
-- matlab-edu
-Â
-To get the FEATUREs of a license take a look into the corresponding
-state file ([see above](#Licence)), or use
-Application
-List of provided features
-ansys
-$ grep -v "#" /apps/user/licenses/ansys_features_state.txt | cut -f1 -d' '
-comsol
-$ grep -v "#" /apps/user/licenses/comsol_features_state.txt | cut -f1 -d' '
-comsol-edu
-$ grep -v "#" /apps/user/licenses/comsol-edu_features_state.txt | cut -f1 -d' '
-matlab
-$ grep -v "#" /apps/user/licenses/matlab_features_state.txt | cut -f1 -d' '
-matlab-edu
-$ grep -v "#" /apps/user/licenses/matlab-edu_features_state.txt | cut -f1 -d' '
-Â
-Example of PBS Pro resource name, based on APP and FEATURE name
-Application
-Feature
-PBS Pro resource name
-ansys
-acfd
-feature__ansys__acfd
-ansys
-aa_r
-feature__ansys__aa_r
-comsol
-COMSOL
-feature__comsol__COMSOL
-comsol
-HEATTRANSFER
-feature__comsol__HEATTRANSFER
-comsol-edu
-COMSOLBATCH
-feature__comsol-edu__COMSOLBATCH
-comsol-edu
-STRUCTURALMECHANICS
-feature__comsol-edu__STRUCTURALMECHANICS
-matlab
-MATLAB
-feature__matlab__MATLAB
-matlab
-Image_Toolbox
-feature__matlab__Image_Toolbox
-matlab-edu
-MATLAB_Distrib_Comp_Engine
-feature__matlab-edu__MATLAB_Distrib_Comp_Engine
-matlab-edu
-Image_Acquisition_Toolbox
-feature__matlab-edu__Image_Acquisition_Toolbox
-**Be aware, that the resource names in PBS Pro are CASE SENSITIVE!**
-### Example of qsub statement
-Run an interactive PBS job with 1 Matlab EDU license, 1 Distributed
-Computing Toolbox and 32 Distributed Computing Engines (running on 32
-cores)
- $ qsub -I -q qprod -A PROJECT_ID -l select=2ncpus=16 -l feature__matlab-edu__MATLAB=1 -l feature__matlab-edu__Distrib_Computing_Toolbox=1 -l feature__matlab-edu__MATLAB_Distrib_Comp_Engine=32
-The license is used and accounted only with the real usage of the
-product. So in this example, the general Matlab is used after Matlab is
-run vy the user and not at the time, when the shell of the interactive
-job is started. Also the Distributed Computing licenses are used at the
-time, when the user uses the distributed parallel computation in Matlab
-(e. g. issues pmode start, matlabpool, etc.).
-Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage-1.html)
-
- - [Network](../network.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](virtualization.html)
-
diff --git a/anselm-cluster-documentation/software/java.md b/anselm-cluster-documentation/software/java.md
deleted file mode 100644
index 0607cfc2b36c8f9fa75c6a34f8d053a67b856409..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/java.md
+++ /dev/null
@@ -1,84 +0,0 @@
-Java on ANSELM
-
-
-Java is available on Anselm cluster. Activate java by loading the java
-module
- $ module load java
-Note that the java module must be loaded on the compute nodes as well,
-in order to run java on compute nodes.
-Check for java version and path
- $ java -version
- $ which java
-With the module loaded, not only the runtime environment (JRE), but also
-the development environment (JDK) with the compiler is available.
- $ javac -version
- $ which javac
-Java applications may use MPI for interprocess communication, in
-conjunction with OpenMPI. Read more
-on .
-This functionality is currently not supported on Anselm cluster. In case
-you require the java interface to MPI, please contact [Anselm
-support](https//support.it4i.cz/rt/).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage-1.html)
-
- - [Network](../network.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](virtualization.html)
-
diff --git a/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.md b/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.md
deleted file mode 100644
index dc6acf4053dcd24544c460d74c90cae545cba610..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.md
+++ /dev/null
@@ -1,144 +0,0 @@
-MPI4Py (MPI for Python)
-=======================
-OpenMPI interface to Python
-
-
-Introduction
-------------
-MPI for Python provides bindings of the Message Passing Interface (MPI)
-standard for the Python programming language, allowing any Python
-program to exploit multiple processors.
-This package is constructed on top of the MPI-1/2 specifications and
-provides an object oriented interface which closely follows MPI-2 C++
-bindings. It supports point-to-point (sends, receives) and collective
-(broadcasts, scatters, gathers) communications of any picklable Python
-object, as well as optimized communications of Python object exposing
-the single-segment buffer interface (NumPy arrays, builtin
-bytes/string/array objects).
-On Anselm MPI4Py is available in standard Python modules.
-Modules
--------
-MPI4Py is build for OpenMPI. Before you start with MPI4Py you need to
-load Python and OpenMPI modules.
- $ module load python
- $ module load openmpi
-Execution
----------
-You need to import MPI to your python program. Include the following
-line to the python script
- from mpi4py import MPI
-The MPI4Py enabled python programs [execute as any other
-OpenMPI](Running_OpenMPI.html) code.The simpliest way is
-to run
- $ mpiexec python .py
-For example
- $ mpiexec python hello_world.py
-Examples
---------
-### Hello world!
- from mpi4py import MPI
- comm = MPI.COMM_WORLD
- print "Hello! I'm rank %d from %d running in total..." % (comm.rank, comm.size)
- comm.Barrier() Â # wait for everybody to synchronize
-### Collective Communication with NumPy arrays
- from mpi4py import MPI
- from __future__ import division
- import numpy as np
- comm = MPI.COMM_WORLD
- print("-"*78)
- print(" Running on %d cores" % comm.size)
- print("-"*78)
- comm.Barrier()
- # Prepare a vector of N=5 elements to be broadcasted...
- N = 5
- if comm.rank == 0
- Â Â A = np.arange(N, dtype=np.float64) Â Â # rank 0 has proper data
- else
- Â Â A = np.empty(N, dtype=np.float64) Â Â # all other just an empty array
- # Broadcast A from rank 0 to everybody
- comm.Bcast( [A, MPI.DOUBLE] )
- # Everybody should now have the same...
- print "[%02d] %s" % (comm.rank, A)
-Execute the above code as
- $ qsub -q qexp -l select=4ncpus=16mpiprocs=16ompthreads=1 -I
- $ module load python openmpi
- $ mpiexec -bycore -bind-to-core python hello_world.py
-In this example, we run MPI4Py enabled code on 4 nodes, 16 cores per
-node (total of 64 processes), each python process is bound to a
-different core.
-More examples and documentation can be found on [MPI for Python
-webpage](https//pythonhosted.org/mpi4py/usrman/index.html).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
- .navTreeFolderish
- .contenttype-folder}
- - [Running
- OpenMPI](Running_OpenMPI.html)
-
- - [Running
- MPICH2](running-mpich2.html)
-
- - [MPI4Py (MPI
- for Python)](mpi4py-mpi-for-python.html "OpenMPI interface to Python")
-
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/numerical-languages.md b/anselm-cluster-documentation/software/numerical-languages.md
deleted file mode 100644
index 522b91428e8d7d5721f8209a427ad6f9a6098823..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/numerical-languages.md
+++ /dev/null
@@ -1,103 +0,0 @@
-Interpreted languages for numerical computations and analysis
-
-
-Introduction
-------------
-This section contains a collection of high-level interpreted languages,
-primarily intended for numerical computations.
-Matlab
-------
-MATLAB^®^ is a high-level language and interactive environment for
-numerical computation, visualization, and programming.
- $ module load MATLAB/2015b-EDU
- $ matlab
-Read more at the [Matlab
-page](numerical-languages/matlab.html).
-Octave
-------
-GNU Octave is a high-level interpreted language, primarily intended for
-numerical computations. The Octave language is quite similar to Matlab
-so that most programs are easily portable.
- $ module load Octave
- $ octave
-Read more at the [Octave
-page](numerical-languages/octave.html).
-R
--
-The R is an interpreted language and environment for statistical
-computing and graphics.
- $ module load R
- $ R
-Read more at the [R page](numerical-languages/r.html).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage-1.html)
-
- - [Network](../network.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](numerical-languages.html "Interpreted languages for numerical computations")
-
-
- - [Matlab](numerical-languages/copy_of_matlab.html)
-
- - [Matlab
- 2013-2014](numerical-languages/matlab.html)
-
- - [Octave](numerical-languages/octave.html)
-
- - [R](numerical-languages/r.html)
-
- - [Virtualization](virtualization.html)
diff --git a/anselm-cluster-documentation/software/numerical-languages/introduction.md b/anselm-cluster-documentation/software/numerical-languages/introduction.md
deleted file mode 100644
index 4704775e491242d042649213a3130e81930dad70..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/numerical-languages/introduction.md
+++ /dev/null
@@ -1,103 +0,0 @@
-Interpreted languages for numerical computations and analysis
-
-
-Introduction
-------------
-This section contains a collection of high-level interpreted languages,
-primarily intended for numerical computations.
-Matlab
-------
-MATLAB^®^ is a high-level language and interactive environment for
-numerical computation, visualization, and programming.
- $ module load MATLAB/2015b-EDU
- $ matlab
-Read more at the [Matlab
-page](matlab.html).
-Octave
-------
-GNU Octave is a high-level interpreted language, primarily intended for
-numerical computations. The Octave language is quite similar to Matlab
-so that most programs are easily portable.
- $ module load Octave
- $ octave
-Read more at the [Octave page](octave.html).
-R
--
-The R is an interpreted language and environment for statistical
-computing and graphics.
- $ module load R
- $ R
-Read more at the [R page](r.html).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
-
- - [Matlab](copy_of_matlab.html)
-
- - [Matlab
- 2013-2014](matlab.html)
-
- - [Octave](octave.html)
-
- - [R](r.html)
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/numerical-libraries.md b/anselm-cluster-documentation/software/numerical-libraries.md
deleted file mode 100644
index 4b516d83c06a1ca0efebdd432d15a58ed39cbd13..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/numerical-libraries.md
+++ /dev/null
@@ -1,104 +0,0 @@
-Libraries for numerical computations
-Nebyla ještě nahrána žádná alba ani fotografie.
- [Intel numerical libraries](numerical-libraries/intel-numerical-libraries.html){.contenttype-document .state-published .url}
- Intel libraries for high performance in
- numerical computing
- [GSL](numerical-libraries/gsl.html){.contenttype-document .state-published .url}
- The GNU Scientific Library. Provides a
- wide range of mathematical routines.
- [HDF5](numerical-libraries/hdf5.html){.contenttype-document .state-published .url}
- Hierarchical Data Format library. Serial
- and MPI parallel version.
- [FFTW](numerical-libraries/fftw.html){.contenttype-document .state-published .url}
- The discrete Fourier transform in one or
- more dimensions, MPI parallel
- [MAGMA for Intel Xeon Phi](numerical-libraries/magma-for-intel-xeon-phi.html){.contenttype-document .state-published .url}
- Next generation dense algebra library for
- heterogeneous systems with accelerators
- [PETSc](numerical-libraries/petsc.html){.contenttype-document .state-published .url}
- PETSc is a suite of building blocks for
- the scalable solution of scientific and engineering applications
- modelled by partial differential equations. It supports MPI, shared
- memory, and GPUs through CUDA or OpenCL, as well as hybrid
- MPI-shared memory or MPI-GPU parallelism.
- [Trilinos](numerical-libraries/trilinos.html){.contenttype-document .state-published .url}
- Packages for large scale scientific and
- engineering problems. Provides MPI and
- hybrid parallelization.
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage-1.html)
-
- - [Network](../network.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](numerical-libraries.html "Libraries for numerical computations")
-
-
- - [Intel numerical
- libraries](numerical-libraries/intel-numerical-libraries.html "Intel libraries for high performance in numerical computing")
-
- - [GSL](numerical-libraries/gsl.html "The GNU Scientific Library. Provides a wide range of mathematical routines.")
-
- - [HDF5](numerical-libraries/hdf5.html "Hierarchical Data Format library. Serial and MPI parallel version.")
-
- - [FFTW](numerical-libraries/fftw.html "The discrete Fourier transform in one or more dimensions, MPI parallel")
-
- - [MAGMA for Intel Xeon
- Phi](numerical-libraries/magma-for-intel-xeon-phi.html "Next generation dense algebra library for heterogeneous systems with accelerators
- ")
- - [PETSc](numerical-libraries/petsc.html "PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism.")
-
- - [Trilinos](numerical-libraries/trilinos.html " Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization.")
-
- - [Numerical
- languages](numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](virtualization.html)
diff --git a/anselm-cluster-documentation/software/numerical-libraries/fftw.md b/anselm-cluster-documentation/software/numerical-libraries/fftw.md
deleted file mode 100644
index 6bd89032913467beca067a4d82872af455b5d4c8..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/numerical-libraries/fftw.md
+++ /dev/null
@@ -1,184 +0,0 @@
-FFTW
-====
-The discrete Fourier transform in one or more dimensions, MPI parallel
-
-
-Â
-FFTW is a C subroutine library for computing the discrete Fourier
-transform in one or more dimensions, of arbitrary input size, and of
-both real and complex data (as well as of even/odd data, i.e. the
-discrete cosine/sine transforms or DCT/DST). The FFTW library allows for
-MPI parallel, in-place discrete Fourier transform, with data distributed
-over number of nodes.****
-**
-**Two versions, **3.3.3** and **2.1.5** of FFTW are available on Anselm,
-each compiled for **Intel MPI** and **OpenMPI** using **intel** and
-**gnu** compilers. These are available via modules
-Version
-Parallelization
-module
-linker options
-FFTW3 gcc
-3.3.3
-pthread, OpenMP
-fftw3/3.3.3-gcc
--lfftw3, -lfftw3_threads
--lfftw3_omp
-FFTW3 icc
-3.3.3
-pthread, OpenMP
-fftw3
--lfftw3, -lfftw3_threads
--lfftw3_omp
-FFTW2 gcc
-2.1.5
-pthread
-fftw2/2.1.5-gcc
--lfftw, -lfftw_threads
-FFTW2 icc
-2.1.5
-pthread
-fftw2
--lfftw, -lfftw_threads
-FFTW3 gcc
-3.3.3
-OpenMPI
-fftw-mpi3/3.3.3-gcc
--lfftw3_mpi
-FFTW3 icc
-3.3.3
-Intel MPI
-fftw3-mpi
--lfftw3_mpi
-FFTW2 gcc
-2.1.5
-OpenMPI
-fftw2-mpi/2.1.5-gcc
--lfftw_mpi
-FFTW2 gcc
-2.1.5
-IntelMPI
-fftw2-mpi/2.1.5-gcc
--lfftw_mpi
- $ module load fftw3
-The module sets up environment variables, required for linking and
-running fftw enabled applications. Make sure that the choice of fftw
-module is consistent with your choice of MPI library. Mixing MPI of
-different implementations may have unpredictable results.
-Example
--------
- #include
- int main(int argc, char **argv)
- {
- Â Â Â const ptrdiff_t N0 = 100, N1 = 1000;
- Â Â Â fftw_plan plan;
- Â Â Â fftw_complex *data;
- Â Â Â ptrdiff_t alloc_local, local_n0, local_0_start, i, j;
- Â Â Â MPI_Init(&argc, &argv);
- Â Â Â fftw_mpi_init();
- Â Â Â /* get local data size and allocate */
- Â Â Â alloc_local = fftw_mpi_local_size_2d(N0, N1, MPI_COMM_WORLD,
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â &local_n0, &local_0_start);
- Â Â Â data = fftw_alloc_complex(alloc_local);
- Â Â Â /* create plan for in-place forward DFT */
- Â Â Â plan = fftw_mpi_plan_dft_2d(N0, N1, data, data, MPI_COMM_WORLD,
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â FFTW_FORWARD, FFTW_ESTIMATE);
- Â Â Â /* initialize data */
- Â Â Â for (i = 0; i < local_n0; ++i) for (j = 0; j < N1; ++j)
- Â Â Â {Â Â data[i*N1 + j][0] = i;
- Â Â Â Â Â Â Â data[i*N1 + j][1] = j; }
- Â Â Â /* compute transforms, in-place, as many times as desired */
- Â Â Â fftw_execute(plan);
- Â Â Â fftw_destroy_plan(plan);
- Â Â Â MPI_Finalize();
- }
-Load modules and compile
- $ module load impi intel
- $ module load fftw3-mpi
- $ mpicc testfftw3mpi.c -o testfftw3mpi.x -Wl,-rpath=$LIBRARY_PATH -lfftw3_mpi
-Run the example as [Intel MPI
-program](../mpi-1/running-mpich2.html).
-Read more on FFTW usage on the [FFTW
-website.](http//www.fftw.org/fftw3_doc/)
-
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
- .navTreeFolderish
- .contenttype-folder}
- - [Intel numerical
- libraries](intel-numerical-libraries.html "Intel libraries for high performance in numerical computing")
-
- - [GSL](gsl.html "The GNU Scientific Library. Provides a wide range of mathematical routines.")
-
- - [HDF5](hdf5.html "Hierarchical Data Format library. Serial and MPI parallel version.")
-
- - [FFTW](fftw.html "The discrete Fourier transform in one or more dimensions, MPI parallel")
-
-
- - [MAGMA for Intel Xeon
- Phi](magma-for-intel-xeon-phi.html "Next generation dense algebra library for heterogeneous systems with accelerators
- ")
- - [PETSc](petsc.html "PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism.")
-
- - [Trilinos](trilinos.html " Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization.")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/numerical-libraries/hdf5.md b/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
deleted file mode 100644
index 7cf8f8b48a72d21bfd809c6ac8502b41452decb9..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
+++ /dev/null
@@ -1,211 +0,0 @@
-HDF5
-====
-Hierarchical Data Format library. Serial and MPI parallel version.
-Â
-[HDF5 (Hierarchical Data Format)](http//www.hdfgroup.org/HDF5/) is a
-general purpose library and file format for storing scientific data.
-HDF5 can store two primary objects datasets and groups. A dataset is
-essentially a multidimensional array of data elements, and a group is a
-structure for organizing objects in an HDF5 file. Using these two basic
-objects, one can create and store almost any kind of scientific data
-structure, such as images, arrays of vectors, and structured and
-unstructured grids. You can also mix and match them in HDF5 files
-according to your needs.
-Versions **1.8.11** and **1.8.13** of HDF5 library are available on
-Anselm, compiled for **Intel MPI** and **OpenMPI** using **intel** and
-**gnu** compilers. These are available via modules
-Version
-Parallelization
-module
-C linker options
-C++ linker options
-Fortran linker options
-HDF5 icc serial
-pthread
-hdf5/1.8.11
-$HDF5_INC $HDF5_SHLIB
-$HDF5_INC $HDF5_CPP_LIB
-$HDF5_INC $HDF5_F90_LIB
-HDF5 icc parallel MPI
-pthread, IntelMPI
-hdf5-parallel/1.8.11
-$HDF5_INC $HDF5_SHLIB
-Not supported
-$HDF5_INC $HDF5_F90_LIB
-HDF5 icc serial
-pthread
-hdf5/1.8.13
-$HDF5_INC $HDF5_SHLIB
-$HDF5_INC $HDF5_CPP_LIB
-$HDF5_INC $HDF5_F90_LIB
-HDF5 icc parallel MPI
-pthread, IntelMPI
-hdf5-parallel/1.8.13
-$HDF5_INC $HDF5_SHLIB
-Not supported
-$HDF5_INC $HDF5_F90_LIB
-HDF5 gcc parallel MPI
-pthread, OpenMPI 1.6.5, gcc 4.8.1
-hdf5-parallel/1.8.11-gcc
-$HDF5_INC $HDF5_SHLIB
-Not supported
-$HDF5_INC $HDF5_F90_LIB
-HDF5 gcc parallel MPI
-pthread, OpenMPI 1.6.5, gcc 4.8.1
-hdf5-parallel/1.8.13-gcc
-$HDF5_INC $HDF5_SHLIB
-Not supported
-$HDF5_INC $HDF5_F90_LIB
-HDF5 gcc parallel MPI
-pthread, OpenMPI 1.8.1, gcc 4.9.0
-hdf5-parallel/1.8.13-gcc49
-$HDF5_INC $HDF5_SHLIB
-Not supported
-$HDF5_INC $HDF5_F90_LIB
-Â
- $ module load hdf5-parallel
-The module sets up environment variables, required for linking and
-running HDF5 enabled applications. Make sure that the choice of HDF5
-module is consistent with your choice of MPI library. Mixing MPI of
-different implementations may have unpredictable results.
-Be aware, that GCC version of **HDF5 1.8.11** has serious performance
-issues, since it's compiled with -O0 optimization flag. This version is
-provided only for testing of code compiled only by GCC and IS NOT
-recommended for production computations. For more informations, please
-see
-
-All GCC versions of **HDF5 1.8.13** are not affected by the bug, are
-compiled with -O3 optimizations and are recommended for production
-computations.
-Example
--------
- #include "hdf5.h"
- #define FILE "dset.h5"
- int main() {
- hid_t file_id, dataset_id, dataspace_id; /* identifiers */
- hsize_t dims[2];
- herr_t status;
- int i, j, dset_data[4][6];
- /* Create a new file using default properties. */
- file_id = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
- /* Create the data space for the dataset. */
- dims[0] = 4;
- dims[1] = 6;
- dataspace_id = H5Screate_simple(2, dims, NULL);
- /* Initialize the dataset. */
- for (i = 0; i < 4; i++)
- for (j = 0; j < 6; j++)
- dset_data[i][j] = i * 6 + j + 1;
- /* Create the dataset. */
- dataset_id = H5Dcreate2(file_id, "/dset", H5T_STD_I32BE, dataspace_id,
- H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
- /* Write the dataset. */
- status = H5Dwrite(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
- dset_data);
- status = H5Dread(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
- dset_data);
- /* End access to the dataset and release resources used by it. */
- status = H5Dclose(dataset_id);
- /* Terminate access to the data space. */
- status = H5Sclose(dataspace_id);
- /* Close the file. */
- status = H5Fclose(file_id);
- }
-Load modules and compile
- $ module load intel impi
- $ module load hdf5-parallel
- $ mpicc hdf5test.c -o hdf5test.x -Wl,-rpath=$LIBRARY_PATH $HDF5_INC $HDF5_SHLIB
-Run the example as [Intel MPI
-program](../anselm-cluster-documentation/software/mpi-1/running-mpich2.html).
-For further informations, please see the website
-Â
-Â
-Â
-
-class="smarterwiki-popup-bubble smarterwiki-popup-bubble-active smarterwiki-popup-bubble-flipped">
-class="smarterwiki-popup-bubble-tip">
-class="smarterwiki-popup-bubble-body">
-class="smarterwiki-popup-bubble-links-container">
-class="smarterwiki-popup-bubble-links">
-class="smarterwiki-popup-bubble-links-row">[{.smarterwiki-popup-bubble-link-favicon}](http//maps.google.com/maps?q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB "Search Google Maps"){.smarterwiki-popup-bubble-link}[{.smarterwiki-popup-bubble-link-favicon}](http//www.google.com/search?q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB "Search Google"){.smarterwiki-popup-bubble-link}[](http//www.google.com/search?hl=com&btnI=I'm+Feeling+Lucky&q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB+wikipedia "Search Wikipedia"){.smarterwiki-popup-bubble-link}
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
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- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
- .navTreeFolderish
- .contenttype-folder}
- - [Intel numerical
- libraries](intel-numerical-libraries.html "Intel libraries for high performance in numerical computing")
-
- - [GSL](gsl.html "The GNU Scientific Library. Provides a wide range of mathematical routines.")
-
- - [HDF5](hdf5.html "Hierarchical Data Format library. Serial and MPI parallel version.")
-
-
- - [FFTW](fftw.html "The discrete Fourier transform in one or more dimensions, MPI parallel")
-
- - [MAGMA for Intel Xeon
- Phi](magma-for-intel-xeon-phi.html "Next generation dense algebra library for heterogeneous systems with accelerators
- ")
- - [PETSc](petsc.html "PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism.")
-
- - [Trilinos](trilinos.html " Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization.")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md b/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
deleted file mode 100644
index 370be1163ae18983e77a60efecb17eac7a44e44a..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
+++ /dev/null
@@ -1,122 +0,0 @@
-
-Intel numerical libraries
-=========================
-Intel libraries for high performance in numerical computing
-
-
-Intel Math Kernel Library
--------------------------
-Intel Math Kernel Library (Intel MKL) is a library of math kernel
-subroutines, extensively threaded and optimized for maximum performance.
-Intel MKL unites and provides these basic components BLAS, LAPACK,
-ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and
-many more.
- $ module load mkl
-Read more at the [Intel
-MKL](../intel-suite/intel-mkl.html) page.
-Intel Integrated Performance Primitives
----------------------------------------
-Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX
-is available, via module ipp. The IPP is a library of highly optimized
-algorithmic building blocks for media and data applications. This
-includes signal, image and frame processing algorithms, such as FFT,
-FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many
-more.
- $ module load ipp
-Read more at the [Intel
-IPP](../intel-suite/intel-integrated-performance-primitives.html)
-page.
-Intel Threading Building Blocks
--------------------------------
-Intel Threading Building Blocks (Intel TBB) is a library that supports
-scalable parallel programming using standard ISO C++ code. It does not
-require special languages or compilers. It is designed to promote
-scalable data parallel programming. Additionally, it fully supports
-nested parallelism, so you can build larger parallel components from
-smaller parallel components. To use the library, you specify tasks, not
-threads, and let the library map tasks onto threads in an efficient
-manner.
- $ module load tbb
-Read more at the [Intel
-TBB](../intel-suite/intel-tbb.html) page.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
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- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
- .navTreeFolderish
- .contenttype-folder}
- - [Intel numerical
- libraries](intel-numerical-libraries.html "Intel libraries for high performance in numerical computing")
-
-
- - [GSL](gsl.html "The GNU Scientific Library. Provides a wide range of mathematical routines.")
-
- - [HDF5](hdf5.html "Hierarchical Data Format library. Serial and MPI parallel version.")
-
- - [FFTW](fftw.html "The discrete Fourier transform in one or more dimensions, MPI parallel")
-
- - [MAGMA for Intel Xeon
- Phi](magma-for-intel-xeon-phi.html "Next generation dense algebra library for heterogeneous systems with accelerators
- ")
- - [PETSc](petsc.html "PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism.")
-
- - [Trilinos](trilinos.html " Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization.")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md b/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
deleted file mode 100644
index 8a2027e649c6bb17512f5d43971bc4680958abdb..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
+++ /dev/null
@@ -1,150 +0,0 @@
-
-MAGMA for Intel Xeon Phi
-========================
-Next generation dense algebra library for heterogeneous systems with
-accelerators
-### Compiling and linking with MAGMA
-To be able to compile and link code with MAGMA library user has to load
-following module
- $ module load magma/1.3.0-mic
-To make compilation more user friendly module also sets these two
-environment variables
-MAGMA_INC - contains paths to the MAGMA header files (to be used for
-compilation step)
-
-MAGMA_LIBS - contains paths to MAGMA libraries (to be used for linking
-step). Â
-Compilation example
- $ icc -mkl -O3 -DHAVE_MIC -DADD_ -Wall $MAGMA_INC -c testing_dgetrf_mic.cpp -o testing_dgetrf_mic.o
- $ icc -mkl -O3 -DHAVE_MIC -DADD_ -Wall -fPIC -Xlinker -zmuldefs -Wall -DNOCHANGE -DHOST testing_dgetrf_mic.o -o testing_dgetrf_mic $MAGMA_LIBS
-Â
-### Running MAGMA code
-MAGMA implementation for Intel MIC requires a MAGMA server running on
-accelerator prior to executing the user application. The server can be
-started and stopped using following scripts
-To start MAGMA server use
-**$MAGMAROOT/start_magma_server**
-
-To stop the server use
-**$MAGMAROOT/stop_magma_server**
-
-For deeper understanding how the MAGMA server is started, see the
-following script
-**$MAGMAROOT/launch_anselm_from_mic.sh**
-To test if the MAGMA server runs properly we can run one of examples
-that are part of the MAGMA installation
- [user@cn204 ~]$ $MAGMAROOT/testing/testing_dgetrf_mic
- [user@cn204 ~]$ export OMP_NUM_THREADS=16
- [lriha@cn204 ~]$ $MAGMAROOT/testing/testing_dgetrf_mic
- Usage /apps/libs/magma-mic/magmamic-1.3.0/testing/testing_dgetrf_mic [options] [-h|--help]
- Â MÂ Â Â Â NÂ Â Â Â CPU GFlop/s (sec)Â Â MAGMA GFlop/s (sec)Â Â ||PA-LU||/(||A||*N)
- =========================================================================
- Â 1088Â 1088Â Â Â Â ---Â Â (Â ---Â )Â Â Â Â 13.93 (Â Â 0.06)Â Â Â Â ---
- Â 2112Â 2112Â Â Â Â ---Â Â (Â ---Â )Â Â Â Â 77.85 (Â Â 0.08)Â Â Â Â ---
- Â 3136Â 3136Â Â Â Â ---Â Â (Â ---Â )Â Â Â 183.21 (Â Â 0.11)Â Â Â Â ---
- Â 4160Â 4160Â Â Â Â ---Â Â (Â ---Â )Â Â Â 227.52 (Â Â 0.21)Â Â Â Â ---
- Â 5184Â 5184Â Â Â Â ---Â Â (Â ---Â )Â Â Â 258.61 (Â Â 0.36)Â Â Â Â ---
- Â 6208Â 6208Â Â Â Â ---Â Â (Â ---Â )Â Â Â 333.12 (Â Â 0.48)Â Â Â Â ---
- Â 7232Â 7232Â Â Â Â ---Â Â (Â ---Â )Â Â Â 416.52 (Â Â 0.61)Â Â Â Â ---
- Â 8256Â 8256Â Â Â Â ---Â Â (Â ---Â )Â Â Â 446.97 (Â Â 0.84)Â Â Â Â ---
- Â 9280Â 9280Â Â Â Â ---Â Â (Â ---Â )Â Â Â 461.15 (Â Â 1.16)Â Â Â Â ---
- 10304 10304Â Â Â Â ---Â Â (Â ---Â )Â Â Â 500.70 (Â Â 1.46)Â Â Â Â ---
-Â
-Please note MAGMA contains several benchmarks and examples that can be
-found in
-**$MAGMAROOT/testing/**
-MAGMA relies on the performance of all CPU cores as well as on the
-performance of the accelerator. Therefore on Anselm number of CPU OpenMP
-threads has to be set to 16 Â **
-export OMP_NUM_THREADS=16**
-Â
-See more details at [MAGMA home
-page](http//icl.cs.utk.edu/magma/).
-References
-----------
-[1] MAGMA MIC Linear Algebra Library for Intel Xeon Phi Coprocessors,
-Jack Dongarra et. al,Â
-[http//icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf
-](http//icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf)
-
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
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- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
- .navTreeFolderish
- .contenttype-folder}
- - [Intel numerical
- libraries](intel-numerical-libraries.html "Intel libraries for high performance in numerical computing")
-
- - [GSL](gsl.html "The GNU Scientific Library. Provides a wide range of mathematical routines.")
-
- - [HDF5](hdf5.html "Hierarchical Data Format library. Serial and MPI parallel version.")
-
- - [FFTW](fftw.html "The discrete Fourier transform in one or more dimensions, MPI parallel")
-
- - [MAGMA for Intel Xeon
- Phi](magma-for-intel-xeon-phi.html "Next generation dense algebra library for heterogeneous systems with accelerators
- ")
-
- - [PETSc](petsc.html "PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism.")
-
- - [Trilinos](trilinos.html " Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization.")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/numerical-libraries/petsc.md b/anselm-cluster-documentation/software/numerical-libraries/petsc.md
deleted file mode 100644
index 0aa3c15dbe1fd56d0358837df64cd99479a8ebb0..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/numerical-libraries/petsc.md
+++ /dev/null
@@ -1,171 +0,0 @@
-PETSc
-=====
-PETSc is a suite of building blocks for the scalable solution of
-scientific and engineering applications modelled by partial differential
-equations. It supports MPI, shared memory, and GPUs through CUDA or
-OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism.
-
-
-Introduction
-------------
-PETSc (Portable, Extensible Toolkit for Scientific Computation) is a
-suite of building blocks (data structures and routines) for the scalable
-solution of scientific and engineering applications modelled by partial
-differential equations. It allows thinking in terms of high-level
-objects (matrices) instead of low-level objects (raw arrays). Written in
-C language but can also be called from FORTRAN, C++, Python and Java
-codes. It supports MPI, shared memory, and GPUs through CUDA or OpenCL,
-as well as hybrid MPI-shared memory or MPI-GPU parallelism.
-Resources
----------
-- [project webpage](http//www.mcs.anl.gov/petsc/)
-- [documentation](http//www.mcs.anl.gov/petsc/documentation/)
- - [PETSc Users
- Manual (PDF)](http//www.mcs.anl.gov/petsc/petsc-current/docs/manual.pdf)
- - [index of all manual
- pages](http//www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/singleindex.html)
-- PRACE Video Tutorial [part
- 1](http//www.youtube.com/watch?v=asVaFg1NDqY), [part
- 2](http//www.youtube.com/watch?v=ubp_cSibb9I), [part
- 3](http//www.youtube.com/watch?v=vJAAAQv-aaw), [part
- 4](http//www.youtube.com/watch?v=BKVlqWNh8jY), [part
- 5](http//www.youtube.com/watch?v=iXkbLEBFjlM)
-Modules
--------
-You can start using PETSc on Anselm by loading the PETSc module. Module
-names obey this pattern
- # module load petsc/version-compiler-mpi-blas-variant, e.g.
- module load petsc/3.4.4-icc-impi-mkl-opt
-where `variant` is replaced by one of
-`{dbg, opt, threads-dbg, threads-opt}`. The `opt` variant is compiled
-without debugging information (no `-g` option) and with aggressive
-compiler optimizations (`-O3 -xAVX`). This variant is suitable for
-performance measurements and production runs. In all other cases use the
-debug (`dbg`) variant, because it contains debugging information,
-performs validations and self-checks, and provides a clear stack trace
-and message in case of an error. The other two variants `threads-dbg`
-and `threads-opt` are `dbg` and `opt`, respectively, built with [OpenMP
-and pthreads threading
-support](http//www.mcs.anl.gov/petsc/features/threads.html).
-External libraries
-------------------
-PETSc needs at least MPI, BLAS and LAPACK. These dependencies are
-currently satisfied with Intel MPI and Intel MKL in Anselm `petsc`
-modules.
-PETSc can be linked with a plethora of [external numerical
-libraries](http//www.mcs.anl.gov/petsc/miscellaneous/external.html),
-extending PETSc functionality, e.g. direct linear system solvers,
-preconditioners or partitioners. See below a list of libraries currently
-included in Anselm `petsc` modules.
-All these libraries can be used also alone, without PETSc. Their static
-or shared program libraries are available in
-`$PETSC_DIR/$PETSC_ARCH/lib` and header files in
-`$PETSC_DIR/$PETSC_ARCH/include`. `PETSC_DIR` and `PETSC_ARCH` are
-environment variables pointing to a specific PETSc instance based on the
-petsc module loaded.
-### Libraries linked to PETSc on Anselm (as of 11 April 2015)
-- dense linear algebra
- - [Elemental](http//libelemental.org/)
-- sparse linear system solvers
- - [Intel MKL
- Pardiso](https//software.intel.com/en-us/node/470282)
- - [MUMPS](http//mumps.enseeiht.fr/)
- - [PaStiX](http//pastix.gforge.inria.fr/)
- - [SuiteSparse](http//faculty.cse.tamu.edu/davis/suitesparse.html)
- - [SuperLU](http//crd.lbl.gov/~xiaoye/SuperLU/#superlu)
- - [SuperLU_Dist](http//crd.lbl.gov/~xiaoye/SuperLU/#superlu_dist)
-- input/output
- - [ExodusII](http//sourceforge.net/projects/exodusii/)
- - [HDF5](http//www.hdfgroup.org/HDF5/)
- - [NetCDF](http//www.unidata.ucar.edu/software/netcdf/)
-- partitioning
- - [Chaco](http//www.cs.sandia.gov/CRF/chac.html)
- - [METIS](http//glaros.dtc.umn.edu/gkhome/metis/metis/overview)
- - [ParMETIS](http//glaros.dtc.umn.edu/gkhome/metis/parmetis/overview)
- - [PT-Scotch](http//www.labri.fr/perso/pelegrin/scotch/)
-- preconditioners & multigrid
- - [Hypre](http//acts.nersc.gov/hypre/)
- - [Trilinos ML](http//trilinos.sandia.gov/packages/ml/)
- - [SPAI - Sparse Approximate
- Inverse](https//bitbucket.org/petsc/pkg-spai)
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
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-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
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- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
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-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
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- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
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- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
- .navTreeFolderish
- .contenttype-folder}
- - [Intel numerical
- libraries](intel-numerical-libraries.html "Intel libraries for high performance in numerical computing")
-
- - [GSL](gsl.html "The GNU Scientific Library. Provides a wide range of mathematical routines.")
-
- - [HDF5](hdf5.html "Hierarchical Data Format library. Serial and MPI parallel version.")
-
- - [FFTW](fftw.html "The discrete Fourier transform in one or more dimensions, MPI parallel")
-
- - [MAGMA for Intel Xeon
- Phi](magma-for-intel-xeon-phi.html "Next generation dense algebra library for heterogeneous systems with accelerators
- ")
- - [PETSc](petsc.html "PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism.")
-
-
- - [Trilinos](trilinos.html " Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization.")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/numerical-libraries/trilinos.md b/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
deleted file mode 100644
index 94872dc6c09ceee2fac21a98eb294d04549041de..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
+++ /dev/null
@@ -1,135 +0,0 @@
-Trilinos
-========
-Packages for large scale scientific and engineering problems. Provides
-MPI and hybrid parallelization.
-### Introduction
-Trilinos is a collection of software packages for the numerical solution
-of large scale scientific and engineering problems. It is based on C++
-and feautures modern object-oriented design. Both serial as well as
-parallel computations based on MPI and hybrid parallelization are
-supported within Trilinos packages.
-### Installed packages
-Current Trilinos installation on ANSELM contains (among others) the
-following main packages
-- **Epetra** - core linear algebra package containing classes for
- manipulation with serial and distributed vectors, matrices,
- and graphs. Dense linear solvers are supported via interface to BLAS
- and LAPACK (Intel MKL on ANSELM). Its extension **EpetraExt**
- contains e.g. methods for matrix-matrix multiplication.
-- **Tpetra** - next-generation linear algebra package. Supports 64bit
- indexing and arbitrary data type using C++ templates.
-- **Belos** - library of various iterative solvers (CG, block CG,
- GMRES, block GMRES etc.).
-- **Amesos** - interface to direct sparse solvers.
-- **Anasazi** - framework for large-scale eigenvalue algorithms.
-- **IFPACK** - distributed algebraic preconditioner (includes e.g.
- incomplete LU factorization)
-- **Teuchos** - common tools packages. This package contains classes
- for memory management, output, performance monitoring, BLAS and
- LAPACK wrappers etc.
-For the full list of Trilinos packages, descriptions of their
-capabilities, and user manuals see
-[http//trilinos.sandia.gov.](http//trilinos.sandia.gov/)
-### Installed version
-Currently, Trilinos in version 11.2.3 compiled with Intel Compiler is
-installed on ANSELM.
-### Compilling against Trilinos
-First, load the appropriate module
- $ module load trilinos
-For the compilation of CMake-aware project, Trilinos provides the
-FIND_PACKAGE( Trilinos ) capability, which makes it easy to build
-against Trilinos, including linking against the correct list of
-libraries. For details, see
-For compiling using simple makefiles, Trilinos provides Makefile.export
-system, which allows users to include important Trilinos variables
-directly into their makefiles. This can be done simply by inserting the
-following line into the makefile
- include Makefile.export.Trilinos
-or
- include Makefile.export.
-if you are interested only in a specific Trilinos package. This will
-give you access to the variables such as Trilinos_CXX_COMPILER,
-Trilinos_INCLUDE_DIRS, Trilinos_LIBRARY_DIRS etc. For the detailed
-description and example makefile see
-.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
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-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
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- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
- .navTreeFolderish
- .contenttype-folder}
- - [Intel numerical
- libraries](intel-numerical-libraries.html "Intel libraries for high performance in numerical computing")
-
- - [GSL](gsl.html "The GNU Scientific Library. Provides a wide range of mathematical routines.")
-
- - [HDF5](hdf5.html "Hierarchical Data Format library. Serial and MPI parallel version.")
-
- - [FFTW](fftw.html "The discrete Fourier transform in one or more dimensions, MPI parallel")
-
- - [MAGMA for Intel Xeon
- Phi](magma-for-intel-xeon-phi.html "Next generation dense algebra library for heterogeneous systems with accelerators
- ")
- - [PETSc](petsc.html "PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism.")
-
- - [Trilinos](trilinos.html " Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization.")
-
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/omics-master-1.md b/anselm-cluster-documentation/software/omics-master-1.md
deleted file mode 100644
index 6d8c4f6a7c0578e31dbf522f7c212f8d35d209d5..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/omics-master-1.md
+++ /dev/null
@@ -1,78 +0,0 @@
- [Overview](omics-master-1/overview.html){.contenttype-document .state-published .url}
- The human NGS data processing solution
-
- [images](omics-master-1/images.html){.contenttype-folder .state-published .url}
-
- [Diagnostic component (TEAM)](omics-master-1/diagnostic-component-team.html){.contenttype-document .state-published .url}
-
- [Priorization component (BiERApp)](omics-master-1/priorization-component-bierapp.html){.contenttype-document .state-published .url}
-
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage-1.html)
-
- - [Network](../network.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](virtualization.html)
-
- - [Compilers](compilers.html "Available compilers, including GNU, INTEL and UPC compilers")
-
- - [Intel Xeon
- Phi](intel-xeon-phi.html "A guide to Intel Xeon Phi usage")
-
- - [ISV
- Licenses](isv_licenses.html "A guide to managing Independent Software Vendor licences")
-
diff --git a/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md b/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md
deleted file mode 100644
index ae2aa156ef14bfb2824383271f2eefa1505ba44c..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md
+++ /dev/null
@@ -1,112 +0,0 @@
-
-Diagnostic component (TEAM)
-===========================
-
-
-### Access
-TEAM is available at the following address
-Â
-The address is accessible only via
-[VPN. ](../../accessing-the-cluster/vpn-access.html)
-### Diagnostic component (TEAM) {#diagnostic-component-team}
-VCF files are scanned by this diagnostic tool for known diagnostic
-disease-associated variants. When no diagnostic mutation is found, the
-file can be sent to the disease-causing gene discovery tool to see
-wheter new disease associated variants can be found.
-TEAMÂ (27)Â is an intuitive and easy-to-use web tool that
-fills the gap between the predicted mutations and the final diagnostic
-in targeted enrichment sequencing analysis. The tool searches for known
-diagnostic mutations, corresponding to a disease panel, among the
-predicted patient’s variants. Diagnostic variants for the disease are
-taken from four databases of disease-related variants (HGMD-public,
-HUMSAVAR , ClinVar and COSMIC) If no primary diagnostic variant is
-found, then a list of secondary findings that can help to establish a
-diagnostic is produced. TEAM also provides with an interface for the
-definition of and customization of panels, by means of which, genes and
-mutations can be added or discarded to adjust panel definitions.Â
-
-Â
-***Figure 5. ****Interface of the application. Panels for defining
-targeted regions of interest can be set up by just drag and drop known
-disease genes or disease definitions from the lists. Thus, virtual
-panels can be interactively improved as the knowledge of the disease
-increases.*
-*
-*
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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- ") .navTreeFolderish
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diff --git a/anselm-cluster-documentation/software/omics-master-1/images.md b/anselm-cluster-documentation/software/omics-master-1/images.md
deleted file mode 100644
index d5f9cbe78473ee91df36b55adb4f0fe71d31c97b..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/omics-master-1/images.md
+++ /dev/null
@@ -1,168 +0,0 @@
-images
-======
- {width="16" height="16"} [Fig 1](images/fig1.png/view.html){.contenttype-image .state-missing-value .url}
- OMICS MASTER solution overview. Data is
- produced in the external labs and comes to IT4I (represented by the
- blue dashed line). The data pre-processor converts raw data into a
- list of variants and annotations for each sequenced patient. These
- lists files together with primary and secondary (alignment) data
- files are stored in IT4I sequence DB and uploaded to the discovery
- (candidate priorization) or diagnostic component where they can be
- analysed directly by the user that produced them, depending of the
- experimental design carried out.
- {width="16" height="16"} [fig2.png](images/fig2.png/view.html){.contenttype-image .state-missing-value .url}
- FASTQ file.
- {width="16" height="16"} [table1.png](images/table1.png/view.html){.contenttype-image .state-missing-value .url}
- Mandatory fields in the SAM format.
- {width="16" height="16"} [fig3.png](images/fig3.png/view.html){.contenttype-image .state-missing-value .url}
- SAM format file. The â€@SQ’ line in the
- header section gives the order of reference sequences. Notably, r001
- is the name of a read pair. According to FLAG 163 (=1+2+32+128), the
- read mapped to position 7 is the second read in the pair (128) and
- regarded as properly paired (1 + 2); its mate is mapped to 37 on the
- reverse strand (32). Read r002 has three soft-clipped (unaligned)
- bases. The coordinate shown in SAM is the position of the first
- aligned base. The CIGAR string for this alignment contains a
- P (padding) operation which correctly aligns the inserted sequences.
- Padding operations can be absent when an aligner does not support
- multiple sequence alignment. The last six bases of read r003 map to
- position 9, and the first five to position 29 on the reverse strand.
- The hard clipping operation H indicates that the clipped sequence is
- not present in the sequence field. The NM tag gives the number
- of mismatches. Read r004 is aligned across an intron, indicated by
- the N operation.
- {width="16" height="16"} [fig4.png](images/fig4.png/view.html){.contenttype-image .state-missing-value .url}
- a) Example of valid VCF. The header lines
- ##fileformat and #CHROM are mandatory, the rest is optional but
- strongly recommended. Each line of the body describes variants
- present in the sampled population at one genomic position or region.
- All alternate alleles are listed in the ALT column and referenced
- from the genotype fields as 1-based indexes to this list; the
- reference haplotype is designated as 0. For multiploid data, the
- separator indicates whether the data are phased (|) or unphased (/).
- Thus, the two alleles C and G at the positions 2 and 5 in this
- figure occur on the same chromosome in SAMPLE1. The first data line
- shows an example of a deletion (present in SAMPLE1) and a
- replacement of two bases by another base (SAMPLE2); the second line
- shows a SNP and an insertion; the third a SNP; the fourth a large
- structural variant described by the annotation in the INFO column,
- the coordinate is that of the base before the variant. (b–f )
- Alignments and VCF representations of different sequence variants
- SNP, insertion, deletion, replacement, and a large deletion. The REF
- columns shows the reference bases replaced by the haplotype in the
- ALT column. The coordinate refers to the first reference base. (g)
- Users are advised to use simplest representation possible and lowest
- coordinate in cases where the position is ambiguous.
- {width="16" height="16"} [fig5.png](images/fig5.png/view.html){.contenttype-image .state-missing-value .url}
- Interface of the application. Panels for
- defining targeted regions of interest can be set up by just drag and
- drop known disease genes or disease definitions from the lists.
- Thus, virtual panels can be interactively improved as the knowledge
- of the disease increases.
- {width="16" height="16"} [fig6.png](images/fig6.png/view.html){.contenttype-image .state-missing-value .url}
- Web interface to the prioritization tool.
- This figure shows the interface of the web tool for candidate gene
- prioritization with the filters available. The tool includes a
- genomic viewer (Genome Maps 30) that enables the representation of
- the variants in the corresponding genomic coordinates.
- {width="16" height="16"} [fig7.png](images/fig7.png/view.html){.contenttype-image .state-missing-value .url}
- TEAM upload panel. Once the file has been
- uploaded, a panel must be chosen from the Panel list. Then, pressing
- the Run button the diagnostic process starts.
- {width="16" height="16"} [fig7x.png](images/fig7x.png/view.html){.contenttype-image .state-missing-value .url}
- The panel manager. The elements used to
- define a panel are (A) disease terms, (B) diagnostic mutations
- and (C) genes. Arrows represent actions that can be taken in the
- panel manager. Panels can be defined by using the known mutations
- and genes of a particular disease. This can be done by dragging them
- to the Primary Diagnostic box (action D). This action, in addition
- to defining the diseases in the Primary Diagnostic box,
- automatically adds the corresponding genes to the Genes box. The
- panels can be customized by adding new genes (action F) or removing
- undesired genes (action G). New disease mutations can be added
- independently or associated to an already existing disease term
- (action E). Disease terms can be removed by simply dragging themback
- (action H).
- {width="16" height="16"} [fig8.png](images/fig8.png/view.html){.contenttype-image .state-missing-value .url}
- BierApp VCF upload panel. It is
- recommended to choose a name for the job as well as a description.
-
- {width="16" height="16"} [fig9.png](images/fig9.png/view.html){.contenttype-image .state-missing-value .url}
- This picture shows all the information
- associated to the variants. If a variant has an associated phenotype
- we could see it in the last column. In this case, the variant
- 7132481242 C>T is associated to the phenotype large
- intestine tumor.
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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diff --git a/anselm-cluster-documentation/software/omics-master-1/images/fig1.png/image.png b/anselm-cluster-documentation/software/omics-master-1/images/fig1.png/image.png
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--- a/anselm-cluster-documentation/software/omics-master-1/images/fig1.png/view.md
+++ /dev/null
@@ -1,101 +0,0 @@
-Info
-
-Fig 1
-=====
-OMICS MASTER solution overview. Data is produced in the external labs
-and comes to IT4I (represented by the blue dashed line). The data
-pre-processor converts raw data into a list of variants and annotations
-for each sequenced patient. These lists files together with primary and
-secondary (alignment) data files are stored in IT4I sequence DB and
-uploaded to the discovery (candidate priorization) or diagnostic
-component where they can be analysed directly by the user that produced
-them, depending of the experimental design carried out.
-[{width="400" height="249"}
-](image_view_fullscreen.html) id="plone-image-details"
-class="discreet visualNoPrint"> Velikost
-obrázku v plné velikosti 153 KB | [
-class="visualNoPrint"> 
-ZobrazenĂ ](image_view_fullscreen.html) [
-class="visualNoPrint"> 
-Stáhnout ](fig1.png)
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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- Nodes](../../../../compute-nodes.html)
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- ") .navTreeFolderish
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diff --git a/anselm-cluster-documentation/software/omics-master-1/images/fig2.png/image.png b/anselm-cluster-documentation/software/omics-master-1/images/fig2.png/image.png
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index 9908cb44ad5bbd8b61bf84d9dd4c9bc343c18eae..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/omics-master-1/images/fig2.png/view.md
+++ /dev/null
@@ -1,94 +0,0 @@
-Info
-
-fig2.png
-========
-FASTQ file.
-[{width="400" height="117"}
-](image_view_fullscreen.html) id="plone-image-details"
-class="discreet visualNoPrint"> Velikost
-obrázku v plné velikosti 38 KB | [
-class="visualNoPrint"> 
-ZobrazenĂ ](image_view_fullscreen.html) [
-class="visualNoPrint"> 
-Stáhnout ](fig2.png)
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-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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- Nodes](../../../../compute-nodes.html)
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- ") .navTreeFolderish
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diff --git a/anselm-cluster-documentation/software/omics-master-1/images/fig3.png/image.png b/anselm-cluster-documentation/software/omics-master-1/images/fig3.png/image.png
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index 281373458aef1ad9616d54b6aef213ca7978ab63..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/omics-master-1/images/fig3.png/view.md
+++ /dev/null
@@ -1,108 +0,0 @@
-Info
-
-fig3.png
-========
-SAM format file. The â€@SQ’ line in the header section gives the order of
-reference sequences. Notably, r001 is the name of a read pair. According
-to FLAG 163 (=1+2+32+128), the read mapped to position 7 is the second
-read in the pair (128) and regarded as properly paired (1 + 2); its mate
-is mapped to 37 on the reverse strand (32). Read r002 has three
-soft-clipped (unaligned) bases. The coordinate shown in SAM is the
-position of the first aligned base. The CIGAR string for this alignment
-contains a P (padding) operation which correctly aligns the inserted
-sequences. Padding operations can be absent when an aligner does not
-support multiple sequence alignment. The last six bases of read r003 map
-to position 9, and the first five to position 29 on the reverse strand.
-The hard clipping operation H indicates that the clipped sequence is not
-present in the sequence field. The NM tag gives the number of
-mismatches. Read r004 is aligned across an intron, indicated by the N
-operation.
-[{width="400" height="96"}
-](image_view_fullscreen.html) id="plone-image-details"
-class="discreet visualNoPrint"> Velikost
-obrázku v plné velikosti 33 KB | [
-class="visualNoPrint"> 
-ZobrazenĂ ](image_view_fullscreen.html) [
-class="visualNoPrint"> 
-Stáhnout ](fig3.png)
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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- Execution](../../../../resource-allocation-and-job-execution.html)
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- - [Compute
- Nodes](../../../../compute-nodes.html)
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- ") .navTreeFolderish
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-
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-
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- CUDA](../../../nvidia-cuda.html "A guide to nVidia CUDA programming and GPU usage")
-
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diff --git a/anselm-cluster-documentation/software/omics-master-1/images/fig4.png/image.png b/anselm-cluster-documentation/software/omics-master-1/images/fig4.png/image.png
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index 4ecb13728a0cf816dc8cc8f8bb18d0c02fa1ea79..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/omics-master-1/images/fig4.png/view.md
+++ /dev/null
@@ -1,112 +0,0 @@
-Info
-
-
-a) Example of valid VCF. The header lines ##fileformat and #CHROM are
-mandatory, the rest is optional but strongly recommended. Each line of
-the body describes variants present in the sampled population at one
-genomic position or region. All alternate alleles are listed in the ALT
-column and referenced from the genotype fields as 1-based indexes to
-this list; the reference haplotype is designated as 0. For multiploid
-data, the separator indicates whether the data are phased (|) or
-unphased (/). Thus, the two alleles C and G at the positions 2 and 5 in
-this figure occur on the same chromosome in SAMPLE1. The first data line
-shows an example of a deletion (present in SAMPLE1) and a replacement of
-two bases by another base (SAMPLE2); the second line shows a SNP and an
-insertion; the third a SNP; the fourth a large structural variant
-described by the annotation in the INFO column, the coordinate is that
-of the base before the variant. (b–f ) Alignments and VCF
-representations of different sequence variants SNP, insertion,
-deletion, replacement, and a large deletion. The REF columns shows the
-reference bases replaced by the haplotype in the ALT column. The
-coordinate refers to the first reference base. (g) Users are advised to
-use simplest representation possible and lowest coordinate in cases
-where the position is ambiguous.
-[{width="400" height="306"}
-](image_view_fullscreen.html) id="plone-image-details"
-class="discreet visualNoPrint"> Velikost
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-
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- ") .navTreeFolderish
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-
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-
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-
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-
- - [Compilers](../../../compilers.html "Available compilers, including GNU, INTEL and UPC compilers")
-
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- Phi](../../../intel-xeon-phi.html "A guide to Intel Xeon Phi usage")
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- Licenses](../../../isv_licenses.html "A guide to managing Independent Software Vendor licences")
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- CUDA](../../../nvidia-cuda.html "A guide to nVidia CUDA programming and GPU usage")
-
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- Master](../../../omics-master-1.html)
- .navTreeFolderish
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diff --git a/anselm-cluster-documentation/software/omics-master-1/images/fig5.png/view.md b/anselm-cluster-documentation/software/omics-master-1/images/fig5.png/view.md
deleted file mode 100644
index 5479e9f0ecbc1d3e54bffd39652a4dabc0be4fb1..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/omics-master-1/images/fig5.png/view.md
+++ /dev/null
@@ -1,97 +0,0 @@
-Info
-
-fig5.png
-========
-Interface of the application. Panels for defining targeted regions of
-interest can be set up by just drag and drop known disease genes or
-disease definitions from the lists. Thus, virtual panels can be
-interactively improved as the knowledge of the disease increases.
-[{width="400" height="235"}
-](image_view_fullscreen.html) id="plone-image-details"
-class="discreet visualNoPrint"> Velikost
-obrázku v plné velikosti 302 KB | [
-class="visualNoPrint"> 
-ZobrazenĂ ](image_view_fullscreen.html) [
-class="visualNoPrint"> 
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- New](../../../../../whats-new.html)
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-
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- Documentation](../../../../../salomon.html)
-
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- Documentation](../../../../../anselm-cluster-documentation.html)
-
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- Overview](../../../../hardware-overview.html)
-
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- Cluster](../../../../accessing-the-cluster/shell-and-data-access.html)
-
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- Modules](../../../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../../compute-nodes.html)
-
- - [Storage](../../../../storage-1.html)
-
- - [Network](../../../../network.html)
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- - [Software](../../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
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-
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-
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- science](../../../chemistry.html "Tools for computational chemistry.")
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- studio](../../../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../../../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
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- Libraries](../../../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../../../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../../../virtualization.html)
-
- - [Compilers](../../../compilers.html "Available compilers, including GNU, INTEL and UPC compilers")
-
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- Phi](../../../intel-xeon-phi.html "A guide to Intel Xeon Phi usage")
-
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- Licenses](../../../isv_licenses.html "A guide to managing Independent Software Vendor licences")
-
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-
- - [nVidia
- CUDA](../../../nvidia-cuda.html "A guide to nVidia CUDA programming and GPU usage")
-
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diff --git a/anselm-cluster-documentation/software/omics-master-1/images/fig6.png/view.md b/anselm-cluster-documentation/software/omics-master-1/images/fig6.png/view.md
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--- a/anselm-cluster-documentation/software/omics-master-1/images/fig6.png/view.md
+++ /dev/null
@@ -1,98 +0,0 @@
-Info
-
-fig6.png
-========
-Web interface to the prioritization tool. This figure shows the
-interface of the web tool for candidate gene prioritization with the
-filters available. The tool includes a genomic viewer (Genome Maps 30)
-that enables the representation of the variants in the corresponding
-genomic coordinates.
-[{width="400" height="295"}
-](image_view_fullscreen.html) id="plone-image-details"
-class="discreet visualNoPrint"> Velikost
-obrázku v plné velikosti 510 KB | [
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- New](../../../../../whats-new.html)
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- IT4Innovations](../../../../../get-started-with-it4innovations.html)
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- Documentation](../../../../../salomon.html)
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- Documentation](../../../../../anselm-cluster-documentation.html)
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- Overview](../../../../hardware-overview.html)
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- Cluster](../../../../accessing-the-cluster/shell-and-data-access.html)
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- Execution](../../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../../compute-nodes.html)
-
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- ") .navTreeFolderish
- .contenttype-folder}
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- science](../../../chemistry.html "Tools for computational chemistry.")
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- studio](../../../intel-suite.html "The Intel Parallel Studio XE")
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-
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- Libraries](../../../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../../../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../../../virtualization.html)
-
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diff --git a/anselm-cluster-documentation/software/omics-master-1/images/fig7.png/image.png b/anselm-cluster-documentation/software/omics-master-1/images/fig7.png/image.png
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--- a/anselm-cluster-documentation/software/omics-master-1/images/fig7.png/view.md
+++ /dev/null
@@ -1,96 +0,0 @@
-Info
-
-fig7.png
-========
-TEAM upload panel. Once the file has been uploaded, a panel must be
-chosen from the Panel list. Then, pressing the Run button the diagnostic
-process starts.
-[{width="400" height="71"}
-](image_view_fullscreen.html) id="plone-image-details"
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- New](../../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../../get-started-with-it4innovations.html)
-
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- Documentation](../../../../../salomon.html)
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- Documentation](../../../../../anselm-cluster-documentation.html)
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- Overview](../../../../hardware-overview.html)
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- Cluster](../../../../accessing-the-cluster/shell-and-data-access.html)
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- Modules](../../../../environment-and-modules.html)
-
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- Execution](../../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../../compute-nodes.html)
-
- - [Storage](../../../../storage-1.html)
-
- - [Network](../../../../network.html)
-
- - [Software](../../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../../ansys.html "An engineering simulation software ")
-
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- profilers](../../../debuggers.html "A collection of development tools")
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- science](../../../chemistry.html "Tools for computational chemistry.")
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- studio](../../../intel-suite.html "The Intel Parallel Studio XE")
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- Libraries](../../../numerical-libraries.html "Libraries for numerical computations")
-
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- languages](../../../numerical-languages.html "Interpreted languages for numerical computations")
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-
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diff --git a/anselm-cluster-documentation/software/omics-master-1/images/fig7x.png/image.png b/anselm-cluster-documentation/software/omics-master-1/images/fig7x.png/image.png
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--- a/anselm-cluster-documentation/software/omics-master-1/images/fig7x.png/view.md
+++ /dev/null
@@ -1,104 +0,0 @@
-Info
-
-fig7x.png
-=========
-The panel manager. The elements used to define a panel are (A) disease
-terms, (B) diagnostic mutations and (C) genes. Arrows represent actions
-that can be taken in the panel manager. Panels can be defined by using
-the known mutations and genes of a particular disease. This can be done
-by dragging them to the Primary Diagnostic box (action D). This action,
-in addition to defining the diseases in the Primary Diagnostic box,
-automatically adds the corresponding genes to the Genes box. The panels
-can be customized by adding new genes (action F) or removing undesired
-genes (action G). New disease mutations can be added independently or
-associated to an already existing disease term (action E). Disease terms
-can be removed by simply dragging themback (action H).
-[{width="400" height="286"}
-](image_view_fullscreen.html) id="plone-image-details"
-class="discreet visualNoPrint"> Velikost
-obrázku v plné velikosti 156 KB | [
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- New](../../../../../whats-new.html)
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-
- - [Salomon Cluster
- Documentation](../../../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../../../hardware-overview.html)
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- - [Accessing the
- Cluster](../../../../accessing-the-cluster/shell-and-data-access.html)
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- Modules](../../../../environment-and-modules.html)
-
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- Execution](../../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../../compute-nodes.html)
-
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- ") .navTreeFolderish
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- science](../../../chemistry.html "Tools for computational chemistry.")
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- studio](../../../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../../../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
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- Libraries](../../../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../../../numerical-languages.html "Interpreted languages for numerical computations")
-
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-
- - [Compilers](../../../compilers.html "Available compilers, including GNU, INTEL and UPC compilers")
-
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- Phi](../../../intel-xeon-phi.html "A guide to Intel Xeon Phi usage")
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- - [nVidia
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diff --git a/anselm-cluster-documentation/software/omics-master-1/images/fig8.png/image.png b/anselm-cluster-documentation/software/omics-master-1/images/fig8.png/image.png
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--- a/anselm-cluster-documentation/software/omics-master-1/images/fig8.png/view.md
+++ /dev/null
@@ -1,95 +0,0 @@
-Info
-
-fig8.png
-========
-BierApp VCF upload panel. It is recommended to choose a name for the job
-as well as a description.
-[{width="400" height="227"}
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- Execution](../../../../resource-allocation-and-job-execution.html)
-
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- Nodes](../../../../compute-nodes.html)
-
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-
- - [Network](../../../../network.html)
-
- - [Software](../../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../../ansys.html "An engineering simulation software ")
-
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-
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-
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-
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-
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-
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-
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-
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-
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- .navTreeFolderish
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diff --git a/anselm-cluster-documentation/software/omics-master-1/images/fig9.png/image.png b/anselm-cluster-documentation/software/omics-master-1/images/fig9.png/image.png
deleted file mode 100755
index 406e0dbb156d0f8e75f6230f66dfccc58fed457b..0000000000000000000000000000000000000000
Binary files a/anselm-cluster-documentation/software/omics-master-1/images/fig9.png/image.png and /dev/null differ
diff --git a/anselm-cluster-documentation/software/omics-master-1/images/fig9.png/view.md b/anselm-cluster-documentation/software/omics-master-1/images/fig9.png/view.md
deleted file mode 100644
index f60da7fbe7691ce586f11836a8115b7563b83083..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/omics-master-1/images/fig9.png/view.md
+++ /dev/null
@@ -1,97 +0,0 @@
-Info
-
-fig9.png
-========
-This picture shows all the information associated to the variants. If a
-variant has an associated phenotype we could see it in the last column.
-In this case, the variant 7132481242 C>T is associated to the
-phenotype large intestine tumor.
-[{width="400" height="171"}
-](image_view_fullscreen.html) id="plone-image-details"
-class="discreet visualNoPrint"> Velikost
-obrázku v plné velikosti 268 KB | [
-class="visualNoPrint"> 
-ZobrazenĂ ](image_view_fullscreen.html) [
-class="visualNoPrint"> 
-Stáhnout ](fig9.png)
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
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- [Navigace](../../../../../sitemap.html)
- - [What's
- New](../../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../../compute-nodes.html)
-
- - [Storage](../../../../storage-1.html)
-
- - [Network](../../../../network.html)
-
- - [Software](../../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../../../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../../../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../../../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../../../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../../../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../../../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../../../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../../../virtualization.html)
-
- - [Compilers](../../../compilers.html "Available compilers, including GNU, INTEL and UPC compilers")
-
- - [Intel Xeon
- Phi](../../../intel-xeon-phi.html "A guide to Intel Xeon Phi usage")
-
- - [ISV
- Licenses](../../../isv_licenses.html "A guide to managing Independent Software Vendor licences")
-
- - [Java](../../../java.html "Java on ANSELM")
-
- - [nVidia
- CUDA](../../../nvidia-cuda.html "A guide to nVidia CUDA programming and GPU usage")
-
- - [OMICS
- Master](../../../omics-master-1.html)
- .navTreeFolderish
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diff --git a/anselm-cluster-documentation/software/omics-master-1/images/table1.png/view.md b/anselm-cluster-documentation/software/omics-master-1/images/table1.png/view.md
deleted file mode 100644
index 3c97abe80f6053026038fe043a5a93bcd94f2813..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/omics-master-1/images/table1.png/view.md
+++ /dev/null
@@ -1,93 +0,0 @@
-Info
-
-
-Mandatory fields in the SAM format.
-[{width="400" height="222"}
-](image_view_fullscreen.html) id="plone-image-details"
-class="discreet visualNoPrint"> Velikost
-obrázku v plné velikosti 128 KB | [
-class="visualNoPrint"> 
-ZobrazenĂ ](image_view_fullscreen.html) [
-class="visualNoPrint"> 
-Stáhnout ](table1.png)
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
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- - [What's
- New](../../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
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-
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- Execution](../../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../../compute-nodes.html)
-
- - [Storage](../../../../storage-1.html)
-
- - [Network](../../../../network.html)
-
- - [Software](../../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../../../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../../../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../../../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../../../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../../../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../../../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../../../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../../../virtualization.html)
-
- - [Compilers](../../../compilers.html "Available compilers, including GNU, INTEL and UPC compilers")
-
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- Phi](../../../intel-xeon-phi.html "A guide to Intel Xeon Phi usage")
-
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- Licenses](../../../isv_licenses.html "A guide to managing Independent Software Vendor licences")
-
- - [Java](../../../java.html "Java on ANSELM")
-
- - [nVidia
- CUDA](../../../nvidia-cuda.html "A guide to nVidia CUDA programming and GPU usage")
-
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- Master](../../../omics-master-1.html)
- .navTreeFolderish
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diff --git a/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.md b/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.md
deleted file mode 100644
index 59438810b2835186500a548ba480c42896c42c75..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.md
+++ /dev/null
@@ -1,107 +0,0 @@
-
-Priorization component (BiERApp)
-================================
-### Access
-BiERApp is available at the following address
-Â
-The address is accessible only
-via [VPN. ](../../accessing-the-cluster/vpn-access.html)
-### BiERApp
-### This tool is aimed to discover new disease genes or variants by studying affected families or cases and controls. It carries out a filtering process to sequentially remove (i) variants which are not no compatible with the disease because are not expected to have impact on the protein function; (ii) variants that exist at frequencies incompatible with the disease; (iii) variants that do not segregate with the disease. The result is a reduced set of disease gene candidates that should be further validated experimentally.
-BiERapp (28) efficiently helps in the identification of
-causative variants in family and sporadic genetic diseases. The program
-reads lists of predicted variants (nucleotide substitutions and indels)
-in affected individuals or tumor samples and controls. In family
-studies, different modes of inheritance can easily be defined to filter
-out variants that do not segregate with the disease along the family.
-Moreover, BiERapp integrates additional information such as allelic
-frequencies in the general population and the most popular damaging
-scores to further narrow down the number of putative variants in
-successive filtering steps. BiERapp provides an interactive and
-user-friendly interface that implements the filtering strategy used in
-the context of a large-scale genomic project carried out by the Spanish
-Network for Research, in Rare Diseases (CIBERER) and the Medical Genome
-Project. in which more than 800 exomes have been analyzed.
-
-***Figure 6***. *Web interface to the prioritization tool.* *This
-figure*Â *shows the interface of the web tool for candidate gene
-prioritization with the filters available. The tool includes a genomic
-viewer (Genome Maps 30) that enables the representation of
-the variants in the corresponding genomic coordinates.*
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
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- New](../../../whats-new.html)
-
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- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
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- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
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- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
-
- - [Compilers](../compilers.html "Available compilers, including GNU, INTEL and UPC compilers")
-
- - [Intel Xeon
- Phi](../intel-xeon-phi.html "A guide to Intel Xeon Phi usage")
-
- - [ISV
- Licenses](../isv_licenses.html "A guide to managing Independent Software Vendor licences")
-
- - [Java](../java.html "Java on ANSELM")
diff --git a/anselm-cluster-documentation/software/openfoam.md b/anselm-cluster-documentation/software/openfoam.md
deleted file mode 100644
index 5d9d664a8bd7f2ca1bc7f6baceaa1c0d5f9fe935..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/openfoam.md
+++ /dev/null
@@ -1,230 +0,0 @@
-A free, open source CFD software package
-
-
-**Introduction**
-----------------
-OpenFOAM is a free, open source CFD software package developed
-by [**OpenCFD Ltd**](http//www.openfoam.com/about) at [**ESI
-Group**](http//www.esi-group.com/) and distributed by the [**OpenFOAM
-Foundation **](http//www.openfoam.org/). It has a large user base
-across most areas of engineering and science, from both commercial and
-academic organisations.Â
-Homepage
-### **Installed version**
-Currently, several version compiled by GCC/ICC compilers in
-single/double precision with several version of openmpi are available on
-Anselm.
-For example syntax of available OpenFOAM module is
-< openfoam/2.2.1-icc-openmpi1.6.5-DP >
-this means openfoam version 2.2.1 compiled by
-ICC compiler with openmpi1.6.5 in double
-precision.
-Naming convection of the installed versions is following
-Â Â
-openfoam/<VERSION>-<COMPILER>-<openmpiVERSION>-<PRECISION>
-- <VERSION> - version of
- openfoam
-- <COMPILER> - version of used
- compiler
-- <openmpiVERSION> - version of used
- openmpi/impi
-- <PRECISION> - DP/SP –
- double/single precision
-### **Available OpenFOAM modules**
-To check available modules use
- $ module avail
-In /opt/modules/modulefiles/engineering you can see installed
-engineering softwares
- ------------------------------------ /opt/modules/modulefiles/engineering -------------------------------------------------------------
- ansys/14.5.x              matlab/R2013a-COM                               openfoam/2.2.1-icc-impi4.1.1.036-DP
- comsol/43b-COMÂ Â Â Â Â Â Â Â Â Â Â Â matlab/R2013a-EDUÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â openfoam/2.2.1-icc-openmpi1.6.5-DP
- comsol/43b-EDUÂ Â Â Â Â Â Â Â Â Â Â Â openfoam/2.2.1-gcc481-openmpi1.6.5-DPÂ Â Â Â Â Â Â Â Â Â Â paraview/4.0.1-gcc481-bullxmpi1.2.4.1-osmesa10.0
- lsdyna/7.x.x              openfoam/2.2.1-gcc481-openmpi1.6.5-SP
-For information how to use modules please [look
-here](../environment-and-modules.html "Environment and Modules ").
-**Getting Started**
--------------------
-To create OpenFOAM environment on ANSELM give the commands
- $ module load openfoam/2.2.1-icc-openmpi1.6.5-DP
- $ source $FOAM_BASHRC
-Pleas load correct module with your requirements “compiler - GCC/ICC,
-precision - DP/SP”.
-Create a project directory within the $HOME/OpenFOAM directory
-named <USER>-<OFversion> and create a directory
-named run within it, e.g. by typing
- $ mkdir -p $FOAM_RUN
-Project directory is now available by typing
- $ cd /home//OpenFOAM/-/run
-<OFversion> - for example <2.2.1>
-or
- $ cd $FOAM_RUN
-Copy the tutorial examples directory in the OpenFOAM distribution to
-the run directory
- $ cp -r $FOAM_TUTORIALS $FOAM_RUN
-Now you can run the first case for example incompressible laminar flow
-in a cavity.
-**Running Serial Applications**
--------------------------------
-Create a Bash script test.shÂ
-
- #!/bin/bash
- module load openfoam/2.2.1-icc-openmpi1.6.5-DP
- source $FOAM_BASHRC
- # source to run functions
- . $WM_PROJECT_DIR/bin/tools/RunFunctions
- cd $FOAM_RUN/tutorials/incompressible/icoFoam/cavity
- runApplication blockMesh
- runApplication icoFoam
-
-
-Job submission
-
- $ qsub -A OPEN-0-0 -q qprod -l select=1ncpus=16,walltime=030000 test.sh
-
- For information about job submission please [look
-here](../resource-allocation-and-job-execution/job-submission-and-execution.html "Job submission").
-**Running applications in parallel**
--------------------------------------------------
-Run the second case for example external incompressible turbulent
-flow - case - motorBike.
-First we must run serial application bockMesh and decomposePar for
-preparation of parallel computation.
-
-Create a Bash scrip test.sh
-
- #!/bin/bash
- module load openfoam/2.2.1-icc-openmpi1.6.5-DP
- source $FOAM_BASHRC
- # source to run functions
- . $WM_PROJECT_DIR/bin/tools/RunFunctions
- cd $FOAM_RUN/tutorials/incompressible/simpleFoam/motorBike
- runApplication blockMesh
- runApplication decomposePar
-
-
-Job submission
-
- $ qsub -A OPEN-0-0 -q qprod -l select=1ncpus=16,walltime=030000 test.sh
-
-This job create simple block mesh and domain decomposition.
-Check your decomposition, and submit parallel computation
-Create a PBS script
-testParallel.pbs
-
- #!/bin/bash
- #PBS -N motorBike
- #PBS -l select=2ncpus=16
- #PBS -l walltime=010000
- #PBS -q qprod
- #PBS -A OPEN-0-0
- module load openfoam/2.2.1-icc-openmpi1.6.5-DP
- source $FOAM_BASHRC
- cd $FOAM_RUN/tutorials/incompressible/simpleFoam/motorBike
- nproc = 32
- mpirun -hostfile ${PBS_NODEFILE} -np $nproc snappyHexMesh -overwrite -parallel | tee snappyHexMesh.log
- mpirun -hostfile ${PBS_NODEFILE} -np $nproc potentialFoam -noFunctionObject-writep -parallel | tee potentialFoam.log
- mpirun -hostfile ${PBS_NODEFILE} -np $nproc simpleFoam -parallel | tee simpleFoam.log
-
-nproc – number of subdomains
-Job submission
-
- $ qsub testParallel.pbs
-
-**Compile your own solver**
-----------------------------------------
-Initialize OpenFOAM environment before compiling your solver
-
- $ module load openfoam/2.2.1-icc-openmpi1.6.5-DP
- $ source $FOAM_BASHRC
- $ cd $FOAM_RUN/
-Create directory applications/solvers in user directory
-
- $ mkdir -p applications/solvers
- $ cd applications/solvers
-
-Copy icoFoam solver’s source files
-
- $ cp -r $FOAM_SOLVERS/incompressible/icoFoam/ My_icoFoam
- $ cd My_icoFoam
-Rename icoFoam.C to My_icoFOAM.C
-
- $ mv icoFoam.C My_icoFoam.C
-
-Edit *files* file in *Make* directory
-
- icoFoam.C
- EXE = $(FOAM_APPBIN)/icoFoam
-and change to
- My_icoFoam.C
- EXE = $(FOAM_USER_APPBIN)/My_icoFoam
-In directory My_icoFoam give the compilation command
-
- $ wmake
-------------------------------------------------------------------------
-Â
-**Â Have a fun with OpenFOAM )**
-Â
-Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage-1.html)
-
- - [Network](../network.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](virtualization.html)
-
diff --git a/anselm-cluster-documentation/software/operating-system.md b/anselm-cluster-documentation/software/operating-system.md
deleted file mode 100644
index 827b5747ebb440478570f8fe03ea5927ea697cfc..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/operating-system.md
+++ /dev/null
@@ -1,70 +0,0 @@
-The operating system, deployed on ANSELM
-
-
-The operating system on Anselm is Linux - bullx Linux Server release
-6.3.
-bullx Linux is based on Red Hat Enterprise Linux. bullx Linux is a Linux
-distribution provided by Bull and dedicated to HPC applications.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage-1.html)
-
- - [Network](../network.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](virtualization.html)
-
diff --git a/anselm-cluster-documentation/software/paraview.md b/anselm-cluster-documentation/software/paraview.md
deleted file mode 100644
index f2d62fc047f2d095d9ca5a2bde9b28f465897c2a..0000000000000000000000000000000000000000
--- a/anselm-cluster-documentation/software/paraview.md
+++ /dev/null
@@ -1,147 +0,0 @@
-An open-source, multi-platform data analysis and visualization
-application
-
-
-Introduction
-------------
-**ParaView**Â is an open-source, multi-platform data analysis and
-visualization application. ParaView users can quickly build
-visualizations to analyze their data using qualitative and quantitative
-techniques. The data exploration can be done interactively in 3D or
-programmatically using ParaView's batch processing capabilities.
-ParaView was developed to analyze extremely large datasets using
-distributed memory computing resources. It can be run on supercomputers
-to analyze datasets of exascale size as well as on laptops for smaller
-data.
-Homepage Â
-Installed version
------------------
-Currently, version 4.0.1 compiled with GCC 4.8.1 against Bull MPI
-library and OSMesa 10.0 is installed on Anselm.
-Usage
------
-On Anselm, ParaView is to be used in client-server mode. A parallel
-ParaView server is launched on compute nodes by the user, and client is
-launched on your desktop PC to control and view the visualization.
-Download ParaView client application for your OS here
-Â . Important
-**your version must match the version number installed on Anselm** !
-(currently v4.0.1)
-### Launching server
-To launch the server, you must first allocate compute nodes, for example
-Â
- $ qsub -I -q qprod -A OPEN-0-0 -l select=2
-to launch an interactive session on 2 nodes. Refer to [Resource
-Allocation and Job
-Execution](../resource-allocation-and-job-execution/introduction.html)
-for details.
-After the interactive session is opened, load the ParaView module
- $ module add paraview
-Now launch the parallel server, with number of nodes times 16 processes
-
- $ mpirun -np 32 pvserver --use-offscreen-rendering
- Waiting for client...
- Connection URL cs//cn7711111
- Accepting connection(s) cn7711111
-Â Note the that the server is listening on compute node cn77 in this
-case, we shall use this information later.
-### Client connection
-Because a direct connection is not allowed to compute nodes on Anselm,
-you must establish a SSH tunnel to connect to the server. Choose a port
-number on your PC to be forwarded to ParaView server, for example 12345.
-If your PC is running Linux, use this command to estabilish a SSH tunnel
-
- ssh -TN -L 12345cn7711111 username@anselm.it4i.cz
-replace username with your login and cn77
-with the name of compute node your ParaView server is running on (see
-previous step). If you use PuTTY on Windows, load Anselm connection
-configuration, then go to Connection->
-class="highlightedSearchTerm">SSH->Tunnels to set up the
-port forwarding. Click Remote radio button. Insert 12345 to Source port
-textbox. Insert cn7711111. Click Add button, then Open. [Read
-more about port
-forwarding.](resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html)
-Now launch ParaView client installed on your desktop PC. Select
-File->Connect..., click Add Server. Fill in the following
-Name Anselm tunnel
-Server Type Client/Server
-Host localhost
-Port 12345
-Click Configure, Save, the configuration is now saved for later use. Now
-click Connect to connect to the ParaView server. In your terminal where
-you have interactive session with ParaView server launched, you should
-see
- Client connected.
-You can now use Parallel ParaView.
-### Close server
-Remember to close the interactive session after you finish working with
-ParaView server, as it will remain launched even after your client is
-disconnected and will continue to consume resources.
-GPU support
------------
-Currently, GPU acceleration is not supported in the server and ParaView
-will not take advantage of accelerated nodes on Anselm. Support for GPU
-acceleration might be added in the future.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage-1.html)
-
- - [Network](../network.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](virtualization.html)
-
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diff --git a/++resource++jquery-ui-themes/sunburst/images/ui-icons_ffffff_256x240.png b/docs.it4i.cz/++resource++jquery-ui-themes/sunburst/images/ui-icons_ffffff_256x240.png
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diff --git a/RSS b/docs.it4i.cz/RSS
old mode 100755
new mode 100644
similarity index 96%
rename from RSS
rename to docs.it4i.cz/RSS
index 23f11db081a31c8da4084a8459de7340cd393284..f44409f3cde6ad63181bbb25565a36025b32b955
--- a/RSS
+++ b/docs.it4i.cz/RSS
@@ -101,8 +101,8 @@
<div id="parent-fieldname-text-50ee0f8999e14a08822bd423d24de7ef" class="">
- <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
-<h2 class=" "><img title="Vampir screenshot" class="image-inline" alt="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
+ <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
+<h2 class=" "><img alt="Vampir screenshot" class="image-inline" title="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
<h2 class=" ">Installed versions</h2>
<p>Version 8.5.0 is currently installed as module <span class="monospace">Vampir/8.5.0</span> :</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir &</pre>
@@ -153,8 +153,8 @@
<div id="parent-fieldname-text-f6e25102d1244fb4ab355175867747b5" class="">
- <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
-<h2 class=" "><img title="Vampir screenshot" class="image-inline" alt="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
+ <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
+<h2 class=" "><img alt="Vampir screenshot" class="image-inline" title="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
<h2 class=" ">Installed versions</h2>
<p>Version 8.5.0 is currently installed as module <span class="monospace">Vampir/8.5.0</span> :</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir &</pre>
@@ -295,8 +295,8 @@
<pre class="prettyprint lang-sh"><span style="text-align: left; float: none; ">[usename@login1.anselm ~]$ gnome-session &<br />[1] 23691<br />[<span style="text-align: left; float: none; ">usename</span>@login1.anselm ~]$ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused<br />PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused<br /><br />** (gnome-session:23691): WARNING **: Cannot open display:<br /></span></pre>
<p><span style="text-align: left; float: none; ">Â </span></p>
<ol>
-<li><span style="text-align: left; float: none; ">Locate and modify <span style="text-align: left; float: none; ">Cygwin shortcut that uses<span class="Apple-converted-space">Â </span></span><a href="http://x.cygwin.com/docs/man1/startxwin.1.html" rel="nofollow" style="text-align: left; ">startxwin</a><br />locate<br />C:\cygwin64\bin\XWin.exe<br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">change it to</span></span></span><br />C:\<i class="moz-txt-slash">cygwin64\bin\XWin.exe -listen tcp</i><br /><br /><img title="XWin-listen-tcp.png" class="image-inline" alt="XWin-listen-tcp.png" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/XWinlistentcp.png" /><br /></span><br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span></span></li>
-<li><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">Check Putty settings:<br /><span style="text-align: left; float: none; ">Enable X11 forwarding</span><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span><span class="Apple-converted-space"><br /></span></span><br /><a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding"><img title="" class="image-inline" alt="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwinX11forwarding.png/@@images/0f5b58e3-253c-4f87-a3b2-16f75cbf090f.png" /></a><br /></span></span></li>
+<li><span style="text-align: left; float: none; ">Locate and modify <span style="text-align: left; float: none; ">Cygwin shortcut that uses<span class="Apple-converted-space">Â </span></span><a href="http://x.cygwin.com/docs/man1/startxwin.1.html" rel="nofollow" style="text-align: left; ">startxwin</a><br />locate<br />C:\cygwin64\bin\XWin.exe<br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">change it to</span></span></span><br />C:\<i class="moz-txt-slash">cygwin64\bin\XWin.exe -listen tcp</i><br /><br /><img alt="XWin-listen-tcp.png" class="image-inline" title="XWin-listen-tcp.png" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/XWinlistentcp.png" /><br /></span><br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span></span></li>
+<li><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">Check Putty settings:<br /><span style="text-align: left; float: none; ">Enable X11 forwarding</span><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span><span class="Apple-converted-space"><br /></span></span><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding"><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwinX11forwarding.png/@@images/0f5b58e3-253c-4f87-a3b2-16f75cbf090f.png" /></a><br /></span></span></li>
</ol>
<p>Â </p>
@@ -361,7 +361,7 @@
<div id="parent-fieldname-text" class="plain">
- <p>We have implemented a new way to run parallel MATLAB jobs. Unlike the previously documented method, it does not submit a separate new job to run the workers, all is done within a single job. Read about it here:Â <a target="_self" title="" class="external-link" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6">https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6</a></p>
+ <p>We have implemented a new way to run parallel MATLAB jobs. Unlike the previously documented method, it does not submit a separate new job to run the workers, all is done within a single job. Read about it here:Â <a title="" class="external-link" target="_self" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6">https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6</a></p>
</div>
@@ -652,13 +652,13 @@
<pre class="prettyprint lang-sh">$ module load phono3py/0.9.14-ictce-7.3.5-Python-2.7.9</pre>
<h2>Example of calculating thermal conductivity of Si using VASP code.</h2>
<h3>Calculating force constants</h3>
-<p>One needs to calculate second order and third order force constants using the diamond structure of silicon stored in <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/poscar-si">POSCAR</a>Â (the same form as in VASP) using single displacement calculations within supercell.</p>
+<p>One needs to calculate second order and third order force constants using the diamond structure of silicon stored in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/poscar-si">POSCAR</a>Â (the same form as in VASP) using single displacement calculations within supercell.</p>
<pre class="prettyprint lang-sh">$ cat POSCAR<br />Â Si<br />Â Â 1.0<br />Â Â Â Â 5.4335600309153529Â Â Â 0.0000000000000000Â Â Â 0.0000000000000000<br />Â Â Â Â 0.0000000000000000Â Â Â 5.4335600309153529Â Â Â 0.0000000000000000<br />Â Â Â Â 0.0000000000000000Â Â Â 0.0000000000000000Â Â Â 5.4335600309153529<br />Â Si<br />Â Â 8<br />Direct<br />Â Â 0.8750000000000000Â 0.8750000000000000Â 0.8750000000000000<br />Â Â 0.8750000000000000Â 0.3750000000000000Â 0.3750000000000000<br />Â Â 0.3750000000000000Â 0.8750000000000000Â 0.3750000000000000<br />Â Â 0.3750000000000000Â 0.3750000000000000Â 0.8750000000000000<br />Â Â 0.1250000000000000Â 0.1250000000000000Â 0.1250000000000000<br />Â Â 0.1250000000000000Â 0.6250000000000000Â 0.6250000000000000<br />Â Â 0.6250000000000000Â 0.1250000000000000Â 0.6250000000000000<br />Â Â 0.6250000000000000Â 0.6250000000000000Â 0.1250000000000000<br /><br /></pre>
<h3>Generating displacement using 2x2x2 supercell for both second and third order force constants</h3>
<pre class="prettyprint lang-sh">$ <span class="n">phono3py</span> <span class="o">-</span><span class="n">d</span> <span class="o">--</span><span class="n">dim</span><span class="o">=</span><span class="s2">"2 2 2"</span> <span class="o">-</span><span class="n">c</span> <span class="n">POSCAR</span><span class="o"></span><span class="n"></span></pre>
<p class=" "><span class="n">111 displacements is created stored in <span class="n">disp_fc3.yaml</span>, and the structure input files with this displacements are POSCAR-00XXX, where the XXX=111.<br /></span></p>
<pre class="prettyprint lang-sh"><span class="n">disp_fc3.yaml POSCAR-00008 POSCAR-00017 POSCAR-00026 POSCAR-00035 POSCAR-00044 POSCAR-00053 POSCAR-00062 POSCAR-00071 POSCAR-00080 POSCAR-00089 POSCAR-00098 POSCAR-00107<br />POSCAR        POSCAR-00009 POSCAR-00018 POSCAR-00027 POSCAR-00036 POSCAR-00045 POSCAR-00054 POSCAR-00063 POSCAR-00072 POSCAR-00081 POSCAR-00090 POSCAR-00099 POSCAR-00108<br />POSCAR-00001  POSCAR-00010 POSCAR-00019 POSCAR-00028 POSCAR-00037 POSCAR-00046 POSCAR-00055 POSCAR-00064 POSCAR-00073 POSCAR-00082 POSCAR-00091 POSCAR-00100 POSCAR-00109<br />POSCAR-00002  POSCAR-00011 POSCAR-00020 POSCAR-00029 POSCAR-00038 POSCAR-00047 POSCAR-00056 POSCAR-00065 POSCAR-00074 POSCAR-00083 POSCAR-00092 POSCAR-00101 POSCAR-00110<br />POSCAR-00003  POSCAR-00012 POSCAR-00021 POSCAR-00030 POSCAR-00039 POSCAR-00048 POSCAR-00057 POSCAR-00066 POSCAR-00075 POSCAR-00084 POSCAR-00093 POSCAR-00102 POSCAR-00111<br />POSCAR-00004  POSCAR-00013 POSCAR-00022 POSCAR-00031 POSCAR-00040 POSCAR-00049 POSCAR-00058 POSCAR-00067 POSCAR-00076 POSCAR-00085 POSCAR-00094 POSCAR-00103<br />POSCAR-00005  POSCAR-00014 POSCAR-00023 POSCAR-00032 POSCAR-00041 POSCAR-00050 POSCAR-00059 POSCAR-00068 POSCAR-00077 POSCAR-00086 POSCAR-00095 POSCAR-00104<br />POSCAR-00006  POSCAR-00015 POSCAR-00024 POSCAR-00033 POSCAR-00042 POSCAR-00051 POSCAR-00060 POSCAR-00069 POSCAR-00078 POSCAR-00087 POSCAR-00096 POSCAR-00105<br />POSCAR-00007  POSCAR-00016 POSCAR-00025 POSCAR-00034 POSCAR-00043 POSCAR-00052 POSCAR-00061 POSCAR-00070 POSCAR-00079 POSCAR-00088 POSCAR-00097 POSCAR-00106</span></pre>
-<p class=" "><span class="n"> For each displacement the forces needs to be calculated, i.e. in form of the output file of VASP (vasprun.xml). For a single VASP calculations one needs <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/KPOINTS">KPOINTS</a>, <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/POTCAR">POTCAR</a>, <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/INCAR">INCAR</a> in your case directory (where you have POSCARS) and those 111 displacements calculations can be generated by <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/prepare.sh">prepare.sh</a> script. Then each of the single 111 calculations is submitted <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/run.sh">run.sh</a> by <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/submit.sh">submit.sh</a>.</span></p>
+<p class=" "><span class="n"> For each displacement the forces needs to be calculated, i.e. in form of the output file of VASP (vasprun.xml). For a single VASP calculations one needs <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/KPOINTS">KPOINTS</a>, <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/POTCAR">POTCAR</a>, <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/INCAR">INCAR</a> in your case directory (where you have POSCARS) and those 111 displacements calculations can be generated by <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/prepare.sh">prepare.sh</a> script. Then each of the single 111 calculations is submitted <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/run.sh">run.sh</a> by <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/submit.sh">submit.sh</a>.</span></p>
<pre class="prettyprint lang-sh"><span class="n">$./prepare.sh<br />$ls<br />disp-00001Â disp-00009Â disp-00017Â disp-00025Â disp-00033Â disp-00041Â disp-00049Â disp-00057Â disp-00065Â disp-00073Â disp-00081Â disp-00089Â disp-00097Â disp-00105Â Â Â Â INCAR<br />disp-00002Â disp-00010Â disp-00018Â disp-00026Â disp-00034Â disp-00042Â disp-00050Â disp-00058Â disp-00066Â disp-00074Â disp-00082Â disp-00090Â disp-00098Â disp-00106Â Â Â Â KPOINTS<br />disp-00003Â disp-00011Â disp-00019Â disp-00027Â disp-00035Â disp-00043Â disp-00051Â disp-00059Â disp-00067Â disp-00075Â disp-00083Â disp-00091Â disp-00099Â disp-00107Â Â Â Â POSCAR<br />disp-00004Â disp-00012Â disp-00020Â disp-00028Â disp-00036Â disp-00044Â disp-00052Â disp-00060Â disp-00068Â disp-00076Â disp-00084Â disp-00092Â disp-00100Â disp-00108Â Â Â Â POTCAR<br />disp-00005Â disp-00013Â disp-00021Â disp-00029Â disp-00037Â disp-00045Â disp-00053Â disp-00061Â disp-00069Â disp-00077Â disp-00085Â disp-00093Â disp-00101Â disp-00109Â Â Â Â prepare.sh<br />disp-00006Â disp-00014Â disp-00022Â disp-00030Â disp-00038Â disp-00046Â disp-00054Â disp-00062Â disp-00070Â disp-00078Â disp-00086Â disp-00094Â disp-00102Â disp-00110Â Â Â Â run.sh<br />disp-00007Â disp-00015Â disp-00023Â disp-00031Â disp-00039Â disp-00047Â disp-00055Â disp-00063Â disp-00071Â disp-00079Â disp-00087Â disp-00095Â disp-00103Â disp-00111Â Â Â Â submit.sh<br />disp-00008Â disp-00016Â disp-00024Â disp-00032Â disp-00040Â disp-00048Â disp-00056Â disp-00064Â disp-00072Â disp-00080Â disp-00088Â disp-00096Â disp-00104Â disp_fc3.yaml<br /></span></pre>
<p class=" "><span class="n">Taylor your run.sh script to fit into your project and other needs and submit all 111 calculations using submit.sh script</span></p>
<pre class="prettyprint lang-sh"><span class="n">$ ./submit.sh</span></pre>
@@ -675,7 +675,7 @@
<pre class="prettyprint lang-sh">$ grep grid_point ir_grid_points.yaml<br />num_reduced_ir_grid_points: 35<br />ir_grid_points:Â # [address, weight]<br />- grid_point: 0<br />- grid_point: 1<br />- grid_point: 2<br />- grid_point: 3<br />- grid_point: 4<br />- grid_point: 10<br />- grid_point: 11<br />- grid_point: 12<br />- grid_point: 13<br />- grid_point: 20<br />- grid_point: 21<br />- grid_point: 22<br />- grid_point: 30<br />- grid_point: 31<br />- grid_point: 40<br />- grid_point: 91<br />- grid_point: 92<br />- grid_point: 93<br />- grid_point: 94<br />- grid_point: 101<br />- grid_point: 102<br />- grid_point: 103<br />- grid_point: 111<br />- grid_point: 112<br />- grid_point: 121<br />- grid_point: 182<br />- grid_point: 183<br />- grid_point: 184<br />- grid_point: 192<br />- grid_point: 193<br />- grid_point: 202<br />- grid_point: 273<br />- grid_point: 274<br />- grid_point: 283<br />- grid_point: 364</pre>
<p>one finds which grid points needed to be calculated, for instance using following</p>
<pre class="prettyprint lang-sh"><span class="n">$ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCARÂ --sigma 0.1 --br --write-gamma --gp="0 1 2</span></pre>
-<p><span class="n">one calculates grid points 0, 1, 2. To automize one can use for instance scripts to submit 5 points in series, see <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/gofree-cond1.sh">gofree-cond1.sh </a></span></p>
+<p><span class="n">one calculates grid points 0, 1, 2. To automize one can use for instance scripts to submit 5 points in series, see <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/gofree-cond1.sh">gofree-cond1.sh </a></span></p>
<pre class="prettyprint lang-sh"><span class="n">$ qsub gofree-cond1.sh</span></pre>
<p><span class="n">Finally the thermal conductivity result is produced by grouping single conductivity per grid calculations using </span></p>
<pre class="prettyprint lang-sh"><span class="n">$ <span class="n">phono3py</span> <span class="o">--</span><span class="n">fc3</span> <span class="o">--</span><span class="n">fc2</span> <span class="o">--</span><span class="n">dim</span><span class="o">=</span><span class="s2">"2 2 2"</span> <span class="o">--</span><span class="n">mesh</span><span class="o">=</span><span class="s2">"</span>9 9 9" <span class="o">--</span><span class="n">br</span> <span class="o">--</span><span class="n">read_gamma</span></span></pre>
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@@ -87,9 +84,9 @@
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@@ -220,11 +217,11 @@
<div id="parent-fieldname-text-519a21511a404ed6acc09c81711a65aa" class="">
- <p>Welcome to Anselm supercomputer cluster. The Anselm cluster consists of 209 compute nodes, totaling 3344 compute cores with 15TB RAM and giving over 94 Tflop/s theoretical peak performance. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 16 cores, at least 64GB RAM, and 500GB harddrive. Nodes are interconnected by fully non-blocking fat-tree Infiniband network and equipped with Intel Sandy Bridge processors. A few nodes are also equipped with NVIDIA Kepler GPU or Intel Xeon Phi MIC accelerators. Read more in <a target="_self" title="" class="internal-link" href="anselm-cluster-documentation/hardware-overview.html">Hardware Overview</a>.</p>
-<p>The cluster runs bullx Linux <a class="external-link" href="http://www.bull.com/bullx-logiciels/systeme-exploitation.html" target="_self" title=""><span class="WYSIWYG_LINK"></span></a><a target="_self" title="" class="internal-link" href="anselm-cluster-documentation/software/operating-system.html">operating system</a>, which is compatible with the <span class="WYSIWYG_LINK">RedHat</span> <a class="external-link" href="http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg" target="_self" title=""><span class="WYSIWYG_LINK">Linux family.</span></a> We have installed a wide range of <a target="_self" title="" class="internal-link" href="anselm-cluster-documentation/software.html">software</a> packages targeted at different scientific domains. These packages are accessible via the <a target="_self" title="" class="internal-link" href="anselm-cluster-documentation/environment-and-modules.html">modules environment</a>.</p>
+ <p>Welcome to Anselm supercomputer cluster. The Anselm cluster consists of 209 compute nodes, totaling 3344 compute cores with 15TB RAM and giving over 94 Tflop/s theoretical peak performance. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 16 cores, at least 64GB RAM, and 500GB harddrive. Nodes are interconnected by fully non-blocking fat-tree Infiniband network and equipped with Intel Sandy Bridge processors. A few nodes are also equipped with NVIDIA Kepler GPU or Intel Xeon Phi MIC accelerators. Read more in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">Hardware Overview</a>.</p>
+<p>The cluster runs bullx Linux <a class="external-link" href="http://www.bull.com/bullx-logiciels/systeme-exploitation.html" target="_self" title=""><span class="WYSIWYG_LINK"></span></a><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">operating system</a>, which is compatible with the <span class="WYSIWYG_LINK">RedHat</span> <a class="external-link" href="http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg" target="_self" title=""><span class="WYSIWYG_LINK">Linux family.</span></a> We have installed a wide range of <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software">software</a> packages targeted at different scientific domains. These packages are accessible via the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">modules environment</a>.</p>
<p>User data shared file-system (HOME, 320TB) and job data shared file-system (SCRATCH, 146TB) are available to users.</p>
-<p>The PBS Professional workload manager provides <a target="_self" title="" class="internal-link" href="anselm-cluster-documentation/resource-allocation-and-job-execution.html">computing resources allocations and job execution</a>.</p>
-<p>Read more on how to <a target="_self" title="" class="internal-link" href="get-started-with-it4innovations/applying-for-resources.html">apply for resources</a>, <a target="_self" title="" class="internal-link" href="get-started-with-it4innovations/obtaining-login-credentials.html">obtain login credentials,</a> and <a target="_self" title="" class="internal-link" href="anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access.html">access the cluster</a>.</p>
+<p>The PBS Professional workload manager provides <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">computing resources allocations and job execution</a>.</p>
+<p>Read more on how to <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources">apply for resources</a>, <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">obtain login credentials,</a> and <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">access the cluster</a>.</p>
</div>
@@ -300,7 +297,7 @@
<dt class="portletHeader hiddenStructure">
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+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -332,7 +329,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -348,7 +345,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -364,7 +361,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="anselm-cluster-documentation.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -380,7 +377,7 @@
- <a title="" class="state-published contenttype-document" href="anselm-cluster-documentation/hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -396,7 +393,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -412,7 +409,7 @@
- <a title="" class="state-published contenttype-document" href="anselm-cluster-documentation/environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -428,7 +425,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="anselm-cluster-documentation/resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -444,7 +441,7 @@
- <a title="" class="state-published contenttype-document" href="anselm-cluster-documentation/compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -460,7 +457,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="anselm-cluster-documentation/storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -476,7 +473,7 @@
- <a title="" class="state-published contenttype-document" href="anselm-cluster-documentation/network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -492,10 +489,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="anselm-cluster-documentation/software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -511,7 +508,7 @@
- <a title="" class="state-published contenttype-document" href="anselm-cluster-documentation/remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -527,7 +524,7 @@
- <a title="" class="state-published contenttype-document" href="anselm-cluster-documentation/prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -552,7 +549,7 @@
- <a title="" class="state-published contenttype-document" href="links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -568,7 +565,7 @@
- <a title="" class="state-published contenttype-collection" href="changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -584,7 +581,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
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+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -652,12 +649,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -673,7 +670,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:15:55 GMT -->
</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation.md b/docs.it4i.cz/anselm-cluster-documentation.md
new file mode 100644
index 0000000000000000000000000000000000000000..7d1bde3e9229026bb5cd0d102710e86979641d53
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation.md
@@ -0,0 +1,34 @@
+Introduction
+============
+
+Welcome to Anselm supercomputer cluster. The Anselm cluster consists of
+209 compute nodes, totaling 3344 compute cores with 15TB RAM and giving
+over 94 Tflop/s theoretical peak performance. Each node is a <span
+class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 16
+cores, at least 64GB RAM, and 500GB harddrive. Nodes are interconnected
+by fully non-blocking fat-tree Infiniband network and equipped with
+Intel Sandy Bridge processors. A few nodes are also equipped with NVIDIA
+Kepler GPU or Intel Xeon Phi MIC accelerators. Read more in [Hardware
+Overview](https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview).
+The cluster runs bullx Linux [<span
+class="WYSIWYG_LINK"></span>](http://www.bull.com/bullx-logiciels/systeme-exploitation.html)[operating
+system](https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system),
+which is compatible with the <span class="WYSIWYG_LINK">RedHat</span>
+[<span class="WYSIWYG_LINK">Linux
+family.</span>](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
+We have installed a wide range of
+[software](https://docs.it4i.cz/anselm-cluster-documentation/software)
+packages targeted at different scientific domains. These packages are
+accessible via the [modules
+environment](https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules).
+User data shared file-system (HOME, 320TB) and job data shared
+file-system (SCRATCH, 146TB) are available to users.
+The PBS Professional workload manager provides [computing resources
+allocations and job
+execution](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution).
+Read more on how to [apply for
+resources](https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources),
+[obtain login
+credentials,](https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials)
+and [access the
+cluster](https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster).
diff --git a/anselm-cluster-documentation/Anselm profile.jpg b/docs.it4i.cz/anselm-cluster-documentation/Anselmprofile.jpg
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/Anselm profile.jpg
rename to docs.it4i.cz/anselm-cluster-documentation/Anselmprofile.jpg
diff --git a/anselm-cluster-documentation/Authorization_chain.png b/docs.it4i.cz/anselm-cluster-documentation/Authorization_chain.png
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/Authorization_chain.png
rename to docs.it4i.cz/anselm-cluster-documentation/Authorization_chain.png
diff --git a/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access.html b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster.html
old mode 100755
new mode 100644
similarity index 70%
rename from anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access.html
rename to docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster.html
index 2e2b86e22a492d69e5cca1ddaf748cbae5ea7c6f..573237aed354a3c8ce5474edef48acc7f4319f74
--- a/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:49 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Shell access and data transfer — IT4I Docs</title>
- <link rel="canonical" href="shell-and-data-access.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="shell-and-data-access.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="shell-and-data-access.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="shell-and-data-access.html">Accessing the Cluster</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">Accessing the Cluster</a>
<span class="breadcrumbSeparator">
/
@@ -265,7 +262,7 @@
</tr>
</tbody>
</table>
-<p>The authentication is by the <a target="_self" title="" class="internal-link" href="../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html">private key</a></p>
+<p>The authentication is by the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">private key</a></p>
<p class="callout">Please verify SSH fingerprints during the first logon. They are identical on all login nodes:<span class="monospace"><br />29:b3:f4:64:b0:73:f5:6f:a7:85:0f:e0:0d:be:76:bf (DSA)<br />d4:6f:5c:18:f4:3f:70:ef:bc:fc:cc:2b:fd:13:36:b7 (RSA)</span></p>
<p>Â </p>
<p>Private keys authentication:</p>
@@ -273,10 +270,10 @@
<pre class="prettyprint lang-sh">local $ ssh -i /path/to/id_rsa username@anselm.it4i.cz</pre>
<p>If you see warning message "UNPROTECTED PRIVATE KEY FILE!", use this command to set lower permissions to private key file.</p>
<pre class="prettyprint lang-sh">local $ chmod 600 /path/to/id_rsa</pre>
-<p>On <strong>Windows</strong>, use <a target="_self" title="" class="internal-link" href="../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html">PuTTY ssh client</a>.</p>
+<p>On <strong>Windows</strong>, use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty">PuTTY ssh client</a>.</p>
<p>After logging in, you will see the command prompt:</p>
<pre class=" "> _<br /> /\ | |<br /> / \ _ __ ___ ___| |_ __ ___<br /> / /\ \ | '_ \/ __|/ _ \ | '_ ` _ \<br /> / ____ \| | | \__ \ __/ | | | | | |<br /> /_/ \_\_| |_|___/\___|_|_| |_| |_|<br /><br /><br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â http://www.it4i.cz/?lang=en<br /><br /><br />Last login: Tue Jul 9 15:57:38 2013 from your-host.example.com<br />[username@login2.anselm ~]$</pre>
-<p class="callout">The environment is <strong>not</strong> shared between login nodes, except for <a target="_self" title="" class="external-link" href="storage-1.html#section-1">shared filesystems</a>.</p>
+<p class="callout">The environment is <strong>not</strong> shared between login nodes, except for <a title="" class="external-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1#section-1">shared filesystems</a>.</p>
<h2 class=" ">Data Transfer</h2>
<p>Data in and out of the system may be transferred by the <a class="external-link" href="http://en.wikipedia.org/wiki/Secure_copy" target="_self" title="">scp</a> and sftp protocols. <span class="discreet">(Not available yet.) In case large volumes of data are transferred, use dedicated data mover node dm1.anselm.it4i.cz for increased performance.</span></p>
<table class="listing">
@@ -304,7 +301,7 @@
</tr>
</tbody>
</table>
-<p>Â The authentication is by the <a target="_self" title="" class="internal-link" href="../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html">private key</a></p>
+<p>Â The authentication is by the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">private key</a></p>
<p class="callout">Data transfer rates up to <strong>160MB/s</strong> can be achieved with scp or sftp. 1TB may be transferred in 1:50h.</p>
<p>To achieve 160MB/s transfer rates, the end user must be connected by 10G line all the way to IT4Innovations and use computer with fast processor for the transfer. Using Gigabit ethernet connection, up to 110MB/s may be expected. Fast cipher (aes128-ctr) should be used.</p>
<p class="callout">If you experience degraded data transfer performance, consult your local network provider.</p>
@@ -319,7 +316,7 @@
<p>Learn more on ssh, scp and sshfs by reading the manpages</p>
<pre class="prettyprint lang-sh">$ man ssh<br />$ man scp<br />$ man sshfs</pre>
<p>On Windows, use <a class="external-link" href="http://winscp.net/eng/download.php" target="_self" title="">WinSCP client</a> to transfer the data. The <a class="external-link" href="http://code.google.com/p/win-sshfs/" target="_self" title="">win-sshfs client</a> provides a way to mount the Anselm filesystems directly as an external disc.</p>
-<p>More information about the shared file systems is available <a target="_self" title="" class="internal-link" href="../storage-1/storage.html">here</a>.</p>
+<p>More information about the shared file systems is available <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage">here</a>.</p>
</div>
@@ -395,7 +392,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -411,7 +408,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -427,7 +424,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -443,7 +440,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -459,7 +456,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -475,7 +472,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -491,7 +488,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="shell-and-data-access.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -507,7 +504,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="shell-and-data-access.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access">
<span>Shell access and data transfer</span>
</a>
@@ -523,7 +520,7 @@
- <a title="" class="state-published contenttype-link" href="../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html">
+ <a class="state-published contenttype-link" title="" href="/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface">
<span>Graphical User Interface</span>
</a>
@@ -539,7 +536,7 @@
- <a title="" class="state-published contenttype-document" href="vpn-access.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access">
<span>VPN Access</span>
</a>
@@ -555,7 +552,7 @@
- <a title="" class="state-published contenttype-document" href="outgoing-connections.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections">
<span>Outgoing connections</span>
</a>
@@ -580,7 +577,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -596,7 +593,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -612,7 +609,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -628,7 +625,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -644,7 +641,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -660,10 +657,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -679,7 +676,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -695,7 +692,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -720,7 +717,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -736,7 +733,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -752,7 +749,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -791,14 +788,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -820,12 +817,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -841,7 +838,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:50 GMT -->
</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster.md b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster.md
new file mode 100644
index 0000000000000000000000000000000000000000..f94bc1f2798e621608141717061437963f15a297
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster.md
@@ -0,0 +1,100 @@
+Shell access and data transfer
+==============================
+
+Interactive Login
+-----------------
+The Anselm cluster is accessed by SSH protocol via login nodes login1
+and login2 at address anselm.it4i.cz. The login nodes may be addressed
+specifically, by prepending the login node name to the address.
+ Login address Port Protocol Login node
+ ------ ----------
+ anselm.it4i.cz 22 ssh round-robin DNS record for login1 and login2
+ login1.anselm.it4i.cz 22 ssh login1
+ login2.anselm.it4i.cz 22 ssh login2
+The authentication is by the [private
+key](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys)
+Please verify SSH fingerprints during the first logon. They are
+identical on all login nodes:<span class="monospace">
+29:b3:f4:64:b0:73:f5:6f:a7:85:0f:e0:0d:be:76:bf (DSA)
+d4:6f:5c:18:f4:3f:70:ef:bc:fc:cc:2b:fd:13:36:b7Â (RSA)</span>
+Â
+Private keys authentication:
+On **Linux** or **Mac**, use
+``` {.prettyprint .lang-sh}
+local $ ssh -i /path/to/id_rsa username@anselm.it4i.cz
+```
+If you see warning message "UNPROTECTED PRIVATE KEY FILE!", use this
+command to set lower permissions to private key file.
+``` {.prettyprint .lang-sh}
+local $ chmod 600 /path/to/id_rsa
+```
+On **Windows**, use [PuTTY ssh
+client](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty).
+After logging in, you will see the command prompt:
+ _
+ / | |
+ / _ __ ___ ___| |_ __ ___
+ / / | '_ / __|/ _ | '_ ` _
+ / ____ | | | __ __/ | | | | | |
+ /_/ __| |_|___/___|_|_| |_| |_|
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â http://www.it4i.cz/?lang=en
+ Last loginTue Jul 9 15:57:38 2013 from your-host.example.com
+ [username@login2.anselm ~]$
+The environment is **not** shared between login nodes, except for
+[shared
+filesystems](https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1#section-1).
+Data Transfer
+-------------
+Data in and out of the system may be transferred by the
+[scp](http://en.wikipedia.org/wiki/Secure_copy) and sftp
+protocols. <span class="discreet">(Not available yet.) In case large
+volumes of data are transferred, use dedicated data mover node
+dm1.anselm.it4i.cz for increased performance.</span>
+ Address Port Protocol
+ ---- ----------- ------------------
+ anselm.it4i.cz 22 scp, sftp
+ login1.anselm.it4i.cz 22 scp, sftp
+ login2.anselm.it4i.cz 22 scp, sftp
+ <span class="discreet">dm1.anselm.it4i.cz</span> <span class="discreet">22</span> <span class="discreet">scp, sftp</span>
+Â The authentication is by the [private
+key](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys)
+Data transfer rates up to **160MB/s** can be achieved with scp or sftp.
+1TB may be transferred in 1:50h.
+To achieve 160MB/s transfer rates, the end user must be connected by 10G
+line all the way to IT4Innovations and use computer with fast processor
+for the transfer. Using Gigabit ethernet connection, up to 110MB/s may
+be expected. Fast cipher (aes128-ctr) should be used.
+If you experience degraded data transfer performance, consult your local
+network provider.
+On linux or Mac, use scp or sftp client to transfer the data to Anselm:
+``` {.prettyprint .lang-sh}
+local $ scp -i /path/to/id_rsa my-local-file username@anselm.it4i.cz:directory/file
+```
+``` {.prettyprint .lang-sh}
+local $ scp -i /path/to/id_rsa -r my-local-dir username@anselm.it4i.cz:directory
+```
+> or
+``` {.prettyprint .lang-sh}
+local $ sftp -o IdentityFile=/path/to/id_rsa username@anselm.it4i.cz
+```
+Very convenient way to transfer files in and out of the Anselm computer
+is via the fuse filesystem
+[sshfs](http://linux.die.net/man/1/sshfs)
+``` {.prettyprint .lang-sh}
+local $ sshfs -o IdentityFile=/path/to/id_rsa username@anselm.it4i.cz:. mountpoint
+```
+Using sshfs, the users Anselm home directory will be mounted on your
+local computer, just like an external disk.
+Learn more on ssh, scp and sshfs by reading the manpages
+``` {.prettyprint .lang-sh}
+$ man ssh
+$ man scp
+$ man sshfs
+```
+On Windows, use [WinSCP
+client](http://winscp.net/eng/download.php) to transfer
+the data. The [win-sshfs
+client](http://code.google.com/p/win-sshfs/) provides a
+way to mount the Anselm filesystems directly as an external disc.
+More information about the shared file systems is available
+[here](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage).
diff --git a/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.html b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.html
old mode 100755
new mode 100644
similarity index 74%
rename from anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.html
rename to docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.html
index ab9caff833da0d63ef877a5b529b072456257d19..f96f5ddeb3a81b1478f528ea4964e85ebeb1a778
--- a/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.html
@@ -10,45 +10,42 @@
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
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- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
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<title>Outgoing connections — IT4I Docs</title>
- <link rel="canonical" href="outgoing-connections.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="outgoing-connections.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="outgoing-connections.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="shell-and-data-access.html">Accessing the Cluster</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">Accessing the Cluster</a>
<span class="breadcrumbSeparator">
/
@@ -366,7 +363,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -382,7 +379,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -398,7 +395,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -414,7 +411,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -430,7 +427,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -446,7 +443,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -462,7 +459,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="shell-and-data-access.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -478,7 +475,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access">
<span>Shell access and data transfer</span>
</a>
@@ -494,7 +491,7 @@
- <a title="" class="state-published contenttype-link" href="../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html">
+ <a class="state-published contenttype-link" title="" href="/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface">
<span>Graphical User Interface</span>
</a>
@@ -510,7 +507,7 @@
- <a title="" class="state-published contenttype-document" href="vpn-access.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access">
<span>VPN Access</span>
</a>
@@ -526,7 +523,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="outgoing-connections.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections">
<span>Outgoing connections</span>
</a>
@@ -551,7 +548,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -567,7 +564,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -583,7 +580,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -599,7 +596,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -615,7 +612,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -631,10 +628,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -650,7 +647,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -666,7 +663,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -691,7 +688,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -707,7 +704,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -723,7 +720,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -762,14 +759,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -791,12 +788,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -812,7 +809,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:37 GMT -->
</html>
diff --git a/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md
similarity index 58%
rename from anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md
rename to docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md
index 86b2e480acdad05ed0275637b6055221867c58f2..1e00ffd80682c075f62a187afed313ff757d94c5 100644
--- a/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md
@@ -1,9 +1,9 @@
-
-
+Outgoing connections
+====================
+
Connection restrictions
------------------------
Outgoing connections, from Anselm Cluster login nodes to the outside
-world, are restricted to following ports
+world, are restricted to following ports:
Port Protocol
------ ----------
22 ssh
@@ -23,25 +23,25 @@ arbitrary remote host and port.
It works by tunneling the connection from Anselm back to users
workstation and forwarding from the workstation to the remote host.
Pick some unused port on Anselm login node (for example 6000) and
-establish the port forwarding
+establish the port forwarding:
```
-local $ ssh -R 6000remote.host.com1234 anselm.it4i.cz
+local $ ssh -R 6000:remote.host.com:1234 anselm.it4i.cz
```
In this example, we establish port forwarding between port 6000 on
Anselm and port 1234 on the remote.host.com. By accessing
-localhost6000 on Anselm, an application will see response of
-remote.host.com1234. The traffic will run via users local workstation.
+localhost:6000 on Anselm, an application will see response of
+remote.host.com:1234. The traffic will run via users local workstation.
Port forwarding may be done **using PuTTY** as well. On the PuTTY
Configuration screen, load your Anselm configuration first. Then go to
Connection->SSH->Tunnels to set up the port forwarding. Click
Remote radio button. Insert 6000 to Source port textbox. Insert
-remote.host.com1234. Click Add button, then Open.
+remote.host.com:1234. Click Add button, then Open.
Port forwarding may be established directly to the remote host. However,
this requires that user has ssh access to remote.host.com
```
-$ ssh -L 6000localhost1234 remote.host.com
+$ ssh -L 6000:localhost:1234 remote.host.com
```
-Note Port number 6000 is chosen as an example only. Pick any free port.
+NotePort number 6000 is chosen as an example only. Pick any free port.
### []()Port forwarding from compute nodes
Remote port forwarding from compute nodes allows applications running on
the compute nodes to access hosts outside Anselm Cluster.
@@ -50,12 +50,12 @@ First, establish the remote port forwarding form the login node, as
Second, invoke port forwarding from the compute node to the login node.
Insert following line into your jobscript or interactive shell
```
-$ ssh -TN -f -L 6000localhost6000 login1
+$ ssh -TN -f -L 6000:localhost:6000 login1
```
-In this example, we assume that port forwarding from login16000 to
-remote.host.com1234 has been established beforehand. By accessing
-localhost6000, an application running on a compute node will see
-response of remote.host.com1234
+In this example, we assume that port forwarding from login1:6000 to
+remote.host.com:1234 has been established beforehand. By accessing
+localhost:6000, an application running on a compute node will see
+response of remote.host.com:1234
### Using proxy servers
Port forwarding is static, each single port is mapped to a particular
port on remote host. Connection to other remote host, requires new
@@ -65,44 +65,18 @@ remote hosts, via single proxy server.
To establish local proxy server on your workstation, install and run
SOCKS proxy server software. On Linux, sshd demon provides the
functionality. To establish SOCKS proxy server listening on port 1080
-run
+run:
```
local $ ssh -D 1080 localhost
```
On Windows, install and run the free, open source [Sock
-Puppet](http//sockspuppet.com/) server.
+Puppet](http://sockspuppet.com/) server.
Once the proxy server is running, establish ssh port forwarding from
Anselm to the proxy server, port 1080, exactly as [described
above](#port-forwarding-from-login-nodes).
```
-local $ ssh -R 6000localhost1080 anselm.it4i.cz
+local $ ssh -R 6000:localhost:1080 anselm.it4i.cz
```
-Now, configure the applications proxy settings to **localhost6000**.
+Now, configure the applications proxy settings to **localhost:6000**.
Use port forwarding to access the [proxy server from compute
nodes](#port-forwarding-from-compute-nodes) as well .
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
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- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
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-
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- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](shell-and-data-access.html)
-
- - [Shell access and data
- transfer](shell-and-data-access.html)
diff --git a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html
new file mode 100644
index 0000000000000000000000000000000000000000..81b67436924a860235b90c6ec028c8ec05f1d237
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+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html
@@ -0,0 +1,842 @@
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+</head>
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+
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+
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+
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+
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+ <input id="searchbox_currentfolder_only" class="noborder" type="checkbox" name="path" value="/docs/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access" />
+ <label for="searchbox_currentfolder_only" style="cursor: pointer">pouze v aktuálnà sekci</label>
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+
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
+ <span class="breadcrumbSeparator">
+ /
+
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+
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+ <span id="breadcrumbs-2" dir="ltr">
+
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">Accessing the Cluster</a>
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+
+ </span>
+
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+ <span id="breadcrumbs-3" dir="ltr">
+
+
+
+ <span id="breadcrumbs-current">Shell access and data transfer</span>
+
+ </span>
+
+</div>
+</div>
+
+
+ <div class="">
+
+
+
+
+
+ <dl class="portalMessage info" id="kssPortalMessage" style="display:none">
+ <dt>Info</dt>
+ <dd></dd>
+ </dl>
+
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+
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+
+
+ <div id="viewlet-above-content-title"></div>
+
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+
+ <h1 id="parent-fieldname-title" class="documentFirstHeading">
+ Shell access and data transfer
+ </h1>
+
+
+
+
+ <div id="viewlet-below-content-title">
+</div>
+
+
+
+
+
+
+
+
+
+
+
+ <div id="viewlet-above-content-body">
+<dl id="document-toc" class="portlet toc" style="display: none">
+ <dt class="portletHeader">Obsah</dt>
+ <dd class="portletItem">
+ </dd>
+</dl>
+</div>
+ <div id="content-core">
+
+
+
+ <div id="parent-fieldname-text-ceca9cfaad22488eaa73549210740832" class="">
+ <h2 class=" ">Interactive Login</h2>
+<p>The Anselm cluster is accessed by SSH protocol via login nodes login1 and login2 at address anselm.it4i.cz. The login nodes may be addressed specifically, by prepending the login node name to the address.</p>
+<table class="listing">
+<tbody>
+<tr><th>Login address</th><th>Port</th><th>Protocol</th><th>Login node</th></tr>
+<tr class="even">
+<td>anselm.it4i.cz</td>
+<td>22</td>
+<td>ssh</td>
+<td>round-robin DNS record for login1 and login2</td>
+</tr>
+<tr class="odd">
+<td>login1.anselm.it4i.cz</td>
+<td>22</td>
+<td>ssh</td>
+<td>login1</td>
+</tr>
+<tr class="even">
+<td>login2.anselm.it4i.cz</td>
+<td>22</td>
+<td>ssh</td>
+<td>login2</td>
+</tr>
+</tbody>
+</table>
+<p>The authentication is by the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">private key</a></p>
+<p class="callout">Please verify SSH fingerprints during the first logon. They are identical on all login nodes:<span class="monospace"><br />29:b3:f4:64:b0:73:f5:6f:a7:85:0f:e0:0d:be:76:bf (DSA)<br />d4:6f:5c:18:f4:3f:70:ef:bc:fc:cc:2b:fd:13:36:b7 (RSA)</span></p>
+<p>Â </p>
+<p>Private keys authentication:</p>
+<p>On <strong>Linux</strong> or <strong>Mac</strong>, use</p>
+<pre class="prettyprint lang-sh">local $ ssh -i /path/to/id_rsa username@anselm.it4i.cz</pre>
+<p>If you see warning message "UNPROTECTED PRIVATE KEY FILE!", use this command to set lower permissions to private key file.</p>
+<pre class="prettyprint lang-sh">local $ chmod 600 /path/to/id_rsa</pre>
+<p>On <strong>Windows</strong>, use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty">PuTTY ssh client</a>.</p>
+<p>After logging in, you will see the command prompt:</p>
+<pre class=" "> _<br /> /\ | |<br /> / \ _ __ ___ ___| |_ __ ___<br /> / /\ \ | '_ \/ __|/ _ \ | '_ ` _ \<br /> / ____ \| | | \__ \ __/ | | | | | |<br /> /_/ \_\_| |_|___/\___|_|_| |_| |_|<br /><br /><br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â http://www.it4i.cz/?lang=en<br /><br /><br />Last login: Tue Jul 9 15:57:38 2013 from your-host.example.com<br />[username@login2.anselm ~]$</pre>
+<p class="callout">The environment is <strong>not</strong> shared between login nodes, except for <a title="" class="external-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1#section-1">shared filesystems</a>.</p>
+<h2 class=" ">Data Transfer</h2>
+<p>Data in and out of the system may be transferred by the <a class="external-link" href="http://en.wikipedia.org/wiki/Secure_copy" target="_self" title="">scp</a> and sftp protocols. <span class="discreet">(Not available yet.) In case large volumes of data are transferred, use dedicated data mover node dm1.anselm.it4i.cz for increased performance.</span></p>
+<table class="listing">
+<tbody>
+<tr><th>Address</th><th>Port</th><th>Protocol</th></tr>
+<tr class="even">
+<td>anselm.it4i.cz</td>
+<td>22</td>
+<td>scp, sftp</td>
+</tr>
+<tr class="odd">
+<td>login1.anselm.it4i.cz</td>
+<td>22</td>
+<td>scp, sftp</td>
+</tr>
+<tr class="even">
+<td>login2.anselm.it4i.cz</td>
+<td>22</td>
+<td>scp, sftp</td>
+</tr>
+<tr class="odd">
+<td><span class="discreet">dm1.anselm.it4i.cz</span></td>
+<td><span class="discreet">22</span></td>
+<td><span class="discreet">scp, sftp</span></td>
+</tr>
+</tbody>
+</table>
+<p>Â The authentication is by the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">private key</a></p>
+<p class="callout">Data transfer rates up to <strong>160MB/s</strong> can be achieved with scp or sftp. 1TB may be transferred in 1:50h.</p>
+<p>To achieve 160MB/s transfer rates, the end user must be connected by 10G line all the way to IT4Innovations and use computer with fast processor for the transfer. Using Gigabit ethernet connection, up to 110MB/s may be expected. Fast cipher (aes128-ctr) should be used.</p>
+<p class="callout">If you experience degraded data transfer performance, consult your local network provider.</p>
+<p>On linux or Mac, use scp or sftp client to transfer the data to Anselm:</p>
+<pre class="prettyprint lang-sh">local $ scp -i /path/to/id_rsa my-local-file username@anselm.it4i.cz:directory/file</pre>
+<pre class="prettyprint lang-sh">local $ scp -i /path/to/id_rsa -r my-local-dir username@anselm.it4i.cz:directory</pre>
+<blockquote>or</blockquote>
+<pre class="prettyprint lang-sh">local $ sftp -o IdentityFile=/path/to/id_rsa username@anselm.it4i.cz</pre>
+<p>Very convenient way to transfer files in and out of the Anselm computer is via the fuse filesystem <a class="external-link" href="http://linux.die.net/man/1/sshfs" target="_self" title="">sshfs</a></p>
+<pre class="prettyprint lang-sh">local $ sshfs -o IdentityFile=/path/to/id_rsa username@anselm.it4i.cz:. mountpoint</pre>
+<p>Using sshfs, the users Anselm home directory will be mounted on your local computer, just like an external disk.</p>
+<p>Learn more on ssh, scp and sshfs by reading the manpages</p>
+<pre class="prettyprint lang-sh">$ man ssh<br />$ man scp<br />$ man sshfs</pre>
+<p>On Windows, use <a class="external-link" href="http://winscp.net/eng/download.php" target="_self" title="">WinSCP client</a> to transfer the data. The <a class="external-link" href="http://code.google.com/p/win-sshfs/" target="_self" title="">win-sshfs client</a> provides a way to mount the Anselm filesystems directly as an external disc.</p>
+<p>More information about the shared file systems is available <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage">here</a>.</p>
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diff --git a/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access.md b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
similarity index 58%
rename from anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access.md
rename to docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
index 8db1ad892c145b11cf15ab0ecafa61eb63bb99d8..f94bc1f2798e621608141717061437963f15a297 100644
--- a/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
@@ -1,24 +1,24 @@
+Shell access and data transfer
==============================
-
-
+
Interactive Login
-----------------
The Anselm cluster is accessed by SSH protocol via login nodes login1
and login2 at address anselm.it4i.cz. The login nodes may be addressed
specifically, by prepending the login node name to the address.
Login address Port Protocol Login node
- ----------------------- ------ ---------- ----------------------------------------------
+ ------ ----------
anselm.it4i.cz 22 ssh round-robin DNS record for login1 and login2
login1.anselm.it4i.cz 22 ssh login1
login2.anselm.it4i.cz 22 ssh login2
The authentication is by the [private
-key](../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+key](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys)
Please verify SSH fingerprints during the first logon. They are
-identical on all login nodes
-29b3f464b073f56fa7850fe00dbe76bf (DSA)
-d46f5c18f43f70efbcfccc2bfd1336b7Â (RSA)
+identical on all login nodes:<span class="monospace">
+29:b3:f4:64:b0:73:f5:6f:a7:85:0f:e0:0d:be:76:bf (DSA)
+d4:6f:5c:18:f4:3f:70:ef:bc:fc:cc:2b:fd:13:36:b7Â (RSA)</span>
Â
-Private keys authentication
+Private keys authentication:
On **Linux** or **Mac**, use
``` {.prettyprint .lang-sh}
local $ ssh -i /path/to/id_rsa username@anselm.it4i.cz
@@ -29,48 +29,49 @@ command to set lower permissions to private key file.
local $ chmod 600 /path/to/id_rsa
```
On **Windows**, use [PuTTY ssh
-client](../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
-After logging in, you will see the command prompt
+client](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty).
+After logging in, you will see the command prompt:
_
/ | |
/ _ __ ___ ___| |_ __ ___
/ / | '_ / __|/ _ | '_ ` _
/ ____ | | | __ __/ | | | | | |
/_/ __| |_|___/___|_|_| |_| |_|
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â http//www.it4i.cz/?lang=en
- Last login Tue Jul 9 155738 2013 from your-host.example.com
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â http://www.it4i.cz/?lang=en
+ Last loginTue Jul 9 15:57:38 2013 from your-host.example.com
[username@login2.anselm ~]$
The environment is **not** shared between login nodes, except for
-[shared filesystems](storage-1.html#section-1).
+[shared
+filesystems](https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1#section-1).
Data Transfer
-------------
Data in and out of the system may be transferred by the
-[scp](http//en.wikipedia.org/wiki/Secure_copy) and sftp
-protocols. (Not available yet.) In case large
+[scp](http://en.wikipedia.org/wiki/Secure_copy) and sftp
+protocols. <span class="discreet">(Not available yet.) In case large
volumes of data are transferred, use dedicated data mover node
-dm1.anselm.it4i.cz for increased performance.
+dm1.anselm.it4i.cz for increased performance.</span>
Address Port Protocol
- -------------------------------------------------- ---------------------------------- -----------------------------------------
+ ---- ----------- ------------------
anselm.it4i.cz 22 scp, sftp
login1.anselm.it4i.cz 22 scp, sftp
login2.anselm.it4i.cz 22 scp, sftp
- dm1.anselm.it4i.cz 22 scp, sftp
+ <span class="discreet">dm1.anselm.it4i.cz</span> <span class="discreet">22</span> <span class="discreet">scp, sftp</span>
 The authentication is by the [private
-key](../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+key](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys)
Data transfer rates up to **160MB/s** can be achieved with scp or sftp.
-1TB may be transferred in 150h.
+1TB may be transferred in 1:50h.
To achieve 160MB/s transfer rates, the end user must be connected by 10G
line all the way to IT4Innovations and use computer with fast processor
for the transfer. Using Gigabit ethernet connection, up to 110MB/s may
be expected. Fast cipher (aes128-ctr) should be used.
If you experience degraded data transfer performance, consult your local
network provider.
-On linux or Mac, use scp or sftp client to transfer the data to Anselm
+On linux or Mac, use scp or sftp client to transfer the data to Anselm:
``` {.prettyprint .lang-sh}
-local $ scp -i /path/to/id_rsa my-local-file username@anselm.it4i.czdirectory/file
+local $ scp -i /path/to/id_rsa my-local-file username@anselm.it4i.cz:directory/file
```
``` {.prettyprint .lang-sh}
-local $ scp -i /path/to/id_rsa -r my-local-dir username@anselm.it4i.czdirectory
+local $ scp -i /path/to/id_rsa -r my-local-dir username@anselm.it4i.cz:directory
```
> or
``` {.prettyprint .lang-sh}
@@ -78,9 +79,9 @@ local $ sftp -o IdentityFile=/path/to/id_rsa username@anselm.it4i.cz
```
Very convenient way to transfer files in and out of the Anselm computer
is via the fuse filesystem
-[sshfs](http//linux.die.net/man/1/sshfs)
+[sshfs](http://linux.die.net/man/1/sshfs)
``` {.prettyprint .lang-sh}
-local $ sshfs -o IdentityFile=/path/to/id_rsa username@anselm.it4i.cz. mountpoint
+local $ sshfs -o IdentityFile=/path/to/id_rsa username@anselm.it4i.cz:. mountpoint
```
Using sshfs, the users Anselm home directory will be mounted on your
local computer, just like an external disk.
@@ -91,35 +92,9 @@ $ man scp
$ man sshfs
```
On Windows, use [WinSCP
-client](http//winscp.net/eng/download.php) to transfer
+client](http://winscp.net/eng/download.php) to transfer
the data. The [win-sshfs
-client](http//code.google.com/p/win-sshfs/) provides a
+client](http://code.google.com/p/win-sshfs/) provides a
way to mount the Anselm filesystems directly as an external disc.
More information about the shared file systems is available
-[here](../storage-1/storage.html).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](shell-and-data-access.html)
-
- - [Shell access and data
- transfer](shell-and-data-access.html)
+[here](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage).
diff --git a/anselm-cluster-documentation/accessing-the-cluster/storage-1.html b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1.html
old mode 100755
new mode 100644
similarity index 83%
rename from anselm-cluster-documentation/accessing-the-cluster/storage-1.html
rename to docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1.html
index a912ae83d033d3605eeb880e4d21abb89dfb6a75..c0bf7ecf45474408754fa21733ab48c91d90d548
--- a/anselm-cluster-documentation/accessing-the-cluster/storage-1.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1 by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:03 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/IEFixes-cachekey-ec9b60024fd235ff2c883b4b54db91cb.css" />
<![endif]-->
- <style type="text/css" media="screen">@import url(../../portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Storage — IT4I Docs</title>
- <link rel="canonical" href="../storage-1.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="storage-1.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="storage-1.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -232,11 +229,11 @@
<div id="parent-fieldname-text-1d1e813ad5694098ada90d35a6148610" class="">
<p>There are two main shared file systems on Anselm cluster, the <a class="anchor-link" href="#home" target="_self" title="">HOME</a> and <a class="anchor-link" href="#scratch" target="_self" title="">SCRATCH</a>. All login and compute nodes may access same data on shared filesystems. Compute nodes are also equipped with local (non-shared) scratch, ramdisk and tmp filesystems.</p>
<h2 class=" ">Archiving</h2>
-<p>Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use <a target="_self" title="" class="internal-link" href="../storage-1/cesnet-data-storage.html">CESNET storage service</a>, which is available via SSHFS.</p>
+<p>Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage">CESNET storage service</a>, which is available via SSHFS.</p>
<h2 class=" ">Shared Filesystems</h2>
<p class=" ">Anselm computer provides two main shared filesystems, the <a class="anchor-link" href="#home" target="_self" title="">HOME filesystem</a> and the <a class="anchor-link" href="#scratch" target="_self" title="">SCRATCH filesystem</a>. Both HOME and SCRATCH filesystems are realized as a parallel Lustre filesystem. Both shared file systems are accessible via the Infiniband network. Extended ACLs are provided on both Lustre filesystems for the purpose of sharing data with other users using fine-grained control.</p>
<h3 class=" ">Understanding the Lustre Filesystems</h3>
-<p>(source <a class="external-link" href="http://www.nas.nasa.gov/" target="_self" title="">http://www.nas.nasa.gov</a>)</p>
+<p>(source <a class="external-link" href="http://www.nas.nasa.gov" target="_self" title="">http://www.nas.nasa.gov</a>)</p>
<p>A user file on the Lustre filesystem can be divided into multiple chunks (stripes) and stored across a subset of the object storage targets (OSTs) (disks). The stripes are distributed among the OSTs in a round-robin fashion to ensure load balancing.</p>
<p>When a client (a <span class="glossaryItem">compute <span class="glossaryItem">node</span></span> from your job) needs to create or access a file, the client queries the metadata server (<span class="glossaryItem">MDS</span>) and the metadata target (<span class="glossaryItem">MDT</span>) for the layout and location of the <a href="http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping">file's stripes</a>. Once the file is opened and the client obtains the striping information, the <span class="glossaryItem">MDS</span> is no longer involved in the file I/O process. The client interacts directly with the object storage servers (OSSes) and OSTs to perform I/O operations such as locking, disk allocation, storage, and retrieval.</p>
<p>If multiple clients try to read and write the same part of a file at the same time, the Lustre distributed lock manager enforces coherency so that all clients see consistent results.</p>
@@ -305,7 +302,7 @@
<p>The HOME filesystem is mounted in directory /home. Users home directories /home/username reside on this filesystem. Accessible capacity is 320TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 250GB per user. <span>If 250GB should prove as insufficient for particular user, please contact</span>Â <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">support</a>, the quota may be lifted upon request.</p>
<p class="callout">The HOME filesystem is intended for preparation, evaluation, processing and storage of data generated by active Projects.</p>
<p>The HOME filesystem should not be used to archive data of past Projects or other unrelated data.</p>
-<p>The files on HOME filesystem will not be deleted until end of the <a target="_self" title="" class="internal-link" href="../../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html">users lifecycle</a>.</p>
+<p>The files on HOME filesystem will not be deleted until end of the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials">users lifecycle</a>.</p>
<p class=" ">The filesystem is backed up, such that it can be restored in case of catasthropic failure resulting in significant data loss. This backup however is not intended to restore old versions of user data or to restore (accidentaly) deleted files. </p>
<p class=" ">The HOME filesystem is realized as Lustre parallel filesystem and is available on all login and computational nodes. <br />Default stripe size is 1MB, stripe count is 1. There are 22 OSTs dedicated for the HOME filesystem.</p>
<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
@@ -592,7 +589,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -608,7 +605,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -624,7 +621,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -640,7 +637,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -656,7 +653,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -672,7 +669,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -688,7 +685,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -704,7 +701,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -720,7 +717,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -736,7 +733,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -752,7 +749,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -768,7 +765,7 @@
- <a title="" class="state-published contenttype-document" href="../storage-1/cesnet-data-storage.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage">
<span>CESNET Data Storage</span>
</a>
@@ -793,7 +790,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -809,10 +806,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -828,7 +825,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -844,7 +841,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -869,7 +866,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -885,7 +882,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -901,7 +898,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -940,14 +937,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -969,12 +966,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -990,7 +987,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1 by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:03 GMT -->
</html>
diff --git a/anselm-cluster-documentation/storage-1.md b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1.md
similarity index 77%
rename from anselm-cluster-documentation/storage-1.md
rename to docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1.md
index 1423b551f30a04d25356739699fd871f1fcbd2b9..8fca8932e4dd28e96ea3b96c0c2383987a62c404 100644
--- a/anselm-cluster-documentation/storage-1.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1.md
@@ -1,3 +1,6 @@
+Storage
+=======
+
There are two main shared file systems on Anselm cluster, the
[HOME](#home) and [SCRATCH](#scratch). All
login and compute nodes may access same data on shared filesystems.
@@ -8,8 +11,8 @@ Archiving
Please don't use shared filesystems as a backup for large amount of data
or long-term archiving mean. The academic staff and students of research
institutions in the Czech Republic can use [CESNET storage
-service](storage-1/cesnet-data-storage.html), which is
-available via SSHFS.
+service](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage),
+which is available via SSHFS.
Shared Filesystems
------------------
Anselm computer provides two main shared filesystems, the [HOME
@@ -20,21 +23,20 @@ are accessible via the Infiniband network. Extended ACLs are provided on
both Lustre filesystems for the purpose of sharing data with other users
using fine-grained control.
### Understanding the Lustre Filesystems
-(source
-[http//www.nas.nasa.gov](http//www.nas.nasa.gov/))
+(source <http://www.nas.nasa.gov>)
A user file on the Lustre filesystem can be divided into multiple chunks
(stripes) and stored across a subset of the object storage targets
(OSTs) (disks). The stripes are distributed among the OSTs in a
round-robin fashion to ensure load balancing.
-When a client (a compute
-class="glossaryItem">node from your job) needs to create
-or access a file, the client queries the metadata server (
-class="glossaryItem">MDS) and the metadata target (
-class="glossaryItem">MDT) for the layout and location of the
+When a client (a <span class="glossaryItem">compute <span
+class="glossaryItem">node</span></span> from your job) needs to create
+or access a file, the client queries the metadata server (<span
+class="glossaryItem">MDS</span>) and the metadata target (<span
+class="glossaryItem">MDT</span>) for the layout and location of the
[file's
-stripes](http//www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping).
+stripes](http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping).
Once the file is opened and the client obtains the striping information,
-the MDS is no longer involved in the
+the <span class="glossaryItem">MDS</span> is no longer involved in the
file I/O process. The client interacts directly with the object storage
servers (OSSes) and OSTs to perform I/O operations such as locking, disk
allocation, storage, and retrieval.
@@ -43,16 +45,16 @@ same time, the Lustre distributed lock manager enforces coherency so
that all clients see consistent results.
There is default stripe configuration for Anselm Lustre filesystems.
However, users can set the following stripe parameters for their own
-directories or files to get optimum I/O performance
-1. stripe_size the size of the chunk in bytes; specify with k, m, or
+directories or files to get optimum I/O performance:
+1. stripe_sizethe size of the chunk in bytes; specify with k, m, or
g to use units of KB, MB, or GB, respectively; the size must be an
even multiple of 65,536 bytes; default is 1MB for all Anselm Lustre
filesystems
2. stripe_count the number of OSTs to stripe across; default is 1 for
Anselm Lustre filesystems one can specify -1 to use all OSTs in
the filesystem.
-3. stripe_offset The index of the
- class="glossaryItem">OST where the first stripe is to be
+3. stripe_offset The index of the <span
+ class="glossaryItem">OST</span> where the first stripe is to be
placed; default is -1 which results in random selection; using a
non-default value is NOT recommended.
Â
@@ -66,15 +68,15 @@ access patterns.Â
$ lfs getstripe dir|filename
$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir|filename
```
-Example
+Example:
``` {.prettyprint .lang-sh}
$ lfs getstripe /scratch/username/
/scratch/username/
-stripe_count 1 stripe_size 1048576 stripe_offset -1
+stripe_count 1 stripe_size 1048576 stripe_offset -1
$ lfs setstripe -c -1 /scratch/username/
$ lfs getstripe /scratch/username/
/scratch/username/
-stripe_count 10 stripe_size 1048576 stripe_offset -1
+stripe_count 10 stripe_size 1048576 stripe_offset -1
```
In this example, we view current stripe setting of the
/scratch/username/ directory. The stripe count is changed to all OSTs,
@@ -109,30 +111,31 @@ part of a file. However, it can be counterproductive in some cases if it
does not match your I/O pattern. The choice of stripe size has no effect
on a single-stripe file.
Read more on
+<http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html>
### Lustre on Anselm
The architecture of Lustre on Anselm is composed of two metadata
servers (MDS) and four data/object storage servers (OSS). Two object
storage servers are used for file system HOME and another two object
storage servers are used for file system SCRATCH.
-Configuration of the storages
-- HOME Lustre object storage
-
+<span class="emphasis">Configuration of the storages</span>
+- <span class="emphasis">HOME Lustre object storage</span>
+ <div class="itemizedlist">
- One disk array NetApp E5400
- 22 OSTs
- 227 2TB NL-SAS 7.2krpm disks
- 22 groups of 10 disks in RAID6 (8+2)
- 7 hot-spare disks
-- SCRATCH Lustre object storage
-
+- <span class="emphasis">SCRATCH Lustre object storage</span>
+ <div class="itemizedlist">
- Two disk arrays NetApp E5400
- 10 OSTs
- 106 2TB NL-SAS 7.2krpm disks
- 10 groups of 10 disks in RAID6 (8+2)
- 6 hot-spare disks
-- Lustre metadata storage
-
+- <span class="emphasis">Lustre metadata storage</span>
+ <div class="itemizedlist">
- One disk array NetApp E2600
- 12 300GB SAS 15krpm disks
- 2 groups of 5 disks in RAID5
@@ -142,16 +145,16 @@ Configuration of the storages
The HOME filesystem is mounted in directory /home. Users home
directories /home/username reside on this filesystem. Accessible
capacity is 320TB, shared among all users. Individual users are
-restricted by filesystem usage quotas, set to 250GB per user. If
+restricted by filesystem usage quotas, set to 250GB per user. <span>If
250GB should prove as insufficient for particular user, please
-contact [support](https//support.it4i.cz/rt),
+contact</span>Â [support](https://support.it4i.cz/rt),
the quota may be lifted upon request.
The HOME filesystem is intended for preparation, evaluation, processing
and storage of data generated by active Projects.
The HOME filesystem should not be used to archive data of past Projects
or other unrelated data.
The files on HOME filesystem will not be deleted until end of the [users
-lifecycle](../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html).
+lifecycle](https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials).
The filesystem is backed up, such that it can be restored in case ofÂ
catasthropic failure resulting in significant data loss. This backup
however is not intended to restore old versions of user data or to
@@ -183,19 +186,17 @@ freely create subdirectories and files on the filesystem. Accessible
capacity is 146TB, shared among all users. Individual users are
restricted by filesystem usage quotas, set to 100TB per user. The
purpose of this quota is to prevent runaway programs from filling the
-entire filesystem and deny service to other users. If 100TB should
+entire filesystem and deny service to other users. <span>If 100TB should
prove as insufficient for particular user, please contact
-[support](https//support.it4i.cz/rt), the quota may be
-lifted upon request.Â
+[support](https://support.it4i.cz/rt), the quota may be
+lifted upon request. </span>
The Scratch filesystem is intended for temporary scratch data generated
during the calculation as well as for high performance access to input
and output files. All I/O intensive jobs must use the SCRATCH filesystem
as their working directory.
-
Users are advised to save the necessary data from the SCRATCH filesystem
to HOME filesystem after the calculations and clean up the scratch
files.
-
Files on the SCRATCH filesystem that are **not accessed for more than 90
days** will be automatically **deleted**.
The SCRATCH filesystem is realized as Lustre parallel filesystem and is
@@ -219,31 +220,31 @@ Default stripe count
1
Number of OSTs
10
-### Disk usage and quota commands
-User quotas on the file systems can be checked and reviewed using
-following command
+### <span>Disk usage and quota commands</span>
+<span>User quotas on the file systems can be checked and reviewed using
+following command:</span>
``` {.prettyprint .lang-sh}
$ lfs quota dir
```
-Example for Lustre HOME directory
+Example for Lustre HOME directory:
``` {.prettyprint .lang-sh}
$ lfs quota /home
-Disk quotas for user user001 (uid 1234)
+Disk quotas for user user001 (uid 1234):
Filesystem kbytes quota limit grace files quota limit grace
/home 300096 0 250000000 - 2102 0 500000 -
-Disk quotas for group user001 (gid 1234)
+Disk quotas for group user001 (gid 1234):
Filesystem kbytes quota limit grace files quota limit grace
/home 300096 0 0 - 2102 0 0 -
```
In this example, we view current quota size limit of 250GB and 300MB
currently used by user001.
-Example for Lustre SCRATCH directory
+Example for Lustre SCRATCH directory:
``` {.prettyprint .lang-sh}
$ lfs quota /scratch
-Disk quotas for user user001 (uid 1234)
+Disk quotas for user user001 (uid 1234):
Filesystem kbytes quota limit grace files quota limit grace
 /scratch    8    0 100000000000    -    3    0    0    -
-Disk quotas for group user001 (gid 1234)
+Disk quotas for group user001 (gid 1234):
Filesystem kbytes quota limit grace files quota limit grace
/scratch    8    0    0    -    3    0    0    -
```
@@ -255,7 +256,7 @@ can use following command to find out.
``` {.prettyprint .lang-sh}
$ du -hs dir
```
-Example for your HOME directory
+Example for your HOME directory:
``` {.prettyprint .lang-sh}
$ cd /home
$ du -hs * .[a-zA-z0-9]* | grep -E "[0-9]*G|[0-9]*M" | sort -hr
@@ -269,9 +270,8 @@ This will list all directories which are having MegaBytes or GigaBytes
of consumed space in your actual (in this example HOME) directory. List
is sorted in descending order from largest to smallest
files/directories.
-
-To have a better understanding of previous commands, you can read
-manpages.
+<span>To have a better understanding of previous commands, you can read
+manpages.</span>
``` {.prettyprint .lang-sh}
$ man lfs
```
@@ -291,33 +291,33 @@ manner. Below, we create a directory and allow a specific user access.
[vop999@login1.anselm ~]$ umask 027
[vop999@login1.anselm ~]$ mkdir test
[vop999@login1.anselm ~]$ ls -ld test
-drwxr-x--- 2 vop999 vop999 4096 Nov 5 1417 test
+drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.anselm ~]$ getfacl test
-# file test
-# owner vop999
-# group vop999
-userrwx
-groupr-x
-other---
-[vop999@login1.anselm ~]$ setfacl -m userjohnsmrwx test
+# filetest
+# ownervop999
+# groupvop999
+user::rwx
+group::r-x
+other::---
+[vop999@login1.anselm ~]$ setfacl -m user:johnsm:rwx test
[vop999@login1.anselm ~]$ ls -ld test
-drwxrwx---+ 2 vop999 vop999 4096 Nov 5 1417 test
+drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.anselm ~]$ getfacl test
-# file test
-# owner vop999
-# group vop999
-userrwx
-userjohnsmrwx
-groupr-x
-maskrwx
-other---
+# filetest
+# ownervop999
+# groupvop999
+user::rwx
+user:johnsm:rwx
+group::r-x
+mask::rwx
+other::---
```
Default ACL mechanism can be used to replace setuid/setgid permissions
on directories. Setting a default ACL on a directory (-d flag to
setfacl) will cause the ACL permissions to be inherited by any newly
created file or subdirectory within the directory. Refer to this page
-for more information on Linux ACL
-[http//www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html ](http//www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html)
+for more information on Linux ACL:
+[http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html ](http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html)
Local Filesystems
-----------------
### Local Scratch
@@ -368,9 +368,9 @@ immediately after the calculation end. Users should take care to save
the output data from within the jobscript.
RAM disk
Mountpoint
-/ramdisk
+<span class="monospace">/ramdisk</span>
Accesspoint
-/ramdisk/$PBS_JOBID
+<span class="monospace">/ramdisk/$PBS_JOBID</span>
Capacity
60GB at compute nodes without accelerator
90GB at compute nodes with accelerator
@@ -388,27 +388,10 @@ files in /tmp directory are automatically purged.
**
----------
Mountpoint Usage Protocol Net Capacity Throughput Limitations Access Services
- ------------------------------------------ --------------------------- ---------- ---------------- ------------ ------------- ------------------------- -----------------------------
- /home home directory Lustre 320 TiB 2 GB/s Quota 250GB Compute and login nodes backed up
- /scratch cluster shared jobs' data Lustre 146 TiB 6 GB/s Quota 100TB Compute and login nodes files older 90 days removed
- /lscratch node local jobs' data local 330 GB 100 MB/s none Compute nodes purged after job ends
- /ramdisk node local jobs' data local 60, 90, 500 GB 5-50 GB/s none Compute nodes purged after job ends
- /tmp local temporary files local 100 MB/s none Compute and login nodes auto purged
+ ------------------- ---- ---------- ---------------- ------------ ------------- -- ------
+ <span class="monospace">/home</span> home directory Lustre 320 TiB 2 GB/s Quota 250GB Compute and login nodes backed up
+ <span class="monospace">/scratch</span> cluster shared jobs' data Lustre 146 TiB 6 GB/s Quota 100TB Compute and login nodes files older 90 days removed
+ <span class="monospace">/lscratch</span> node local jobs' data local 330 GB 100 MB/s none Compute nodes purged after job ends
+ <span class="monospace">/ramdisk</span> node local jobs' data local 60, 90, 500 GB 5-50 GB/s none Compute nodes purged after job ends
+ <span class="monospace">/tmp</span> local temporary files local 100 MB/s none Compute and login nodes auto purged
Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
-
- - [Anselm Cluster
- Documentation](../anselm-cluster-documentation.html)
diff --git a/anselm-cluster-documentation/accessing-the-cluster/vpn-access.html b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.html
old mode 100755
new mode 100644
similarity index 62%
rename from anselm-cluster-documentation/accessing-the-cluster/vpn-access.html
rename to docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.html
index cc66fbbac24078f5f20e55e90891f41bd0867052..afa697e118675faf840b2422de1b455e6302e60e
--- a/anselm-cluster-documentation/accessing-the-cluster/vpn-access.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:34 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
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<title>VPN Access — IT4I Docs</title>
- <link rel="canonical" href="vpn-access.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="vpn-access.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="vpn-access.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="shell-and-data-access.html">Accessing the Cluster</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">Accessing the Cluster</a>
<span class="breadcrumbSeparator">
/
@@ -241,7 +238,7 @@
<div id="parent-fieldname-text-2c3935b8355e4d8fbab23e10e8f9b474" class="">
<h2 class=" ">Accessing IT4Innovations internal resources via VPN</h2>
-<p class="callout"><strong>Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS patch</strong><br />Workaround can be found at <a class="external-link" href="../../vpn-connection-fail-in-win-8.html" target="_self" title="">https://docs.it4i.cz/vpn-connection-fail-in-win-8.1</a></p>
+<p class="callout"><strong>Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS patch</strong><br />Workaround can be found at <a class="external-link" href="https://docs.it4i.cz/vpn-connection-fail-in-win-8.1" target="_self" title="">https://docs.it4i.cz/vpn-connection-fail-in-win-8.1</a></p>
<p class=" ">Â </p>
<p class=" ">For using resources and licenses which are located at IT4Innovations local network, it is necessary to VPN connect to this network.<br />We use Cisco AnyConnect Secure Mobility Client, which is supported on the following operating systems:</p>
<ul>
@@ -255,34 +252,34 @@
<p class=" ">It is impossible to connect to VPN from other operating systems.</p>
<h2 class=" "><span>VPN client installation</span></h2>
<p class=" ">You can install VPN client from web interface after successful login with LDAP credentials on address <a href="https://vpn1.it4i.cz/anselm">https://vpn1.it4i.cz/anselm</a></p>
-<p class=" "><img title="" class="image-inline" alt="" src="../login.jpg/%40%40images/30271119-b392-4db9-a212-309fb41925d6.jpg" /></p>
+<p class=" "><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/anselm-cluster-documentation/login.jpg/@@images/30271119-b392-4db9-a212-309fb41925d6.jpeg" /></p>
<p class=" ">According to the Java settings after login, the client either automatically installs, or downloads installation file for your operating system. It is necessary to allow start of installation tool for automatic installation.</p>
-<p class=" "><img title="Java detection" class="image-inline" alt="Java detection" src="../java_detection.jpg/%40%40images/5498e1ba-2242-4b9c-a799-0377a73f779e.jpg" /></p>
-<p class=" "><img title="Execution access" class="image-inline" alt="Execution access" src="../executionaccess.jpg/%40%40images/4d6e7cb7-9aa7-419c-9583-6dfd92b2c015.jpg" /><img title="Execution access 2" class="image-inline" alt="Execution access 2" src="../executionaccess2.jpg/%40%40images/bed3998c-4b82-4b40-83bd-c3528dde2425.jpg" /></p>
+<p class=" "><img alt="Java detection" class="image-inline" title="Java detection" src="https://docs.it4i.cz/anselm-cluster-documentation/java_detection.jpg/@@images/5498e1ba-2242-4b9c-a799-0377a73f779e.jpeg" /></p>
+<p class=" "><img alt="Execution access" class="image-inline" title="Execution access" src="https://docs.it4i.cz/anselm-cluster-documentation/executionaccess.jpg/@@images/4d6e7cb7-9aa7-419c-9583-6dfd92b2c015.jpeg" /><img alt="Execution access 2" class="image-inline" title="Execution access 2" src="https://docs.it4i.cz/anselm-cluster-documentation/executionaccess2.jpg/@@images/bed3998c-4b82-4b40-83bd-c3528dde2425.jpeg" /></p>
<p class=" ">After successful installation, VPN connection will be established and you can use available resources from IT4I network.</p>
-<p class=" "><img title="Successfull instalation" class="image-inline" alt="Successfull instalation" src="../successfullinstalation.jpg/%40%40images/c6d69ffe-da75-4cb6-972a-0cf4c686b6e1.jpg" /></p>
+<p class=" "><img alt="Successfull instalation" class="image-inline" title="Successfull instalation" src="https://docs.it4i.cz/anselm-cluster-documentation/successfullinstalation.jpg/@@images/c6d69ffe-da75-4cb6-972a-0cf4c686b6e1.jpeg" /></p>
<p class=" ">If your Java setting doesn't allow automatic installation, you can download installation file and install VPN client manually.</p>
-<p class=" "><img title="Installation file" class="image-inline" alt="Installation file" src="../instalationfile.jpg/%40%40images/202d14e9-e2e1-450b-a584-e78c018d6b6a.jpg" /></p>
+<p class=" "><img alt="Installation file" class="image-inline" title="Installation file" src="https://docs.it4i.cz/anselm-cluster-documentation/instalationfile.jpg/@@images/202d14e9-e2e1-450b-a584-e78c018d6b6a.jpeg" /></p>
<p class=" ">After you click on the link, download of installation file will start.</p>
-<p class=" "><img title="Download file successfull" class="image-inline" alt="Download file successfull" src="../downloadfilesuccessfull.jpg/%40%40images/69842481-634a-484e-90cd-d65e0ddca1e8.jpg" /></p>
+<p class=" "><img alt="Download file successfull" class="image-inline" title="Download file successfull" src="https://docs.it4i.cz/anselm-cluster-documentation/downloadfilesuccessfull.jpg/@@images/69842481-634a-484e-90cd-d65e0ddca1e8.jpeg" /></p>
<p class=" ">After successful download of installation file, you have to execute this tool with administrator's rights and install VPN client manually.</p>
<h2 class=" ">Working with VPN client</h2>
<p class=" ">You can use graphical user interface or command line interface to run VPN client on all supported operating systems. We suggest using GUI.</p>
-<p class=" "><img title="Icon" class="image-inline" alt="Icon" src="../icon.jpg" /></p>
+<p class=" "><img alt="Icon" class="image-inline" title="Icon" src="https://docs.it4i.cz/anselm-cluster-documentation/icon.jpg" /></p>
<p>Before the first login to VPN, you have to fill URLÂ <strong>https://vpn1.it4i.cz/anselm</strong> into the text field.</p>
-<p><img title="First run" class="image-inline" alt="First run" src="../first%20run.jpg" /></p>
+<p><img alt="First run" class="image-inline" title="First run" src="https://docs.it4i.cz/anselm-cluster-documentation/firstrun.jpg" /></p>
<p>After you click on the Connect button, you must fill your login credentials.</p>
-<p><img title="Login - GUI" class="image-inline" alt="Login - GUI" src="../login-gui.jpg" /></p>
+<p><img alt="Login - GUI" class="image-inline" title="Login - GUI" src="https://docs.it4i.cz/anselm-cluster-documentation/logingui.jpg" /></p>
<p>After a successful login, the client will minimize to the system tray. If everything works, you can see a lock in the Cisco tray icon.</p>
-<p><img title="Successfull connection" class="image-inline" alt="Successfull connection" src="../anyconnect%20icon.jpg" /></p>
+<p><img alt="Successfull connection" class="image-inline" title="Successfull connection" src="https://docs.it4i.cz/anselm-cluster-documentation/anyconnecticon.jpg" /></p>
<p>If you right-click on this icon, you will see a context menu in which you can control the VPN connection.</p>
-<p><img title="Context menu" class="image-inline" alt="Context menu" src="../anyconnect-contextmenu.jpg" /></p>
+<p><img alt="Context menu" class="image-inline" title="Context menu" src="https://docs.it4i.cz/anselm-cluster-documentation/anyconnectcontextmenu.jpg" /></p>
<p>When you connect to the VPN for the first time, the client downloads the profile and creates a new item "ANSELM" in the connection list. For subsequent connections, it is not necessary to re-enter the URL address, but just select the corresponding item.</p>
-<p><img title="Anselm profile" class="image-inline" alt="Anselm profile" src="../Anselm%20profile.jpg" /></p>
+<p><img alt="Anselm profile" class="image-inline" title="Anselm profile" src="https://docs.it4i.cz/anselm-cluster-documentation/Anselmprofile.jpg" /></p>
<p>Then AnyConnect automatically proceeds like in the case of first logon.</p>
-<p><img title="Login with profile" class="image-inline" alt="Login with profile" src="../loginwithprofile.jpg/%40%40images/a6fd5f3f-bce4-45c9-85e1-8d93c6395eee.jpg" /></p>
+<p><img alt="Login with profile" class="image-inline" title="Login with profile" src="https://docs.it4i.cz/anselm-cluster-documentation/loginwithprofile.jpg/@@images/a6fd5f3f-bce4-45c9-85e1-8d93c6395eee.jpeg" /></p>
<p>After a successful logon, you can see a green circle with a tick mark on the lock icon.</p>
-<p><img title="successful login" class="image-inline" alt="successful login" src="../successfull%20connection.jpg" /></p>
+<p><img alt="successful login" class="image-inline" title="successful login" src="https://docs.it4i.cz/anselm-cluster-documentation/successfullconnection.jpg" /></p>
<p>For disconnecting, right-click on the AnyConnect client icon in the system tray and select <strong>VPN Disconnect</strong>.</p>
</div>
@@ -359,7 +356,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -375,7 +372,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -391,7 +388,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -407,7 +404,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -423,7 +420,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -439,7 +436,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -455,7 +452,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="shell-and-data-access.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -471,7 +468,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access">
<span>Shell access and data transfer</span>
</a>
@@ -487,7 +484,7 @@
- <a title="" class="state-published contenttype-link" href="../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html">
+ <a class="state-published contenttype-link" title="" href="/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface">
<span>Graphical User Interface</span>
</a>
@@ -503,7 +500,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="vpn-access.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access">
<span>VPN Access</span>
</a>
@@ -519,7 +516,7 @@
- <a title="" class="state-published contenttype-document" href="outgoing-connections.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections">
<span>Outgoing connections</span>
</a>
@@ -544,7 +541,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -560,7 +557,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -576,7 +573,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -592,7 +589,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -608,7 +605,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -624,10 +621,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -643,7 +640,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -659,7 +656,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -684,7 +681,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -700,7 +697,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -716,7 +713,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -755,14 +752,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -784,12 +781,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -805,7 +802,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:37 GMT -->
</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
new file mode 100644
index 0000000000000000000000000000000000000000..6dc9839525ee85673376471ea0b5c566e4ce6f64
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
@@ -0,0 +1,84 @@
+VPN Access
+==========
+
+Accessing IT4Innovations internal resources via VPN
+-----
+**Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS
+patch**
+Workaround can be found at
+<https://docs.it4i.cz/vpn-connection-fail-in-win-8.1>
+Â
+For using resources and licenses which are located at IT4Innovations
+local network, it is necessary to VPN connect to this network.
+We use Cisco AnyConnect Secure Mobility Client, which is supported on
+the following operating systems:
+- <span>Windows XP</span>
+- <span>Windows Vista</span>
+- <span>Windows 7</span>
+- <span>Windows 8</span>
+- <span>Linux</span>
+- <span>MacOS</span>
+It is impossible to connect to VPN from other operating systems.
+<span>VPN client installation</span>
+-------------
+You can install VPN client from web interface after successful login
+with LDAP credentials on address <https://vpn1.it4i.cz/anselm>
+
+According to the Java settings after login, the client either
+automatically installs, or downloads installation file for your
+operating system. It is necessary to allow start of installation tool
+for automatic installation.
+
+
+After successful installation, VPN connection will be established and
+you can use available resources from IT4I network.
+
+If your Java setting doesn't allow automatic installation, you can
+download installation file and install VPN client manually.
+
+After you click on the link, download of installation file will start.
+
+After successful download of installation file, you have to execute this
+tool with administrator's rights and install VPN client manually.
+Working with VPN client
+You can use graphical user interface or command line interface to run
+VPN client on all supported operating systems. We suggest using GUI.
+
+Before the first login to VPN, you have to fill
+URLÂ **https://vpn1.it4i.cz/anselm** into the text field.
+
+After you click on the Connect button, you must fill your login
+credentials.
+
+After a successful login, the client will minimize to the system tray.
+If everything works, you can see a lock in the Cisco tray icon.
+
+If you right-click on this icon, you will see a context menu in which
+you can control the VPN connection.
+
+When you connect to the VPN for the first time, the client downloads the
+profile and creates a new item "ANSELM" in the connection list. For
+subsequent connections, it is not necessary to re-enter the URL address,
+but just select the corresponding item.
+
+Then AnyConnect automatically proceeds like in the case of first logon.
+
+After a successful logon, you can see a green circle with a tick mark on
+the lock icon.
+
+For disconnecting, right-click on the AnyConnect client icon in the
+system tray and select **VPN Disconnect**.
diff --git a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc.html b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc.html
new file mode 100644
index 0000000000000000000000000000000000000000..35cf1ad696acf13ac5c8083c479a130569d074e1
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc.html
@@ -0,0 +1,662 @@
+
+<!DOCTYPE html>
+
+<html xmlns="http://www.w3.org/1999/xhtml" lang="cs">
+
+
+
+
+
+
+
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+<p>The X Window system is a principal way to get GUI access to the clusters.</p>
+<p>Read more about configuring <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc"><b>X Window System</b></a>.</p>
+<h2>VNC</h2>
+<p>The <b>Virtual Network Computing</b> (<b>VNC</b>) is a graphical <span class="link-external"><a href="http://en.wikipedia.org/wiki/Desktop_sharing" title="Desktop sharing">desktop sharing</a></span> system that uses the <span class="link-external"><a href="http://en.wikipedia.org/wiki/RFB_protocol" title="RFB protocol">Remote Frame Buffer protocol (RFB)</a></span> to remotely control another <span class="link-external"><a href="http://en.wikipedia.org/wiki/Computer" title="Computer">computer</a></span>.</p>
+<p>Read more about configuring <strong><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc">VNC</a></strong>.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc.md b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc.md
new file mode 100644
index 0000000000000000000000000000000000000000..ff3738063f55085dad7cad70901c9102e176ce07
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc.md
@@ -0,0 +1,21 @@
+Graphical User Interface
+========================
+
+X Window System
+---------------
+The X Window system is a principal way to get GUI access to the
+clusters.
+Read more about configuring [**X Window
+System**](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc).
+VNC
+---
+The **Virtual Network Computing** (**VNC**) is a graphical <span
+class="link-external">[desktop
+sharing](http://en.wikipedia.org/wiki/Desktop_sharing "Desktop sharing")</span>
+system that uses the <span class="link-external">[Remote Frame Buffer
+protocol
+(RFB)](http://en.wikipedia.org/wiki/RFB_protocol "RFB protocol")</span>
+to remotely control another <span
+class="link-external">[computer](http://en.wikipedia.org/wiki/Computer "Computer")</span>.
+Read more about configuring
+**[VNC](https://docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc)**.
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rename from anselm-cluster-documentation/compute-nodes.html
rename to docs.it4i.cz/anselm-cluster-documentation/compute-nodes.html
index fc0e45453b09f8e8279e1e686f7adeb56db7b523..c8a46986d52779f96861535c02c15022fdd63f1a
--- a/anselm-cluster-documentation/compute-nodes.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.html
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
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<title>Compute Nodes — IT4I Docs</title>
- <link rel="canonical" href="compute-nodes.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="compute-nodes.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="compute-nodes.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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@@ -125,13 +122,13 @@
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../index.html">
- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -333,12 +330,12 @@
</div>
<p>Â </p>
<div class="figure">
-<p class="title"><strong><img title="" class="image-inline" alt="" src="bullx-B510.png" /></strong></p>
+<p class="title"><strong><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/anselm-cluster-documentation/bullxB510.png" /></strong></p>
<p class="title"><strong><strong>Figure Anselm bullx B510 servers</strong></strong></p>
<h3 class=" ">Compute Nodes Summary<strong><strong></strong></strong></h3>
<table class="listing">
<tbody>
-<tr><th>Node type</th><th>Count</th><th>Range</th><th>Memory</th><th>Cores</th><th><a target="_self" title="" class="internal-link" href="resource-allocation-and-job-execution/resources-allocation-policy.html">Access</a></th></tr>
+<tr><th>Node type</th><th>Count</th><th>Range</th><th>Memory</th><th>Cores</th><th><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy">Access</a></th></tr>
<tr class="even">
<td>Nodes without accelerator</td>
<td>180</td>
@@ -596,7 +593,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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@@ -612,7 +609,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -628,7 +625,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -644,7 +641,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -660,7 +657,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -676,7 +673,7 @@
- <a title="" class="state-published contenttype-document" href="hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -692,7 +689,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -708,7 +705,7 @@
- <a title="" class="state-published contenttype-document" href="environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -724,7 +721,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -740,7 +737,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="compute-nodes.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -756,7 +753,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -772,7 +769,7 @@
- <a title="" class="state-published contenttype-document" href="network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -788,10 +785,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -807,7 +804,7 @@
- <a title="" class="state-published contenttype-document" href="remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -823,7 +820,7 @@
- <a title="" class="state-published contenttype-document" href="prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -848,7 +845,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -864,7 +861,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -880,7 +877,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -919,14 +916,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -948,12 +945,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -969,7 +966,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/compute-nodes by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:50 GMT -->
</html>
diff --git a/anselm-cluster-documentation/compute-nodes.md b/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md
similarity index 63%
rename from anselm-cluster-documentation/compute-nodes.md
rename to docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md
index 7368c8ff96250d41238f2946227fcdcc68e3e0d6..f1d9d48a85f85f77d6f576d9833258ec4cbc3ca6 100644
--- a/anselm-cluster-documentation/compute-nodes.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md
@@ -1,103 +1,106 @@
+Compute Nodes
+=============
+
Nodes Configuration
-------------------
Anselm is cluster of x86-64 Intel based nodes built on Bull Extreme
Computing bullx technology. The cluster contains four types of compute
nodes.****
### **Compute Nodes Without Accelerator**
--
+- <div class="itemizedlist">
180 nodes
--
+- <div class="itemizedlist">
2880 cores in total
--
+- <div class="itemizedlist">
two Intel Sandy Bridge E5-2665, 8-core, 2.4GHz processors per node
--
+- <div class="itemizedlist">
64 GB of physical memory per node
- one 500GB SATA 2,5” 7,2 krpm HDD per node
--
+- <div class="itemizedlist">
bullx B510 blade servers
--
+- <div class="itemizedlist">
cn[1-180]
### **Compute Nodes With GPU Accelerator**
--
+- <div class="itemizedlist">
23 nodes
--
+- <div class="itemizedlist">
368 cores in total
--
+- <div class="itemizedlist">
two Intel Sandy Bridge E5-2470, 8-core, 2.3GHz processors per node
--
+- <div class="itemizedlist">
96 GB of physical memory per node
- one 500GB SATA 2,5” 7,2 krpm HDD per node
--
+- <div class="itemizedlist">
GPU accelerator 1x NVIDIA Tesla Kepler K20 per node
--
+- <div class="itemizedlist">
bullx B515 blade servers
--
+- <div class="itemizedlist">
cn[181-203]
### **Compute Nodes With MIC Accelerator**
--
+- <div class="itemizedlist">
4 nodes
--
+- <div class="itemizedlist">
64 cores in total
--
+- <div class="itemizedlist">
two Intel Sandy Bridge E5-2470, 8-core, 2.3GHz processors per node
--
+- <div class="itemizedlist">
96 GB of physical memory per node
- one 500GB SATA 2,5” 7,2 krpm HDD per node
--
+- <div class="itemizedlist">
MIC accelerator 1x Intel Phi 5110P per node
--
+- <div class="itemizedlist">
bullx B515 blade servers
--
+- <div class="itemizedlist">
cn[204-207]
### **Fat Compute Nodes**
--
+- <div>
2 nodes
--
+- <div>
32 cores in total
--
+- <div>
2 Intel Sandy Bridge E5-2665, 8-core, 2.4GHz processors per node
--
+- <div>
512 GB of physical memory per node
- two 300GB SAS 3,5”15krpm HDD (RAID1) per node
--
+- <div>
two 100GB SLC SSD per node
--
+- <div>
bullx R423-E3 servers
--
+- <div>
cn[208-209]
Â
-****
+****
****Figure Anselm bullx B510 servers****
### Compute Nodes Summary********
- Node type Count Range Memory Cores [Access](resource-allocation-and-job-execution/resources-allocation-policy.html)
- ---------------------------- ------- --------------- -------- ------------- --------------------------------------------------------------------------------------------------
+ Node type Count Range Memory Cores [Access](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy)
+ ----- ------- --------------- -------- ------------- -----
Nodes without accelerator 180 cn[1-180] 64GB 16 @ 2.4Ghz qexp, qprod, qlong, qfree
Nodes with GPU accelerator 23 cn[181-203] 96GB 16 @ 2.3Ghz qgpu, qprod
Nodes with MIC accelerator 4 cn[204-207] 96GB 16 @ 2.3GHz qmic, qprod
@@ -110,80 +113,66 @@ with accelerator). Processors support Advanced Vector Extensions (AVX)
256-bit instruction set.
### Intel Sandy Bridge E5-2665 Processor
- eight-core
-- speed 2.4 GHz, up to 3.1 GHz using Turbo Boost Technology
-- peak performance 19.2 Gflop/s per
+- speed2.4 GHz, up to 3.1 GHz using Turbo Boost Technology
+- peak performance<span class="emphasis">19.2 Gflop/s</span> per
core
-- caches
+- caches:
+ <div class="itemizedlist">
+ - L2256 KB per core
+ - L320 MB per processor
- - L2 256 KB per core
- - L3 20 MB per processor
-
-- memory bandwidth at the level of the processor 51.2 GB/s
+- memory bandwidth at the level of the processor51.2 GB/s
### Intel Sandy Bridge E5-2470 Processor
- eight-core
-- speed 2.3 GHz, up to 3.1 GHz using Turbo Boost Technology
-- peak performance 18.4 Gflop/s per
+- speed2.3 GHz, up to 3.1 GHz using Turbo Boost Technology
+- peak performance<span class="emphasis">18.4 Gflop/s</span> per
core
-- caches
-
- - L2 256 KB per core
- - L3 20 MB per processor
+- caches:
+ <div class="itemizedlist">
+ - L2256 KB per core
+ - L320 MB per processor
-- memory bandwidth at the level of the processor 38.4 GB/s
+- memory bandwidth at the level of the processor38.4 GB/s
Â
Nodes equipped with Intel Xeon E5-2665 CPU have set PBS resource
attribute cpu_freq = 24, nodes equipped with Intel Xeon E5-2470 CPU
have set PBS resource attribute cpu_freq = 23.
``` {.prettyprint .lang-sh}
-$ qsub -A OPEN-0-0 -q qprod -l select=4ncpus=16cpu_freq=24 -I
+$ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=16:cpu_freq=24 -I
```
In this example, we allocate 4 nodes, 16 cores at 2.4GHhz per node.
Intel Turbo Boost Technology is used by default, you can disable it for
all nodes of job by using resource attribute cpu_turbo_boost.
- $ qsub -A OPEN-0-0 -q qprod -l select=4ncpus=16 -l cpu_turbo_boost=0 -I
+ $ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=16 -l cpu_turbo_boost=0 -I
Memory Architecture
-------------------
### Compute Node Without Accelerator
- 2 sockets
- Memory Controllers are integrated into processors.
-
+ <div class="itemizedlist">
- 8 DDR3 DIMMS per node
- 4 DDR3 DIMMS per CPU
- 1 DDR3 DIMMS per channel
- - Data rate support up to 1600MT/s
+ - Data rate supportup to 1600MT/s
-- Populated memory 8x 8GB DDR3 DIMM 1600Mhz
+- Populated memory8x 8GB DDR3 DIMM 1600Mhz
### Compute Node With GPU or MIC Accelerator
- 2 sockets
- Memory Controllers are integrated into processors.
-
+ <div class="itemizedlist">
- 6 DDR3 DIMMS per node
- 3 DDR3 DIMMS per CPU
- 1 DDR3 DIMMS per channel
- - Data rate support up to 1600MT/s
+ - Data rate supportup to 1600MT/s
-- Populated memory 6x 16GB DDR3 DIMM 1600Mhz
+- Populated memory6x 16GB DDR3 DIMM 1600Mhz
### Fat Compute Node
- 2 sockets
- Memory Controllers are integrated into processors.
-
+ <div class="itemizedlist">
- 16 DDR3 DIMMS per node
- 8 DDR3 DIMMS per CPU
- 2 DDR3 DIMMS per channel
- - Data rate support up to 1600MT/s
-
-- Populated memory 16x 32GB DDR3 DIMM 1600Mhz
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
+ - Data rate supportup to 1600MT/s
+
+- Populated memory16x 32GB DDR3 DIMM 1600Mhz
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diff --git a/anselm-cluster-documentation/environment-and-modules.html b/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.html
old mode 100755
new mode 100644
similarity index 73%
rename from anselm-cluster-documentation/environment-and-modules.html
rename to docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.html
index 276d25b71d24664c2c783ec3a084ce5acc55df59..2502f567aec136966aff9f1844c5ead64e6e623e
--- a/anselm-cluster-documentation/environment-and-modules.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.html
@@ -10,45 +10,42 @@
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Environment and Modules — IT4I Docs</title>
- <link rel="canonical" href="environment-and-modules.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="environment-and-modules.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="environment-and-modules.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../index.html">
- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -332,7 +329,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -348,7 +345,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -364,7 +361,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -380,7 +377,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -396,7 +393,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -412,7 +409,7 @@
- <a title="" class="state-published contenttype-document" href="hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -428,7 +425,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -444,7 +441,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="environment-and-modules.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -460,7 +457,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -476,7 +473,7 @@
- <a title="" class="state-published contenttype-document" href="compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -492,7 +489,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -508,7 +505,7 @@
- <a title="" class="state-published contenttype-document" href="network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -524,10 +521,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -543,7 +540,7 @@
- <a title="" class="state-published contenttype-document" href="remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -559,7 +556,7 @@
- <a title="" class="state-published contenttype-document" href="prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -584,7 +581,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -600,7 +597,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -616,7 +613,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -655,14 +652,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -684,12 +681,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -705,7 +702,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/environment-and-modules by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:49 GMT -->
</html>
diff --git a/anselm-cluster-documentation/environment-and-modules.md b/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md
similarity index 76%
rename from anselm-cluster-documentation/environment-and-modules.md
rename to docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md
index 28adcd2b34696cff2ecf4f0816255ada8b4e1a33..e2a6e796a7dd361342c819e11d5b9e3dcb04c626 100644
--- a/anselm-cluster-documentation/environment-and-modules.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md
@@ -1,3 +1,6 @@
+Environment and Modules
+=======================
+
### Environment Customization
After logging in, you may want to configure the environment. Write your
preferred path definitions, aliases, functions and module loads in the
@@ -20,9 +23,9 @@ fi
Do not run commands outputing to standard output (echo, module list,
etc) in .bashrc for non-interactive SSH sessions. It breaks fundamental
functionality (scp, PBS) of your account! Take care for SSH session
-interactivity for such commands as id="result_box"
-class="short_text">stated
-class="hps">in the previous example.
+interactivity for such commands as <span id="result_box"
+class="short_text"><span class="hps alt-edited">stated</span> <span
+class="hps">in the previous example.</span></span>
### Application Modules
In order to configure your shell for running particular application on
Anselm we use Module package interface.
@@ -65,28 +68,14 @@ with the Intel MPI library
### []()Application Modules Path Expansion
All application modules on Salomon cluster (and further) will be build
using tool called
-[EasyBuild](http//hpcugent.github.io/easybuild/ "EasyBuild").
+[EasyBuild](http://hpcugent.github.io/easybuild/ "EasyBuild").
In case that you want to use some applications that are build by
EasyBuild already, you have to modify your MODULEPATH environment
variable.
``` {.prettyprint .lang-sh}
-export MODULEPATH=$MODULEPATH/apps/easybuild/modules/all/
+export MODULEPATH=$MODULEPATH:/apps/easybuild/modules/all/
```
This command expands your searched paths to modules. You can also add
this command to the .bashrc file to expand paths permanently. After this
command, you can use same commands to list/add/remove modules as is
described above.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
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diff --git a/anselm-cluster-documentation/first run.jpg b/docs.it4i.cz/anselm-cluster-documentation/firstrun.jpg
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/first run.jpg
rename to docs.it4i.cz/anselm-cluster-documentation/firstrun.jpg
diff --git a/anselm-cluster-documentation/hardware-overview.html b/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.html
old mode 100755
new mode 100644
similarity index 74%
rename from anselm-cluster-documentation/hardware-overview.html
rename to docs.it4i.cz/anselm-cluster-documentation/hardware-overview.html
index e2ad03dd7b664124743f155633f616fc946f07f2..65c3ee2422089de6261de828bbf670dd3482f9e0
--- a/anselm-cluster-documentation/hardware-overview.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.html
@@ -10,45 +10,42 @@
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<title>Hardware Overview — IT4I Docs</title>
- <link rel="canonical" href="hardware-overview.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
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- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="hardware-overview.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="hardware-overview.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
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- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -704,11 +701,11 @@
<li>4Â compute nodes with MIC accelerator - equipped with Intel Xeon Phi 5110P</li>
<li>2 fat nodes - equipped with 512GB RAM and two 100GB SSD drives</li>
</ul>
-<p><a target="_self" title="" class="internal-link" href="compute-nodes.html">More about Compute nodes</a>.</p>
-<p>GPU and accelerated nodes are available upon request, see the <a target="_self" title="" class="internal-link" href="resource-allocation-and-job-execution/resources-allocation-policy.html">Resources Allocation Policy</a>.</p>
-<p class="WYSIWYG_LINK">All these nodes are interconnected by fast <span class="WYSIWYG_LINK">InfiniBand <span class="WYSIWYG_LINK">QDR</span> network</span> and Ethernet network. <a target="_self" title="" class="internal-link" href="network.html">More about the <span class="WYSIWYG_LINK">Network</span></a>. Every chassis provides Infiniband switch, marked <strong>isw</strong>, connecting all nodes in the chassis, as well as connecting the chassis to the upper level switches.</p>
-<p class="WYSIWYG_LINK">All nodes share 360TB /home disk storage to store user files. The 146TB shared /scratch storage is available for the scratch data. These file systems are provided by Lustre parallel file system. There is also local disk storage available on all compute nodes /lscratch. <a target="_self" title="" class="internal-link" href="storage-1/storage.html">More about <span class="WYSIWYG_LINK">Storage</span></a>.</p>
-<p>The user access to the Anselm cluster is provided by two login nodes login1, login2, and data mover node dm1. <a target="_self" title="" class="internal-link" href="accessing-the-cluster/shell-and-data-access.html">More about accessing cluster.</a></p>
+<p><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">More about Compute nodes</a>.</p>
+<p>GPU and accelerated nodes are available upon request, see the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy">Resources Allocation Policy</a>.</p>
+<p class="WYSIWYG_LINK">All these nodes are interconnected by fast <span class="WYSIWYG_LINK">InfiniBand <span class="WYSIWYG_LINK">QDR</span> network</span> and Ethernet network. <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/network">More about the <span class="WYSIWYG_LINK">Network</span></a>. Every chassis provides Infiniband switch, marked <strong>isw</strong>, connecting all nodes in the chassis, as well as connecting the chassis to the upper level switches.</p>
+<p class="WYSIWYG_LINK">All nodes share 360TB /home disk storage to store user files. The 146TB shared /scratch storage is available for the scratch data. These file systems are provided by Lustre parallel file system. There is also local disk storage available on all compute nodes /lscratch. <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage">More about <span class="WYSIWYG_LINK">Storage</span></a>.</p>
+<p>The user access to the Anselm cluster is provided by two login nodes login1, login2, and data mover node dm1. <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">More about accessing cluster.</a></p>
<p>Â The parameters are summarized in the following tables:</p>
<table class="listing">
<tbody>
@@ -725,7 +722,7 @@
<td>Operating system</td>
<td>Linux</td>
</tr>
-<tr><th colspan="2"><a target="_self" title="" class="internal-link" href="compute-nodes.html"><strong>Compute nodes</strong></a></th></tr>
+<tr><th colspan="2"><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes"><strong>Compute nodes</strong></a></th></tr>
<tr class="even">
<td>Totally</td>
<td>209</td>
@@ -806,7 +803,7 @@
</tr>
</tbody>
</table>
-<p>Â For more details please refer to the <a target="_self" title="" class="internal-link" href="compute-nodes.html">Compute nodes</a>, <a target="_self" title="" class="internal-link" href="storage-1/storage.html">Storage</a>, and <a target="_self" title="" class="internal-link" href="network.html">Network</a>.</p>
+<p>Â For more details please refer to the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">Compute nodes</a>, <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage">Storage</a>, and <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/network">Network</a>.</p>
</div>
@@ -882,7 +879,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -898,7 +895,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -914,7 +911,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -930,7 +927,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -946,7 +943,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -962,7 +959,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="hardware-overview.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -978,7 +975,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -994,7 +991,7 @@
- <a title="" class="state-published contenttype-document" href="environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -1010,7 +1007,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -1026,7 +1023,7 @@
- <a title="" class="state-published contenttype-document" href="compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -1042,7 +1039,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -1058,7 +1055,7 @@
- <a title="" class="state-published contenttype-document" href="network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -1074,10 +1071,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -1093,7 +1090,7 @@
- <a title="" class="state-published contenttype-document" href="remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1109,7 +1106,7 @@
- <a title="" class="state-published contenttype-document" href="prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1134,7 +1131,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1150,7 +1147,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1166,7 +1163,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1205,14 +1202,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1234,12 +1231,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1255,7 +1252,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/hardware-overview by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:48 GMT -->
</html>
diff --git a/anselm-cluster-documentation/hardware-overview.md b/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md
similarity index 76%
rename from anselm-cluster-documentation/hardware-overview.md
rename to docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md
index 382a6288fe0b8ce48ac568ad6d7c860f4d99f1d9..aff57803f79184d3669e2092a495ac0591ed6e38 100644
--- a/anselm-cluster-documentation/hardware-overview.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md
@@ -1,7 +1,10 @@
+Hardware Overview
+=================
+
The Anselm cluster consists of 209 computational nodes named cn[1-209]
of which 180 are regular compute nodes, 23 GPU Kepler K20 accelerated
nodes, 4 MIC Xeon Phi 5110 accelerated nodes and 2 fat nodes. Each node
-is a powerful x86-64 computer,
+is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer,
equipped with 16 cores (two eight-core Intel Sandy Bridge processors),
at least 64GB RAM, and local hard drive. The user access to the Anselm
cluster is provided by two login nodes login[1,2]. The nodes are
@@ -13,9 +16,9 @@ Virtualization infrastructure provides resources to run long term
servers and services in virtual mode. Fat nodes and virtual servers may
access 45 TB of dedicated block storage. Accelerated nodes, fat nodes,
and virtualization infrastructure are available [upon
-request](https//support.it4i.cz/rt) made by a PI.
+request](https://support.it4i.cz/rt) made by a PI.
Schematic representation of the Anselm cluster. Each box represents a
-node (computer) or storage capacity
+node (computer) or storage capacity:
User-oriented infrastructure
Storage
Management infrastructure
@@ -50,16 +53,27 @@ cn25
cn26
cn27
cn28
-Â
-Â
-Lustre FS
-/home
-320TB
-Â
-Â
-Lustre FS
-/scratch
-146TB
+<table>
+<colgroup>
+<col width="100%" />
+</colgroup>
+<tbody>
+<tr class="odd">
+<td align="left"><p>Â </p>
+<p>Â </p>
+<p>Lustre FS</p>
+<p>/home<br />
+320TB</p>
+<p>Â </p>
+<p>Â </p></td>
+</tr>
+<tr class="even">
+<td align="left"><p>Lustre FS</p>
+<p>/scratch<br />
+146TB</p></td>
+</tr>
+</tbody>
+</table>
Management
nodes
Block storage
@@ -275,21 +289,22 @@ cn136
...
----------------
The cluster compute nodes cn[1-207] are organized within 13 chassis.Â
-There are four types of compute nodes
+There are four types of compute nodes:
- 180 compute nodes without the accelerator
- 23 compute nodes with GPU accelerator - equipped with NVIDIA Tesla
Kepler K20
- 4Â compute nodes with MIC accelerator - equipped with Intel Xeon Phi
5110P
- 2 fat nodes - equipped with 512GB RAM and two 100GB SSD drives
-[More about Compute nodes](compute-nodes.html).
+[More about Compute
+nodes](https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes).
GPU and accelerated nodes are available upon request, see the [Resources
Allocation
-Policy](resource-allocation-and-job-execution/resources-allocation-policy.html).
-All these nodes are interconnected by fast
-class="WYSIWYG_LINK">InfiniBand QDR
-network and Ethernet network. [More about the
-class="WYSIWYG_LINK">Network](network.html).
+Policy](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy).
+All these nodes are interconnected by fast <span
+class="WYSIWYG_LINK">InfiniBand <span class="WYSIWYG_LINK">QDR</span>
+network</span> and Ethernet network. [More about the <span
+class="WYSIWYG_LINK">Network</span>](https://docs.it4i.cz/anselm-cluster-documentation/network).
Every chassis provides Infiniband switch, marked **isw**, connecting all
nodes in the chassis, as well as connecting the chassis to the upper
level switches.
@@ -297,12 +312,12 @@ All nodes share 360TB /home disk storage to store user files. The 146TB
shared /scratch storage is available for the scratch data. These file
systems are provided by Lustre parallel file system. There is also local
disk storage available on all compute nodes /lscratch. [More about
-
-class="WYSIWYG_LINK">Storage](storage-1/storage.html).
+<span
+class="WYSIWYG_LINK">Storage</span>](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage).
The user access to the Anselm cluster is provided by two login nodes
login1, login2, and data mover node dm1. [More about accessing
-cluster.](accessing-the-cluster/shell-and-data-access.html)
-Â The parameters are summarized in the following tables
+cluster.](https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster)
+Â The parameters are summarized in the following tables:
**In general**
Primary purpose
High Performance Computing
@@ -310,7 +325,8 @@ Architecture of compute nodes
x86-64
Operating system
Linux
-[**Compute nodes**](compute-nodes.html)
+[**Compute
+nodes**](https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes)
Totally
209
Processor cores
@@ -337,26 +353,13 @@ Total max. LINPACK performance (Rmax)
Total amount of RAM
15.136 TB
Node Processor Memory Accelerator
- ------------------ --------------------------------------- -------- ----------------------
+ ------------------ ---------------- -------- ----------------------
w/o accelerator 2x Intel Sandy Bridge E5-2665, 2.4GHz 64GB -
GPU accelerated 2x Intel Sandy Bridge E5-2470, 2.3GHz 96GB NVIDIA Kepler K20
MIC accelerated 2x Intel Sandy Bridge E5-2470, 2.3GHz 96GB Intel Xeon Phi P5110
Fat compute node 2x Intel Sandy Bridge E5-2665, 2.4GHz 512GB -
 For more details please refer to the [Compute
-nodes](compute-nodes.html),
-[Storage](storage-1/storage.html), and
-[Network](network.html).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
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- Documentation](../salomon.html)
+nodes](https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes),
+[Storage](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage),
+and
+[Network](https://docs.it4i.cz/anselm-cluster-documentation/network).
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+ <p>Welcome to Anselm supercomputer cluster. The Anselm cluster consists of 209 compute nodes, totaling 3344 compute cores with 15TB RAM and giving over 94 Tflop/s theoretical peak performance. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 16 cores, at least 64GB RAM, and 500GB harddrive. Nodes are interconnected by fully non-blocking fat-tree Infiniband network and equipped with Intel Sandy Bridge processors. A few nodes are also equipped with NVIDIA Kepler GPU or Intel Xeon Phi MIC accelerators. Read more in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">Hardware Overview</a>.</p>
+<p>The cluster runs bullx Linux <a class="external-link" href="http://www.bull.com/bullx-logiciels/systeme-exploitation.html" target="_self" title=""><span class="WYSIWYG_LINK"></span></a><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">operating system</a>, which is compatible with the <span class="WYSIWYG_LINK">RedHat</span> <a class="external-link" href="http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg" target="_self" title=""><span class="WYSIWYG_LINK">Linux family.</span></a> We have installed a wide range of <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software">software</a> packages targeted at different scientific domains. These packages are accessible via the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">modules environment</a>.</p>
+<p>User data shared file-system (HOME, 320TB) and job data shared file-system (SCRATCH, 146TB) are available to users.</p>
+<p>The PBS Professional workload manager provides <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">computing resources allocations and job execution</a>.</p>
+<p>Read more on how to <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources">apply for resources</a>, <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">obtain login credentials,</a> and <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">access the cluster</a>.</p>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
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+<div id="viewlet-cookiepolicy" style="display:none">
+ <h1 id="tlspu_cookiepolicy_title">This Site Uses Cookies</h1>
+ <p id="tlspu_cookiepolicy_message">We may use cookies to record some preference settings and to analyse how you use our web site. We may also use external analysis systems which may set additional cookies to perform their analysis. These cookies are integral to our web site. You can delete or disable these cookies in your web browser if you wish but then our site may not work correctly.</p>
+ <form id="tlspu_cookiepolicy_form">
+ <input type="checkbox" id="tlspu_cookiepolicy_agreed" value="confirmed" />
+ <label for="tlspu_cookiepolicy_agreed">I have read and understood this message.</label>
+ <button disabled="disabled" id="tlspu_cookiepolicy_button" value="hide">Hide this message</button>
+ </form>
+</div>
+
+<script type="text/javascript">
+/*
+*/
+</script>
+
+<div id="portal-footer">
+ <p>
+ <a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
+ <a href="http://prace.it4i.cz/">HPC & PRACE</a>
+ <a href="http://study.it4i.cz/">HPC Study</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
+ <a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
+ <a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
+ </p>
+ <!-- nagios_check_http_expect_string -->
+</div>
+
+ </div>
+ </div>
+
+ <!-- TODO -->
+ <!-- nagios_check_http_expect_string -->
+ <!-- TODO -->
+
+</div>
+</body>
+</html>
+
diff --git a/docs.it4i.cz/anselm-cluster-documentation/introduction.md b/docs.it4i.cz/anselm-cluster-documentation/introduction.md
new file mode 100644
index 0000000000000000000000000000000000000000..7d1bde3e9229026bb5cd0d102710e86979641d53
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/introduction.md
@@ -0,0 +1,34 @@
+Introduction
+============
+
+Welcome to Anselm supercomputer cluster. The Anselm cluster consists of
+209 compute nodes, totaling 3344 compute cores with 15TB RAM and giving
+over 94 Tflop/s theoretical peak performance. Each node is a <span
+class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 16
+cores, at least 64GB RAM, and 500GB harddrive. Nodes are interconnected
+by fully non-blocking fat-tree Infiniband network and equipped with
+Intel Sandy Bridge processors. A few nodes are also equipped with NVIDIA
+Kepler GPU or Intel Xeon Phi MIC accelerators. Read more in [Hardware
+Overview](https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview).
+The cluster runs bullx Linux [<span
+class="WYSIWYG_LINK"></span>](http://www.bull.com/bullx-logiciels/systeme-exploitation.html)[operating
+system](https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system),
+which is compatible with the <span class="WYSIWYG_LINK">RedHat</span>
+[<span class="WYSIWYG_LINK">Linux
+family.</span>](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
+We have installed a wide range of
+[software](https://docs.it4i.cz/anselm-cluster-documentation/software)
+packages targeted at different scientific domains. These packages are
+accessible via the [modules
+environment](https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules).
+User data shared file-system (HOME, 320TB) and job data shared
+file-system (SCRATCH, 146TB) are available to users.
+The PBS Professional workload manager provides [computing resources
+allocations and job
+execution](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution).
+Read more on how to [apply for
+resources](https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources),
+[obtain login
+credentials,](https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials)
+and [access the
+cluster](https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster).
diff --git a/anselm-cluster-documentation/java_detection.jpg/@@images/5498e1ba-2242-4b9c-a799-0377a73f779e.jpg b/docs.it4i.cz/anselm-cluster-documentation/java_detection.jpg/@@images/5498e1ba-2242-4b9c-a799-0377a73f779e.jpeg
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/java_detection.jpg/@@images/5498e1ba-2242-4b9c-a799-0377a73f779e.jpg
rename to docs.it4i.cz/anselm-cluster-documentation/java_detection.jpg/@@images/5498e1ba-2242-4b9c-a799-0377a73f779e.jpeg
diff --git a/anselm-cluster-documentation/legend.png b/docs.it4i.cz/anselm-cluster-documentation/legend.png
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/legend.png
rename to docs.it4i.cz/anselm-cluster-documentation/legend.png
diff --git a/anselm-cluster-documentation/login.jpg/@@images/30271119-b392-4db9-a212-309fb41925d6.jpg b/docs.it4i.cz/anselm-cluster-documentation/login.jpg/@@images/30271119-b392-4db9-a212-309fb41925d6.jpeg
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/login.jpg/@@images/30271119-b392-4db9-a212-309fb41925d6.jpg
rename to docs.it4i.cz/anselm-cluster-documentation/login.jpg/@@images/30271119-b392-4db9-a212-309fb41925d6.jpeg
diff --git a/anselm-cluster-documentation/login-gui.jpg b/docs.it4i.cz/anselm-cluster-documentation/logingui.jpg
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/login-gui.jpg
rename to docs.it4i.cz/anselm-cluster-documentation/logingui.jpg
diff --git a/anselm-cluster-documentation/loginwithprofile.jpg/@@images/a6fd5f3f-bce4-45c9-85e1-8d93c6395eee.jpg b/docs.it4i.cz/anselm-cluster-documentation/loginwithprofile.jpg/@@images/a6fd5f3f-bce4-45c9-85e1-8d93c6395eee.jpeg
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/loginwithprofile.jpg/@@images/a6fd5f3f-bce4-45c9-85e1-8d93c6395eee.jpg
rename to docs.it4i.cz/anselm-cluster-documentation/loginwithprofile.jpg/@@images/a6fd5f3f-bce4-45c9-85e1-8d93c6395eee.jpeg
diff --git a/anselm-cluster-documentation/network.html b/docs.it4i.cz/anselm-cluster-documentation/network.html
old mode 100755
new mode 100644
similarity index 71%
rename from anselm-cluster-documentation/network.html
rename to docs.it4i.cz/anselm-cluster-documentation/network.html
index 16bcbeaebdc7f62f178f12a76847ebe10f8c626b..281c302ac34e82b2346a9e287ff69502e2b9a238
--- a/anselm-cluster-documentation/network.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/network.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/network by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:50 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/network" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/IEFixes-cachekey-ec9b60024fd235ff2c883b4b54db91cb.css" />
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- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Network — IT4I Docs</title>
- <link rel="canonical" href="network.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/network" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="network.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/network#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="network.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/network#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../index.html">
- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -316,7 +313,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -332,7 +329,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -348,7 +345,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -364,7 +361,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -380,7 +377,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -396,7 +393,7 @@
- <a title="" class="state-published contenttype-document" href="hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -412,7 +409,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -428,7 +425,7 @@
- <a title="" class="state-published contenttype-document" href="environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -444,7 +441,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -460,7 +457,7 @@
- <a title="" class="state-published contenttype-document" href="compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -476,7 +473,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -492,7 +489,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="network.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -508,10 +505,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -527,7 +524,7 @@
- <a title="" class="state-published contenttype-document" href="remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -543,7 +540,7 @@
- <a title="" class="state-published contenttype-document" href="prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -568,7 +565,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -584,7 +581,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -600,7 +597,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -639,14 +636,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -668,12 +665,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -689,7 +686,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/anselm-cluster-documentation/network.md b/docs.it4i.cz/anselm-cluster-documentation/network.md
similarity index 67%
rename from anselm-cluster-documentation/network.md
rename to docs.it4i.cz/anselm-cluster-documentation/network.md
index 5ffbe8b00ea28ac452170dc369f9edd299c77eca..33ccce93e0eea6756576de1fe33f9cd4a5f51c7e 100644
--- a/anselm-cluster-documentation/network.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/network.md
@@ -1,13 +1,16 @@
+Network
+=======
+
All compute and login nodes of Anselm are interconnected by
-[Infiniband](http//en.wikipedia.org/wiki/InfiniBand)
+[Infiniband](http://en.wikipedia.org/wiki/InfiniBand)
QDR network and by Gigabit
-[Ethernet](http//en.wikipedia.org/wiki/Ethernet)
+[Ethernet](http://en.wikipedia.org/wiki/Ethernet)
network. Both networks may be used to transfer user data.
Infiniband Network
------------------
All compute and login nodes of Anselm are interconnected by a
high-bandwidth, low-latency
-[Infiniband](http//en.wikipedia.org/wiki/InfiniBand)
+[Infiniband](http://en.wikipedia.org/wiki/InfiniBand)
QDR network (IB 4x QDR, 40 Gbps). The network topology is a fully
non-blocking fat-tree.
The compute nodes may be accessed via the Infiniband network using ib0
@@ -27,29 +30,15 @@ The network provides **114MB/s** transfer rates via the TCP connection.
Example
-------
``` {.prettyprint .lang-sh}
-$ qsub -q qexp -l select=4ncpus=16 -N Name0 ./myjob
+$ qsub -q qexp -l select=4:ncpus=16 -N Name0 ./myjob
$ qstat -n -u username
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
-15209.srv11 username qexp Name0 5530 4 64 -- 0100 R 0000
+15209.srv11 username qexp Name0 5530 4 64 -- 01:00 R 00:00
cn17/0*16+cn108/0*16+cn109/0*16+cn110/0*16
$ ssh 10.2.1.110
$ ssh 10.1.1.108
```
In this example, we access the node cn110 by Infiniband network via the
ib0 interface, then from cn110 to cn108 by Ethernet network.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
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- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
diff --git a/anselm-cluster-documentation/prace.html b/docs.it4i.cz/anselm-cluster-documentation/prace.html
old mode 100755
new mode 100644
similarity index 76%
rename from anselm-cluster-documentation/prace.html
rename to docs.it4i.cz/anselm-cluster-documentation/prace.html
index d788ea95b485c2e4525992f36f0ba55b36db0f14..9a923e9610be8d7f67613fe531cfbd575164df67
--- a/anselm-cluster-documentation/prace.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/prace.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/prace by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:52 GMT -->
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- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>PRACE User Support — IT4I Docs</title>
- <link rel="canonical" href="prace.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/prace" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="prace.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/prace#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="prace.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/prace#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../index.html">
- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -231,14 +228,14 @@
<div id="parent-fieldname-text-79d0c039774f4e6391e5446ec00492f1" class="">
<h2 class=" ">Intro</h2>
-<p>PRACE users coming to Anselm as to TIER-1 system offered through the DECI calls are in general treated as standard users and so most of the general documentation applies to them as well. This section shows the main differences for quicker orientation, but often uses references to the original documentation. PRACE users who don't undergo the full procedure (including signing the IT4I AuP on top of the PRACE AuP) will not have a password and thus access to some services intended for regular users. This can lower their comfort, but otherwise they should be able to use the TIER-1 system as intended. Please see the <a target="_self" title="" class="internal-link" href="../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html">Obtaining Login Credentials section</a>, if the same level of access is required.</p>
+<p>PRACE users coming to Anselm as to TIER-1 system offered through the DECI calls are in general treated as standard users and so most of the general documentation applies to them as well. This section shows the main differences for quicker orientation, but often uses references to the original documentation. PRACE users who don't undergo the full procedure (including signing the IT4I AuP on top of the PRACE AuP) will not have a password and thus access to some services intended for regular users. This can lower their comfort, but otherwise they should be able to use the TIER-1 system as intended. Please see the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials">Obtaining Login Credentials section</a>, if the same level of access is required.</p>
<p>All general <a class="external-link" href="http://www.prace-ri.eu/user-documentation/" target="_self" title="">PRACE User Documentation</a> should be read before continuing reading the local documentation here.</p>
<h2 class=" "><a name="help-and-support"></a>Help and Support</h2>
<p>If you have any troubles, need information, request support or want to install additional software, please use <a class="external-link" href="http://www.prace-ri.eu/helpdesk-guide264/" target="_self" title="">PRACE Helpdesk</a>.</p>
-<p>Information about the local services are provided in the <a target="_self" title="" class="internal-link" href="introduction.html">introduction of general user documentation</a>. Please keep in mind, that standard PRACE accounts don't have a password to access the web interface of the local (IT4Innovations) request tracker and thus a new ticket should be created by sending an e-mail to support[at]it4i.cz.</p>
+<p>Information about the local services are provided in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/introduction">introduction of general user documentation</a>. Please keep in mind, that standard PRACE accounts don't have a password to access the web interface of the local (IT4Innovations) request tracker and thus a new ticket should be created by sending an e-mail to support[at]it4i.cz.</p>
<h2 class=" ">Obtaining Login Credentials</h2>
<p>In general PRACE users already have a PRACE account setup through their HOMESITE (institution from their country) as a result of rewarded PRACE project proposal. This includes signed PRACE AuP, generated and registered certificates, etc.</p>
-<p>If there's a special need a PRACE user can get a standard (local) account at IT4Innovations. To get an account on the Anselm cluster, the user needs to obtain the login credentials. The procedure is the same as for general users of the cluster, so please see the corresponding <a target="_self" title="" class="internal-link" href="../get-started-with-it4innovations/obtaining-login-credentials.html">section of the general documentation here</a>.</p>
+<p>If there's a special need a PRACE user can get a standard (local) account at IT4Innovations. To get an account on the Anselm cluster, the user needs to obtain the login credentials. The procedure is the same as for general users of the cluster, so please see the corresponding <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">section of the general documentation here</a>.</p>
<h2 class=" ">Accessing the cluster</h2>
<h3 class=" ">Access with GSI-SSH</h3>
<p>For all PRACE users the method for interactive access (login) and data transfer based on grid services from Globus Toolkit (GSI SSH and GridFTP) is supported.</p>
@@ -323,13 +320,13 @@
<pre>$ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ anselm-prace.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_</pre>
<pre>$ gsiscp -P 2222 anselm-prace.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_ </pre>
<h3 class=" ">Access to X11 applications (VNC)</h3>
-<p>If the user needs to run X11 based graphical application and does not have a X11 server, the applications can be run using VNC service. If the user is using regular SSH based access, please see the <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html">section in general documentation</a>.</p>
-<p>If the user uses GSI SSH based access, then the procedure is similar to the SSH based access (<a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html">look here</a>), only the port forwarding must be done using GSI SSH:</p>
+<p>If the user needs to run X11 based graphical application and does not have a X11 server, the applications can be run using VNC service. If the user is using regular SSH based access, please see the <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">section in general documentation</a>.</p>
+<p>If the user uses GSI SSH based access, then the procedure is similar to the SSH based access (<a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">look here</a>), only the port forwarding must be done using GSI SSH:</p>
<pre class=" ">$ gsissh -p 2222 anselm.it4i.cz -L 5961:localhost:5961</pre>
<h3 class=" ">Access with SSH</h3>
-<p class=" ">After successful obtainment of login credentials for the local IT4Innovations account, the PRACE users can access the cluster as regular users using SSH. For more information please see the <a target="_self" title="" class="internal-link" href="resolveuid/5d3d6f3d873a42e584cbf4365c4e251b.html">section in general documentation</a>.</p>
+<p class=" ">After successful obtainment of login credentials for the local IT4Innovations account, the PRACE users can access the cluster as regular users using SSH. For more information please see the <a title="" class="internal-link" target="_self" href="resolveuid/5d3d6f3d873a42e584cbf4365c4e251b">section in general documentation</a>.</p>
<h2 class=" "><a name="file-transfers"></a>File transfers</h2>
-<p>PRACE users can use the same transfer mechanisms as regular users (if they've undergone the full registration procedure). For information about this, please see <a target="_self" title="" class="internal-link" href="resolveuid/5d3d6f3d873a42e584cbf4365c4e251b.html">the section in the general documentation</a>.</p>
+<p>PRACE users can use the same transfer mechanisms as regular users (if they've undergone the full registration procedure). For information about this, please see <a title="" class="internal-link" target="_self" href="resolveuid/5d3d6f3d873a42e584cbf4365c4e251b">the section in the general documentation</a>.</p>
<p>Apart from the standard mechanisms, for PRACE users to transfer data to/from Anselm cluster, a GridFTP server running Globus Toolkit GridFTP service is available. The service is available from public Internet as well as from the internal PRACE network (accessible only from other PRACE partners).</p>
<p>There's one control server and three backend servers for striping and/or backup in case one of them would fail.</p>
<p><strong>Access from PRACE network:</strong></p>
@@ -418,17 +415,17 @@
</tr>
</tbody>
</table>
-<p class=" ">More information about the shared file systems is available <a target="_self" title="" class="internal-link" href="storage-1/storage.html">here</a>.</p>
+<p class=" ">More information about the shared file systems is available <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/storage">here</a>.</p>
<h2 class=" ">Usage of the cluster</h2>
<p>There are some limitations for PRACE user when using the cluster. By default PRACE users aren't allowed to access special queues in the PBS Pro to have high priority or exclusive access to some special equipment like accelerated nodes and high memory (fat) nodes. There may be also restrictions obtaining a working license for the commercial software installed on the cluster, mostly because of the license agreement or because of insufficient amount of licenses.</p>
-<p>For production runs always use scratch file systems, either the global shared or the local ones. The available file systems are described <a target="_self" title="" class="internal-link" href="hardware-overview.html">here</a>.</p>
+<p>For production runs always use scratch file systems, either the global shared or the local ones. The available file systems are described <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">here</a>.</p>
<h3 class=" ">Software, Modules and PRACE Common Production Environment</h3>
-<p>All system wide installed software on the cluster is made available to the users via the modules. The information about the environment and modules usage is in this <a target="_self" title="" class="internal-link" href="environment-and-modules.html">section of general documentation</a>.</p>
+<p>All system wide installed software on the cluster is made available to the users via the modules. The information about the environment and modules usage is in this <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">section of general documentation</a>.</p>
<p>PRACE users can use the "prace" module to use the <a class="external-link" href="http://www.prace-ri.eu/PRACE-common-production" target="_self" title="">PRACE Common Production Environment</a>.</p>
<pre class=" ">$ module load prace</pre>
<p>Â </p>
<h3 class=" ">Resource Allocation and Job Execution</h3>
-<p>General information about the resource allocation, job queuing and job execution is in this <a target="_self" title="" class="internal-link" href="resource-allocation-and-job-execution/introduction.html">section of general documentation</a>.</p>
+<p>General information about the resource allocation, job queuing and job execution is in this <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction">section of general documentation</a>.</p>
<p>For PRACE users, the default production run queue is "qprace". PRACE users can also use two other queues "qexp" and "qfree".</p>
<table class="listing">
<tbody>
@@ -464,7 +461,7 @@
</table>
<p class=" "><strong>qprace</strong>, the PRACE Production queue<strong></strong>: This queue is intended for normal production runs. It is required that active project with nonzero remaining resources is specified to enter the qprace. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qprace is 12 hours. If the job needs longer time, it must use checkpoint/restart functionality.</p>
<h3 class=" ">Accounting & Quota</h3>
-<p>The resources that are currently subject to accounting are the core hours. The core hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. See <a target="_self" title="" class="internal-link" href="resource-allocation-and-job-execution/resources-allocation-policy.html">example in the general documentation</a>.</p>
+<p>The resources that are currently subject to accounting are the core hours. The core hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. See <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy">example in the general documentation</a>.</p>
<p>PRACE users should check their project accounting using the <a class="external-link" href="http://www.prace-ri.eu/accounting-report-tool/" target="_self" title="">PRACE Accounting Tool (DART)</a>.</p>
<p>Users who have undergone the full local registration procedure (including signing the IT4Innovations Acceptable Use Policy) and who have received local password may check at any time, how many core-hours have been consumed by themselves and their projects using the command "it4ifree". Please note that you need to know your user password to use the command and that the displayed core hours are "system core hours" which differ from PRACE "standardized core hours".</p>
<p class="callout">The <strong>it4ifree</strong> command is a part of it4i.portal.clients package, located here:<br /><a class="external-link" href="https://pypi.python.org/pypi/it4i.portal.clients" target="_self" title="">https://pypi.python.org/pypi/it4i.portal.clients</a></p>
@@ -550,7 +547,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -566,7 +563,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -582,7 +579,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -598,7 +595,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -614,7 +611,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -630,7 +627,7 @@
- <a title="" class="state-published contenttype-document" href="hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -646,7 +643,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -662,7 +659,7 @@
- <a title="" class="state-published contenttype-document" href="environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -678,7 +675,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -694,7 +691,7 @@
- <a title="" class="state-published contenttype-document" href="compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -710,7 +707,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -726,7 +723,7 @@
- <a title="" class="state-published contenttype-document" href="network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -742,10 +739,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -761,7 +758,7 @@
- <a title="" class="state-published contenttype-document" href="remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -777,7 +774,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="prace.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -802,7 +799,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -818,7 +815,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -834,7 +831,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -873,14 +870,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -902,12 +899,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -923,7 +920,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/prace by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:54 GMT -->
</html>
diff --git a/anselm-cluster-documentation/prace.md b/docs.it4i.cz/anselm-cluster-documentation/prace.md
similarity index 67%
rename from anselm-cluster-documentation/prace.md
rename to docs.it4i.cz/anselm-cluster-documentation/prace.md
index c512ede6dab21c39d54e059491a7b4428afd30a1..8e0d19d89e3595aceb42675ca183d571af75a7a6 100644
--- a/anselm-cluster-documentation/prace.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/prace.md
@@ -1,3 +1,6 @@
+PRACE User Support
+==================
+
Intro
-----
PRACE users coming to Anselm as to TIER-1 system offered through the
@@ -10,24 +13,25 @@ not have a password and thus access to some services intended for
regular users. This can lower their comfort, but otherwise they should
be able to use the TIER-1 system as intended. Please see the [Obtaining
Login Credentials
-section](../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html),
+section](https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials),
if the same level of access is required.
All general [PRACE User
-Documentation](http//www.prace-ri.eu/user-documentation/)
+Documentation](http://www.prace-ri.eu/user-documentation/)
should be read before continuing reading the local documentation here.
[]()Help and Support
--------------------
If you have any troubles, need information, request support or want to
install additional software, please use [PRACE
-Helpdesk](http//www.prace-ri.eu/helpdesk-guide264/).
+Helpdesk](http://www.prace-ri.eu/helpdesk-guide264/).
Information about the local services are provided in the [introduction
-of general user documentation](introduction.html).
+of general user
+documentation](https://docs.it4i.cz/anselm-cluster-documentation/introduction).
Please keep in mind, that standard PRACE accounts don't have a password
to access the web interface of the local (IT4Innovations) request
tracker and thus a new ticket should be created by sending an e-mail to
support[at]it4i.cz.
Obtaining Login Credentials
----------------------------
+----
In general PRACE users already have a PRACE account setup through their
HOMESITE (institution from their country) as a result of rewarded PRACE
project proposal. This includes signed PRACE AuP, generated and
@@ -37,7 +41,7 @@ account at IT4Innovations. To get an account on the Anselm cluster, the
user needs to obtain the login credentials. The procedure is the same as
for general users of the cluster, so please see the corresponding
[section of the general documentation
-here](../get-started-with-it4innovations/obtaining-login-credentials.html).
+here](https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials).
Accessing the cluster
---------------------
### Access with GSI-SSH
@@ -48,90 +52,90 @@ The user will need a valid certificate and to be present in the PRACE
LDAP (please contact your HOME SITE or the primary investigator of your
project for LDAP account creation).
Most of the information needed by PRACE users accessing the Anselm
-TIER-1 system can be found here
+TIER-1 system can be found here:
- [General user's
- FAQ](http//www.prace-ri.eu/Users-General-FAQs)
+ FAQ](http://www.prace-ri.eu/Users-General-FAQs)
- [Certificates
- FAQ](http//www.prace-ri.eu/Certificates-FAQ)
+ FAQ](http://www.prace-ri.eu/Certificates-FAQ)
- [Interactive access using
- GSISSH](http//www.prace-ri.eu/Interactive-Access-Using-gsissh)
+ GSISSH](http://www.prace-ri.eu/Interactive-Access-Using-gsissh)
- [Data transfer with
- GridFTP](http//www.prace-ri.eu/Data-Transfer-with-GridFTP-Details)
+ GridFTP](http://www.prace-ri.eu/Data-Transfer-with-GridFTP-Details)
- [Data transfer with
- gtransfer](http//www.prace-ri.eu/Data-Transfer-with-gtransfer)
+ gtransfer](http://www.prace-ri.eu/Data-Transfer-with-gtransfer)
Â
Before you start to use any of the services don't forget to create a
-proxy certificate from your certificate
+proxy certificate from your certificate:
$ grid-proxy-init
To check whether your proxy certificate is still valid (by default it's
-valid 12 hours), use
+valid 12 hours), use:
$ grid-proxy-info
Â
To access Anselm cluster, two login nodes running GSI SSH service are
available. The service is available from public Internet as well as from
the internal PRACE network (accessible only from other PRACE partners).
-**Access from PRACE network**
-It is recommended to use the single DNS name
-class="monospace">anselm-prace.it4i.cz which is distributed
+**Access from PRACE network:**
+It is recommended to use the single DNS name <span
+class="monospace">anselm-prace.it4i.cz</span> which is distributed
between the two login nodes. If needed, user can login directly to one
-of the login nodes. The addresses are
+of the login nodes. The addresses are:
Login address Port Protocol Login node
- ----------------------------- ------ ---------- ------------------
+ ------ ------ ---------- ------------------
anselm-prace.it4i.cz 2222 gsissh login1 or login2
login1-prace.anselm.it4i.cz 2222 gsissh login1
login2-prace.anselm.it4i.cz 2222 gsissh login2
Â
$ gsissh -p 2222 anselm-prace.it4i.cz
When logging from other PRACE system, the prace_service script can be
-used
+used:
$ gsissh `prace_service -i -s anselm`
Â
-**Access from public Internet**
-It is recommended to use the single DNS name
-class="monospace">anselm.it4i.cz which is distributed between the
+**Access from public Internet:**
+It is recommended to use the single DNS name <span
+class="monospace">anselm.it4i.cz</span> which is distributed between the
two login nodes. If needed, user can login directly to one of the login
-nodes. The addresses are
+nodes. The addresses are:
Login address Port Protocol Login node
- ----------------------- ------ ---------- ------------------
+ ------ ---------- ------------------
anselm.it4i.cz 2222 gsissh login1 or login2
login1.anselm.it4i.cz 2222 gsissh login1
login2.anselm.it4i.cz 2222 gsissh login2
$ gsissh -p 2222 anselm.it4i.cz
-When logging from other PRACE system, the
-class="monospace">prace_service script can be used
+When logging from other PRACE system, the <span
+class="monospace">prace_service</span> script can be used:
$ gsissh `prace_service -e -s anselm`
Â
Although the preferred and recommended file transfer mechanism is [using
GridFTP](#file-transfers), the GSI SSH implementation on
Anselm supports also SCP, so for small files transfer gsiscp can be
-used
- $ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ anselm.it4i.cz_ANSELM_PATH_TO_YOUR_FILE_
- $ gsiscp -P 2222 anselm.it4i.cz_ANSELM_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_
- $ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ anselm-prace.it4i.cz_ANSELM_PATH_TO_YOUR_FILE_
- $ gsiscp -P 2222 anselm-prace.it4i.cz_ANSELM_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_
+used:
+ $ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ anselm.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_
+ $ gsiscp -P 2222 anselm.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_
+ $ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ anselm-prace.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_
+ $ gsiscp -P 2222 anselm-prace.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_
### Access to X11 applications (VNC)
If the user needs to run X11 based graphical application and does not
have a X11 server, the applications can be run using VNC service. If the
user is using regular SSH based access, please see the [section in
general
-documentation](resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html).
+documentation](resolveuid/11e53ad0d2fd4c5187537f4baeedff33).
If the user uses GSI SSH based access, then the procedure is similar to
the SSH based access ([look
-here](resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html)),
-only the port forwarding must be done using GSI SSH
- $ gsissh -p 2222 anselm.it4i.cz -L 5961localhost5961
+here](resolveuid/11e53ad0d2fd4c5187537f4baeedff33)),
+only the port forwarding must be done using GSI SSH:
+ $ gsissh -p 2222 anselm.it4i.cz -L 5961:localhost:5961
### Access with SSH
After successful obtainment of login credentials for the local
IT4Innovations account, the PRACE users can access the cluster as
regular users using SSH. For more information please see the [section in
general
-documentation](resolveuid/5d3d6f3d873a42e584cbf4365c4e251b.html).
+documentation](resolveuid/5d3d6f3d873a42e584cbf4365c4e251b).
[]()File transfers
------------------
PRACE users can use the same transfer mechanisms as regular users (if
they've undergone the full registration procedure). For information
about this, please see [the section in the general
-documentation](resolveuid/5d3d6f3d873a42e584cbf4365c4e251b.html).
+documentation](resolveuid/5d3d6f3d873a42e584cbf4365c4e251b).
Apart from the standard mechanisms, for PRACE users to transfer data
to/from Anselm cluster, a GridFTP server running Globus Toolkit GridFTP
service is available. The service is available from public Internet as
@@ -139,47 +143,47 @@ well as from the internal PRACE network (accessible only from other
PRACE partners).
There's one control server and three backend servers for striping and/or
backup in case one of them would fail.
-**Access from PRACE network**
+**Access from PRACE network:**
Login address Port Node role
- ------------------------------ ------ -----------------------------
+ ------- ------ ------
gridftp-prace.anselm.it4i.cz 2812 Front end /control server
login1-prace.anselm.it4i.cz 2813 Backend / data mover server
login2-prace.anselm.it4i.cz 2813 Backend / data mover server
dm1-prace.anselm.it4i.cz 2813 Backend / data mover server
Copy files **to** Anselm by running the following commands on your local
-machine
- $ globus-url-copy file//_LOCAL_PATH_TO_YOUR_FILE_ gsiftp//gridftp-prace.anselm.it4i.cz2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_
-Or by using prace_service script
- $ globus-url-copy file//_LOCAL_PATH_TO_YOUR_FILE_ gsiftp//`prace_service -i -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_
-Copy files **from** Anselm
- $ globus-url-copy gsiftp//gridftp-prace.anselm.it4i.cz2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file//_LOCAL_PATH_TO_YOUR_FILE_
-Or by using prace_service script
- $ globus-url-copy gsiftp//`prace_service -i -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file//_LOCAL_PATH_TO_YOUR_FILE_
+machine:
+ $ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://gridftp-prace.anselm.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_
+Or by using <span class="monospace">prace_service</span> script:
+ $ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://`prace_service -i -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_
+Copy files **from** Anselm:
+ $ globus-url-copy gsiftp://gridftp-prace.anselm.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
+Or by using <span class="monospace">prace_service</span> script:
+ $ globus-url-copy gsiftp://`prace_service -i -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
Â
-**Access from public Internet**
+**Access from public Internet:**
Login address Port Node role
- ------------------------ ------ -----------------------------
+ - ------ ------
gridftp.anselm.it4i.cz 2812 Front end /control server
login1.anselm.it4i.cz 2813 Backend / data mover server
login2.anselm.it4i.cz 2813 Backend / data mover server
dm1.anselm.it4i.cz 2813 Backend / data mover server
Copy files **to** Anselm by running the following commands on your local
-machine
- $ globus-url-copy file//_LOCAL_PATH_TO_YOUR_FILE_ gsiftp//gridftp.anselm.it4i.cz2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_
-Or by using prace_service script
- $ globus-url-copy file//_LOCAL_PATH_TO_YOUR_FILE_ gsiftp//`prace_service -e -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_
-Copy files **from** Anselm
- $ globus-url-copy gsiftp//gridftp.anselm.it4i.cz2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file//_LOCAL_PATH_TO_YOUR_FILE_
-Or by using prace_service script
- $ globus-url-copy gsiftp//`prace_service -e -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file//_LOCAL_PATH_TO_YOUR_FILE_
+machine:
+ $ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://gridftp.anselm.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_
+Or by using <span class="monospace">prace_service</span> script:
+ $ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://`prace_service -e -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_
+Copy files **from** Anselm:
+ $ globus-url-copy gsiftp://gridftp.anselm.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
+Or by using <span class="monospace">prace_service</span> script:
+ $ globus-url-copy gsiftp://`prace_service -e -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
Â
-Generally both shared file systems are available through GridFTP
+Generally both shared file systems are available through GridFTP:
File system mount point Filesystem Comment
- ------------------------- ------------ ----------------------------------------------------------------
+ -- ------------ ------------------
/home Lustre Default HOME directories of users in format /home/prace/login/
/scratch Lustre Shared SCRATCH mounted on the whole cluster
More information about the shared file systems is available
-[here](storage-1/storage.html).
+[here](https://docs.it4i.cz/anselm-cluster-documentation/storage).
Usage of the cluster
--------------------
There are some limitations for PRACE user when using the cluster. By
@@ -191,24 +195,24 @@ installed on the cluster, mostly because of the license agreement or
because of insufficient amount of licenses.
For production runs always use scratch file systems, either the global
shared or the local ones. The available file systems are described
-[here](hardware-overview.html).
+[here](https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview).
### Software, Modules and PRACE Common Production Environment
All system wide installed software on the cluster is made available to
the users via the modules. The information about the environment and
modules usage is in this [section of general
-documentation](environment-and-modules.html).
+documentation](https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules).
PRACE users can use the "prace" module to use the [PRACE Common
Production
-Environment](http//www.prace-ri.eu/PRACE-common-production).
+Environment](http://www.prace-ri.eu/PRACE-common-production).
$ module load prace
Â
### Resource Allocation and Job Execution
General information about the resource allocation, job queuing and job
execution is in this [section of general
-documentation](resource-allocation-and-job-execution/introduction.html).
+documentation](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction).
For PRACE users, the default production run queue is "qprace". PRACE
users can also use two other queues "qexp" and "qfree".
- -------------------------------------------------------------------------------------------------------------------------
+ ------
queue Active project Project resources Nodes priority authorization walltime
default/max
--------------------- ---------------- ------------------- --------------------- ---------- --------------- -------------
@@ -219,8 +223,8 @@ users can also use two other queues "qexp" and "qfree".
**qfree** yes none required 178 w/o accelerator very low no 12 / 12h
Free resource queue
- -------------------------------------------------------------------------------------------------------------------------
-**qprace**, the PRACE Production queue**** This queue is intended for
+ ------
+**qprace**, the PRACE Production queue****This queue is intended for
normal production runs. It is required that active project with nonzero
remaining resources is specified to enter the qprace. The queue runs
with medium priority and no special authorization is required to use it.
@@ -233,10 +237,10 @@ accounting runs whenever the computational cores are allocated or
blocked via the PBS Pro workload manager (the qsub command), regardless
of whether the cores are actually used for any calculation. See [example
in the general
-documentation](resource-allocation-and-job-execution/resources-allocation-policy.html).
+documentation](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy).
PRACE users should check their project accounting using the [PRACE
Accounting Tool
-(DART)](http//www.prace-ri.eu/accounting-report-tool/).
+(DART)](http://www.prace-ri.eu/accounting-report-tool/).
Users who have undergone the full local registration procedure
(including signing the IT4Innovations Acceptable Use Policy) and who
have received local password may check at any time, how many core-hours
@@ -245,9 +249,10 @@ have been consumed by themselves and their projects using the command
the command and that the displayed core hours are "system core hours"
which differ from PRACE "standardized core hours".
The **it4ifree** command is a part of it4i.portal.clients package,
-located here
+located here:
+<https://pypi.python.org/pypi/it4i.portal.clients>
$ it4ifree
- Password
+ Password:
    PID  Total Used ...by me Free
  -------- ------- ------ -------- -------
  OPEN-0-0 1500000 400644  225265 1099356
@@ -261,17 +266,3 @@ If the quota is insufficient, please contact the
[support](#help-and-support) and request an increase.
Â
Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
diff --git a/anselm-cluster-documentation/quality-1.png b/docs.it4i.cz/anselm-cluster-documentation/quality1.png
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/quality-1.png
rename to docs.it4i.cz/anselm-cluster-documentation/quality1.png
diff --git a/anselm-cluster-documentation/quality-2.png b/docs.it4i.cz/anselm-cluster-documentation/quality2.png
old mode 100755
new mode 100644
similarity index 100%
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old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/quality-3.png
rename to docs.it4i.cz/anselm-cluster-documentation/quality3.png
diff --git a/anselm-cluster-documentation/remote-visualization.html b/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.html
old mode 100755
new mode 100644
similarity index 75%
rename from anselm-cluster-documentation/remote-visualization.html
rename to docs.it4i.cz/anselm-cluster-documentation/remote-visualization.html
index b855cc9616959b9a2a98d417cb5847e534ade268..8e2dd7f0fc6f90bce0e9d62910da1f8f3a06a99e
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization" /><!--[if lt IE 7]></base><![endif]-->
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Remote visualization service — IT4I Docs</title>
- <link rel="canonical" href="remote-visualization.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="remote-visualization.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="remote-visualization.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -232,7 +229,7 @@
<p>Currently two compute nodes are dedicated for this service with following configuration for each node:</p>
<table class="listing">
<tbody>
-<tr class="odd"><th colspan="2"><a target="_self" title="" class="internal-link" href="compute-nodes.html"><strong>Visualization node configuration</strong></a></th></tr>
+<tr class="odd"><th colspan="2"><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes"><strong>Visualization node configuration</strong></a></th></tr>
<tr class="even">
<td>CPU</td>
<td>2x Intel Sandy Bridge E5-2670, 2.6GHz</td>
@@ -260,15 +257,15 @@
</tbody>
</table>
<h2>Schematic overview</h2>
-<p><img title="rem_vis_scheme" class="image-inline" alt="rem_vis_scheme" src="scheme.png" /></p>
-<p><img title="rem_vis_legend" class="image-inline" alt="rem_vis_legend" src="legend.png" /></p>
+<p><img alt="rem_vis_scheme" class="image-inline" title="rem_vis_scheme" src="https://docs.it4i.cz/anselm-cluster-documentation/scheme.png" /></p>
+<p><img alt="rem_vis_legend" class="image-inline" title="rem_vis_legend" src="https://docs.it4i.cz/anselm-cluster-documentation/legend.png" /></p>
<h2 class=" " id="setup-and-start-your-own-turbovnc-server">How to use the service</h2>
<h3>Setup and start your own TurboVNC server.</h3>
<p>TurboVNC is designed and implemented for cooperation with VirtualGL and available for free for all major platforms. For more information and download, please refer to: <a href="http://sourceforge.net/projects/turbovnc/">http://sourceforge.net/projects/turbovnc/</a></p>
<p><strong>Always use TurboVNC on both sides</strong> (server and client) <strong>don't mix TurboVNC and other VNC implementations</strong> (TightVNC, TigerVNC, ...) as the VNC protocol implementation may slightly differ and diminish your user experience by introducing picture artifacts, etc.</p>
<p>The procedure is:</p>
<h4 id="1-connect-to-a-login-node">1. Connect to a login node.</h4>
-<p>Please <a target="_self" title="" class="internal-link" href="resolveuid/5d3d6f3d873a42e584cbf4365c4e251b.html">follow the documentation</a>.</p>
+<p>Please <a title="" class="internal-link" target="_self" href="resolveuid/5d3d6f3d873a42e584cbf4365c4e251b">follow the documentation</a>.</p>
<h4 id="2-run-your-own-instance-of-turbovnc-server">2. Run your own instance of TurboVNC server.</h4>
<p>To have the OpenGL acceleration, <strong>24 bit color depth must be used</strong>. Otherwise only the geometry (desktop size) definition is needed.</p>
<p><em>At first VNC server run you need to define a password.</em></p>
@@ -287,7 +284,7 @@
<h4 id="6-connect-to-the-login-node-where-your-vnc-server-runs-with-ssh-to-tunnel-your-vnc-session">6. Connect to the login node where your VNC server runs with SSH to tunnel your VNC session.</h4>
<p>Tunnel the TCP port on which your VNC server is listenning.</p>
<pre class="code highlight white shell"><code>$ ssh login2.anselm.it4i.cz -L 5901:localhost:5901 </code></pre>
-<p><em>If you use Windows and Putty, please refer to port forwarding setup <span class="internal-link">in the documentation</span>:</em> <a href="../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html#section-12">https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc#section-12</a></p>
+<p><em>If you use Windows and Putty, please refer to port forwarding setup <span class="internal-link">in the documentation</span>:</em> <a href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc#section-12">https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc#section-12</a></p>
<h4 id="7-if-you-don-t-have-turbo-vnc-installed-on-your-workstation">7. If you don't have Turbo VNC installed on your workstation.</h4>
<p>Get it from: <a href="http://sourceforge.net/projects/turbovnc/">http://sourceforge.net/projects/turbovnc/</a></p>
<h4 id="8-run-turbovnc-viewer-from-your-workstation">8. Run TurboVNC Viewer from your workstation.</h4>
@@ -344,14 +341,14 @@
<p>Just logout from the visualization node and exit both opened terminals and end your VNC server session as described above.</p>
<h2 class=" ">Tips and Tricks</h2>
<p>If you want to increase the responsibility of the visualization, please adjust your TurboVNC client settings in this way:</p>
-<p><img title="rem_vis_settings" class="image-inline" alt="rem_vis_settings" src="turbovnc-client-setting.png" /></p>
+<p><img alt="rem_vis_settings" class="image-inline" title="rem_vis_settings" src="https://docs.it4i.cz/anselm-cluster-documentation/turbovncclientsetting.png" /></p>
<p>To have an idea how the settings are affecting the resulting picture quality three levels of "JPEG image quality" are demonstrated:</p>
<p>1. JPEG image quality = 30</p>
-<p><img title="rem_vis_q3" class="image-inline" alt="rem_vis_q3" src="quality-3.png" /></p>
+<p><img alt="rem_vis_q3" class="image-inline" title="rem_vis_q3" src="https://docs.it4i.cz/anselm-cluster-documentation/quality3.png" /></p>
<p>2. JPEG image quality = 15</p>
-<p><img title="rem_vis_q2" class="image-inline" alt="rem_vis_q2" src="quality-2.png" /></p>
+<p><img alt="rem_vis_q2" class="image-inline" title="rem_vis_q2" src="https://docs.it4i.cz/anselm-cluster-documentation/quality2.png" /></p>
<p>3. JPEG image quality = 10</p>
-<p><img title="rem_vis_q1" class="image-inline" alt="rem_vis_q1" src="quality-1.png" /></p>
+<p><img alt="rem_vis_q1" class="image-inline" title="rem_vis_q1" src="https://docs.it4i.cz/anselm-cluster-documentation/quality1.png" /></p>
<p><br /><br /></p>
</div>
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<dt class="portletHeader hiddenStructure">
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- <a href="../sitemap.html" class="tile">Navigace</a>
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<span>What's New</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -476,7 +473,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -492,7 +489,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -508,7 +505,7 @@
- <a title="" class="state-published contenttype-document" href="hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -524,7 +521,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -540,7 +537,7 @@
- <a title="" class="state-published contenttype-document" href="environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -556,7 +553,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -572,7 +569,7 @@
- <a title="" class="state-published contenttype-document" href="compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -588,7 +585,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -604,7 +601,7 @@
- <a title="" class="state-published contenttype-document" href="network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -620,10 +617,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -639,7 +636,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="remote-visualization.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -655,7 +652,7 @@
- <a title="" class="state-published contenttype-document" href="prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -680,7 +677,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -696,7 +693,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -712,7 +709,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -751,14 +748,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -780,12 +777,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -801,7 +798,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/remote-visualization by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:52 GMT -->
</html>
diff --git a/anselm-cluster-documentation/remote-visualization.md b/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md
similarity index 71%
rename from anselm-cluster-documentation/remote-visualization.md
rename to docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md
index 0d73d3123e42437e964ee57f0b94dd42bc54f4c0..f001452634262bd0c4404b4055a0616ea5463b64 100644
--- a/anselm-cluster-documentation/remote-visualization.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md
@@ -1,3 +1,6 @@
+Remote visualization service
+============================
+Introduction {#schematic-overview}
------------
The goal of this service is to provide the users a GPU accelerated use
of OpenGL applications, especially for pre- and post- processing work,
@@ -6,9 +9,9 @@ shared file systems of the cluster and a reasonable amount of RAM.
The service is based on integration of open source tools VirtualGL and
TurboVNC together with the cluster's job scheduler PBS Professional.
Currently two compute nodes are dedicated for this service with
-following configuration for each node
+following configuration for each node:
[**Visualization node
-configuration**](compute-nodes.html)
+configuration**](https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes)
CPU
2x Intel Sandy Bridge E5-2670, 2.6GHz
Processor cores
@@ -23,22 +26,22 @@ Compute network
InfiniBand QDR
Schematic overview
------------------
-
-
+
+
How to use the service {#setup-and-start-your-own-turbovnc-server}
----------------------
### Setup and start your own TurboVNC server.
TurboVNC is designed and implemented for cooperation with VirtualGL and
available for free for all major platforms. For more information and
-download, please refer to
+download, please refer to<http://sourceforge.net/projects/turbovnc/>
**Always use TurboVNC on both sides** (server and client) **don't mix
TurboVNC and other VNC implementations** (TightVNC, TigerVNC, ...) as
the VNC protocol implementation may slightly differ and diminish your
user experience by introducing picture artifacts, etc.
-The procedure is
+The procedure is:
#### 1. Connect to a login node. {#1-connect-to-a-login-node}
Please [follow the
-documentation](resolveuid/5d3d6f3d873a42e584cbf4365c4e251b.html).
+documentation](resolveuid/5d3d6f3d873a42e584cbf4365c4e251b).
#### 2. Run your own instance of TurboVNC server. {#2-run-your-own-instance-of-turbovnc-server}
To have the OpenGL acceleration, **24 bit color depth must be used**.
Otherwise only the geometry (desktop size) definition is needed.
@@ -48,18 +51,18 @@ color depth.
``` {.code .highlight .white .shell}
$ module load turbovnc/1.2.2
$ vncserver -geometry 1200x700 -depth 24
-Desktop 'TurboVNC login21 (username)' started on display login21
+Desktop 'TurboVNClogin2:1 (username)' started on display login2:1
Starting applications specified in /home/username/.vnc/xstartup.turbovnc
-Log file is /home/username/.vnc/login21.log
+Log file is /home/username/.vnc/login2:1.log
```
#### 3. Remember which display number your VNC server runs (you will need it in the future to stop the server). {#3-remember-which-display-number-your-vnc-server-runs-you-will-need-it-in-the-future-to-stop-the-server}
``` {.code .highlight .white .shell}
$ vncserver -list
-TurboVNC server sessions
+TurboVNC server sessions
X DISPLAY # PROCESS ID
-1 23269
+:1 23269
```
-In this example the VNC server runs on display **1**.
+In this example the VNC server runs on display **:1**.
#### 4. Remember the exact login node, where your VNC server runs. {#4-remember-the-exact-login-node-where-your-vnc-server-runs}
``` {.code .highlight .white .shell}
$ uname -n
@@ -69,28 +72,28 @@ In this example the VNC server runs on **login2**.
#### 5. Remember on which TCP port your own VNC server is running. {#5-remember-on-which-tcp-port-your-own-vnc-server-is-running}
To get the port you have to look to the log file of your VNC server.
``` {.code .highlight .white .shell}
-$ grep -E "VNC.*port" /home/username/.vnc/login21.log
-20/02/2015 144641 Listening for VNC connections on TCP port 5901
+$ grep -E "VNC.*port" /home/username/.vnc/login2:1.log
+20/02/2015 14:46:41 Listening for VNC connections on TCP port 5901
```
In this example the VNC server listens on TCP port **5901**.
#### 6. Connect to the login node where your VNC server runs with SSH to tunnel your VNC session. {#6-connect-to-the-login-node-where-your-vnc-server-runs-with-ssh-to-tunnel-your-vnc-session}
Tunnel the TCP port on which your VNC server is listenning.
``` {.code .highlight .white .shell}
-$ ssh login2.anselm.it4i.cz -L 5901localhost5901
+$ ssh login2.anselm.it4i.cz -L 5901:localhost:5901
```
*If you use Windows and Putty, please refer to port forwarding setup
-in the documentation*
-[https//docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc#section-12](../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html#section-12)
+<span class="internal-link">in the documentation</span>:*
+<https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc#section-12>
#### 7. If you don't have Turbo VNC installed on your workstation. {#7-if-you-don-t-have-turbo-vnc-installed-on-your-workstation}
-Get it from
+Get it from<http://sourceforge.net/projects/turbovnc/>
#### 8. Run TurboVNC Viewer from your workstation. {#8-run-turbovnc-viewer-from-your-workstation}
Mind that you should connect through the SSH tunneled port. In this
example it is 5901 on your workstation (localhost).
``` {.code .highlight .white .shell}
-$ vncviewer localhost5901
+$ vncviewer localhost:5901
```
*If you use Windows version of TurboVNC Viewer, just run the Viewer and
-use address **localhost5901**.*
+use address **localhost:5901**.*
#### 9. Proceed to the chapter "Access the visualization node." {#9-proceed-to-the-chapter-access-the-visualization-node}
*Now you should have working TurboVNC session connected to your
workstation.*
@@ -98,29 +101,49 @@ workstation.*
*Don't forget to correctly shutdown your own VNC server on the login
node!*
``` {.code .highlight .white .shell}
-$ vncserver -kill 1
+$ vncserver -kill :1
```
Access the visualization node
------------------------------
+------
To access the node use a dedicated PBS Professional scheduler queue
-**qviz**. The queue has following properties
-queue
-active project
-project resources
-nodes
-min ncpus*
-priority
-authorization
-walltime
-default/max
-qviz              Visualization queue
-yes
-none required
-2
-4
-150
-no
-1 hour / 2 hours
+**qviz**. The queue has following properties:
+<table>
+<colgroup>
+<col width="12%" />
+<col width="12%" />
+<col width="12%" />
+<col width="12%" />
+<col width="12%" />
+<col width="12%" />
+<col width="12%" />
+<col width="12%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">queue</th>
+<th align="left">active project</th>
+<th align="left">project resources</th>
+<th align="left">nodes</th>
+<th align="left">min ncpus*</th>
+<th align="left">priority</th>
+<th align="left">authorization</th>
+<th align="left">walltime<br />
+default/max</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><p><strong>qviz              </strong> Visualization queue</p></td>
+<td align="left">yes</td>
+<td align="left">none required</td>
+<td align="left">2</td>
+<td align="left">4</td>
+<td align="left"><span><em>150</em></span></td>
+<td align="left">no</td>
+<td align="left">1 hour / 2 hours</td>
+</tr>
+</tbody>
+</table>
Currently when accessing the node, each user gets 4 cores of a CPU
allocated, thus approximately 16 GB of RAM and 1/4 of the GPU capacity.
*If more GPU power or RAM is required, it is recommended to allocate one
@@ -128,7 +151,7 @@ whole node per user, so that all 16 cores, whole RAM and whole GPU is
exclusive. This is currently also the maximum allowed allocation per one
user. One hour of work is allocated by default, the user may ask for 2
hours maximum.*
-To access the visualization node, follow these steps
+To access the visualization node, follow these steps:
#### 1. In your VNC session, open a terminal and allocate a node using PBSPro qsub command. {#1-in-your-vnc-session-open-a-terminal-and-allocate-a-node-using-pbspro-qsub-command}
*This step is necessary to allow you to proceed with next steps.*
``` {.code .highlight .white .shell}
@@ -137,7 +160,7 @@ $ qsub -I -q qviz -A PROJECT_ID
In this example the default values for CPU cores and usage time are
used.
``` {.code .highlight .white .shell}
-$ qsub -I -q qviz -A PROJECT_ID -l select=1ncpus=16 -l walltime=020000
+$ qsub -I -q qviz -A PROJECT_ID -l select=1:ncpus=16 -l walltime=02:00:00
```
*Substitute **PROJECT_ID** with the assigned project identification
string.*
@@ -168,7 +191,7 @@ $ vglrun glxgears
Please note, that if you want to run an OpenGL application which is
available through modules, you need at first load the respective module.
E. g. to run the **Mentat** OpenGL application from **MARC** software
-package use
+package use:
``` {.code .highlight .white .shell}
$ module load marc/2013.1
$ vglrun mentat
@@ -179,29 +202,13 @@ and end your VNC server session as described above.
Tips and Tricks
---------------
If you want to increase the responsibility of the visualization, please
-adjust your TurboVNC client settings in this way
-
+adjust your TurboVNC client settings in this way:
+
To have an idea how the settings are affecting the resulting picture
-quality three levels of "JPEG image quality" are demonstrated
+quality three levels of "JPEG image quality" are demonstrated:
1. JPEG image quality = 30
-
+
2. JPEG image quality = 15
-
+
3. JPEG image quality = 10
-
-
-
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
+
diff --git a/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.html b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution.html
old mode 100755
new mode 100644
similarity index 63%
rename from anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.html
rename to docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution.html
index 8e50984175a176086c956fc2194e4ec582ec638a..ab1fa6392df77de00881290a5c8ebe27e2de97e5
--- a/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:03 GMT -->
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- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Resource Allocation and Job Execution — IT4I Docs</title>
- <link rel="canonical" href="../resource-allocation-and-job-execution.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="introduction.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="introduction.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -230,9 +227,9 @@
<div id="parent-fieldname-text-85dbd3a3056441709e60b0b74d70f00b" class="">
- <p>To run a <a target="_self" title="" class="internal-link" href="../introduction.html">job</a>, <a target="_self" title="" class="internal-link" href="../introduction.html">computational resources</a> for this particular job must be allocated. This is done via the PBS Pro job workload manager software, which efficiently distributes workloads across the supercomputer. Extensive informations about PBS Pro can be found in the <a target="_self" title="" class="internal-link" href="../../pbspro-documentation.html">official documentation here</a>, especially in the <a target="_self" title="" class="internal-link" href="../../pbspro-documentation/PBSProUserGuide12.pdf">PBS Pro User's Guide</a>.</p>
+ <p>To run a <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/introduction">job</a>, <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/introduction">computational resources</a> for this particular job must be allocated. This is done via the PBS Pro job workload manager software, which efficiently distributes workloads across the supercomputer. Extensive informations about PBS Pro can be found in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/pbspro-documentation">official documentation here</a>, especially in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/pbspro-documentation/pbspro-users-guide">PBS Pro User's Guide</a>.</p>
<h2 class=" ">Resources Allocation Policy</h2>
-<p>The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. <a target="_self" title="" class="internal-link" href="job-priority.html">The Fairshare</a> at Anselm ensures that individual users may consume approximately equal amount of resources per week. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following queues are available to Anselm users:</p>
+<p>The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority">The Fairshare</a> at Anselm ensures that individual users may consume approximately equal amount of resources per week. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following queues are available to Anselm users:</p>
<ul>
<li><strong>qexp</strong>, the Express queue</li>
<li><strong>qprod</strong>, the Production queue<strong></strong></li>
@@ -241,15 +238,15 @@
<li><strong>qfree, </strong>the Free resource utilization queue</li>
</ul>
<p class="callout">Check the queue status at <a class="external-link" href="https://extranet.it4i.cz/anselm/" target="_self" title="">https://extranet.it4i.cz/anselm/</a></p>
-<p>Read more on the <a target="_self" title="" class="internal-link" href="resources-allocation-policy.html">Resource Allocation Policy</a> page.</p>
+<p>Read more on the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy">Resource Allocation Policy</a> page.</p>
<h2 class=" ">Job submission and execution</h2>
<p class="callout">Use the <strong>qsub</strong> command to submit your jobs.</p>
<p class=" ">The qsub submits the job into the queue. The qsub command creates a request to the PBS Job manager for allocation of specified resources. The <strong>smallest allocation unit is entire node, 16 cores</strong>, with exception of the qexp queue. The resources will be allocated when available, subject to allocation policies and constraints. <strong>After the resources are allocated the jobscript or interactive shell is executed on first of the allocated nodes.</strong></p>
-<p class=" ">Read more on the <a target="_self" title="" class="internal-link" href="job-submission-and-execution.html">Job submission and execution</a> page.</p>
+<p class=" ">Read more on the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">Job submission and execution</a> page.</p>
<h2 class=" ">Capacity computing</h2>
<p class="callout">Use Job arrays when running huge number of jobs.<br />Use GNU Parallel and/or Job arrays when running (many) single core jobs.</p>
<p>In many cases, it is useful to submit huge (<span>100+</span>) number of computational jobs into the PBS queue system. Huge number of (small) jobs is one of the most effective ways to execute embarrassingly parallel calculations, achieving best runtime, throughput and computer utilization. In this chapter, we discuss the the recommended way to run huge number of jobs, including <strong>ways to run huge number of single core jobs</strong>.</p>
-<p>Read more on <a target="_self" title="" class="internal-link" href="capacity-computing.html">Capacity computing</a> page.</p>
+<p>Read more on <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing">Capacity computing</a> page.</p>
</div>
@@ -325,7 +322,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -341,7 +338,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -357,7 +354,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -373,7 +370,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -389,7 +386,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -405,7 +402,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -421,7 +418,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -437,7 +434,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -453,7 +450,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -469,7 +466,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy">
<span>Resources Allocation Policy</span>
</a>
@@ -485,7 +482,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">
<span>Job submission and execution</span>
</a>
@@ -501,7 +498,7 @@
- <a title="" class="state-published contenttype-document" href="job-priority.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority">
<span>Job scheduling</span>
</a>
@@ -517,7 +514,7 @@
- <a title="" class="state-published contenttype-document" href="capacity-computing.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing">
<span>Capacity computing</span>
</a>
@@ -542,7 +539,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -574,7 +571,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
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- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -609,7 +606,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -650,7 +647,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
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+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
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- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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_paq.push(['setTrackerUrl', u+'piwik.php']);
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var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</div>
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution.md b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution.md
new file mode 100644
index 0000000000000000000000000000000000000000..c0a7da2ce7d24a1e84a791be4fcaf30966945bd2
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution.md
@@ -0,0 +1,61 @@
+Resource Allocation and Job Execution
+=====================================
+
+To run a
+[job](https://docs.it4i.cz/anselm-cluster-documentation/introduction),
+[computational
+resources](https://docs.it4i.cz/anselm-cluster-documentation/introduction)
+for this particular job must be allocated. This is done via the PBS Pro
+job workload manager software, which efficiently distributes workloads
+across the supercomputer. Extensive informations about PBS Pro can be
+found in the [official documentation
+here](https://docs.it4i.cz/pbspro-documentation),
+especially in the [PBS Pro User's
+Guide](https://docs.it4i.cz/pbspro-documentation/pbspro-users-guide).
+Resources Allocation Policy
+----
+The resources are allocated to the job in a fairshare fashion, subject
+to constraints set by the queue and resources available to the Project.
+[The
+Fairshare](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority)
+at Anselm ensures that individual users may consume approximately equal
+amount of resources per week. The resources are accessible via several
+queues for queueing the jobs. The queues provide prioritized and
+exclusive access to the computational resources. Following queues are
+available to Anselm users:
+- **qexp**, the Express queue
+- **qprod**, the Production queue****
+- **qlong**, the Long queue, regula
+- **qnvidia, qmic, qfat**, the Dedicated queues
+- **qfree,** the Free resource utilization queue
+Check the queue status at <https://extranet.it4i.cz/anselm/>
+Read more on the [Resource Allocation
+Policy](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy)
+page.
+Job submission and execution
+-----
+Use the **qsub** command to submit your jobs.
+The qsub submits the job into the queue. The qsub command creates a
+request to the PBS Job manager for allocation of specified resources.Â
+The **smallest allocation unit is entire node, 16 cores**, with
+exception of the qexp queue. The resources will be allocated when
+available, subject to allocation policies and constraints. **After the
+resources are allocated the jobscript or interactive shell is executed
+on first of the allocated nodes.**
+Read more on the [Job submission and
+execution](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution)
+page.
+Capacity computing
+------------------
+Use Job arrays when running huge number of jobs.
+Use GNU Parallel and/or Job arrays when running (many) single core jobs.
+In many cases, it is useful to submit huge (<span>100+</span>) number of
+computational jobs into the PBS queue system. Huge number of (small)
+jobs is one of the most effective ways to execute embarrassingly
+parallel calculations, achieving best runtime, throughput and computer
+utilization. In this chapter, we discuss the the recommended way to run
+huge number of jobs, including **ways to run huge number of single core
+jobs**.
+Read more on [Capacity
+computing](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing)
+page.
diff --git a/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity.zip b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing-examples
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/resource-allocation-and-job-execution/capacity.zip
rename to docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing-examples
diff --git a/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.html b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.html
old mode 100755
new mode 100644
similarity index 79%
rename from anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.html
rename to docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.html
index 4eced333134e5485d7533edb1009138fc25e3623..c443de93d313198eb2f874d7e521db0c77bcb029
--- a/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing" /><!--[if lt IE 7]></base><![endif]-->
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- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
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<title>Capacity computing — IT4I Docs</title>
- <link rel="canonical" href="capacity-computing.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="capacity-computing.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="capacity-computing.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
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- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../resource-allocation-and-job-execution.html">Resource Allocation and Job Execution</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">Resource Allocation and Job Execution</a>
<span class="breadcrumbSeparator">
/
@@ -293,7 +290,7 @@
<pre class="prettyprint lang-sh">$ qstat -u $USER -t</pre>
<p>Display status information for all user's subjobs.</p>
<pre class="prettyprint lang-sh">$ qstat -u $USER -tJ</pre>
-<p>Read more on job arrays in the <a target="_self" title="" class="internal-link" href="../../pbspro-documentation.html">PBSPro Users guide</a>.</p>
+<p>Read more on job arrays in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/pbspro-documentation">PBSPro Users guide</a>.</p>
<h2 class=" "><a name="gnu-parallel"></a>GNU parallel</h2>
<p class="callout">Use GNU parallel to run many single core tasks on one node.</p>
<p class=" ">GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input. GNU parallel is most useful in running single core jobs via the queue system on Anselm.</p>
@@ -341,7 +338,7 @@
<p>In this example, we submit a job array of 31 subjobs. Note the -J 1-992:<strong>32</strong>, this must be the same as the number sent to numtasks file. Each subjob will run on full node and process 16 input files in parallel, 32 in total per subjob. Every subjob is assumed to complete in less than 2 hours.</p>
<p>Please note the #PBS directives in the beginning of the jobscript file, dont' forget to set your valid PROJECT_ID and desired queue.</p>
<h2 class=" ">Examples</h2>
-<p>Download the examples in <a target="_self" title="" class="internal-link" href="capacity.zip">capacity.zip</a>, illustrating the above listed ways to run huge number of jobs. We recommend to try out the examples, before using this for running production jobs.</p>
+<p>Download the examples in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing-examples">capacity.zip</a>, illustrating the above listed ways to run huge number of jobs. We recommend to try out the examples, before using this for running production jobs.</p>
<p>Unzip the archive in an empty directory on Anselm and follow the instructions in the README file</p>
<pre class="prettyprint lang-sh">$ unzip capacity.zip<br />$ cat README</pre>
<p>Â </p>
@@ -420,7 +417,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
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@@ -436,7 +433,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -452,7 +449,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -468,7 +465,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -484,7 +481,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -500,7 +497,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -516,7 +513,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -532,7 +529,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -548,7 +545,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -564,7 +561,7 @@
- <a title="" class="state-published contenttype-document" href="resources-allocation-policy.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy">
<span>Resources Allocation Policy</span>
</a>
@@ -580,7 +577,7 @@
- <a title="" class="state-published contenttype-document" href="job-submission-and-execution.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">
<span>Job submission and execution</span>
</a>
@@ -596,7 +593,7 @@
- <a title="" class="state-published contenttype-document" href="job-priority.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority">
<span>Job scheduling</span>
</a>
@@ -612,7 +609,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="capacity-computing.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing">
<span>Capacity computing</span>
</a>
@@ -637,7 +634,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -653,7 +650,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -669,7 +666,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -685,10 +682,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -704,7 +701,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -720,7 +717,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -745,7 +742,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -761,7 +758,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -777,7 +774,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -816,14 +813,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -845,12 +842,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -866,7 +863,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:39 GMT -->
</html>
diff --git a/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md
similarity index 86%
rename from anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md
rename to docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md
index 28cb59e2827a833f4894ff424529fd2a4209a3a2..c26533581b5d3f9a1b1c44a851860f2642874dcd 100644
--- a/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md
@@ -1,9 +1,9 @@
+Capacity computing
==================
-
-
+
Introduction
------------
-In many cases, it is useful to submit huge (100+) number of
+In many cases, it is useful to submit huge (<span>100+</span>) number of
computational jobs into the PBS queue system. Huge number of (small)
jobs is one of the most effective ways to execute embarrassingly
parallel calculations, achieving best runtime, throughput and computer
@@ -14,7 +14,7 @@ scheduling and overall degradation of performance and user experience,
for all users. For this reason, the number of jobs is **limited to 100
per user, 1000 per job array**
Please follow one of the procedures below, in case you wish to schedule
-more than 100 jobs at a time.
+more than <span>100</span> jobs at a time.
- Use [Job arrays](#job-arrays) when running huge number
of [multithread](#shared-jobscript-on-one-node) (bound
to one node only) or multinode (multithread across several nodes)
@@ -34,7 +34,7 @@ Policy
Huge number of jobs may be easily submitted and managed as a job array.
A job array is a compact representation of many jobs, called subjobs.
The subjobs share the same job script, and have the same values for all
-attributes and resources, with the following exceptions
+attributes and resources, with the following exceptions:
- each subjob has a unique index, $PBS_ARRAY_INDEX
- job Identifiers of subjobs only differ by their indices
- the state of subjobs can differ (R,Q,...etc.)
@@ -46,21 +46,21 @@ managed by qdel, qalter, qhold, qrls and qsig commands as a single job.
All subjobs in job array use the very same, single jobscript. Each
subjob runs its own instance of the jobscript. The instances execute
different work controlled by $PBS_ARRAY_INDEX variable.
-[]()Example
+[]()Example:
Assume we have 900 input files with name beginning with "file" (e. g.
file001, ..., file900). Assume we would like to use each of these input
files with program executable myprog.x, each as a separate job.
First, we create a tasklist file (or subjobs list), listing all tasks
-(subjobs) - all input files in our example
+(subjobs) - all input files in our example:
``` {.prettyprint .lang-sh}
$ find . -name 'file*' > tasklist
```
-Then we create jobscript
+Then we create jobscript:
``` {.prettyprint .lang-sh}
#!/bin/bash
#PBS -A PROJECT_ID
#PBS -q qprod
-#PBS -l select=1ncpus=16,walltime=020000
+#PBS -l select=1:ncpus=16,walltime=02:00:00
# change to local scratch directory
SCR=/lscratch/$PBS_JOBID
mkdir -p $SCR ; cd $SCR || exit
@@ -69,7 +69,7 @@ TASK=$(sed -n "${PBS_ARRAY_INDEX}p" $PBS_O_WORKDIR/tasklist)
# copy input file and executable to scratch
cp $PBS_O_WORKDIR/$TASK input ; cp $PBS_O_WORKDIR/myprog.x .
# execute the calculation
-./myprog.x output
+./myprog.x < input > output
# copy output file to submit directory
cp output $PBS_O_WORKDIR/$TASK.out
```
@@ -77,7 +77,7 @@ In this example, the submit directory holds the 900 input files,
executable myprog.x and the jobscript file. As input for each run, we
take the filename of input file from created tasklist file. We copy the
input file to local scratch /lscratch/$PBS_JOBID, execute the myprog.x
-and copy the output file back to the submit directory,
+and copy the output file back to <span>the submit directory</span>,
under the $TASK.out name. The myprog.x runs on one node only and must
use threads to run in parallel. Be aware, that if the myprog.x **is not
multithreaded**, then all the **jobs are run as single thread programs
@@ -93,7 +93,7 @@ run has to be used properly.
### Submit the job array
To submit the job array, use the qsub -J command. The 900 jobs of the
[example above](#array_example) may be submitted like
-this
+this:
``` {.prettyprint .lang-sh}
$ qsub -N JOBNAME -J 1-900 jobscript
12345[].dm2
@@ -103,9 +103,9 @@ run on full node and is assumed to take less than 2 hours (please note
the #PBS directives in the beginning of the jobscript file, dont'
forget to set your valid PROJECT_ID and desired queue).
Sometimes for testing purposes, you may need to submit only one-element
-array. This is not allowed by PBSPro, but there's a workaround
+array. This is not allowed by PBSPro, but there's a workaround:
``` {.prettyprint .lang-sh}
-$ qsub -N JOBNAME -J 9-102 jobscript
+$ qsub -N JOBNAME -J 9-10:2 jobscript
```
This will only choose the lower index (9 in this example) for
submitting/running your job.
@@ -113,27 +113,27 @@ submitting/running your job.
Check status of the job array by the qstat command.
``` {.prettyprint .lang-sh}
$ qstat -a 12345[].dm2
-dm2
+dm2:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
-12345[].dm2 user2 qprod xx 13516 1 16 -- 0050 B 0002
+12345[].dm2 user2 qprod xx 13516 1 16 -- 00:50 B 00:02
```
The status B means that some subjobs are already running.
Check status of the first 100 subjobs by the qstat command.
``` {.prettyprint .lang-sh}
$ qstat -a 12345[1-100].dm2
-dm2
+dm2:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
-12345[1].dm2 user2 qprod xx 13516 1 16 -- 0050 R 0002
-12345[2].dm2 user2 qprod xx 13516 1 16 -- 0050 R 0002
-12345[3].dm2 user2 qprod xx 13516 1 16 -- 0050 R 0001
-12345[4].dm2 user2 qprod xx 13516 1 16 -- 0050 Q --
+12345[1].dm2 user2 qprod xx 13516 1 16 -- 00:50 R 00:02
+12345[2].dm2 user2 qprod xx 13516 1 16 -- 00:50 R 00:02
+12345[3].dm2 user2 qprod xx 13516 1 16 -- 00:50 R 00:01
+12345[4].dm2 user2 qprod xx 13516 1 16 -- 00:50 Q --
. . . . . . . . . . .
, . . . . . . . . . .
-12345[100].dm2 user2 qprod xx 13516 1 16 -- 0050 Q --
+12345[100].dm2 user2 qprod xx 13516 1 16 -- 00:50 Q --
```
Delete the entire job array. Running subjobs will be killed, queueing
subjobs will be deleted.
@@ -150,7 +150,7 @@ Display status information for all user's subjobs.
$ qstat -u $USER -tJ
```
Read more on job arrays in the [PBSPro Users
-guide](../../pbspro-documentation.html).
+guide](https://docs.it4i.cz/pbspro-documentation).
[]()GNU parallel
----------------
Use GNU parallel to run many single core tasks on one node.
@@ -158,7 +158,7 @@ GNU parallel is a shell tool for executing jobs in parallel using one or
more computers. A job can be a single command or a small script that has
to be run for each of the lines in the input. GNU parallel is most
useful in running single core jobs via the queue system on Anselm.
-For more information and examples see the parallel man page
+For more information and examples see the parallel man page:
``` {.prettyprint .lang-sh}
$ module add parallel
$ man parallel
@@ -167,22 +167,22 @@ $ man parallel
The GNU parallel shell executes multiple instances of the jobscript
using all cores on the node. The instances execute different work,
controlled by the $PARALLEL_SEQ variable.
-[]()Example
+[]()Example:
Assume we have 101 input files with name beginning with "file" (e. g.
file001, ..., file101). Assume we would like to use each of these input
files with program executable myprog.x, each as a separate single core
job. We call these single core jobs tasks.
First, we create a tasklist file, listing all tasks - all input files in
-our example
+our example:
``` {.prettyprint .lang-sh}
$ find . -name 'file*' > tasklist
```
-Then we create jobscript
+Then we create jobscript:
``` {.prettyprint .lang-sh}
#!/bin/bash
#PBS -A PROJECT_ID
#PBS -q qprod
-#PBS -l select=1ncpus=16,walltime=020000
+#PBS -l select=1:ncpus=16,walltime=02:00:00
[ -z "$PARALLEL_SEQ" ] &&
{ module add parallel ; exec parallel -a $PBS_O_WORKDIR/tasklist $0 ; }
# change to local scratch directory
@@ -208,7 +208,7 @@ and copy the output file back to the submit directory, under the
$TASK.out name.Â
### Submit the job
To submit the job, use the qsub command. The 101 tasks' job of the
-[example above](#gp_example) may be submitted like this
+[example above](#gp_example) may be submitted like this:
``` {.prettyprint .lang-sh}
$ qsub -N JOBNAME jobscript
12345.dm2
@@ -219,7 +219,7 @@ complete in less than 2 hours.
Please note the #PBS directives in the beginning of the jobscript file,
dont' forget to set your valid PROJECT_ID and desired queue.
[]()Job arrays and GNU parallel
--------------------------------
+--------
Combine the Job arrays and GNU parallel for best throughput of single
core jobs
While job arrays are able to utilize all available computational nodes,
@@ -234,13 +234,13 @@ is submitted to the queuing system. The subjobs run GNU parallel. The
GNU parallel shell executes multiple instances of the jobscript using
all cores on the node. The instances execute different work, controlled
by the $PBS_JOB_ARRAY and $PARALLEL_SEQ variables.
-[]()Example
+[]()Example:
Assume we have 992 input files with name beginning with "file" (e. g.
file001, ..., file992). Assume we would like to use each of these input
files with program executable myprog.x, each as a separate single core
job. We call these single core jobs tasks.
First, we create a tasklist file, listing all tasks - all input files in
-our example
+our example:
``` {.prettyprint .lang-sh}
$ find . -name 'file*' > tasklist
```
@@ -249,12 +249,12 @@ one subjob
``` {.prettyprint .lang-sh}
$ seq 32 > numtasks
```
-Then we create jobscript
+Then we create jobscript:
``` {.prettyprint .lang-sh}
#!/bin/bash
#PBS -A PROJECT_ID
#PBS -q qprod
-#PBS -l select=1ncpus=16,walltime=020000
+#PBS -l select=1:ncpus=16,walltime=02:00:00
[ -z "$PARALLEL_SEQ" ] &&
{ module add parallel ; exec parallel -a $PBS_O_WORKDIR/numtasks $0 ; }
# change to local scratch directory
@@ -279,7 +279,7 @@ submit directory, under the $TASK.out name. The numtasks file controls
how many tasks will be run per subjob. Once an task is finished, new
task starts, until the number of tasks in numtasks file is reached.
Select subjob walltime and number of tasks per subjob carefully
-Â When deciding this values, think about following guiding rules
+Â When deciding this values, think about following guiding rules :
1. Let n=N/16. Inequality (n+1) * T < W should hold. The N is
number of tasks per subjob, T is expected single task walltime and W
is subjob walltime. Short subjob walltime improves scheduling and
@@ -290,13 +290,13 @@ Select subjob walltime and number of tasks per subjob carefully
### Submit the job array
To submit the job array, use the qsub -J command. The 992 tasks' job of
the [example above](#combined_example) may be submitted
-like this
+like this:
``` {.prettyprint .lang-sh}
-$ qsub -N JOBNAME -J 1-99232 jobscript
+$ qsub -N JOBNAME -J 1-992:32 jobscript
12345[].dm2
```
In this example, we submit a job array of 31 subjobs. Note the -J
-1-992**32**, this must be the same as the number sent to numtasks file.
+1-992:**32**, this must be the same as the number sent to numtasks file.
Each subjob will run on full node and process 16 input files in
parallel, 32 in total per subjob. Every subjob is assumed to complete
in less than 2 hours.
@@ -304,7 +304,8 @@ Please note the #PBS directives in the beginning of the jobscript file,
dont' forget to set your valid PROJECT_ID and desired queue.
Examples
--------
-Download the examples in [capacity.zip](capacity.zip),Â
+Download the examples in
+[capacity.zip](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing-examples),Â
illustrating the above listed ways to run huge number of jobs. We
recommend to try out the examples, before using this for running
production jobs.
@@ -315,29 +316,3 @@ $ unzip capacity.zip
$ cat README
```
Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
diff --git a/anselm-cluster-documentation/resource-allocation-and-job-execution/fairshare_formula.png b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/fairshare_formula.png
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/resource-allocation-and-job-execution/fairshare_formula.png
rename to docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/fairshare_formula.png
diff --git a/anselm-cluster-documentation/resource-allocation-and-job-execution.html b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.html
old mode 100755
new mode 100644
similarity index 63%
rename from anselm-cluster-documentation/resource-allocation-and-job-execution.html
rename to docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.html
index e724109125e85988bc21b107fdaa32aa032d8b25..3ec96cfe8297547683bc9d328e9899a4b310739c
--- a/anselm-cluster-documentation/resource-allocation-and-job-execution.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.html
@@ -10,45 +10,42 @@
-
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
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+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
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<title>Resource Allocation and Job Execution — IT4I Docs</title>
- <link rel="canonical" href="resource-allocation-and-job-execution.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="resource-allocation-and-job-execution.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="resource-allocation-and-job-execution.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
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- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
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@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -230,9 +227,9 @@
<div id="parent-fieldname-text-85dbd3a3056441709e60b0b74d70f00b" class="">
- <p>To run a <a target="_self" title="" class="internal-link" href="introduction.html">job</a>, <a target="_self" title="" class="internal-link" href="introduction.html">computational resources</a> for this particular job must be allocated. This is done via the PBS Pro job workload manager software, which efficiently distributes workloads across the supercomputer. Extensive informations about PBS Pro can be found in the <a target="_self" title="" class="internal-link" href="../pbspro-documentation.html">official documentation here</a>, especially in the <a target="_self" title="" class="internal-link" href="../pbspro-documentation/PBSProUserGuide12.pdf">PBS Pro User's Guide</a>.</p>
+ <p>To run a <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/introduction">job</a>, <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/introduction">computational resources</a> for this particular job must be allocated. This is done via the PBS Pro job workload manager software, which efficiently distributes workloads across the supercomputer. Extensive informations about PBS Pro can be found in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/pbspro-documentation">official documentation here</a>, especially in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/pbspro-documentation/pbspro-users-guide">PBS Pro User's Guide</a>.</p>
<h2 class=" ">Resources Allocation Policy</h2>
-<p>The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. <a target="_self" title="" class="internal-link" href="resource-allocation-and-job-execution/job-priority.html">The Fairshare</a> at Anselm ensures that individual users may consume approximately equal amount of resources per week. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following queues are available to Anselm users:</p>
+<p>The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority">The Fairshare</a> at Anselm ensures that individual users may consume approximately equal amount of resources per week. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following queues are available to Anselm users:</p>
<ul>
<li><strong>qexp</strong>, the Express queue</li>
<li><strong>qprod</strong>, the Production queue<strong></strong></li>
@@ -241,15 +238,15 @@
<li><strong>qfree, </strong>the Free resource utilization queue</li>
</ul>
<p class="callout">Check the queue status at <a class="external-link" href="https://extranet.it4i.cz/anselm/" target="_self" title="">https://extranet.it4i.cz/anselm/</a></p>
-<p>Read more on the <a target="_self" title="" class="internal-link" href="resource-allocation-and-job-execution/resources-allocation-policy.html">Resource Allocation Policy</a> page.</p>
+<p>Read more on the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy">Resource Allocation Policy</a> page.</p>
<h2 class=" ">Job submission and execution</h2>
<p class="callout">Use the <strong>qsub</strong> command to submit your jobs.</p>
<p class=" ">The qsub submits the job into the queue. The qsub command creates a request to the PBS Job manager for allocation of specified resources. The <strong>smallest allocation unit is entire node, 16 cores</strong>, with exception of the qexp queue. The resources will be allocated when available, subject to allocation policies and constraints. <strong>After the resources are allocated the jobscript or interactive shell is executed on first of the allocated nodes.</strong></p>
-<p class=" ">Read more on the <a target="_self" title="" class="internal-link" href="resource-allocation-and-job-execution/job-submission-and-execution.html">Job submission and execution</a> page.</p>
+<p class=" ">Read more on the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">Job submission and execution</a> page.</p>
<h2 class=" ">Capacity computing</h2>
<p class="callout">Use Job arrays when running huge number of jobs.<br />Use GNU Parallel and/or Job arrays when running (many) single core jobs.</p>
<p>In many cases, it is useful to submit huge (<span>100+</span>) number of computational jobs into the PBS queue system. Huge number of (small) jobs is one of the most effective ways to execute embarrassingly parallel calculations, achieving best runtime, throughput and computer utilization. In this chapter, we discuss the the recommended way to run huge number of jobs, including <strong>ways to run huge number of single core jobs</strong>.</p>
-<p>Read more on <a target="_self" title="" class="internal-link" href="resource-allocation-and-job-execution/capacity-computing.html">Capacity computing</a> page.</p>
+<p>Read more on <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing">Capacity computing</a> page.</p>
</div>
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<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
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- <a title="" class="state-published contenttype-document" href="hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -437,7 +434,7 @@
- <a title="" class="state-published contenttype-document" href="environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -453,7 +450,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -469,7 +466,7 @@
- <a title="" class="state-published contenttype-document" href="resource-allocation-and-job-execution/resources-allocation-policy.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy">
<span>Resources Allocation Policy</span>
</a>
@@ -485,7 +482,7 @@
- <a title="" class="state-published contenttype-document" href="resource-allocation-and-job-execution/job-submission-and-execution.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">
<span>Job submission and execution</span>
</a>
@@ -501,7 +498,7 @@
- <a title="" class="state-published contenttype-document" href="resource-allocation-and-job-execution/job-priority.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority">
<span>Job scheduling</span>
</a>
@@ -517,7 +514,7 @@
- <a title="" class="state-published contenttype-document" href="resource-allocation-and-job-execution/capacity-computing.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing">
<span>Capacity computing</span>
</a>
@@ -542,7 +539,7 @@
- <a title="" class="state-published contenttype-document" href="compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -558,7 +555,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -574,7 +571,7 @@
- <a title="" class="state-published contenttype-document" href="network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -590,10 +587,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -609,7 +606,7 @@
- <a title="" class="state-published contenttype-document" href="remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -625,7 +622,7 @@
- <a title="" class="state-published contenttype-document" href="prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -650,7 +647,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -666,7 +663,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -682,7 +679,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['enableLinkTracking']);
(function() {
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -750,12 +747,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -771,7 +768,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md
new file mode 100644
index 0000000000000000000000000000000000000000..c0a7da2ce7d24a1e84a791be4fcaf30966945bd2
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md
@@ -0,0 +1,61 @@
+Resource Allocation and Job Execution
+=====================================
+
+To run a
+[job](https://docs.it4i.cz/anselm-cluster-documentation/introduction),
+[computational
+resources](https://docs.it4i.cz/anselm-cluster-documentation/introduction)
+for this particular job must be allocated. This is done via the PBS Pro
+job workload manager software, which efficiently distributes workloads
+across the supercomputer. Extensive informations about PBS Pro can be
+found in the [official documentation
+here](https://docs.it4i.cz/pbspro-documentation),
+especially in the [PBS Pro User's
+Guide](https://docs.it4i.cz/pbspro-documentation/pbspro-users-guide).
+Resources Allocation Policy
+----
+The resources are allocated to the job in a fairshare fashion, subject
+to constraints set by the queue and resources available to the Project.
+[The
+Fairshare](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority)
+at Anselm ensures that individual users may consume approximately equal
+amount of resources per week. The resources are accessible via several
+queues for queueing the jobs. The queues provide prioritized and
+exclusive access to the computational resources. Following queues are
+available to Anselm users:
+- **qexp**, the Express queue
+- **qprod**, the Production queue****
+- **qlong**, the Long queue, regula
+- **qnvidia, qmic, qfat**, the Dedicated queues
+- **qfree,** the Free resource utilization queue
+Check the queue status at <https://extranet.it4i.cz/anselm/>
+Read more on the [Resource Allocation
+Policy](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy)
+page.
+Job submission and execution
+-----
+Use the **qsub** command to submit your jobs.
+The qsub submits the job into the queue. The qsub command creates a
+request to the PBS Job manager for allocation of specified resources.Â
+The **smallest allocation unit is entire node, 16 cores**, with
+exception of the qexp queue. The resources will be allocated when
+available, subject to allocation policies and constraints. **After the
+resources are allocated the jobscript or interactive shell is executed
+on first of the allocated nodes.**
+Read more on the [Job submission and
+execution](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution)
+page.
+Capacity computing
+------------------
+Use Job arrays when running huge number of jobs.
+Use GNU Parallel and/or Job arrays when running (many) single core jobs.
+In many cases, it is useful to submit huge (<span>100+</span>) number of
+computational jobs into the PBS queue system. Huge number of (small)
+jobs is one of the most effective ways to execute embarrassingly
+parallel calculations, achieving best runtime, throughput and computer
+utilization. In this chapter, we discuss the the recommended way to run
+huge number of jobs, including **ways to run huge number of single core
+jobs**.
+Read more on [Capacity
+computing](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing)
+page.
diff --git a/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.html b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.html
old mode 100755
new mode 100644
similarity index 70%
rename from anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.html
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index 5374b8c07c22098176b6adbb508221ee94590836..f073fee73feb8c8de21a622c991e06656c643b83
--- a/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.html
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@@ -10,45 +10,42 @@
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<title>Job scheduling — IT4I Docs</title>
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">Resource Allocation and Job Execution</a>
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@@ -252,7 +249,7 @@
<p>Fairshare priority is priority calculated on recent usage of resources. Fairshare priority is calculated per project, all members of project share same fairshare priority. Projects with higher recent usage have lower fairshare priority than projects with lower or none recent usage.</p>
<p>Fairshare priority is used for ranking jobs with equal queue priority.</p>
<p>Fairshare priority is calculated as</p>
-<p class=" "><img title="" class="image-inline" alt="" src="fairshare_formula.png" /></p>
+<p class=" "><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/fairshare_formula.png" /></p>
<p class=" ">where MAX_FAIRSHARE has value 1E6,<br />usage<sub>Project</sub> is cumulated usage by all members of selected project,<br /> usage<sub>Total</sub> is total usage by all users, by all projects.</p>
<p class=" ">Usage counts allocated corehours (ncpus*walltime). Usage is decayed, or cut in half periodically, at the interval 168 hours (one week).<br />Jobs queued in queue qexp are not calculated to project's usage.</p>
<p class="callout"><span>Calculated usage and fairshare priority can be seen at <a class="external-link" href="https://extranet.it4i.cz/anselm/projects" target="_self" title="">https://extranet.it4i.cz/anselm/projects</a>.</span></p>
@@ -263,7 +260,7 @@
<p><span><span>Eligible time can be seen as eligible_time attribute of job.</span></span></p>
<h3 class=" ">Formula</h3>
<p class=" ">Job execution priority (job sort formula) is calculated as:</p>
-<p class=" "><img title="" class="image-inline" alt="" src="job_sort_formula.png" /></p>
+<p class=" "><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job_sort_formula.png" /></p>
<h3 class=" ">Job backfilling</h3>
<p><span>Anselm cluster uses job backfilling.</span></p>
<p>Backfilling means fitting smaller jobs around the higher-priority jobs that the scheduler is going to run next, in such a way that the higher-priority jobs are not delayed. Backfilling allows us to keep resources from becoming idle when the top job (job with the highest execution priority) cannot run.</p>
@@ -346,7 +343,7 @@
<dt class="portletHeader hiddenStructure">
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- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
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</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
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</a>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -442,7 +439,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
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@@ -458,7 +455,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -474,7 +471,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
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@@ -490,7 +487,7 @@
- <a title="" class="state-published contenttype-document" href="resources-allocation-policy.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy">
<span>Resources Allocation Policy</span>
</a>
@@ -506,7 +503,7 @@
- <a title="" class="state-published contenttype-document" href="job-submission-and-execution.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">
<span>Job submission and execution</span>
</a>
@@ -522,7 +519,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="job-priority.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority">
<span>Job scheduling</span>
</a>
@@ -538,7 +535,7 @@
- <a title="" class="state-published contenttype-document" href="capacity-computing.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing">
<span>Capacity computing</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
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- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -630,7 +627,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -646,7 +643,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -671,7 +668,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -687,7 +684,7 @@
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+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -703,7 +700,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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<div id="portal-footer">
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
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+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
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+ <a href="https://extranet.it4i.cz">Extranet</a>
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<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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diff --git a/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
similarity index 65%
rename from anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
rename to docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
index 83d2c324409b64633ce233764852ac91df70b0c9..89ae4286f09a2062a591e9bb67d46d74f9a7b13d 100644
--- a/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
@@ -1,10 +1,11 @@
+Job scheduling
==============
Job execution priority
----------------------
Scheduler gives each job an execution priority and then uses this job
execution priority to select which job(s) to run.
Job execution priority on Anselm is determined by these job properties
-(in order of importance)
+(in order of importance):
1. queue priority
2. fairshare priority
3. eligible time
@@ -16,7 +17,7 @@ Execution priority of jobs in higher priority queues is always greater
than execution priority of jobs in lower priority queues. Other
properties of job used for determining job execution priority (fairshare
priority, eligible time) cannot compete with queue priority.
-Queue priorities can be seen at
+Queue priorities can be seen at <https://extranet.it4i.cz/anselm/queues>
### Fairshare priority
Fairshare priority is priority calculated on recent usage of resources.
Fairshare priority is calculated per project, all members of project
@@ -24,33 +25,34 @@ share same fairshare priority. Projects with higher recent usage have
lower fairshare priority than projects with lower or none recent usage.
Fairshare priority is used for ranking jobs with equal queue priority.
Fairshare priority is calculated as
-
+
where MAX_FAIRSHARE has value 1E6,
usage~Project~ is cumulated usage by all members of selected project,
usage~Total~ is total usage by all users, by all projects.
Usage counts allocated corehours (ncpus*walltime). Usage is decayed, or
cut in half periodically, at the interval 168 hours (one week).
Jobs queued in queue qexp are not calculated to project's usage.
-Calculated usage and fairshare priority can be seen at
-.
-
-Calculated fairshare priority can be also seen as
-Resource_List.fairshare attribute of a job.
-### Eligible time
+<span>Calculated usage and fairshare priority can be seen at
+<https://extranet.it4i.cz/anselm/projects>.</span>
+<span>
+<span>Calculated fairshare priority can be also seen as
+Resource_List.fairshare attribute of a job.</span>
+</span>
+### <span>Eligible time</span>
Eligible time is amount (in seconds) of eligible time job accrued while
waiting to run. Jobs with higher eligible time gains higher
-priority.
+pri<span><span></span></span>ority.
Eligible time has the least impact on execution priority. Eligible time
is used for sorting jobs with equal queue priority and fairshare
-priority. It is very, very difficult for eligible time to
+priority. It is very, very difficult for <span>eligible time</span> to
compete with fairshare priority.
-Eligible time can be seen as eligible_time attribute of
-job.
+<span><span>Eligible time can be seen as eligible_time attribute of
+job.</span></span>
### Formula
-Job execution priority (job sort formula) is calculated as
-
+Job execution priority (job sort formula) is calculated as:
+
### Job backfilling
-Anselm cluster uses job backfilling.
+<span>Anselm cluster uses job backfilling.</span>
Backfilling means fitting smaller jobs around the higher-priority jobs
that the scheduler is going to run next, in such a way that the
higher-priority jobs are not delayed. Backfilling allows us to keep
@@ -69,29 +71,3 @@ It is **very beneficial to specify the walltime** when submitting jobs.
Specifying more accurate walltime enables better schedulling, better
execution times and better resource usage. Jobs with suitable (small)
walltime could be backfilled - and overtake job(s) with higher priority.
-------------------------------------------------------------------------
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- Documentation](../../salomon.html)
-
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- Documentation](../../anselm-cluster-documentation.html)
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- Overview](../hardware-overview.html)
-
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- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
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- Modules](../environment-and-modules.html)
diff --git a/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.html b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.html
old mode 100755
new mode 100644
similarity index 78%
rename from anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.html
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index 6fc2b9d02039c971203bcd5ced1e988b3a7292d7..52f136f76433e9b3f9b3678565dadc13a134c598
--- a/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.html
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<title>Job submission and execution — IT4I Docs</title>
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- <a href="../resource-allocation-and-job-execution.html">Resource Allocation and Job Execution</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">Resource Allocation and Job Execution</a>
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@@ -301,8 +298,8 @@
<div class="titlepage">
<div>In this example, we allocate 4 nodes, 16 cores, selecting only the nodes with Intel Xeon E5-2665 CPU.</div>
<h3 class=" ">Placement by IB switch</h3>
-<div>Groups of computational nodes are connected to chassis integrated Infiniband switches. These switches form the leaf switch layer of the <a target="_self" title="" class="internal-link" href="../network.html">Infiniband network</a> <span class="internal-link">fat</span> tree topology. Nodes sharing the leaf switch can communicate most efficiently. Sharing the same switch prevents hops in the network and provides for unbiased, most efficient network communication.<br /><br /></div>
-<div>Nodes sharing the same switch may be selected via the PBS resource attribute ibswitch. Values of this attribute are iswXX, where XX is the switch number. The node-switch mapping can be seen at <a target="_self" title="" class="internal-link" href="../hardware-overview.html">Hardware Overview</a> section.<br /><br /></div>
+<div>Groups of computational nodes are connected to chassis integrated Infiniband switches. These switches form the leaf switch layer of the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/network">Infiniband network</a> <span class="internal-link">fat</span> tree topology. Nodes sharing the leaf switch can communicate most efficiently. Sharing the same switch prevents hops in the network and provides for unbiased, most efficient network communication.<br /><br /></div>
+<div>Nodes sharing the same switch may be selected via the PBS resource attribute ibswitch. Values of this attribute are iswXX, where XX is the switch number. The node-switch mapping can be seen at <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">Hardware Overview</a> section.<br /><br /></div>
<div>We recommend allocating compute nodes of a single switch when best possible computational network performance is required to run the job efficiently:</div>
<pre class=" ">qsub -A OPEN-0-0 -q qprod -l select=18:ncpus=16:ibswitch=isw11 ./myjob</pre>
<div>In this example, we request all the 18 nodes sharing the isw11 switch for 24 hours. Full chassis will be allocated.</div>
@@ -361,20 +358,20 @@
<p>The recommended way to run production jobs is to change to /scratch directory early in the jobscript, copy all inputs to /scratch, execute the calculations and copy outputs to home directory.</p>
<pre class="prettyprint lang-sh">#!/bin/bash<br /><br /># change to scratch directory, exit on failure<br />SCRDIR=/scratch/$USER/myjob<br />mkdir -p $SCRDIR<br />cd $SCRDIR || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/input .<br />cp $PBS_O_WORKDIR/mympiprog.x .<br /><br /># load the mpi module<br />module load openmpi<br /><br /># execute the calculation<br />mpiexec -pernode ./mympiprog.x<br /><br /># copy output file to home<br />cp output $PBS_O_WORKDIR/.<br /><br />#exit<br />exit</pre>
<p class=" ">In this example, some directory on the /home holds the input file input and executable mympiprog.x . We create a directory myjob on the /scratch filesystem, copy input and executable files from the /home directory where the qsub was invoked ($PBS_O_WORKDIR) to /scratch, execute the MPI programm mympiprog.x and copy the output file back to the /home directory. The mympiprog.x is executed as one process per node, on all allocated nodes.</p>
-<p class="callout">Consider preloading inputs and executables onto <a target="_self" title="" class="internal-link" href="../storage-1/storage.html">shared scratch</a> before the calculation starts.</p>
+<p class="callout">Consider preloading inputs and executables onto <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage">shared scratch</a> before the calculation starts.</p>
<p>In some cases, it may be impractical to copy the inputs to scratch and outputs to home. This is especially true when very large input and output files are expected, or when the files should be reused by a subsequent calculation. In such a case, it is users responsibility to preload the input files on shared /scratch before the job submission and retrieve the outputs manually, after all calculations are finished.</p>
<p class="callout"><a name="PBSsaved"></a>Store the qsub options within the jobscript. <br />Use <strong>mpiprocs</strong> and <strong>ompthreads</strong> qsub options to control the MPI job execution.</p>
<p>Example jobscript for an MPI job with preloaded inputs and executables, options for qsub are stored within the script :</p>
<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -q qprod<br />#PBS -N MYJOB<br />#PBS -l select=100:ncpus=16:mpiprocs=1:ompthreads=16<br />#PBS -A OPEN-0-0<br /><br /># change to scratch directory, exit on failure<br />SCRDIR=/scratch/$USER/myjob<br />cd $SCRDIR || exit<br /><br /><br /># load the mpi module<br />module load openmpi<br /><br /># execute the calculation<br />mpiexec ./mympiprog.x<br /><br /><br />#exit<br />exit</pre>
<p class=" ">In this example, input and executable files are assumed preloaded manually in /scratch/$USER/myjob directory. Note the <strong>mpiprocs</strong> and <strong>ompthreads</strong> qsub options, controlling behavior of the MPI execution. The mympiprog.x is executed as one process per node, on all 100 allocated nodes. If mympiprog.x implements OpenMP threads, it will run 16 threads per node.</p>
-<p class=" ">More information is found in the <a target="_self" title="" class="internal-link" href="../software/mpi-1/Running_OpenMPI.html">Running OpenMPI</a> and <a target="_self" title="" class="internal-link" href="../software/mpi-1/running-mpich2.html">Running MPICH2</a> sections.</p>
+<p class=" ">More information is found in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI">Running OpenMPI</a> and <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2">Running MPICH2</a> sections.</p>
<h3 class=" ">Example Jobscript for Single Node Calculation<a name="JobscriptLocal"></a></h3>
<p class="callout">Local scratch directory is often useful for single node jobs. Local scratch will be deleted immediately after the job ends.</p>
-<p>Example jobscript for single node calculation, using <a target="_self" title="" class="internal-link" href="../storage-1/storage.html">local scratch</a> on the node:</p>
+<p>Example jobscript for single node calculation, using <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage">local scratch</a> on the node:</p>
<pre class="prettyprint lang-sh">#!/bin/bash<br /><br /># change to local scratch directory<br />cd /lscratch/$PBS_JOBID || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/input .<br />cp $PBS_O_WORKDIR/myprog.x .<br /><br /># execute the calculation<br />./myprog.x<br /><br /># copy output file to home<br />cp output $PBS_O_WORKDIR/.<br /><br />#exit<br />exit</pre>
<p class=" ">In this example, some directory on the home holds the input file input and executable myprog.x . We copy input and executable files from the home directory where the qsub was invoked ($PBS_O_WORKDIR) to local scratch /lscratch/$PBS_JOBID, execute the myprog.x and copy the output file back to the /home directory. The myprog.x runs on one node only and may use threads.</p>
<h3 class=" ">Other Jobscript Examples</h3>
-<p>Further jobscript examples may be found in the <a target="_self" title="" class="internal-link" href="../software.html">Software</a> section and the <a target="_self" title="" class="internal-link" href="capacity-computing.html">Capacity computing</a> section.</p>
+<p>Further jobscript examples may be found in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a> section and the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing">Capacity computing</a> section.</p>
<p>Â </p>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
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+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
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@@ -563,7 +560,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
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@@ -579,7 +576,7 @@
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+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy">
<span>Resources Allocation Policy</span>
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@@ -611,7 +608,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="job-submission-and-execution.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">
<span>Job submission and execution</span>
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@@ -627,7 +624,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority">
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@@ -643,7 +640,7 @@
- <a title="" class="state-published contenttype-document" href="capacity-computing.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing">
<span>Capacity computing</span>
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@@ -668,7 +665,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
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@@ -684,7 +681,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
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@@ -700,7 +697,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
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@@ -716,10 +713,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -735,7 +732,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -751,7 +748,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
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@@ -776,7 +773,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
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@@ -792,7 +789,7 @@
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+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
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@@ -808,7 +805,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -897,7 +894,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:38 GMT -->
</html>
diff --git a/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md
similarity index 80%
rename from anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md
rename to docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md
index 8e82a3ad601add88bfbb18dc75c9a57b3fe8d139..e461362995d2f3cbe41560a58de9a1e73626c0ab 100644
--- a/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md
@@ -1,7 +1,6 @@
Job submission and execution
============================
-
-
+
Job Submission
--------------
When allocating computational resources for the job, please specify
@@ -14,9 +13,9 @@ When allocating computational resources for the job, please specify
6. Jobscript or interactive switch
Use the **qsub** command to submit your job to a queue for allocation of
the computational resources.
-Submit the job using the qsub command
+Submit the job using the qsub command:
``` {.prettyprint .lang-sh}
-$ qsub -A Project_ID -q queue -l select=xncpus=y,walltime=[[hh]mm]ss[.ms] jobscript
+$ qsub -A Project_ID -q queue -l select=x:ncpus=y,walltime=[[hh:]mm:]ss[.ms] jobscript
```
The qsub submits the job into the queue, in another words the qsub
command creates a request to the PBS Job manager for allocation of
@@ -26,7 +25,7 @@ resources are allocated the jobscript or interactive shell is executed
on first of the allocated nodes.**
### Job Submission Examples
``` {.prettyprint .lang-sh}
-$ qsub -A OPEN-0-0 -q qprod -l select=64ncpus=16,walltime=030000 ./myjob
+$ qsub -A OPEN-0-0 -q qprod -l select=64:ncpus=16,walltime=03:00:00 ./myjob
```
In this example, we allocate 64 nodes, 16 cores per node, for 3 hours.
We allocate these resources via the qprod queue, consumed resources will
@@ -34,21 +33,21 @@ be accounted to the Project identified by Project ID OPEN-0-0. Jobscript
myjob will be executed on the first node in the allocation.
Â
``` {.prettyprint .lang-sh}
-$ qsub -q qexp -l select=4ncpus=16 -I
+$ qsub -q qexp -l select=4:ncpus=16 -I
```
In this example, we allocate 4 nodes, 16 cores per node, for 1 hour. We
allocate these resources via the qexp queue. The resources will be
available interactively
Â
``` {.prettyprint .lang-sh}
-$ qsub -A OPEN-0-0 -q qnvidia -l select=10ncpus=16 ./myjob
+$ qsub -A OPEN-0-0 -q qnvidia -l select=10:ncpus=16 ./myjob
```
In this example, we allocate 10 nvidia accelerated nodes, 16 cores per
node, for 24 hours. We allocate these resources via the qnvidia queue.
Jobscript myjob will be executed on the first node in the allocation.
Â
``` {.prettyprint .lang-sh}
-$ qsub -A OPEN-0-0 -q qfree -l select=10ncpus=16 ./myjob
+$ qsub -A OPEN-0-0 -q qfree -l select=10:ncpus=16 ./myjob
```
In this example, we allocate 10Â nodes, 16 cores per node, for 12 hours.
We allocate these resources via the qfree queue. It is not required that
@@ -64,7 +63,7 @@ $ qsub ./myjob
```
Â
By default, the PBS batch system sends an e-mail only when the job is
-aborted. Disabling mail events completely can be done like this
+aborted. Disabling mail events completely can be done like this:
``` {.prettyprint .lang-sh}
$ qsub -m n
```
@@ -73,7 +72,7 @@ Advanced job placement
### Placement by name
Specific nodes may be allocated via the PBS
``` {.prettyprint .lang-sh}
-qsub -A OPEN-0-0 -q qprod -l select=1ncpus=16host=cn171+1ncpus=16host=cn172 -I
+qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=16:host=cn171+1:ncpus=16:host=cn172 -I
```
In this example, we allocate nodes cn171 and cn172, all 16 cores per
node, for 24 hours. Consumed resources will be accounted to the Project
@@ -83,36 +82,36 @@ interactively.
Nodes equipped with Intel Xeon E5-2665 CPU have base clock frequency
2.4GHz, nodes equipped with Intel Xeon E5-2470 CPU have base frequency
2.3 GHz (see section Compute Nodes for details). Nodes may be selected
-via the PBS resource attribute
-class="highlightedSearchTerm">cpu_freq .
+via the PBS resource attribute <span
+class="highlightedSearchTerm">cpu_freq</span> .
CPU Type base freq. Nodes cpu_freq attribute
- -------------------- ------------ ---------------------------- ---------------------
+ -------------------- ------------ ----- ---------------------
Intel Xeon E5-2665 2.4GHz cn[1-180], cn[208-209] 24
Intel Xeon E5-2470 2.3GHz cn[181-207] 23
Â
```
-$ qsub -A OPEN-0-0 -q qprod -l select=4ncpus=16cpu_freq=24 -I
+$ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=16:cpu_freq=24 -I
```
In this example, we allocate 4 nodes, 16 cores, selecting only the nodes
with Intel Xeon E5-2665 CPU.
### Placement by IB switch
Groups of computational nodes are connected to chassis integrated
Infiniband switches. These switches form the leaf switch layer of the
-[Infiniband network](../network.html)
-class="internal-link">fat tree topology. Nodes sharing the leaf
-switch can communicate most efficiently. Sharing the same switch
+[InfinibandÂ
+network](https://docs.it4i.cz/anselm-cluster-documentation/network)
+<span class="internal-link">fat</span> tree topology. Nodes sharing the
+leaf switch can communicate most efficiently. Sharing the same switch
prevents hops in the network and provides for unbiased, most efficient
network communication.
-
Nodes sharing the same switch may be selected via the PBS resource
attribute ibswitch. Values of this attribute are iswXX, where XX is the
switch number. The node-switch mapping can be seen at [Hardware
-Overview](../hardware-overview.html) section.
-
+Overview](https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview)
+section.
We recommend allocating compute nodes of a single switch when best
possible computational network performance is required to run the job
-efficiently
- qsub -A OPEN-0-0 -q qprod -l select=18ncpus=16ibswitch=isw11 ./myjob
+efficiently:
+ qsub -A OPEN-0-0 -q qprod -l select=18:ncpus=16:ibswitch=isw11 ./myjob
In this example, we request all the 18 nodes sharing the isw11 switch
for 24 hours. Full chassis will be allocated.
Advanced job handling
@@ -123,16 +122,16 @@ keeping the default.Â
If necessary (such as in case of benchmarking) you can disable the Turbo
for all nodes of the job by using the PBS resource attribute
cpu_turbo_boost
- $ qsub -A OPEN-0-0 -q qprod -l select=4ncpus=16 -l cpu_turbo_boost=0 -I
+ $ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=16 -l cpu_turbo_boost=0 -I
More about the Intel Turbo Boost in the TurboBoost section
### Advanced examples
In the following example, we select an allocation for benchmarking a
very special and demanding MPI program. We request Turbo off, 2 full
chassis of compute nodes (nodes sharing the same IB switches) for 30
-minutes
+minutes:
$ qsub -A OPEN-0-0 -q qprod
- -l select=18ncpus=16ibswitch=isw10mpiprocs=1ompthreads=16+18ncpus=16ibswitch=isw20mpiprocs=16ompthreads=1
- -l cpu_turbo_boost=0,walltime=003000
+ -l select=18:ncpus=16:ibswitch=isw10:mpiprocs=1:ompthreads=16+18:ncpus=16:ibswitch=isw20:mpiprocs=16:ompthreads=1
+ -l cpu_turbo_boost=0,walltime=00:30:00
-N Benchmark ./mybenchmark
The MPI processes will be distributed differently on the nodes connected
to the two switches. On the isw10 nodes, we will run 1 MPI process per
@@ -150,16 +149,16 @@ $ qstat -a -u username
$ qstat -an -u username
$ qstat -f 12345.srv11
```
-[]()Example
+[]()Example:
``` {.prettyprint .lang-sh}
$ qstat -a
-srv11
+srv11:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
-16287.srv11 user1 qlong job1 6183 4 64 -- 1440 R 3825
-16468.srv11 user1 qlong job2 8060 4 64 -- 1440 R 1744
-16547.srv11 user2 qprod job3x 13516 2 32 -- 4800 R 0058
+16287.srv11 user1 qlong job1 6183 4 64 -- 144:0 R 38:25
+16468.srv11 user1 qlong job2 8060 4 64 -- 144:0 R 17:44
+16547.srv11 user2 qprod job3x 13516 2 32 -- 48:00 R 00:58
```
In this example user1 and user2 are running jobs named job1, job2 and
job3x. The jobs job1 and job2 are using 4 nodes, 16 cores per node each.
@@ -179,14 +178,14 @@ $ check-pbs-jobs --print-job-out --print-job-err
$ check-pbs-jobs --jobid JOBID --check-all --print-all
$ check-pbs-jobs --jobid JOBID --tailf-job-out
```
-Examples
+Examples:
``` {.prettyprint .lang-sh}
$ check-pbs-jobs --check-all
JOB 35141.dm2, session_id 71995, user user2, nodes cn164,cn165
-Check session id OK
+Check session idOK
Check processes
-cn164 OK
-cn165 No process
+cn164OK
+cn165No process
```
In this example we see that job 35141.dm2 currently runs no process on
allocated node cn165, which may indicate an execution error.
@@ -194,13 +193,13 @@ allocated node cn165, which may indicate an execution error.
$ check-pbs-jobs --print-load --print-processes
JOB 35141.dm2, session_id 71995, user user2, nodes cn164,cn165
Print load
-cn164 LOAD 16.01, 16.01, 16.00
-cn165 LOAD 0.01, 0.00, 0.01
+cn164LOAD16.01, 16.01, 16.00
+cn165LOAD 0.01, 0.00, 0.01
Print processes
%CPU CMD
-cn164 0.0 -bash
-cn164 0.0 /bin/bash /var/spool/PBS/mom_priv/jobs/35141.dm2.SC
-cn164 99.7 run-task
+cn164 0.0 -bash
+cn164 0.0 /bin/bash /var/spool/PBS/mom_priv/jobs/35141.dm2.SC
+cn16499.7 run-task
...
```
In this example we see that job 35141.dm2 currently runs process
@@ -209,10 +208,10 @@ empty, which may indicate an execution error.
``` {.prettyprint .lang-sh}
$ check-pbs-jobs --jobid 35141.dm2 --print-job-out
JOB 35141.dm2, session_id 71995, user user2, nodes cn164,cn165
-Print job standard output
+Print job standard output:
======================== Job start ==========================
-Started at   Fri Aug 30 024753 CEST 2013
-Script name  script
+Started at   Fri Aug 30 02:47:53 CEST 2013
+Script name  script
Run loop 1
Run loop 2
Run loop 3
@@ -245,13 +244,13 @@ manager.
The jobscript or interactive shell is executed on first of the allocated
nodes.
``` {.prettyprint .lang-sh}
-$ qsub -q qexp -l select=4ncpus=16 -N Name0 ./myjob
+$ qsub -q qexp -l select=4:ncpus=16 -N Name0 ./myjob
$ qstat -n -u username
-srv11
+srv11:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
-15209.srv11 username qexp Name0 5530 4 64 -- 0100 R 0000
+15209.srv11 username qexp Name0 5530 4 64 -- 01:00 R 00:00
cn17/0*16+cn108/0*16+cn109/0*16+cn110/0*16
```
 In this example, the nodes cn17, cn108, cn109 and cn110 were allocated
@@ -261,9 +260,9 @@ use as well.
The jobscript or interactive shell is by default executed in home
directory
``` {.prettyprint .lang-sh}
-$ qsub -q qexp -l select=4ncpus=16 -I
-qsub waiting for job 15210.srv11 to start
-qsub job 15210.srv11 ready
+$ qsub -q qexp -l select=4:ncpus=16 -I
+qsubwaiting for job 15210.srv11 to start
+qsubjob 15210.srv11 ready
$ pwd
/home/username
```
@@ -277,9 +276,9 @@ Calculations on allocated nodes may be executed remotely via the MPI,
ssh, pdsh or clush. You may find out which nodes belong to the
allocation by reading the $PBS_NODEFILE file
``` {.prettyprint .lang-sh}
-qsub -q qexp -l select=4ncpus=16 -I
-qsub waiting for job 15210.srv11 to start
-qsub job 15210.srv11 ready
+qsub -q qexp -l select=4:ncpus=16 -I
+qsubwaiting for job 15210.srv11 to start
+qsubjob 15210.srv11 ready
$ pwd
/home/username
$ sort -u $PBS_NODEFILE
@@ -289,10 +288,10 @@ cn109.bullx
cn110.bullx
$ pdsh -w cn17,cn[108-110] hostname
-cn17 cn17
-cn108 cn108
-cn109 cn109
-cn110 cn110
+cn17cn17
+cn108cn108
+cn109cn109
+cn110cn110
```
In this example, the hostname program is executed via pdsh from the
interactive shell. The execution runs on all four allocated nodes. The
@@ -329,8 +328,8 @@ MPI programm mympiprog.x and copy the output file back to the /home
directory. The mympiprog.x is executed as one process per node, on all
allocated nodes.
Consider preloading inputs and executables onto [shared
-scratch](../storage-1/storage.html) before the
-calculation starts.
+scratch](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage)
+before the calculation starts.
In some cases, it may be impractical to copy the inputs to scratch and
outputs to home. This is especially true when very large input and
output files are expected, or when the files should be reused by a
@@ -341,12 +340,12 @@ retrieve the outputs manually, after all calculations are finished.
Use **mpiprocs** and **ompthreads** qsub options to control the MPI job
execution.
Example jobscript for an MPI job with preloaded inputs and executables,
-options for qsub are stored within the script
+options for qsub are stored within the script :
``` {.prettyprint .lang-sh}
#!/bin/bash
#PBS -q qprod
#PBS -N MYJOB
-#PBS -l select=100ncpus=16mpiprocs=1ompthreads=16
+#PBS -l select=100:ncpus=16:mpiprocs=1:ompthreads=16
#PBS -A OPEN-0-0
# change to scratch directory, exit on failure
SCRDIR=/scratch/$USER/myjob
@@ -365,14 +364,16 @@ The mympiprog.x is executed as one process per node, on all 100
allocated nodes. If mympiprog.x implements OpenMP threads, it will run
16 threads per node.
More information is found in the [Running
-OpenMPI](../software/mpi-1/Running_OpenMPI.html) and
-[Running MPICH2](../software/mpi-1/running-mpich2.html)
+OpenMPI](https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI)
+and [Running
+MPICH2](https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2)
sections.
### Example Jobscript for Single Node Calculation[]()
Local scratch directory is often useful for single node jobs. Local
scratch will be deleted immediately after the job ends.
Example jobscript for single node calculation, using [local
-scratch](../storage-1/storage.html) on the node
+scratch](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage)
+on the node:
``` {.prettyprint .lang-sh}
#!/bin/bash
# change to local scratch directory
@@ -395,32 +396,8 @@ file back to the /home directory. The myprog.x runs on one node only and
may use threads.
### Other Jobscript Examples
Further jobscript examples may be found in the
-[Software](../software.html) section and the [Capacity
-computing](capacity-computing.html) section.
+[Software](https://docs.it4i.cz/anselm-cluster-documentation/software)
+section and the [Capacity
+computing](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing)
+section.
Â
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-**[Komentáře](#plone-discussions){#plone-discussions-href}**
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-class="portletWrapper"
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- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
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-
- - [Hardware
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-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
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diff --git a/anselm-cluster-documentation/resource-allocation-and-job-execution/job_sort_formula.png b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job_sort_formula.png
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/resource-allocation-and-job-execution/job_sort_formula.png
rename to docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job_sort_formula.png
diff --git a/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.html b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.html
old mode 100755
new mode 100644
similarity index 74%
rename from anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.html
rename to docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.html
index ea9fea88b2d2a062c3d228482562790d83fec3be..c864b5f355ca6bbccc1de34db55b59c95612f5bd
--- a/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.html
@@ -10,45 +10,42 @@
-
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@@ -87,9 +84,9 @@
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<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="resources-allocation-policy.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="resources-allocation-policy.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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@@ -125,13 +122,13 @@
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- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
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- <a href="../../index.html">Ăšvod</a>
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@@ -153,7 +150,7 @@
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<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
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@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../resource-allocation-and-job-execution.html">Resource Allocation and Job Execution</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">Resource Allocation and Job Execution</a>
<span class="breadcrumbSeparator">
/
@@ -241,7 +238,7 @@
<div id="parent-fieldname-text-d035f997ef984ebb97f6e7aabd57f8be" class="">
<h2 class=" ">Resources Allocation Policy</h2>
-<p>The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. The Fairshare at Anselm ensures that individual users may consume approximately equal amount of resources per week. Detailed information in the <a target="_self" title="" class="internal-link" href="job-priority.html">Job scheduling</a> section. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following table provides the queue partitioning overview:Â Â Â </p>
+<p>The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. The Fairshare at Anselm ensures that individual users may consume approximately equal amount of resources per week. Detailed information in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority">Job scheduling</a> section. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following table provides the queue partitioning overview:Â Â Â </p>
<table class="listing">
<tbody>
<tr><th>queue</th><th>active project</th><th>project resources</th><th>nodes</th><th>min ncpus*</th><th>priority</th><th>authorization</th><th>walltime<br />default/max</th></tr>
@@ -315,18 +312,18 @@
<li><strong>qfree</strong>, The Free resource queue<strong></strong>: The queue qfree is intended for utilization of free resources, after a Project exhausted all its allocated computational resources (Does not apply to DD projects by default. DD projects have to request for persmission on qfree after exhaustion of computational resources.). It is required that active project is specified to enter the queue, however no remaining resources are required. Consumed resources will be accounted to the Project. Only 178 nodes without accelerator may be accessed from this queue. Full nodes, 16 cores per node are allocated. The queue runs with very low priority and no special authorization is required to use it. The maximum runtime in qfree is 12 hours.</li>
</ul>
<h3 class=" ">Notes <strong><br /></strong></h3>
-<p>The job wall clock time defaults to<strong> half the maximum time</strong>, see table above. Longer wall time limits can be <a target="_self" title="" class="internal-link" href="job-submission-and-execution.html">set manually, see examples</a>. <br /><br />Jobs that exceed the reserved wall clock time (Req'd Time) get killed automatically. Wall clock time limit can be changed for queuing jobs (state Q) using the qalter command, however can not be changed for a running job (state R).</p>
+<p>The job wall clock time defaults to<strong> half the maximum time</strong>, see table above. Longer wall time limits can be <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">set manually, see examples</a>. <br /><br />Jobs that exceed the reserved wall clock time (Req'd Time) get killed automatically. Wall clock time limit can be changed for queuing jobs (state Q) using the qalter command, however can not be changed for a running job (state R).</p>
<p>Anselm users may check current queue configuration at <a class="external-link" href="https://extranet.it4i.cz/anselm/queues" target="_self" title="">https://extranet.it4i.cz/anselm/queues</a>.</p>
<h3 class=" ">Queue status</h3>
<p class="callout">Check the status of jobs, queues and compute nodes at <a class="external-link" href="https://extranet.it4i.cz/anselm/" target="_self" title="">https://extranet.it4i.cz/anselm/</a></p>
-<p class=" "><img title="" class="image-inline" alt="rspbs web interface" src="rsweb.png" /></p>
+<p class=" "><img alt="rspbs web interface" class="image-inline" title="" src="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/rsweb.png" /></p>
<p>Display the queue status on Anselm:</p>
<pre class="prettyprint lang-sh">$ qstat -q</pre>
<p class=" ">The PBS allocation overview may be obtained also using the rspbs command.</p>
<pre class="prettyprint lang-sh">$ rspbs<br />Usage: rspbs [options]<br /><br />Options:<br /> --version            show program's version number and exit<br /> -h, --help           show this help message and exit<br /> --get-node-ncpu-chart<br />                       Print chart of allocated ncpus per node<br /> --summary            Print summary<br /> --get-server-details Print server<br /> --get-queues         Print queues<br /> --get-queues-details Print queues details<br /> --get-reservations   Print reservations<br /> --get-reservations-details<br />                       Print reservations details<br /> --get-nodes          Print nodes of PBS complex<br /> --get-nodeset        Print nodeset of PBS complex<br /> --get-nodes-details  Print nodes details<br /> --get-jobs           Print jobs<br /> --get-jobs-details   Print jobs details<br /> --get-jobs-check-params<br />                       Print jobid, job state, session_id, user, nodes<br /> --get-users          Print users of jobs<br /> --get-allocated-nodes<br />                       Print allocated nodes of jobs<br /> --get-allocated-nodeset<br />                       Print allocated nodeset of jobs<br /> --get-node-users     Print node users<br /> --get-node-jobs      Print node jobs<br /> --get-node-ncpus     Print number of ncpus per node<br /> --get-node-allocated-ncpus<br />                       Print number of allocated ncpus per node<br /> --get-node-qlist     Print node qlist<br /> --get-node-ibswitch  Print node ibswitch<br /> --get-user-nodes     Print user nodes<br /> --get-user-nodeset   Print user nodeset<br /> --get-user-jobs      Print user jobs<br /> --get-user-jobc      Print number of jobs per user<br /> --get-user-nodec     Print number of allocated nodes per user<br /> --get-user-ncpus     Print number of allocated ncpus per user<br /> --get-qlist-nodes    Print qlist nodes<br /> --get-qlist-nodeset  Print qlist nodeset<br /> --get-ibswitch-nodes Print ibswitch nodes<br /> --get-ibswitch-nodeset<br />                       Print ibswitch nodeset<br /> --state=STATE        Only for given job state<br /> --jobid=JOBID        Only for given job ID<br /> --user=USER          Only for given user<br /> --node=NODE          Only for given node<br /> --nodestate=NODESTATE<br />                       Only for given node state (affects only --get-node*<br />                       --get-qlist-* --get-ibswitch-* actions)<br /> --incl-finished      Include finished jobs<br /><br /></pre>
<h2 class=" "><a name="resources-accounting-policy"></a>Resources Accounting Policy</h2>
<h3 class=" ">The Core-Hour</h3>
-<p>The resources that are currently subject to accounting are the core-hours. The core-hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. 1 core-hour is defined as 1 processor core allocated for 1 hour of wall clock time. Allocating a full node (16 cores) for 1 hour accounts to 16 core-hours. See example in the <a target="_self" title="" class="internal-link" href="job-submission-and-execution.html">Job submission and execution</a> section.</p>
+<p>The resources that are currently subject to accounting are the core-hours. The core-hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. 1 core-hour is defined as 1 processor core allocated for 1 hour of wall clock time. Allocating a full node (16 cores) for 1 hour accounts to 16 core-hours. See example in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">Job submission and execution</a> section.</p>
<h3 class=" ">Check consumed resources</h3>
<p class="callout">The <strong>it4ifree</strong> command is a part of it4i.portal.clients package, located here:<br /><a class="external-link" href="https://pypi.python.org/pypi/it4i.portal.clients" target="_self" title="">https://pypi.python.org/pypi/it4i.portal.clients</a></p>
<p>User may check at any time, how many core-hours have been consumed by himself/herself and his/her projects. The command is available on clusters' login nodes.</p>
@@ -407,7 +404,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -423,7 +420,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -439,7 +436,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -455,7 +452,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -471,7 +468,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -487,7 +484,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -503,7 +500,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -519,7 +516,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -535,7 +532,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -551,7 +548,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="resources-allocation-policy.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy">
<span>Resources Allocation Policy</span>
</a>
@@ -567,7 +564,7 @@
- <a title="" class="state-published contenttype-document" href="job-submission-and-execution.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">
<span>Job submission and execution</span>
</a>
@@ -583,7 +580,7 @@
- <a title="" class="state-published contenttype-document" href="job-priority.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority">
<span>Job scheduling</span>
</a>
@@ -599,7 +596,7 @@
- <a title="" class="state-published contenttype-document" href="capacity-computing.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing">
<span>Capacity computing</span>
</a>
@@ -624,7 +621,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -640,7 +637,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -656,7 +653,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -672,10 +669,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -691,7 +688,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -707,7 +704,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -732,7 +729,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -748,7 +745,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -764,7 +761,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -803,14 +800,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<!-- nagios_check_http_expect_string -->
@@ -832,12 +829,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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@@ -853,7 +850,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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diff --git a/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
similarity index 65%
rename from anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
rename to docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
index 700c386660fa369caea1edf3cc1ff13c4c85eba9..1af2116e2f60086a993276503144204d33b74874 100644
--- a/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
@@ -1,75 +1,107 @@
Resources Allocation Policy
===========================
-
-
+
Resources Allocation Policy {#resources-allocation-policy}
----------------------------
+----
The resources are allocated to the job in a fairshare fashion, subject
to constraints set by the queue and resources available to the Project.
The Fairshare at Anselm ensures that individual users may consume
approximately equal amount of resources per week. Detailed information
-in the [Job scheduling](job-priority.html) section. The
-resources are accessible via several queues for queueing the jobs. The
-queues provide prioritized and exclusive access to the computational
-resources. Following table provides the queue partitioning overview Â
-Â
-queue
-active project
-project resources
-nodes
-min ncpus*
-priority
-authorization
-walltime
-default/max
-qexp
-Express queue
-no
-none required
-2 reserved, 31 total
-including MIC, GPU and FAT nodes
-1
-150
-no
-1h
-qprod
-Production queue
-yes
-> 0
-178 nodes w/o accelerator
-16
-0
-no
-24/48h
-qlong
-Long queue
-yes
-> 0
-60 nodes w/o accelerator
-16
-0
-no
-72/144h
-qnvidia, qmic, qfat
-Dedicated queues
-yes
-> 0
-23 total qnvidia
-4 total qmic
-2 total qfat
-16
-200
-yes
-24/48h
-qfree
-Free resource queue
-yes
-none required
-178 w/o accelerator
-16
--1024
-no
-12h
+in the [Job
+scheduling](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority)
+section. The resources are accessible via several queues for queueing
+the jobs. The queues provide prioritized and exclusive access to the
+computational resources. Following table provides the queue partitioning
+overview:Â Â Â
+<table>
+<colgroup>
+<col width="12%" />
+<col width="12%" />
+<col width="12%" />
+<col width="12%" />
+<col width="12%" />
+<col width="12%" />
+<col width="12%" />
+<col width="12%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">queue</th>
+<th align="left">active project</th>
+<th align="left">project resources</th>
+<th align="left">nodes</th>
+<th align="left">min ncpus*</th>
+<th align="left">priority</th>
+<th align="left">authorization</th>
+<th align="left">walltime<br />
+default/max</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>qexp</strong><br />
+Express queue</td>
+<td align="left">no</td>
+<td align="left">none required</td>
+<td align="left">2 reserved, 31 total<br />
+including MIC, GPU and FAT nodes</td>
+<td align="left">1</td>
+<td align="left"><span><em>150</em></span></td>
+<td align="left">no</td>
+<td align="left">1h</td>
+</tr>
+<tr class="even">
+<td align="left"><strong>qprod</strong><br />
+Production queue</td>
+<td align="left">yes<br />
+<br />
+</td>
+<td align="left">> 0</td>
+<td align="left"><p><span><em>178 nodes w/o accelerator</em></span><br />
+<br />
+</p></td>
+<td align="left">16</td>
+<td align="left">0</td>
+<td align="left">no</td>
+<td align="left">24/48h</td>
+</tr>
+<tr class="odd">
+<td align="left"><p><strong>qlong</strong><br />
+Long queue</p></td>
+<td align="left">yes</td>
+<td align="left">> 0</td>
+<td align="left">60 nodes w/o accelerator</td>
+<td align="left">16</td>
+<td align="left">0</td>
+<td align="left">no</td>
+<td align="left">72/144h</td>
+</tr>
+<tr class="even">
+<td align="left"><p><strong>qnvidia, qmic, qfat</strong><br />
+Dedicated queues</p></td>
+<td align="left">yes</td>
+<td align="left"><p>> 0</p></td>
+<td align="left">23 total qnvidia<br />
+4 total qmic<br />
+2 total qfat</td>
+<td align="left">16</td>
+<td align="left"><span><em>200</em></span></td>
+<td align="left">yes</td>
+<td align="left">24/48h</td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>qfree</strong><br />
+Free resource queue</td>
+<td align="left">yes</td>
+<td align="left">none required</td>
+<td align="left">178 w/o accelerator</td>
+<td align="left">16</td>
+<td align="left">-1024</td>
+<td align="left">no</td>
+<td align="left">12h</td>
+</tr>
+</tbody>
+</table>
**The qfree queue is not free of charge**. [Normal
accounting](#resources-accounting-policy) applies.
However, it allows for utilization of free resources, once a Project
@@ -81,47 +113,47 @@ after request for this queue.
clock speed.** Should you need the very same CPU speed, you have to
select the proper nodes during the PSB job submission.
****
-- **qexp**, the Express queue This queue is dedicated for testing and
+- **qexp**, the Express queueThis queue is dedicated for testing and
running very small jobs. It is not required to specify a project to
- enter the qexp. *There are 2 nodes always reserved for
+ enter the qexp. <span>*<span>There are 2 nodes always reserved for
this queue (w/o accelerator), maximum 8 nodes are available via the
qexp for a particular user, from a pool of nodes containing
**Nvidia** accelerated nodes (cn181-203), **MIC** accelerated
nodes (cn204-207) and **Fat** nodes with 512GB RAM (cn208-209). This
enables to test and tune also accelerated code or code with higher
- RAM requirements.* The nodes may be allocated on per
+ RAM requirements</span>.*</span> The nodes may be allocated on per
core basis. No special authorization is required to use it. The
maximum runtime in qexp is 1 hour.
-- **qprod**, the Production queue**** This queue is intended for
+- **qprod**, the Production queue****This queue is intended for
normal production runs. It is required that active project with
nonzero remaining resources is specified to enter the qprod. All
nodes may be accessed via the qprod queue, except the reserved ones.
- *178 nodes without accelerator are
- included.*Â Full nodes, 16 cores per node
+ <span>*<span>178 nodes without accelerator are
+ included</span>.*</span>Â Full nodes, 16 cores per node
are allocated. The queue runs with medium priority and no special
authorization is required to use it. The maximum runtime in qprod is
48 hours.
-- **qlong**, the Long queue**** This queue is intended for long
+- **qlong**, the Long queue****This queue is intended for long
production runs. It is required that active project with nonzero
remaining resources is specified to enter the qlong. Only 60 nodes
without acceleration may be accessed via the qlong queue. Full
nodes, 16 cores per node are allocated. The queue runs with medium
- priority and no special authorization is required to use it.
+ priority and no special authorization is required to use it.<span>
*The maximum runtime in qlong is 144 hours (three times of the
- standard qprod time - 3 * 48 h).*
-- **qnvidia, qmic, qfat**, the Dedicated queues**** The queue qnvidia
+ standard qprod time - 3 * 48 h).*</span>
+- **qnvidia, qmic, qfat**, the Dedicated queues****The queue qnvidia
is dedicated to access the Nvidia accelerated nodes, the qmic to
access MIC nodes and qfat the Fat nodes. It is required that active
project with nonzero remaining resources is specified to enter
these queues. 23 nvidia, 4 mic and 2 fat nodes are included. Full
- nodes, 16 cores per node are allocated. The queues run with
- *very high priority*, the jobs will be scheduled before the
- jobs coming from the *qexp* queue. An PI *needs
- explicitly* ask
- [support](https//support.it4i.cz/rt/) for
+ nodes, 16 cores per node are allocated. The queues run with<span>
+ *very high priority*</span>, the jobs will be scheduled before the
+ jobs coming from the<span> *qexp* </span>queue. An PI<span> *needs
+ explicitly* </span>ask
+ [support](https://support.it4i.cz/rt/) for
authorization to enter the dedicated queues for all users associated
to her/his Project.
-- **qfree**, The Free resource queue**** The queue qfree is intended
+- **qfree**, The Free resource queue****The queue qfree is intended
for utilization of free resources, after a Project exhausted all its
allocated computational resources (Does not apply to DD projects
by default. DD projects have to request for persmission on qfree
@@ -136,18 +168,19 @@ select the proper nodes during the PSB job submission.
**
The job wall clock time defaults to **half the maximum time**, see table
above. Longer wall time limits can be [set manually, see
-examples](job-submission-and-execution.html).
-
+examples](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution).
Jobs that exceed the reserved wall clock time (Req'd Time) get killed
automatically. Wall clock time limit can be changed for queuing jobs
(state Q) using the qalter command, however can not be changed for a
running job (state R).
Anselm users may check current queue configuration at
-.
+<https://extranet.it4i.cz/anselm/queues>.
### Queue status
Check the status of jobs, queues and compute nodes at
-
-Display the queue status on Anselm
+<https://extranet.it4i.cz/anselm/>
+
+Display the queue status on Anselm:
``` {.prettyprint .lang-sh}
$ qstat -q
```
@@ -155,8 +188,8 @@ The PBS allocation overview may be obtained also using the rspbs
command.
``` {.prettyprint .lang-sh}
$ rspbs
-Usage rspbs [options]
-Options
+Usagerspbs [options]
+Options:
 --version            show program's version number and exit
 -h, --help           show this help message and exit
 --get-node-ncpu-chart
@@ -208,7 +241,7 @@ Options
 --incl-finished      Include finished jobs
```
[]()Resources Accounting Policy
--------------------------------
+--------
### The Core-Hour
The resources that are currently subject to accounting are the
core-hours. The core-hours are accounted on the wall clock basis. The
@@ -218,45 +251,21 @@ of whether the cores are actually used for any calculation. 1 core-hour
is defined as 1 processor core allocated for 1 hour of wall clock time.
Allocating a full node (16 cores) for 1 hour accounts to 16 core-hours.
See example in the [Job submission and
-execution](job-submission-and-execution.html) section.
+execution](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution)
+section.
### Check consumed resources
The **it4ifree** command is a part of it4i.portal.clients package,
-located here
+located here:
+<https://pypi.python.org/pypi/it4i.portal.clients>
User may check at any time, how many core-hours have been consumed by
himself/herself and his/her projects. The command is available on
clusters' login nodes.
``` {.prettyprint .lang-sh}
$ it4ifree
-Password
+Password:
    PID  Total Used ...by me Free
  -------- ------- ------ -------- -------
  OPEN-0-0 1500000 400644  225265 1099356
  DD-13-1   10000 2606 2606 7394
```
Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
diff --git a/anselm-cluster-documentation/resource-allocation-and-job-execution/rsweb.png b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/rsweb.png
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/resource-allocation-and-job-execution/rsweb.png
rename to docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/rsweb.png
diff --git a/anselm-cluster-documentation/scheme.png b/docs.it4i.cz/anselm-cluster-documentation/scheme.png
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/scheme.png
rename to docs.it4i.cz/anselm-cluster-documentation/scheme.png
diff --git a/anselm-cluster-documentation/software.html b/docs.it4i.cz/anselm-cluster-documentation/software.1.html
old mode 100755
new mode 100644
similarity index 67%
rename from anselm-cluster-documentation/software.html
rename to docs.it4i.cz/anselm-cluster-documentation/software.1.html
index 81124aa116e11a17b798866168b702b470758e30..5b663d85284d787f99cbb6f03d77ca2592b877f8
--- a/anselm-cluster-documentation/software.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software.1.html
@@ -10,14 +10,11 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:48 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/" /><!--[if lt IE 7]></base><![endif]-->
@@ -27,31 +24,31 @@
" name="description" />
- <link rel="stylesheet" type="text/css" media="screen" href="../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/IEFixes-cachekey-ec9b60024fd235ff2c883b4b54db91cb.css" />
<![endif]-->
- <style type="text/css" media="screen">@import url(../portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Software — IT4I Docs</title>
- <link rel="canonical" href="software.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -67,7 +64,7 @@
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -90,9 +87,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="software.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="software.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -128,13 +125,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../index.html">
- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -148,7 +145,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -156,7 +153,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -245,7 +242,7 @@
<span class="summary">
- <a href="software/ansys.html" class="contenttype-folder state-published url">ANSYS</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys" class="contenttype-folder state-published url">ANSYS</a>
</span>
<span class="documentByLine">
@@ -271,7 +268,7 @@
<span class="summary">
- <a href="software/comsol.html" class="contenttype-folder state-published url">COMSOL</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol" class="contenttype-folder state-published url">COMSOL</a>
</span>
<span class="documentByLine">
@@ -297,7 +294,7 @@
<span class="summary">
- <a href="software/debuggers.html" class="contenttype-folder state-published url">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers" class="contenttype-folder state-published url">Debuggers and profilers</a>
</span>
<span class="documentByLine">
@@ -323,7 +320,7 @@
<span class="summary">
- <a href="software/chemistry.html" class="contenttype-folder state-published url">Chemistry and Materials science</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry" class="contenttype-folder state-published url">Chemistry and Materials science</a>
</span>
<span class="documentByLine">
@@ -349,7 +346,7 @@
<span class="summary">
- <a href="software/intel-suite.html" class="contenttype-folder state-published url">Intel Parallel studio</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite" class="contenttype-folder state-published url">Intel Parallel studio</a>
</span>
<span class="documentByLine">
@@ -375,7 +372,7 @@
<span class="summary">
- <a href="software/mpi-1.html" class="contenttype-folder state-published url">MPI</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1" class="contenttype-folder state-published url">MPI</a>
</span>
<span class="documentByLine">
@@ -401,7 +398,7 @@
<span class="summary">
- <a href="software/numerical-libraries.html" class="contenttype-folder state-published url">Numerical Libraries</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries" class="contenttype-folder state-published url">Numerical Libraries</a>
</span>
<span class="documentByLine">
@@ -427,7 +424,7 @@
<span class="summary">
- <a href="software/numerical-languages.html" class="contenttype-folder state-published url">Numerical languages</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages" class="contenttype-folder state-published url">Numerical languages</a>
</span>
<span class="documentByLine">
@@ -453,7 +450,7 @@
<span class="summary">
- <a href="software/virtualization.html" class="contenttype-folder state-published url">Virtualization</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization" class="contenttype-folder state-published url">Virtualization</a>
</span>
<span class="documentByLine">
@@ -479,7 +476,7 @@
<span class="summary">
- <a href="software/compilers.html" class="contenttype-document state-published url">Compilers</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers" class="contenttype-document state-published url">Compilers</a>
</span>
<span class="documentByLine">
@@ -505,7 +502,7 @@
<span class="summary">
- <a href="software/intel-xeon-phi.html" class="contenttype-document state-published url">Intel Xeon Phi</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi" class="contenttype-document state-published url">Intel Xeon Phi</a>
</span>
<span class="documentByLine">
@@ -531,7 +528,7 @@
<span class="summary">
- <a href="software/isv_licenses.html" class="contenttype-document state-published url">ISV Licenses</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses" class="contenttype-document state-published url">ISV Licenses</a>
</span>
<span class="documentByLine">
@@ -557,7 +554,7 @@
<span class="summary">
- <a href="software/java.html" class="contenttype-document state-published url">Java</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/java" class="contenttype-document state-published url">Java</a>
</span>
<span class="documentByLine">
@@ -583,7 +580,7 @@
<span class="summary">
- <a href="software/nvidia-cuda.html" class="contenttype-document state-published url">nVidia CUDA</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda" class="contenttype-document state-published url">nVidia CUDA</a>
</span>
<span class="documentByLine">
@@ -609,7 +606,7 @@
<span class="summary">
- <a href="software/omics-master-1.html" class="contenttype-folder state-published url">OMICS Master</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1" class="contenttype-folder state-published url">OMICS Master</a>
</span>
<span class="documentByLine">
@@ -635,7 +632,7 @@
<span class="summary">
- <a href="software/openfoam.html" class="contenttype-document state-published url">OpenFOAM</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam" class="contenttype-document state-published url">OpenFOAM</a>
</span>
<span class="documentByLine">
@@ -661,7 +658,7 @@
<span class="summary">
- <a href="software/operating-system.html" class="contenttype-document state-published url">Operating System</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system" class="contenttype-document state-published url">Operating System</a>
</span>
<span class="documentByLine">
@@ -687,7 +684,7 @@
<span class="summary">
- <a href="software/paraview.html" class="contenttype-document state-published url">ParaView</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview" class="contenttype-document state-published url">ParaView</a>
</span>
<span class="documentByLine">
@@ -713,7 +710,7 @@
<span class="summary">
- <a href="software/gpi2.html" class="contenttype-document state-published url">GPI-2</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2" class="contenttype-document state-published url">GPI-2</a>
</span>
<span class="documentByLine">
@@ -798,7 +795,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -814,7 +811,7 @@
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- <a href="https://extranet.it4i.cz/">Extranet</a>
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+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
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<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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<title>Running MPICH2 — IT4I Docs</title>
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- <a accesskey="6" href="running-mpich2.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<p>In all cases, binding and threading may be verified by executing</p>
<pre class=" ">$ mpirun -bindto numa numactl --show<br />$ mpirun -bindto numa echo $OMP_NUM_THREADS</pre>
<h2 class=" ">Intel MPI on Xeon Phi</h2>
-<p>The<a target="_self" title="" class="internal-link" href="../../../intel-xeon-phi.html"> MPI section of Intel Xeon Phi chapter</a> provides details on how to run Intel MPI code on Xeon Phi architecture.</p>
+<p>The<a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi"> MPI section of Intel Xeon Phi chapter</a> provides details on how to run Intel MPI code on Xeon Phi architecture.</p>
</div>
@@ -353,7 +350,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -369,7 +366,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -385,7 +382,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -401,7 +398,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -417,7 +414,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -433,7 +430,7 @@
- <a title="" class="state-published contenttype-document" href="../../../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -449,7 +446,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -465,7 +462,7 @@
- <a title="" class="state-published contenttype-document" href="../../../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -481,7 +478,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -497,7 +494,7 @@
- <a title="" class="state-published contenttype-document" href="../../../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -513,7 +510,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -529,7 +526,7 @@
- <a title="" class="state-published contenttype-document" href="../../../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -545,10 +542,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -564,7 +561,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../../../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -580,7 +577,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../../../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -596,7 +593,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../../../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -612,7 +609,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../../../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -628,7 +625,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../../../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -644,7 +641,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../mpi-1.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -660,7 +657,7 @@
- <a title="" class="state-published contenttype-document" href="../../../mpi-1/Running_OpenMPI.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI">
<span>Running OpenMPI</span>
</a>
@@ -676,7 +673,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="../../../mpi-1/running-mpich2.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2">
<span>Running MPICH2</span>
</a>
@@ -692,7 +689,7 @@
- <a title="OpenMPI interface to Python" class="state-published contenttype-document" href="../../../mpi-1/mpi4py-mpi-for-python.html">
+ <a class="state-published contenttype-document" title="OpenMPI interface to Python" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python">
<span>MPI4Py (MPI for Python)</span>
</a>
@@ -717,7 +714,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../../../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -733,7 +730,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../../../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -749,7 +746,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -765,7 +762,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../../../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -781,7 +778,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../../../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -797,7 +794,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../../../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -813,7 +810,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../../../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -829,7 +826,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../../../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -845,7 +842,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -861,7 +858,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../../../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -877,7 +874,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../../../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -893,7 +890,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../../../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -909,7 +906,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../../../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -934,7 +931,7 @@
- <a title="" class="state-published contenttype-document" href="../../../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -950,7 +947,7 @@
- <a title="" class="state-published contenttype-document" href="../../../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -975,7 +972,7 @@
- <a title="" class="state-published contenttype-document" href="../../../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -991,7 +988,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1007,7 +1004,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
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+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
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-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1096,7 +1093,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
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</html>
diff --git a/anselm-cluster-documentation/software/mpi-1/running-mpich2.md b/docs.it4i.cz/anselm-cluster-documentation/software/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
similarity index 59%
rename from anselm-cluster-documentation/software/mpi-1/running-mpich2.md
rename to docs.it4i.cz/anselm-cluster-documentation/software/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
index 5ec6a8325fc819b847e6ed67f35e2d9c532d3531..c8d0b2abc90013cd168d0571b9fa0eaaf9d14368 100644
--- a/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
@@ -1,19 +1,18 @@
Running MPICH2
==============
-
-
+
MPICH2 program execution
-------------------------
+-
The MPICH2 programs use mpd daemon or ssh connection to spawn processes,
no PBS support is needed. However the PBS allocation is required to
access compute nodes. On Anselm, the **Intel MPI** and **mpich2 1.9**
are MPICH2 based MPI implementations.
### Basic usage
Use the mpirun to execute the MPICH2 code.
-Example
- $ qsub -q qexp -l select=4ncpus=16 -I
- qsub waiting for job 15210.srv11 to start
- qsub job 15210.srv11 ready
+Example:
+ $ qsub -q qexp -l select=4:ncpus=16 -I
+ qsubwaiting for job 15210.srv11 to start
+ qsubjob 15210.srv11 ready
$ module load impi
$ mpirun -ppn 1 -hostfile $PBS_NODEFILE ./helloworld_mpi.x
Hello world! from rank 0 of 4 on host cn17
@@ -49,7 +48,7 @@ MPI process.
### One MPI process per node
Follow this example to run one MPI process per node, 16 threads per
process. Note that no options to mpirun are needed
- $ qsub -q qexp -l select=4ncpus=16mpiprocs=1ompthreads=16 -I
+ $ qsub -q qexp -l select=4:ncpus=16:mpiprocs=1:ompthreads=16 -I
$ module load mvapich2
$ mpirun ./helloworld_mpi.x
In this example, we demonstrate recommended way to run an MPI
@@ -59,7 +58,7 @@ on 4 nodes.
Follow this example to run two MPI processes per node, 8 threads per
process. Note the options to mpirun for mvapich2. No options are needed
for impi.
- $ qsub -q qexp -l select=4ncpus=16mpiprocs=2ompthreads=8 -I
+ $ qsub -q qexp -l select=4:ncpus=16:mpiprocs=2:ompthreads=8 -I
$ module load mvapich2
$ mpirun -bind-to numa ./helloworld_mpi.x
In this example, we demonstrate recommended way to run an MPI
@@ -70,7 +69,7 @@ node, on 4 nodes
Follow this example to run 16 MPI processes per node, 1 thread per
process. Note the options to mpirun for mvapich2. No options are needed
for impi.
- $ qsub -q qexp -l select=4ncpus=16mpiprocs=16ompthreads=1 -I
+ $ qsub -q qexp -l select=4:ncpus=16:mpiprocs=16:ompthreads=1 -I
$ module load mvapich2
$ mpirun -bind-to core ./helloworld_mpi.x
In this example, we demonstrate recommended way to run an MPI
@@ -81,17 +80,17 @@ Important! Bind every OpenMP thread to a core!
In the previous two examples with one or two MPI processes per node, the
operating system might still migrate OpenMP threads between cores. You
might want to avoid this by setting these environment variable for GCC
-OpenMP
+OpenMP:
$ export GOMP_CPU_AFFINITY="0-15"
-or this one for Intel OpenMP
+or this one for Intel OpenMP:
$ export KMP_AFFINITY=granularity=fine,compact,1,0
As of OpenMP 4.0 (supported by GCC 4.9 and later and Intel 14.0 and
-later) the following variables may be used for Intel or GCC
+later) the following variables may be used for Intel or GCC:
$ export OMP_PROC_BIND=true
$ export OMP_PLACES=cores
Â
MPICH2 Process Mapping and Binding
-----------------------------------
+-----------
The mpirun allows for precise selection of how the MPI processes will be
mapped to the computational nodes and how these processes will bind to
particular processor sockets and cores.
@@ -120,7 +119,7 @@ The Intel MPI automatically binds each process and its threads to the
corresponding portion of cores on the processor socket of the node, no
options needed. The binding is primarily controlled by environment
variables. Read more about mpi process binding on [Intel
-website](https//software.intel.com/sites/products/documentation/hpc/ics/impi/41/lin/Reference_Manual/Environment_Variables_Process_Pinning.htm).
+website](https://software.intel.com/sites/products/documentation/hpc/ics/impi/41/lin/Reference_Manual/Environment_Variables_Process_Pinning.htm).
The MPICH2 uses the -bind-to option Use -bind-to numa or -bind-to core
to bind the process on single core or entire socket.
### Bindings verification
@@ -130,79 +129,5 @@ In all cases, binding and threading may be verified by executing
Intel MPI on Xeon Phi
---------------------
The[MPI section of Intel Xeon Phi
-chapter](../intel-xeon-phi.html) provides details on how
-to run Intel MPI code on Xeon Phi architecture.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
- .navTreeFolderish
- .contenttype-folder}
- - [Running
- OpenMPI](Running_OpenMPI.html)
-
- - [Running
- MPICH2](running-mpich2.html)
-
-
- - [MPI4Py (MPI
- for Python)](mpi4py-mpi-for-python.html "OpenMPI interface to Python")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
+chapter](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi)
+provides details on how to run Intel MPI code on Xeon Phi architecture.
diff --git a/anselm-cluster-documentation/software/ansys.html b/docs.it4i.cz/anselm-cluster-documentation/software/ansys.html
old mode 100755
new mode 100644
similarity index 61%
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rename to docs.it4i.cz/anselm-cluster-documentation/software/ansys.html
index 428142b856a1181763e18864cc0365ab232173ed..d8de0a2db765610ab4a1fc1353fb716c7196d7c6
--- a/anselm-cluster-documentation/software/ansys.html
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<title>Overview of ANSYS Products — IT4I Docs</title>
- <link rel="canonical" href="ansys.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
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<div id="portal-header">
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- <a accesskey="6" href="ansys.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
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<span id="breadcrumbs-2" dir="ltr">
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
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<div id="parent-fieldname-text-23b0fc1f4ce244a2bd48311555b77759" class="">
<p><strong><a class="external-link" href="http://www.svsfem.cz/" target="_blank" title="">SVS FEM</a></strong> as <em><strong><a class="external-link" href="http://www.ansys.com/" target="_self" title="">ANSYS Channel partner</a></strong></em> for Czech Republic provided all ANSYS licenses for ANSELM cluster and supports of all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent, Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging to problem of ANSYS functionality contact please <a class="email-link" href="mailto:hotline@svsfem.cz?subject=Ostrava%20-%20ANSELM" target="_self" title="">hotline@svsfem.cz</a></p>
-<p>Anselm provides as commercial as academic variants. Academic variants are distinguished by "<strong>Academic...</strong>" word in the name of  license or by two letter preposition "<strong>aa_</strong>" in the license feature name. Change of license is realized on command line respectively directly in user's pbs file (see individual products). <a target="_self" title="" class="internal-link" href="../../acl_users/credentials_cookie_auth/require_login888f.html"><span class="short_text" id="result_box"><span class="hps">More</span> <span class="hps">about licensing</span> <span class="hps">here</span></span></a></p>
+<p>Anselm provides as commercial as academic variants. Academic variants are distinguished by "<strong>Academic...</strong>" word in the name of  license or by two letter preposition "<strong>aa_</strong>" in the license feature name. Change of license is realized on command line respectively directly in user's pbs file (see individual products). <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing"><span class="short_text" id="result_box"><span class="hps">More</span> <span class="hps">about licensing</span> <span class="hps">here</span></span></a></p>
<p>To load the latest version of any ANSYS product (Mechanical, Fluent, CFX, MAPDL,...) load the module:</p>
<pre class=" ">$ module load ansys</pre>
<p>ANSYS supports interactive regime, but due to assumed solution of extremely difficult tasks it is not recommended.</p>
@@ -317,7 +314,7 @@
<dt class="portletHeader hiddenStructure">
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<span>Anselm Cluster Documentation</span>
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<span>Accessing the Cluster</span>
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<span>Environment and Modules</span>
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<span>Resource Allocation and Job Execution</span>
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<span>Software</span>
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<span>ANSYS</span>
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<span>ANSYS MAPDL</span>
</a>
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<span>ANSYS CFX</span>
</a>
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<span>ANSYS Fluent</span>
</a>
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<span>ANSYS LS-DYNA</span>
</a>
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<span>LS-DYNA</span>
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<span>ANSYS MAPDL PBS file</span>
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<span>ANSYS CFX PBS file</span>
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- <img width="16" height="16" src="../../sh.png" alt="Soubor" />
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<span>ANSYS Fluent PBS file</span>
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<span>ANSYS LS-DYNA PBS file</span>
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<span>LS-DYNA PBS file</span>
</a>
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- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
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- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
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- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
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- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
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- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
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- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
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- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -857,7 +854,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -873,7 +870,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -889,7 +886,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
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- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
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<span>OMICS Master</span>
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<span>OpenFOAM</span>
</a>
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</a>
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+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
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</a>
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+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1051,7 +1048,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
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- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
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@@ -1083,7 +1080,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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_paq.push(['setTrackerUrl', u+'piwik.php']);
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var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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-
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys.md b/docs.it4i.cz/anselm-cluster-documentation/software/ansys.md
new file mode 100644
index 0000000000000000000000000000000000000000..c8e08155b7b965077a12d582b462273bf2fee7c2
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys.md
@@ -0,0 +1,26 @@
+Overview of ANSYS Products
+==========================
+**[SVS FEM](http://www.svsfem.cz/)** as ***[ANSYS
+Channel partner](http://www.ansys.com/)***Â for Czech
+Republic provided all ANSYS licenses for ANSELM cluster and supports of
+all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent,
+Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging
+to problem of ANSYS functionality contact
+please [hotline@svsfem.cz](mailto:hotline@svsfem.cz?subject=Ostrava%20-%20ANSELM){.email-link}
+Anselm provides as commercial as academic variants. Academic variants
+are distinguished by "**Academic...**" word in the name of  license or
+by two letter preposition "**aa_**" in the license feature name. Change
+of license is realized on command line respectively directly in user's
+pbs file (see individual products). [<span id="result_box"
+class="short_text"><span class="hps">More</span> <span class="hps">about
+licensing</span> <span
+class="hps">here</span></span>](https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing)
+To load the latest version of any ANSYS product (Mechanical, Fluent,
+CFX, MAPDL,...) load the module:
+ $ module load ansys
+ANSYS supports interactive regime, but due to assumed solution of
+extremely difficult tasks it is not recommended.
+If user needs to work in interactive regime we recommend to configure
+the RSM service on the client machine which allows to forward the
+solution to the Anselm directly from the client's Workbench project
+(see ANSYS RSM service).
diff --git a/anselm-cluster-documentation/software/ansys/Fluent_Licence_1.jpg b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/Fluent_Licence_1.jpg
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old mode 100755
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old mode 100755
new mode 100644
similarity index 58%
rename from anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view.html
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index cce36fb6059112d4a477c5a8bcd1eefdeb546938..0aa81960b1e8c4e16ba17e724cf37bbd972859b2
--- a/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file" /><!--[if lt IE 7]></base><![endif]-->
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>ANSYS CFX PBS file — IT4I Docs</title>
- <link rel="canonical" href="../cfx.pbs" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="view.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="view.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../../index.html">
- <img src="../../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../../ansys.html">ANSYS</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">ANSYS</a>
<span class="breadcrumbSeparator">
/
@@ -250,8 +247,8 @@
- <a href="at_download/cfx.pbs">
- <img src="../../../../sh.png" alt="shell script icon" />
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/at_download/file">
+ <img src="https://docs.it4i.cz/sh.png" alt="shell script icon" />
cfx.pbs
</a>
<span class="discreet">
@@ -313,7 +310,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -329,7 +326,7 @@
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<span>What's New</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
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</a>
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<span>Accessing the Cluster</span>
</a>
@@ -425,7 +422,7 @@
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</a>
@@ -441,7 +438,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -457,7 +454,7 @@
- <a title="" class="state-published contenttype-document" href="../../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -473,7 +470,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -489,7 +486,7 @@
- <a title="" class="state-published contenttype-document" href="../../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -505,10 +502,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -524,7 +521,7 @@
- <a title="An engineering simulation software " class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../ansys.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
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</a>
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<span>ANSYS CFX PBS file</span>
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<span>ANSYS Fluent PBS file</span>
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<span>ANSYS LS-DYNA PBS file</span>
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<span>LS-DYNA PBS file</span>
</a>
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<span>COMSOL</span>
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</a>
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<span>ISV Licenses</span>
</a>
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</a>
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<span>nVidia CUDA</span>
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</a>
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</a>
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</a>
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<span>ParaView</span>
</a>
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<span>GPI-2</span>
</a>
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<span>Remote visualization service</span>
</a>
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<span>PRACE User Support</span>
</a>
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<span>Links</span>
</a>
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<span>Changelog</span>
</a>
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<span>PBSPro Documentation</span>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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diff --git a/anselm-cluster-documentation/software/ansys/ansys-cfx.html b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.html
old mode 100755
new mode 100644
similarity index 62%
rename from anselm-cluster-documentation/software/ansys/ansys-cfx.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.html
index 0493835ea2e944888e860d3af77690fca7beeaa1..16f8547aeaa695810aefdc9a2593960914f150c4
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<title>ANSYS CFX — IT4I Docs</title>
- <link rel="canonical" href="ansys-cfx.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx" />
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<script type="text/javascript">
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
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<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="ansys-cfx.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="ansys-cfx.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<div id="portal-personaltools-wrapper">
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<div id="portal-advanced-search" class="hiddenStructure">
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</div>
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+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
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</span>
<span id="breadcrumbs-1" dir="ltr">
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<span id="breadcrumbs-2" dir="ltr">
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/
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</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../ansys.html">ANSYS</a>
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/
@@ -249,9 +246,9 @@
<p><a class="external-link" href="http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+CFX" target="_blank" title="">ANSYS CFX</a> software is a high-performance, general purpose fluid dynamics program that has been applied to solve wide-ranging fluid flow problems for over 20 years. At the heart of ANSYS CFX is its advanced solver technology, the key to achieving reliable and accurate solutions quickly and robustly. The modern, highly parallelized solver is the foundation for an abundant choice of physical models to capture virtually any type of phenomena related to fluid flow. The solver and its many physical models are wrapped in a modern, intuitive, and flexible GUI and user environment, with extensive capabilities for customization and automation using session files, scripting and a powerful expression language.</p>
<p><span>To run ANSYS CFX in batch mode you can utilize/modify the default cfx.pbs script and execute it via the qsub command.</span></p>
<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -l nodes=2:ppn=16<br />#PBS -q qprod<br />#PBS -N $USER-CFX-Project<br />#PBS -A XX-YY-ZZ<br /><br />#! Mail to user when job terminate or abort<br />#PBS -m ae<br /><br />#!change the working directory (default is home directory)<br />#cd <working directory> (working directory must exists)<br />WORK_DIR="/scratch/$USER/work"<br />cd $WORK_DIR<br /><br />echo Running on host `hostname`<br />echo Time is `date`<br />echo Directory is `pwd`<br />echo This jobs runs on the following processors:<br />echo `cat $PBS_NODEFILE`<br /><br />module load ansys<br /><br />#### Set number of processors per host listing<br />#### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)<br />procs_per_host=1<br />#### Create host list<br />hl=""<br />for host in `cat $PBS_NODEFILE`<br />do<br /> if [ "$hl" = "" ]<br /> then hl="$host:$procs_per_host"<br /> else hl="${hl}:$host:$procs_per_host"<br /> fi<br />done<br /><br />echo Machines: $hl<br /><br />#-dev input.def includes the input of CFX analysis in DEF format<br />#-P the name of prefered license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial))<br />/ansys_inc/v145/CFX/bin/cfx5solve -def input.def -size 4 -size-ni 4x -part-large -start-method "Platform MPI Distributed Parallel" -par-dist $hl -P aa_r</pre>
-<p>Header of the pbs file (above) is common and description can be find on <a target="_blank" title="" class="internal-link" href="../../resource-allocation-and-job-execution/job-submission-and-execution.html">this site</a>. SVS FEM recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
+<p>Header of the pbs file (above) is common and description can be find on <a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">this site</a>. SVS FEM recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
<p>Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. <span>Input file has to be defined by common CFX def file which is attached to the cfx solver via parameter -def</span></p>
-<p><strong>License</strong>Â should be selected by parameter -P (Big letter <strong>P</strong>). Licensed products are the following: aa_r (ANSYSÂ <strong>Academic</strong>Â Research), ane3fl (ANSYS Multiphysics)-<strong>Commercial.</strong> <br /><a target="_self" title="" class="internal-link" href="../../../acl_users/credentials_cookie_auth/require_login888f.html"><span class="short_text" id="result_box"><span class="hps">More</span> <span class="hps">about licensing</span> <span class="hps">here</span></span></a></p>
+<p><strong>License</strong>Â should be selected by parameter -P (Big letter <strong>P</strong>). Licensed products are the following: aa_r (ANSYSÂ <strong>Academic</strong>Â Research), ane3fl (ANSYS Multiphysics)-<strong>Commercial.</strong> <br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing"><span class="short_text" id="result_box"><span class="hps">More</span> <span class="hps">about licensing</span> <span class="hps">here</span></span></a></p>
<p>Â </p>
</div>
@@ -328,7 +325,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -344,7 +341,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -360,7 +357,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -376,7 +373,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -392,7 +389,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -408,7 +405,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -424,7 +421,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -440,7 +437,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -456,7 +453,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -472,7 +469,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -488,7 +485,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -504,7 +501,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -520,10 +517,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -539,7 +536,7 @@
- <a title="An engineering simulation software " class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -555,7 +552,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-mechanical-apdl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl">
<span>ANSYS MAPDL</span>
</a>
@@ -571,7 +568,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="ansys-cfx.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx">
<span>ANSYS CFX</span>
</a>
@@ -587,7 +584,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-fluent.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent">
<span>ANSYS Fluent</span>
</a>
@@ -603,7 +600,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-ls-dyna.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna">
<span>ANSYS LS-DYNA</span>
</a>
@@ -619,7 +616,7 @@
- <a title="" class="state-published contenttype-document" href="ls-dyna.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna">
<span>LS-DYNA</span>
</a>
@@ -635,8 +632,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-mapdl-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS MAPDL PBS file</span>
</a>
@@ -651,8 +648,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-cfx-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS CFX PBS file</span>
</a>
@@ -667,8 +664,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-fluent-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS Fluent PBS file</span>
</a>
@@ -683,8 +680,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS LS-DYNA PBS file</span>
</a>
@@ -699,8 +696,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>LS-DYNA PBS file</span>
</a>
@@ -724,7 +721,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -740,7 +737,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -756,7 +753,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -772,7 +769,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -788,7 +785,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -804,7 +801,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -820,7 +817,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -836,7 +833,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -852,7 +849,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -868,7 +865,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -884,7 +881,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -900,7 +897,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -916,7 +913,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -932,7 +929,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -948,7 +945,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -964,7 +961,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -980,7 +977,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -996,7 +993,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1021,7 +1018,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1037,7 +1034,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1062,7 +1059,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1078,7 +1075,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1094,7 +1091,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -1162,12 +1159,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1183,7 +1180,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md
new file mode 100644
index 0000000000000000000000000000000000000000..90931cac41dfd242affef7b9414133c47df1afbf
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md
@@ -0,0 +1,72 @@
+ANSYS CFX
+=========
+[ANSYS
+CFX](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+CFX)
+software is a high-performance, general purpose fluid dynamics program
+that has been applied to solve wide-ranging fluid flow problems for over
+20 years. At the heart of ANSYS CFX is its advanced solver technology,
+the key to achieving reliable and accurate solutions quickly and
+robustly. The modern, highly parallelized solver is the foundation for
+an abundant choice of physical models to capture virtually any type of
+phenomena related to fluid flow. The solver and its many physical models
+are wrapped in a modern, intuitive, and flexible GUI and user
+environment, with extensive capabilities for customization and
+automation using session files, scripting and a powerful expression
+language.
+<span>To run ANSYS CFX in batch mode you can utilize/modify the default
+cfx.pbs script and execute it via the qsub command.</span>
+``` {.prettyprint .lang-sh}
+#!/bin/bash
+#PBS -l nodes=2:ppn=16
+#PBS -q qprod
+#PBS -N $USER-CFX-Project
+#PBS -A XX-YY-ZZ
+#! Mail to user when job terminate or abort
+#PBS -m ae
+#!change the working directory (default is home directory)
+#cd <working directory> (working directory must exists)
+WORK_DIR="/scratch/$USER/work"
+cd $WORK_DIR
+echo Running on host `hostname`
+echo Time is `date`
+echo Directory is `pwd`
+echo This jobs runs on the following processors:
+echo `cat $PBS_NODEFILE`
+module load ansys
+#### Set number of processors per host listing
+#### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)
+procs_per_host=1
+#### Create host list
+hl=""
+for host in `cat $PBS_NODEFILE`
+do
+ if [ "$hl" = "" ]
+ then hl="$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
+ fi
+done
+echo Machines$hl
+#-dev input.def includes the input of CFX analysis in DEF format
+#-P the name of prefered license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial))
+/ansys_inc/v145/CFX/bin/cfx5solve -def input.def -size 4 -size-ni 4x -part-large -start-method "Platform MPI Distributed Parallel" -par-dist $hl -P aa_r
+```
+Header of the pbs file (above) is common and description can be find
+on [this
+site](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution).
+SVS FEM recommends to utilize sources by keywordsnodes, ppn. These
+keywords allows to address directly the number of nodes (computers) and
+cores (ppn) which will be utilized in the job. Also the rest of code
+assumes such structure of allocated resources.
+Working directory has to be created before sending pbs job into the
+queue. Input file should be in working directory or full path to input
+file has to be specified. <span>Input file has to be defined by common
+CFX def file which is attached to the cfx solver via parameter
+-def</span>
+**License**Â should be selected by parameter -P (Big letter **P**).
+Licensed products are the followingaa_r
+(ANSYSÂ **Academic**Â Research), ane3fl (ANSYS
+Multiphysics)-**Commercial.**
+[<span id="result_box" class="short_text"><span class="hps">More</span>
+<span class="hps">about licensing</span> <span
+class="hps">here</span></span>](https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing)
+Â
diff --git a/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/at_download/fluent.pbs b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file.1
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/at_download/fluent.pbs
rename to docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file.1
diff --git a/anselm-cluster-documentation/software/ansys/fluent.pbs b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/at_download/file
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/software/ansys/fluent.pbs
rename to docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/at_download/file
diff --git a/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view.html b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view.html
old mode 100755
new mode 100644
similarity index 58%
rename from anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view.html
index ceda698c402a94cd8c52012b7ad502c3c3bc5f87..a13c639f743ff960c7412e0e690a6ccdbd6cd9b8
--- a/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:35 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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- <style type="text/css" media="screen">@import url(../../../../portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
- <link rel="stylesheet" type="text/css" href="../../../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="../../../../portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>ANSYS Fluent PBS file — IT4I Docs</title>
- <link rel="canonical" href="../fluent.pbs" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="view.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="view.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../../index.html">
- <img src="../../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../../ansys.html">ANSYS</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">ANSYS</a>
<span class="breadcrumbSeparator">
/
@@ -250,8 +247,8 @@
- <a href="at_download/fluent.pbs">
- <img src="../../../../sh.png" alt="shell script icon" />
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/at_download/file">
+ <img src="https://docs.it4i.cz/sh.png" alt="shell script icon" />
fluent.pbs
</a>
<span class="discreet">
@@ -313,7 +310,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -329,7 +326,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -345,7 +342,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -361,7 +358,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -393,7 +390,7 @@
- <a title="" class="state-published contenttype-document" href="../../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -409,7 +406,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -425,7 +422,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -441,7 +438,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -457,7 +454,7 @@
- <a title="" class="state-published contenttype-document" href="../../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
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<span>Storage</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
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-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -524,7 +521,7 @@
- <a title="An engineering simulation software " class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../ansys.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../ansys-mechanical-apdl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl">
<span>ANSYS MAPDL</span>
</a>
@@ -556,7 +553,7 @@
- <a title="" class="state-published contenttype-document" href="../ansys-cfx.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx">
<span>ANSYS CFX</span>
</a>
@@ -572,7 +569,7 @@
- <a title="" class="state-published contenttype-document" href="../ansys-fluent.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent">
<span>ANSYS Fluent</span>
</a>
@@ -588,7 +585,7 @@
- <a title="" class="state-published contenttype-document" href="../ansys-ls-dyna.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna">
<span>ANSYS LS-DYNA</span>
</a>
@@ -604,7 +601,7 @@
- <a title="" class="state-published contenttype-document" href="../ls-dyna.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna">
<span>LS-DYNA</span>
</a>
@@ -620,8 +617,8 @@
- <a title="" class="state-missing-value contenttype-file" href="../ansys-mapdl-pbs-file/view.html">
- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS MAPDL PBS file</span>
</a>
@@ -636,8 +633,8 @@
- <a title="" class="state-missing-value contenttype-file" href="../ansys-cfx-pbs-file/view.html">
- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS CFX PBS file</span>
</a>
@@ -652,8 +649,8 @@
- <a title="" class="state-missing-value navTreeCurrentItem navTreeCurrentNode contenttype-file" href="view.html">
- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value navTreeCurrentItem navTreeCurrentNode contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS Fluent PBS file</span>
</a>
@@ -668,8 +665,8 @@
- <a title="" class="state-missing-value contenttype-file" href="../ansys-ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS LS-DYNA PBS file</span>
</a>
@@ -684,8 +681,8 @@
- <a title="" class="state-missing-value contenttype-file" href="../ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>LS-DYNA PBS file</span>
</a>
@@ -709,7 +706,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -725,7 +722,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -741,7 +738,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -757,7 +754,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -773,7 +770,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -789,7 +786,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
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<span>Virtualization</span>
</a>
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<span>Compilers</span>
</a>
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<span>Intel Xeon Phi</span>
</a>
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<span>ISV Licenses</span>
</a>
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+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
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<span>nVidia CUDA</span>
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<span>OpenFOAM</span>
</a>
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+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
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</a>
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+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
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+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
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<span>Links</span>
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+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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diff --git a/acl_users/credentials_cookie_auth/require_logind8a8.md b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view.md
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diff --git a/anselm-cluster-documentation/software/ansys/ansys-fluent.html b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.html
old mode 100755
new mode 100644
similarity index 66%
rename from anselm-cluster-documentation/software/ansys/ansys-fluent.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.html
index fd7f0d045e5f7e1f386736d8a541db4d26d438a4..44a814154977c130663c0ecbdcaa93ad1dd480d7
--- a/anselm-cluster-documentation/software/ansys/ansys-fluent.html
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<title>ANSYS Fluent — IT4I Docs</title>
- <link rel="canonical" href="ansys-fluent.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
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+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="ansys-fluent.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="ansys-fluent.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
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- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
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</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
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@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../ansys.html">ANSYS</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">ANSYS</a>
<span class="breadcrumbSeparator">
/
@@ -250,7 +247,7 @@
<h2 class=" "><span>1. Common way to run Fluent over pbs file</span></h2>
<p><span>To run ANSYS Fluent in batch mode you can utilize/modify the default fluent.pbs script and execute it via the qsub command.</span></p>
<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -S /bin/bash<br />#PBS -l nodes=2:ppn=16<br />#PBS -q qprod<br />#PBS -N $USER-Fluent-Project<br />#PBS -A XX-YY-ZZ<br /><br />#! Mail to user when job terminate or abort<br />#PBS -m ae<br /><br />#!change the working directory (default is home directory)<br />#cd <working directory> (working directory must exists)<br />WORK_DIR="/scratch/$USER/work"<br />cd $WORK_DIR<br /><br />echo Running on host `hostname`<br />echo Time is `date`<br />echo Directory is `pwd`<br />echo This jobs runs on the following processors:<br />echo `cat $PBS_NODEFILE`<br /><br />#### Load ansys module so that we find the cfx5solve command<br />module load ansys<br /><br /># Use following line to specify MPI for message-passing instead<br />NCORES=`wc -l $PBS_NODEFILE |awk '{print $1}'`<br /><br />/ansys_inc/v145/fluent/bin/fluent 3d -t$NCORES -cnf=$PBS_NODEFILE -g -i fluent.jou</pre>
-<p>Header of the pbs file (above) is common and description can be find on <a target="_blank" title="" class="internal-link" href="../../resource-allocation-and-job-execution/job-submission-and-execution.html">this site</a>. <a class="external-link" href="http://www.svsfem.cz/" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
+<p>Header of the pbs file (above) is common and description can be find on <a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">this site</a>. <a class="external-link" href="http://www.svsfem.cz" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
<p>Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common Fluent journal file which is attached to the Fluent solver via parameter -i fluent.jou</p>
<p>Journal file with definition of the input geometry and boundary conditions and defined process of solution has e.g. the following structure:</p>
<pre class=" ">/file/read-case aircraft_2m.cas.gz<br />/solve/init<br />init<br />/solve/iterate<br />10<br />/file/write-case-dat aircraft_2m-solution<br />/exit yes</pre>
@@ -330,13 +327,13 @@ mpp="true"</pre>
<p>Fluent could be run in parallel only under Academic Research license. To do so this ANSYS Academic Research license must be placed before ANSYS CFD license in user preferences. To make this change anslic_admin utility should be run</p>
<pre class="prettyprint lang-sh">/ansys_inc/shared_ les/licensing/lic_admin/anslic_admin</pre>
<p>ANSLIC_ADMIN Utility will be run</p>
-<p><img title="" class="image-inline" alt="" src="Fluent_Licence_1.jpg" /></p>
-<p><img title="" class="image-inline" alt="" src="Fluent_Licence_2.jpg" /></p>
-<p><img title="" class="image-inline" alt="" src="Fluent_Licence_3.jpg" /></p>
+<p><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/Fluent_Licence_1.jpg" /></p>
+<p><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/Fluent_Licence_2.jpg" /></p>
+<p><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/Fluent_Licence_3.jpg" /></p>
<p>Â </p>
<p>ANSYS Academic Research license should be moved up to the top of the list.</p>
<p>Â </p>
-<p><img title="" class="image-inline" alt="" src="Fluent_Licence_4.jpg" /></p>
+<p><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/Fluent_Licence_4.jpg" /></p>
</div>
@@ -412,7 +409,7 @@ mpp="true"</pre>
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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@@ -428,7 +425,7 @@ mpp="true"</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -460,7 +457,7 @@ mpp="true"</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -476,7 +473,7 @@ mpp="true"</pre>
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -492,7 +489,7 @@ mpp="true"</pre>
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -508,7 +505,7 @@ mpp="true"</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -524,7 +521,7 @@ mpp="true"</pre>
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -540,7 +537,7 @@ mpp="true"</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -556,7 +553,7 @@ mpp="true"</pre>
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -572,7 +569,7 @@ mpp="true"</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -588,7 +585,7 @@ mpp="true"</pre>
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -604,10 +601,10 @@ mpp="true"</pre>
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -623,7 +620,7 @@ mpp="true"</pre>
- <a title="An engineering simulation software " class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -639,7 +636,7 @@ mpp="true"</pre>
- <a title="" class="state-published contenttype-document" href="ansys-mechanical-apdl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl">
<span>ANSYS MAPDL</span>
</a>
@@ -655,7 +652,7 @@ mpp="true"</pre>
- <a title="" class="state-published contenttype-document" href="ansys-cfx.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx">
<span>ANSYS CFX</span>
</a>
@@ -671,7 +668,7 @@ mpp="true"</pre>
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="ansys-fluent.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent">
<span>ANSYS Fluent</span>
</a>
@@ -687,7 +684,7 @@ mpp="true"</pre>
- <a title="" class="state-published contenttype-document" href="ansys-ls-dyna.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna">
<span>ANSYS LS-DYNA</span>
</a>
@@ -703,7 +700,7 @@ mpp="true"</pre>
- <a title="" class="state-published contenttype-document" href="ls-dyna.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna">
<span>LS-DYNA</span>
</a>
@@ -719,8 +716,8 @@ mpp="true"</pre>
- <a title="" class="state-missing-value contenttype-file" href="ansys-mapdl-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS MAPDL PBS file</span>
</a>
@@ -735,8 +732,8 @@ mpp="true"</pre>
- <a title="" class="state-missing-value contenttype-file" href="ansys-cfx-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS CFX PBS file</span>
</a>
@@ -751,8 +748,8 @@ mpp="true"</pre>
- <a title="" class="state-missing-value contenttype-file" href="ansys-fluent-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS Fluent PBS file</span>
</a>
@@ -767,8 +764,8 @@ mpp="true"</pre>
- <a title="" class="state-missing-value contenttype-file" href="ansys-ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS LS-DYNA PBS file</span>
</a>
@@ -783,8 +780,8 @@ mpp="true"</pre>
- <a title="" class="state-missing-value contenttype-file" href="ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>LS-DYNA PBS file</span>
</a>
@@ -808,7 +805,7 @@ mpp="true"</pre>
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -824,7 +821,7 @@ mpp="true"</pre>
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -840,7 +837,7 @@ mpp="true"</pre>
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -856,7 +853,7 @@ mpp="true"</pre>
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -872,7 +869,7 @@ mpp="true"</pre>
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -888,7 +885,7 @@ mpp="true"</pre>
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -904,7 +901,7 @@ mpp="true"</pre>
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -920,7 +917,7 @@ mpp="true"</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -936,7 +933,7 @@ mpp="true"</pre>
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -952,7 +949,7 @@ mpp="true"</pre>
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -968,7 +965,7 @@ mpp="true"</pre>
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -984,7 +981,7 @@ mpp="true"</pre>
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -1000,7 +997,7 @@ mpp="true"</pre>
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -1016,7 +1013,7 @@ mpp="true"</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -1032,7 +1029,7 @@ mpp="true"</pre>
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -1048,7 +1045,7 @@ mpp="true"</pre>
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1064,7 +1061,7 @@ mpp="true"</pre>
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1080,7 +1077,7 @@ mpp="true"</pre>
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1105,7 +1102,7 @@ mpp="true"</pre>
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1121,7 +1118,7 @@ mpp="true"</pre>
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1146,7 +1143,7 @@ mpp="true"</pre>
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1162,7 +1159,7 @@ mpp="true"</pre>
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1178,7 +1175,7 @@ mpp="true"</pre>
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1217,14 +1214,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1246,12 +1243,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1267,7 +1264,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:34 GMT -->
</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md
new file mode 100644
index 0000000000000000000000000000000000000000..b8b7b424fe32b2abb0fc95bd409bd79835becc8c
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md
@@ -0,0 +1,183 @@
+ANSYS Fluent
+============
+[ANSYS
+Fluent](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent)
+software contains the broad physical modeling capabilities needed to
+model flow, turbulence, heat transfer, and reactions for industrial
+applications ranging from air flow over an aircraft wing to combustion
+in a furnace, from bubble columns to oil platforms, from blood flow to
+semiconductor manufacturing, and from clean room design to wastewater
+treatment plants. Special models that give the software the ability to
+model in-cylinder combustion, aeroacoustics, turbomachinery, and
+multiphase systems have served to broaden its reach.
+<span>1. Common way to run Fluent over pbs file</span>
+--------
+<span>To run ANSYS Fluent in batch mode you can utilize/modify the
+default fluent.pbs script and execute it via the qsub command.</span>
+``` {.prettyprint .lang-sh}
+#!/bin/bash
+#PBS -S /bin/bash
+#PBS -l nodes=2:ppn=16
+#PBS -q qprod
+#PBS -N $USER-Fluent-Project
+#PBS -A XX-YY-ZZ
+#! Mail to user when job terminate or abort
+#PBS -m ae
+#!change the working directory (default is home directory)
+#cd <working directory> (working directory must exists)
+WORK_DIR="/scratch/$USER/work"
+cd $WORK_DIR
+echo Running on host `hostname`
+echo Time is `date`
+echo Directory is `pwd`
+echo This jobs runs on the following processors:
+echo `cat $PBS_NODEFILE`
+#### Load ansys module so that we find the cfx5solve command
+module load ansys
+# Use following line to specify MPI for message-passing instead
+NCORES=`wc -l $PBS_NODEFILE |awk '{print $1}'`
+/ansys_inc/v145/fluent/bin/fluent 3d -t$NCORES -cnf=$PBS_NODEFILE -g -i fluent.jou
+```
+Header of the pbs file (above) is common and description can be find
+on [this
+site](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution).
+[SVS FEM](http://www.svsfem.cz) recommends to utilize
+sources by keywordsnodes, ppn. These keywords allows to address
+directly the number of nodes (computers) and cores (ppn) which will be
+utilized in the job. Also the rest of code assumes such structure of
+allocated resources.
+Working directory has to be created before sending pbs job into the
+queue. Input file should be in working directory or full path to input
+file has to be specified. Input file has to be defined by common Fluent
+journal file which is attached to the Fluent solver via parameter -i
+fluent.jou
+Journal file with definition of the input geometry and boundary
+conditions and defined process of solution has e.g. the following
+structure:
+ /file/read-case aircraft_2m.cas.gz
+ /solve/init
+ init
+ /solve/iterate
+ 10
+ /file/write-case-dat aircraft_2m-solution
+ /exit yes
+<span>The appropriate dimension of the problem has to be set by
+parameter (2d/3d). </span>
+<span>2. Fast way to run Fluent from command line</span>
+----------
+``` {.prettyprint .lang-sh}
+fluent solver_version [FLUENT_options] -i journal_file -pbs
+```
+This syntax will start the ANSYS FLUENT job under PBS Professional using
+the <span class="monospace">qsub</span>Â command in a batch manner. When
+resources are available, PBS Professional will start the job and return
+a job ID, usually in the form of <span
+class="emphasis">*job_ID.hostname*</span>. This job ID can then be used
+to query, control, or stop the job using standard PBS Professional
+commands, such as <span class="monospace">qstat</span>Â or <span
+class="monospace">qdel</span>. The job will be run out of the current
+working directory, and all output will be written to the file <span
+class="monospace">fluent.o</span><span>Â </span><span
+class="emphasis">*job_ID*</span>. Â Â Â Â
+3. Running Fluent via user's config file
+-----------------
+The sample script uses a configuration file called <span
+class="monospace">pbs_fluent.conf</span> Â if no command line arguments
+are present. This configuration file should be present in the directory
+from which the jobs are submitted (which is also the directory in which
+the jobs are executed). The following is an example of what the content
+of <span class="monospace">pbs_fluent.conf</span>Â can be:
+``` {.screen}
+input="example_small.flin"
+case="Small-1.65m.cas"
+fluent_args="3d -pmyrinet"
+outfile="fluent_test.out"
+mpp="true"
+```
+The following is an explanation of the parameters:
+<span><span class="monospace">input</span> is the name of the input
+file.</span>
+<span class="monospace">case</span> is the name of the <span
+class="monospace">.cas</span>Â file that the input file will utilize.
+<span class="monospace">fluent_args</span> are extra ANSYS FLUENT
+arguments. As shown in the previous example, you can specify the
+interconnect by using the <span class="monospace">-p</span>Â interconnect
+command. The available interconnects include <span
+class="monospace">ethernet</span>Â (the default), <span
+class="monospace">myrinet</span>,<span class="monospace">
+infiniband</span>, <span class="monospace">vendor</span>, <span
+class="monospace">altix</span><span>,</span> and <span
+class="monospace">crayx</span>. The MPI is selected automatically, based
+on the specified interconnect.
+<span class="monospace">outfile</span> is the name of the file to which
+the standard output will be sent.
+<span class="monospace">mpp="true"</span> will tell the job script to
+execute the job across multiple processors. Â Â Â Â Â Â Â Â
+<span>To run ANSYS Fluent in batch mode with user's config file you can
+utilize/modify the following script and execute it via the qsub
+command.</span>
+``` {.prettyprint .lang-sh}
+#!/bin/sh
+#PBS -l nodes=2:ppn=4
+#PBS -1 qprod
+#PBS -N $USE-Fluent-Project
+#PBS -A XX-YY-ZZ
+ cd $PBS_O_WORKDIR
+
+ #We assume that if they didn’t specify arguments then they should use the
+ #config file if [ "xx${input}${case}${mpp}${fluent_args}zz" = "xxzz" ]; then
+ if [ -f pbs_fluent.conf ]; then
+ . pbs_fluent.conf
+ else
+ printf "No command line arguments specified, "
+ printf "and no configuration file found. Exiting n"
+ fi
+ fi
+
+ #Augment the ANSYS FLUENT command line arguments case "$mpp" in
+ true)
+ #MPI job execution scenario
+ num_nodes=â€cat $PBS_NODEFILE | sort -u | wc -lâ€
+ cpus=â€expr $num_nodes * $NCPUSâ€
+ #Default arguments for mpp jobs, these should be changed to suit your
+ #needs.
+ fluent_args="-t${cpus} $fluent_args -cnf=$PBS_NODEFILE"
+ ;;
+ *)
+ #SMP case
+ #Default arguments for smp jobs, should be adjusted to suit your
+ #needs.
+ fluent_args="-t$NCPUS $fluent_args"
+ ;;
+ esac
+ #Default arguments for all jobs
+ fluent_args="-ssh -g -i $input $fluent_args"
+ echo "---------- Going to start a fluent job with the following settings:
+ Input$input
+ Case$case
+ Output$outfile
+ Fluent arguments$fluent_args"
+
+ #run the solver
+ /ansys_inc/v145/fluent/bin/fluent $fluent_args > $outfile
+```
+<span>It runs the jobs out of the directory from which they are
+submitted (PBS_O_WORKDIR).</span>
+4. Running Fluent in parralel
+------
+Fluent could be run in parallel only under Academic Research license. To
+do so this ANSYS Academic Research license must be placed before ANSYS
+CFD license in user preferences. To make this change anslic_admin
+utility should be run
+``` {.prettyprint .lang-sh}
+/ansys_inc/shared_ les/licensing/lic_admin/anslic_admin
+```
+ANSLIC_ADMIN Utility will be run
+
+
+
+Â
+ANSYS Academic Research license should be moved up to the top of the
+list.
+Â
+
diff --git a/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/at_download/ansysdyna.pbs b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file.1
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/at_download/ansysdyna.pbs
rename to docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file.1
diff --git a/anselm-cluster-documentation/software/ansys/ansysdyna.pbs b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/at_download/file
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/software/ansys/ansysdyna.pbs
rename to docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/at_download/file
diff --git a/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view.html b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view.html
old mode 100755
new mode 100644
similarity index 58%
rename from anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view.html
index 51b977a1cde3369290b8aeefebd6b9b185560e56..7531baa784c4e88cac303d2262b5f439dbcfa3ba
--- a/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view.html
@@ -10,45 +10,42 @@
-
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- <link rel="stylesheet" type="text/css" href="../../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
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<title>ANSYS LS-DYNA PBS file — IT4I Docs</title>
- <link rel="canonical" href="../ansysdyna.pbs" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="view.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="view.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../../index.html">
- <img src="../../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
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@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
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@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
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@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../../ansys.html">ANSYS</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">ANSYS</a>
<span class="breadcrumbSeparator">
/
@@ -250,8 +247,8 @@
- <a href="at_download/ansysdyna.pbs">
- <img src="../../../../sh.png" alt="shell script icon" />
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/at_download/file">
+ <img src="https://docs.it4i.cz/sh.png" alt="shell script icon" />
ansysdyna.pbs
</a>
<span class="discreet">
@@ -313,7 +310,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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@@ -329,7 +326,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
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<span>Salomon Cluster Documentation</span>
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+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
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<span>Hardware Overview</span>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
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<span>Environment and Modules</span>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
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<span>Compute Nodes</span>
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<span>Storage</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../../network.html">
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<span>Network</span>
</a>
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-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
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<span>ANSYS</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl">
<span>ANSYS MAPDL</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx">
<span>ANSYS CFX</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../ansys-fluent.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent">
<span>ANSYS Fluent</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../ansys-ls-dyna.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna">
<span>ANSYS LS-DYNA</span>
</a>
@@ -604,7 +601,7 @@
- <a title="" class="state-published contenttype-document" href="../ls-dyna.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna">
<span>LS-DYNA</span>
</a>
@@ -620,8 +617,8 @@
- <a title="" class="state-missing-value contenttype-file" href="../ansys-mapdl-pbs-file/view.html">
- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS MAPDL PBS file</span>
</a>
@@ -636,8 +633,8 @@
- <a title="" class="state-missing-value contenttype-file" href="../ansys-cfx-pbs-file/view.html">
- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS CFX PBS file</span>
</a>
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- <a title="" class="state-missing-value contenttype-file" href="../ansys-fluent-pbs-file/view.html">
- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS Fluent PBS file</span>
</a>
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- <a title="" class="state-missing-value navTreeCurrentItem navTreeCurrentNode contenttype-file" href="view.html">
- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value navTreeCurrentItem navTreeCurrentNode contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS LS-DYNA PBS file</span>
</a>
@@ -684,8 +681,8 @@
- <a title="" class="state-missing-value contenttype-file" href="../ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>LS-DYNA PBS file</span>
</a>
@@ -709,7 +706,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -725,7 +722,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
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- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
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- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
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- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -789,7 +786,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -805,7 +802,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -837,7 +834,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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old mode 100755
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<title>ANSYS LS-DYNA — IT4I Docs</title>
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- <a accesskey="6" href="ansys-ls-dyna.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">ANSYS</a>
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<p><a class="external-link" href="http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/Explicit+Dynamics/ANSYS+LS-DYNA" target="_blank" title="">ANSYS LS-DYNA</a> software provides convenient and easy-to-use access to the technology-rich, time-tested explicit solver without the need to contend with the complex input requirements of this sophisticated program. Introduced in 1996, ANSYS LS-DYNA capabilities have helped customers in numerous industries to resolve highly intricate design issues. <span>ANSYS Mechanical users have been able take advantage of complex explicit solutions for a long time utilizing the traditional ANSYS Parametric Design Language (APDL) environment. <span>These explicit capabilities are available to ANSYS Workbench users as well. The Workbench platform is a powerful, comprehensive, easy-to-use environment for engineering simulation. CAD import from all sources, geometry cleanup, automatic meshing, solution, parametric optimization, result visualization and comprehensive report generation are all available within a single fully interactive modern graphical user environment.</span></span></p>
<p><span>To run ANSYS LS-DYNA in batch mode you can utilize/modify the default ansysdyna.pbs script and execute it via the qsub command.</span></p>
<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -l nodes=2:ppn=16<br />#PBS -q qprod<br />#PBS -N $USER-DYNA-Project<br />#PBS -A XX-YY-ZZ<br /><br />#! Mail to user when job terminate or abort<br />#PBS -m ae<br /><br />#!change the working directory (default is home directory)<br />#cd <working directory><br />WORK_DIR="/scratch/$USER/work"<br />cd $WORK_DIR<br /><br />echo Running on host `hostname`<br />echo Time is `date`<br />echo Directory is `pwd`<br />echo This jobs runs on the following processors:<br />echo `cat $PBS_NODEFILE`<br /><br />#! Counts the number of processors<br />NPROCS=`wc -l < $PBS_NODEFILE`<br /><br />echo This job has allocated $NPROCS nodes<br /><br />module load ansys<br /><br />#### Set number of processors per host listing<br />#### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)<br />procs_per_host=1<br />#### Create host list<br />hl=""<br />for host in `cat $PBS_NODEFILE`<br />do<br /> if [ "$hl" = "" ]<br /> then hl="$host:$procs_per_host"<br /> else hl="${hl}:$host:$procs_per_host"<br /> fi<br />done<br /><br />echo Machines: $hl<br /><br />/ansys_inc/v145/ansys/bin/ansys145 -dis -lsdynampp i=input.k -machines $hl</pre>
-<p><span>Header of the pbs file (above) is common and description can be find on </span><a target="_blank" title="" class="internal-link" href="../../resource-allocation-and-job-execution/job-submission-and-execution.html">this site</a><span>. <a class="external-link" href="http://www.svsfem.cz/" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</span></p>
+<p><span>Header of the pbs file (above) is common and description can be find on </span><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">this site</a><span>. <a class="external-link" href="http://www.svsfem.cz" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</span></p>
<p>Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common LS-DYNA .<strong>k</strong> file which is attached to the ansys solver via parameter i=</p>
<p><span><span>Â </span></span></p>
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-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -538,7 +535,7 @@
- <a title="An engineering simulation software " class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -554,7 +551,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-mechanical-apdl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl">
<span>ANSYS MAPDL</span>
</a>
@@ -570,7 +567,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-cfx.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx">
<span>ANSYS CFX</span>
</a>
@@ -586,7 +583,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-fluent.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent">
<span>ANSYS Fluent</span>
</a>
@@ -602,7 +599,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="ansys-ls-dyna.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna">
<span>ANSYS LS-DYNA</span>
</a>
@@ -618,7 +615,7 @@
- <a title="" class="state-published contenttype-document" href="ls-dyna.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna">
<span>LS-DYNA</span>
</a>
@@ -634,8 +631,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-mapdl-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS MAPDL PBS file</span>
</a>
@@ -650,8 +647,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-cfx-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS CFX PBS file</span>
</a>
@@ -666,8 +663,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-fluent-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS Fluent PBS file</span>
</a>
@@ -682,8 +679,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS LS-DYNA PBS file</span>
</a>
@@ -698,8 +695,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>LS-DYNA PBS file</span>
</a>
@@ -723,7 +720,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -739,7 +736,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -755,7 +752,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -771,7 +768,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -787,7 +784,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -803,7 +800,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -819,7 +816,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -835,7 +832,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -851,7 +848,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -867,7 +864,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -883,7 +880,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -899,7 +896,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -915,7 +912,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -931,7 +928,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -947,7 +944,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -963,7 +960,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -979,7 +976,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -995,7 +992,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1020,7 +1017,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1036,7 +1033,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1061,7 +1058,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1077,7 +1074,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1093,7 +1090,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1132,14 +1129,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1161,12 +1158,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1182,7 +1179,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:34 GMT -->
</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
new file mode 100644
index 0000000000000000000000000000000000000000..736449e2dd3068d85f1db94b6618d088097fd66c
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
@@ -0,0 +1,70 @@
+ANSYS LS-DYNA
+=============
+[ANSYS
+LS-DYNA](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/Explicit+Dynamics/ANSYS+LS-DYNA)
+software provides convenient and easy-to-use access to the
+technology-rich, time-tested explicit solver without the need to contend
+with the complex input requirements of this sophisticated program.
+Introduced in 1996, ANSYS LS-DYNA capabilities have helped customers in
+numerous industries to resolve highly intricate design
+issues. <span>ANSYS Mechanical users have been able take advantage of
+complex explicit solutions for a long time utilizing the traditional
+ANSYS Parametric Design Language (APDL) environment. <span>These
+explicit capabilities are available to ANSYS Workbench users as well.
+The Workbench platform is a powerful, comprehensive, easy-to-use
+environment for engineering simulation. CAD import from all sources,
+geometry cleanup, automatic meshing, solution, parametric optimization,
+result visualization and comprehensive report generation are all
+available within a single fully interactive modern graphical user
+environment.</span></span>
+<span>To run ANSYS LS-DYNA in batch mode you can utilize/modify the
+default ansysdyna.pbs script and execute it via the qsub command.</span>
+``` {.prettyprint .lang-sh}
+#!/bin/bash
+#PBS -l nodes=2:ppn=16
+#PBS -q qprod
+#PBS -N $USER-DYNA-Project
+#PBS -A XX-YY-ZZ
+#! Mail to user when job terminate or abort
+#PBS -m ae
+#!change the working directory (default is home directory)
+#cd <working directory>
+WORK_DIR="/scratch/$USER/work"
+cd $WORK_DIR
+echo Running on host `hostname`
+echo Time is `date`
+echo Directory is `pwd`
+echo This jobs runs on the following processors:
+echo `cat $PBS_NODEFILE`
+#! Counts the number of processors
+NPROCS=`wc -l < $PBS_NODEFILE`
+echo This job has allocated $NPROCS nodes
+module load ansys
+#### Set number of processors per host listing
+#### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)
+procs_per_host=1
+#### Create host list
+hl=""
+for host in `cat $PBS_NODEFILE`
+do
+ if [ "$hl" = "" ]
+ then hl="$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
+ fi
+done
+echo Machines$hl
+/ansys_inc/v145/ansys/bin/ansys145 -dis -lsdynampp i=input.k -machines $hl
+```
+<span>Header of the pbs file (above) is common and description can be
+find on </span>[this
+site](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution)<span>.
+[SVS FEM](http://www.svsfem.cz) recommends to utilize
+sources by keywordsnodes, ppn. These keywords allows to address
+directly the number of nodes (computers) and cores (ppn) which will be
+utilized in the job. Also the rest of code assumes such structure of
+allocated resources.</span>
+Working directory has to be created before sending pbs job into the
+queue. Input file should be in working directory or full path to input
+file has to be specified. Input file has to be defined by common LS-DYNA
+.**k** file which is attached to the ansys solver via parameter i=
+<span><span>Â </span></span>
diff --git a/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/at_download/mapdl.pbs b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file.1
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/at_download/mapdl.pbs
rename to docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file.1
diff --git a/anselm-cluster-documentation/software/ansys/mapdl.pbs b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/at_download/file
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/software/ansys/mapdl.pbs
rename to docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/at_download/file
diff --git a/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view.html b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view.html
old mode 100755
new mode 100644
similarity index 58%
rename from anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view.html
index e61b431a5969cdfd575ebf01d0b22420ad486311..abe495d1a8d5087cdc13848ee0df53fdf1516710
--- a/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view.html
@@ -10,45 +10,42 @@
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
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<title>ANSYS MAPDL PBS file — IT4I Docs</title>
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<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
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+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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diff --git a/anselm-cluster-documentation/software/omics-master-1/images/fig2.png/image_view_fullscreen.md b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view.md
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rename from anselm-cluster-documentation/software/omics-master-1/images/fig2.png/image_view_fullscreen.md
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diff --git a/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.html b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.html
old mode 100755
new mode 100644
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rename from anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.html
index 02846a1345b900ec569c1fccc800e54e7cb07983..bffce6f47c69db5353d741b5d3f1501ebcdd1f5a
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<title>ANSYS MAPDL — IT4I Docs</title>
- <link rel="canonical" href="ansys-mechanical-apdl.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
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<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="ansys-mechanical-apdl.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="ansys-mechanical-apdl.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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<div id="portal-advanced-search" class="hiddenStructure">
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+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
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</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
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@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
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@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../ansys.html">ANSYS</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">ANSYS</a>
<span class="breadcrumbSeparator">
/
@@ -249,9 +246,9 @@
<p><span><strong><a class="external-link" href="http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics" target="_blank" title="">ANSYS Multiphysics</a></strong> software offers a comprehensive product solution for both multiphysics and single-physics analysis. The product includes structural, thermal, fluid and both high- and low-frequency electromagnetic analysis. The product also contains solutions for both direct and sequentially coupled physics problems including direct coupled-field elements and the ANSYS multi-field solver.</span></p>
<p><span>To run ANSYS MAPDL in batch mode you can utilize/modify the default mapdl.pbs script and execute it via the qsub command.</span></p>
<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -l nodes=2:ppn=16<br />#PBS -q qprod<br />#PBS -N $USER-ANSYS-Project<br />#PBS -A XX-YY-ZZ<br /><br />#! Mail to user when job terminate or abort<br />#PBS -m ae<br /><br />#!change the working directory (default is home directory)<br />#cd <working directory> (working directory must exists)<br />WORK_DIR="/scratch/$USER/work"<br />cd $WORK_DIR<br /><br />echo Running on host `hostname`<br />echo Time is `date`<br />echo Directory is `pwd`<br />echo This jobs runs on the following processors:<br />echo `cat $PBS_NODEFILE`<br /><br />module load ansys<br /><br />#### Set number of processors per host listing<br />#### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)<br />procs_per_host=1<br />#### Create host list<br />hl=""<br />for host in `cat $PBS_NODEFILE`<br />do<br /> if [ "$hl" = "" ]<br /> then hl="$host:$procs_per_host"<br /> else hl="${hl}:$host:$procs_per_host"<br /> fi<br />done<br /><br />echo Machines: $hl<br /><br />#-i input.dat includes the input of analysis in APDL format<br />#-o file.out is output file from ansys where all text outputs will be redirected <br />#-p the name of license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial), aa_r_dy=Academic AUTODYN)<br />/ansys_inc/v145/ansys/bin/ansys145 -b -dis -p aa_r -i input.dat -o file.out -machines $hl -dir $WORK_DIR</pre>
-<p>Header of the pbs file (above) is common and description can be find on <a target="_blank" title="" class="internal-link" href="../../resource-allocation-and-job-execution/job-submission-and-execution.html">this site</a>. <a class="external-link" href="http://www.svsfem.cz/" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
+<p>Header of the pbs file (above) is common and description can be find on <a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">this site</a>. <a class="external-link" href="http://www.svsfem.cz" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
<p>Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common APDL file which is attached to the ansys solver via parameter -i</p>
-<p><strong>License</strong> should be selected by parameter -p. Licensed products are the following: aa_r (ANSYS <strong>Academic</strong> Research), ane3fl (ANSYS Multiphysics)-<strong>Commercial</strong>, aa_r_dy (ANSYS <strong>Academic</strong> AUTODYN)<span> <br /><a target="_self" title="" class="internal-link" href="../../../acl_users/credentials_cookie_auth/require_login888f.html"><span class="short_text" id="result_box"><span class="hps">More</span> <span class="hps">about licensing</span> <span class="hps">here</span></span></a><br /></span></p>
+<p><strong>License</strong> should be selected by parameter -p. Licensed products are the following: aa_r (ANSYS <strong>Academic</strong> Research), ane3fl (ANSYS Multiphysics)-<strong>Commercial</strong>, aa_r_dy (ANSYS <strong>Academic</strong> AUTODYN)<span> <br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing"><span class="short_text" id="result_box"><span class="hps">More</span> <span class="hps">about licensing</span> <span class="hps">here</span></span></a><br /></span></p>
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<dt class="portletHeader hiddenStructure">
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+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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<span>Anselm Cluster Documentation</span>
</a>
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<span>Hardware Overview</span>
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<span>Accessing the Cluster</span>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
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- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -538,7 +535,7 @@
- <a title="An engineering simulation software " class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -554,7 +551,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="ansys-mechanical-apdl.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl">
<span>ANSYS MAPDL</span>
</a>
@@ -570,7 +567,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx">
<span>ANSYS CFX</span>
</a>
@@ -586,7 +583,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent">
<span>ANSYS Fluent</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna">
<span>ANSYS LS-DYNA</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna">
<span>LS-DYNA</span>
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- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS MAPDL PBS file</span>
</a>
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- <a title="" class="state-missing-value contenttype-file" href="ansys-cfx-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS CFX PBS file</span>
</a>
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- <a title="" class="state-missing-value contenttype-file" href="ansys-fluent-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS Fluent PBS file</span>
</a>
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- <a title="" class="state-missing-value contenttype-file" href="ansys-ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS LS-DYNA PBS file</span>
</a>
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- <a title="" class="state-missing-value contenttype-file" href="ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>LS-DYNA PBS file</span>
</a>
@@ -723,7 +720,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -739,7 +736,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -755,7 +752,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -771,7 +768,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -787,7 +784,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -803,7 +800,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -819,7 +816,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -835,7 +832,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -851,7 +848,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -867,7 +864,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -883,7 +880,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -899,7 +896,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -915,7 +912,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -931,7 +928,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -947,7 +944,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -963,7 +960,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -979,7 +976,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -995,7 +992,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1020,7 +1017,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1036,7 +1033,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1061,7 +1058,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1077,7 +1074,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1093,7 +1090,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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</div>
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-
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
new file mode 100644
index 0000000000000000000000000000000000000000..c29d2617a494e5fa3bff3f9b47f0e01344c6dc6e
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
@@ -0,0 +1,68 @@
+ANSYS MAPDL
+===========
+<span>**[ANSYS
+Multiphysics](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics)**
+software offers a comprehensive product solution for both multiphysics
+and single-physics analysis. The product includes structural, thermal,
+fluid and both high- and low-frequency electromagnetic analysis. The
+product also contains solutions for both direct and sequentially coupled
+physics problems including direct coupled-field elements and the ANSYS
+multi-field solver.</span>
+<span>To run ANSYS MAPDL in batch mode you can utilize/modify the
+default mapdl.pbs script and execute it via the qsub command.</span>
+``` {.prettyprint .lang-sh}
+#!/bin/bash
+#PBS -l nodes=2:ppn=16
+#PBS -q qprod
+#PBS -N $USER-ANSYS-Project
+#PBS -A XX-YY-ZZ
+#! Mail to user when job terminate or abort
+#PBS -m ae
+#!change the working directory (default is home directory)
+#cd <working directory> (working directory must exists)
+WORK_DIR="/scratch/$USER/work"
+cd $WORK_DIR
+echo Running on host `hostname`
+echo Time is `date`
+echo Directory is `pwd`
+echo This jobs runs on the following processors:
+echo `cat $PBS_NODEFILE`
+module load ansys
+#### Set number of processors per host listing
+#### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)
+procs_per_host=1
+#### Create host list
+hl=""
+for host in `cat $PBS_NODEFILE`
+do
+ if [ "$hl" = "" ]
+ then hl="$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
+ fi
+done
+echo Machines$hl
+#-i input.dat includes the input of analysis in APDL format
+#-o file.out is output file from ansys where all text outputs will be redirected
+#-p the name of license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial), aa_r_dy=Academic AUTODYN)
+/ansys_inc/v145/ansys/bin/ansys145 -b -dis -p aa_r -i input.dat -o file.out -machines $hl -dir $WORK_DIR
+```
+Header of the pbs file (above) is common and description can be find on
+[this
+site](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution).
+[SVS FEM](http://www.svsfem.cz) recommends to utilize
+sources by keywordsnodes, ppn. These keywords allows to address
+directly the number of nodes (computers) and cores (ppn) which will be
+utilized in the job. Also the rest of code assumes such structure of
+allocated resources.
+Working directory has to be created before sending pbs job into the
+queue. Input file should be in working directory or full path to input
+file has to be specified. Input file has to be defined by common APDL
+file which is attached to the ansys solver via parameter -i
+**License** should be selected by parameter -p. Licensed products are
+the followingaa_r (ANSYS **Academic** Research), ane3fl (ANSYS
+Multiphysics)-**Commercial**, aa_r_dy (ANSYS **Academic**
+AUTODYN)<span>
+[<span id="result_box" class="short_text"><span class="hps">More</span>
+<span class="hps">about licensing</span> <span
+class="hps">here</span></span>](https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing)
+</span>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.html b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.html
new file mode 100644
index 0000000000000000000000000000000000000000..1361db1994ca8175b8d23b8524d330d6b4f488ad
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.html
@@ -0,0 +1,1173 @@
+
+<!DOCTYPE html>
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+ Overview of ANSYS Products
+ </h1>
+
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+</div>
+
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+ <div id="content-core">
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+ <div id="parent-fieldname-text-23b0fc1f4ce244a2bd48311555b77759" class="">
+ <p><strong><a class="external-link" href="http://www.svsfem.cz/" target="_blank" title="">SVS FEM</a></strong> as <em><strong><a class="external-link" href="http://www.ansys.com/" target="_self" title="">ANSYS Channel partner</a></strong></em> for Czech Republic provided all ANSYS licenses for ANSELM cluster and supports of all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent, Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging to problem of ANSYS functionality contact please <a class="email-link" href="mailto:hotline@svsfem.cz?subject=Ostrava%20-%20ANSELM" target="_self" title="">hotline@svsfem.cz</a></p>
+<p>Anselm provides as commercial as academic variants. Academic variants are distinguished by "<strong>Academic...</strong>" word in the name of  license or by two letter preposition "<strong>aa_</strong>" in the license feature name. Change of license is realized on command line respectively directly in user's pbs file (see individual products). <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing"><span class="short_text" id="result_box"><span class="hps">More</span> <span class="hps">about licensing</span> <span class="hps">here</span></span></a></p>
+<p>To load the latest version of any ANSYS product (Mechanical, Fluent, CFX, MAPDL,...) load the module:</p>
+<pre class=" ">$ module load ansys</pre>
+<p>ANSYS supports interactive regime, but due to assumed solution of extremely difficult tasks it is not recommended.</p>
+<p>If user needs to work in interactive regime we recommend to configure the RSM service on the client machine which allows to forward the solution to the Anselm directly from the client's Workbench project (see ANSYS RSM service).</p>
+
+ </div>
+
+
+ <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
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+<li class="navTreeItem visualNoMarker section-compute-nodes">
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
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+<li class="navTreeItem visualNoMarker navTreeFolderish section-storage-1">
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
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+<li class="navTreeItem visualNoMarker section-network">
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
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+<li class="navTreeItem visualNoMarker navTreeItemInPath navTreeFolderish section-software">
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+
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+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
+
+
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
+
+ <span>Software</span>
+ </a>
+
+
+ <ul class="navTree navTreeLevel2">
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+
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+<li class="navTreeItem visualNoMarker navTreeCurrentNode navTreeFolderish section-ansys">
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+
+
+
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
+
+ <span>ANSYS</span>
+ </a>
+
+
+ <ul class="navTree navTreeLevel3">
+
+
+
+
+<li class="navTreeItem visualNoMarker section-ansys-mechanical-apdl">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl">
+
+ <span>ANSYS MAPDL</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ansys-cfx">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx">
+
+ <span>ANSYS CFX</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ansys-fluent">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent">
+
+ <span>ANSYS Fluent</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ansys-ls-dyna">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna">
+
+ <span>ANSYS LS-DYNA</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ls-dyna">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna">
+
+ <span>LS-DYNA</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ansys-mapdl-pbs-file">
+
+
+
+
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
+ <span>ANSYS MAPDL PBS file</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ansys-cfx-pbs-file">
+
+
+
+
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
+ <span>ANSYS CFX PBS file</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ansys-fluent-pbs-file">
+
+
+
+
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
+ <span>ANSYS Fluent PBS file</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ansys-ls-dyna-pbs-file">
+
+
+
+
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
+ <span>ANSYS LS-DYNA PBS file</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ls-dyna-pbs-file">
+
+
+
+
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
+ <span>LS-DYNA PBS file</span>
+ </a>
+
+
+
+
+</li>
+
+
+
+
+ </ul>
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-comsol">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
+
+ <span>COMSOL</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-debuggers">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
+
+ <span>Debuggers and profilers</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-chemistry">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
+
+ <span>Chemistry and Materials science</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-intel-suite">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
+
+ <span>Intel Parallel studio</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-mpi-1">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
+
+ <span>MPI</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-numerical-libraries">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
+
+ <span>Numerical Libraries</span>
+ </a>
+
+
+
+
+</li>
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+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-numerical-languages">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
+
+ <span>Numerical languages</span>
+ </a>
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+
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+
+</li>
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+<li class="navTreeItem visualNoMarker navTreeFolderish section-virtualization">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
+
+ <span>Virtualization</span>
+ </a>
+
+
+
+
+</li>
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+
+<li class="navTreeItem visualNoMarker section-compilers">
+
+
+
+
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
+
+ <span>Compilers</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-intel-xeon-phi">
+
+
+
+
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
+
+ <span>Intel Xeon Phi</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-isv_licenses">
+
+
+
+
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
+
+ <span>ISV Licenses</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-java">
+
+
+
+
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
+
+ <span>Java</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-nvidia-cuda">
+
+
+
+
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
+
+ <span>nVidia CUDA</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-omics-master-1">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
+
+ <span>OMICS Master</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-openfoam">
+
+
+
+
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
+
+ <span>OpenFOAM</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-operating-system">
+
+
+
+
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
+
+ <span>Operating System</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-paraview">
+
+
+
+
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
+
+ <span>ParaView</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-gpi2">
+
+
+
+
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
+
+ <span>GPI-2</span>
+ </a>
+
+
+
+
+</li>
+
+
+
+
+ </ul>
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-remote-visualization">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
+
+ <span>Remote visualization service</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-prace">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
+
+ <span>PRACE User Support</span>
+ </a>
+
+
+
+
+</li>
+
+
+
+
+ </ul>
+
+
+
+</li>
+
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+<li class="navTreeItem visualNoMarker section-links">
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+ <span>Links</span>
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+
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+
+<li class="navTreeItem visualNoMarker section-changelog">
+
+
+
+
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
+
+ <span>Changelog</span>
+ </a>
+
+
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+</li>
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+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-pbspro-documentation">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
+
+ <span>PBSPro Documentation</span>
+ </a>
+
+
+
+
+</li>
+
+
+
+
+ </ul>
+ <span class="portletBottomLeft"></span>
+ <span class="portletBottomRight"></span>
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+
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+
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md
new file mode 100644
index 0000000000000000000000000000000000000000..c8e08155b7b965077a12d582b462273bf2fee7c2
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md
@@ -0,0 +1,26 @@
+Overview of ANSYS Products
+==========================
+**[SVS FEM](http://www.svsfem.cz/)** as ***[ANSYS
+Channel partner](http://www.ansys.com/)***Â for Czech
+Republic provided all ANSYS licenses for ANSELM cluster and supports of
+all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent,
+Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging
+to problem of ANSYS functionality contact
+please [hotline@svsfem.cz](mailto:hotline@svsfem.cz?subject=Ostrava%20-%20ANSELM){.email-link}
+Anselm provides as commercial as academic variants. Academic variants
+are distinguished by "**Academic...**" word in the name of  license or
+by two letter preposition "**aa_**" in the license feature name. Change
+of license is realized on command line respectively directly in user's
+pbs file (see individual products). [<span id="result_box"
+class="short_text"><span class="hps">More</span> <span class="hps">about
+licensing</span> <span
+class="hps">here</span></span>](https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing)
+To load the latest version of any ANSYS product (Mechanical, Fluent,
+CFX, MAPDL,...) load the module:
+ $ module load ansys
+ANSYS supports interactive regime, but due to assumed solution of
+extremely difficult tasks it is not recommended.
+If user needs to work in interactive regime we recommend to configure
+the RSM service on the client machine which allows to forward the
+solution to the Anselm directly from the client's Workbench project
+(see ANSYS RSM service).
diff --git a/acl_users/credentials_cookie_auth/require_logind8a8.html b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing.html
old mode 100755
new mode 100644
similarity index 68%
rename from acl_users/credentials_cookie_auth/require_logind8a8.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing.html
index fc6cfb239480f05bc42bd0b83110d695755986f8..1d247c089d511aac0e1fbc5e4c9267436e026e50
--- a/acl_users/credentials_cookie_auth/require_logind8a8.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing.html
@@ -10,45 +10,42 @@
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- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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<title>IT4I Docs</title>
- <link rel="canonical" href="../../index.html" />
+ <link rel="canonical" href="https://docs.it4i.cz" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
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+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -63,14 +60,14 @@
- <link rel="alternate" href="../../RSS" title="IT4I Docs - RSS 1.0" type="application/rss+xml" />
+ <link rel="alternate" href="https://docs.it4i.cz/RSS" title="IT4I Docs - RSS 1.0" type="application/rss+xml" />
- <link rel="alternate" href="../../rss.xml" title="IT4I Docs - RSS 2.0" type="application/rss+xml" />
+ <link rel="alternate" href="https://docs.it4i.cz/rss.xml" title="IT4I Docs - RSS 2.0" type="application/rss+xml" />
- <link rel="alternate" href="../../atom.xml" title="IT4I Docs - Atom" type="application/rss+xml" />
+ <link rel="alternate" href="https://docs.it4i.cz/atom.xml" title="IT4I Docs - Atom" type="application/rss+xml" />
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
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@@ -79,7 +76,7 @@
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+ <script type="text/javascript" src="https://docs.it4i.cz/login.js">
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+ <a accesskey="2" href="https://docs.it4i.cz/acl_users/credentials_cookie_auth/require_login?came_from=https%3A//docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="require_logind8a8.html?came_from=https%3A//docs.it4i.cz/salomon/software/isv_licenses#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/acl_users/credentials_cookie_auth/require_login?came_from=https%3A//docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -134,13 +131,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
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+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
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- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -154,7 +151,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
</span>
@@ -196,7 +193,7 @@
<div id="login-form">
- <input type="hidden" name="came_from" value="require_logind8a8.html" />
+ <input type="hidden" name="came_from" value="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing" />
<input type="hidden" name="next" />
@@ -224,7 +221,7 @@
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+ <input type="text" size="15" id="__ac_name" name="__ac_name" value="" />
</div>
@@ -234,7 +231,7 @@
- <input type="password" size="15" name="__ac_password" id="__ac_password" />
+ <input type="password" size="15" id="__ac_password" name="__ac_password" />
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+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -350,7 +347,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/anselm-cluster-documentation/software/omics-master-1/images/fig3.png/image_view_fullscreen.md b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing.md
similarity index 100%
rename from anselm-cluster-documentation/software/omics-master-1/images/fig3.png/image_view_fullscreen.md
rename to docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing.md
diff --git a/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/at_download/lsdyna.pbs b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file.1
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new mode 100644
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rename to docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file.1
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old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/software/ansys/lsdyna.pbs
rename to docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/at_download/file
diff --git a/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view.html b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view.html
old mode 100755
new mode 100644
similarity index 58%
rename from anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view.html
index 951b58cae561cf428eaf34fa5a9c1eaead75425a..cc99e36222517dbd4a901102b8746d271e970d42
--- a/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>LS-DYNA PBS file — IT4I Docs</title>
- <link rel="canonical" href="../lsdyna.pbs" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="view.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="view.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
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-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../../index.html">
- <img src="../../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
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+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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<title>LS-DYNA — IT4I Docs</title>
- <link rel="canonical" href="ls-dyna.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="ls-dyna.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="ls-dyna.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
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</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../ansys.html">ANSYS</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">ANSYS</a>
<span class="breadcrumbSeparator">
/
@@ -250,7 +247,7 @@
<p><span>Anselm provides <strong>1 commercial license of LS-DYNA without HPC</strong> support now. </span></p>
<p><span><span>To run LS-DYNA in batch mode you can utilize/modify the default lsdyna.pbs script and execute it via the qsub command.</span></span></p>
<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -l nodes=1:ppn=16<br />#PBS -q qprod<br />#PBS -N $USER-LSDYNA-Project<br />#PBS -A XX-YY-ZZ<br /><br />#! Mail to user when job terminate or abort<br />#PBS -m ae<br /><br />#!change the working directory (default is home directory)<br />#cd <working directory> (working directory must exists)<br />WORK_DIR="/scratch/$USER/work"<br />cd $WORK_DIR<br /><br />echo Running on host `hostname`<br />echo Time is `date`<br />echo Directory is `pwd`<br /><br />module load lsdyna<br /><br />/apps/engineering/lsdyna/lsdyna700s i=input.k</pre>
-<p>Header of the pbs file (above) is common and description can be find on <a target="_blank" title="" class="internal-link" href="../../resource-allocation-and-job-execution/job-submission-and-execution.html">this site</a>. <a class="external-link" href="http://www.svsfem.cz/" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
+<p>Header of the pbs file (above) is common and description can be find on <a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">this site</a>. <a class="external-link" href="http://www.svsfem.cz" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
<p>Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common LS-DYNA <strong>.k</strong> file which is attached to the LS-DYNA solver via parameter i=</p>
</div>
@@ -327,7 +324,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -343,7 +340,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -407,7 +404,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -439,7 +436,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -471,7 +468,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
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- <a title="In this section we provide overview of installed software and its usage.
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-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
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- <a title="An engineering simulation software " class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
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- <a title="" class="state-published contenttype-document" href="ansys-mechanical-apdl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl">
<span>ANSYS MAPDL</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx">
<span>ANSYS CFX</span>
</a>
@@ -586,7 +583,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-fluent.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent">
<span>ANSYS Fluent</span>
</a>
@@ -602,7 +599,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-ls-dyna.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna">
<span>ANSYS LS-DYNA</span>
</a>
@@ -618,7 +615,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="ls-dyna.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna">
<span>LS-DYNA</span>
</a>
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- <a title="" class="state-missing-value contenttype-file" href="ansys-mapdl-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS MAPDL PBS file</span>
</a>
@@ -650,8 +647,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-cfx-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS CFX PBS file</span>
</a>
@@ -666,8 +663,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-fluent-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS Fluent PBS file</span>
</a>
@@ -682,8 +679,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS LS-DYNA PBS file</span>
</a>
@@ -698,8 +695,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>LS-DYNA PBS file</span>
</a>
@@ -723,7 +720,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -739,7 +736,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -755,7 +752,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -771,7 +768,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -787,7 +784,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -803,7 +800,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -819,7 +816,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -835,7 +832,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -851,7 +848,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -867,7 +864,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -883,7 +880,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -899,7 +896,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -915,7 +912,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -931,7 +928,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -947,7 +944,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -963,7 +960,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -979,7 +976,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -995,7 +992,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1020,7 +1017,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1036,7 +1033,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1061,7 +1058,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1077,7 +1074,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1093,7 +1090,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
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-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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-
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md
new file mode 100644
index 0000000000000000000000000000000000000000..ca41e014650174b552c26e88f9166f24e0e8beb8
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md
@@ -0,0 +1,53 @@
+LS-DYNA
+=======
+[LS-DYNA](http://www.lstc.com/) is a multi-purpose,
+explicit and implicit finite element program used to analyze the
+nonlinear dynamic response of structures. Its fully automated contact
+analysis capability, a wide range of constitutive models to simulate a
+whole range of engineering materials (steels, composites, foams,
+concrete, etc.), error-checking features and the high scalability have
+enabled users worldwide to solve successfully many complex
+problems. <span>Additionally LS-DYNA is extensively used to simulate
+impacts on structures from drop tests, underwater shock, explosions or
+high-velocity impacts. Explosive forming, process engineering, accident
+reconstruction, vehicle dynamics, thermal brake disc analysis or nuclear
+safety are further areas in the broad range of possible applications. In
+leading-edge research LS-DYNA is used to investigate the behaviour of
+materials like composites, ceramics, concrete, or wood. Moreover, it is
+used in biomechanics, human modelling, molecular structures, casting,
+forging, or virtual testing.</span>
+<span>Anselm provides **1 commercial license of LS-DYNA without HPC**
+support now. </span>
+<span><span>To run LS-DYNA in batch mode you can utilize/modify the
+default lsdyna.pbs script and execute it via the qsub
+command.</span></span>
+``` {.prettyprint .lang-sh}
+#!/bin/bash
+#PBS -l nodes=1:ppn=16
+#PBS -q qprod
+#PBS -N $USER-LSDYNA-Project
+#PBS -A XX-YY-ZZ
+#! Mail to user when job terminate or abort
+#PBS -m ae
+#!change the working directory (default is home directory)
+#cd <working directory> (working directory must exists)
+WORK_DIR="/scratch/$USER/work"
+cd $WORK_DIR
+echo Running on host `hostname`
+echo Time is `date`
+echo Directory is `pwd`
+module load lsdyna
+/apps/engineering/lsdyna/lsdyna700s i=input.k
+```
+Header of the pbs file (above) is common and description can be find
+on [this
+site](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution).
+[SVS FEM](http://www.svsfem.cz) recommends to utilize
+sources by keywordsnodes, ppn. These keywords allows to address
+directly the number of nodes (computers) and cores (ppn) which will be
+utilized in the job. Also the rest of code assumes such structure of
+allocated resources.
+Working directory has to be created before sending pbs job into the
+queue. Input file should be in working directory or full path to input
+file has to be specified. Input file has to be defined by common LS-DYNA
+**.k** file which is attached to the LS-DYNA solver via parameter i=
diff --git a/anselm-cluster-documentation/software/chemistry.html b/docs.it4i.cz/anselm-cluster-documentation/software/chemistry.html
old mode 100755
new mode 100644
similarity index 61%
rename from anselm-cluster-documentation/software/chemistry.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/chemistry.html
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--- a/anselm-cluster-documentation/software/chemistry.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/chemistry.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry/" /><!--[if lt IE 7]></base><![endif]-->
<meta content="Tools for computational chemistry." name="description" />
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- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Chemistry and Materials science — IT4I Docs</title>
- <link rel="canonical" href="chemistry.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="chemistry.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="chemistry.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -249,7 +246,7 @@
<span class="summary">
- <a href="chemistry/molpro.html" class="contenttype-document state-published url">Molpro</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro" class="contenttype-document state-published url">Molpro</a>
</span>
<span class="documentByLine">
@@ -275,7 +272,7 @@
<span class="summary">
- <a href="chemistry/nwchem.html" class="contenttype-document state-published url">NWChem</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem" class="contenttype-document state-published url">NWChem</a>
</span>
<span class="documentByLine">
@@ -360,7 +357,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -376,7 +373,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -392,7 +389,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -408,7 +405,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -424,7 +421,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -440,7 +437,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -456,7 +453,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -472,7 +469,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -488,7 +485,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -504,7 +501,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -520,7 +517,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -536,7 +533,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -552,10 +549,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -571,7 +568,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -587,7 +584,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -603,7 +600,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -619,7 +616,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -635,7 +632,7 @@
- <a title="Molpro is a complete system of ab initio programs for molecular electronic structure calculations." class="state-published contenttype-document" href="chemistry/molpro.html">
+ <a class="state-published contenttype-document" title="Molpro is a complete system of ab initio programs for molecular electronic structure calculations." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro">
<span>Molpro</span>
</a>
@@ -651,7 +648,7 @@
- <a title="High-Performance Computational Chemistry" class="state-published contenttype-document" href="chemistry/nwchem.html">
+ <a class="state-published contenttype-document" title="High-Performance Computational Chemistry" href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem">
<span>NWChem</span>
</a>
@@ -676,7 +673,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -692,7 +689,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -708,7 +705,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -724,7 +721,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -740,7 +737,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -756,7 +753,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -772,7 +769,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -788,7 +785,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
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+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
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</a>
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</a>
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<span>ParaView</span>
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+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
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+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
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- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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old mode 100755
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<title>Molpro — IT4I Docs</title>
- <link rel="canonical" href="molpro.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro" />
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<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="molpro.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="molpro.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
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</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
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</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
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@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../chemistry.html">Chemistry and Materials science</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">Chemistry and Materials science</a>
<span class="breadcrumbSeparator">
/
@@ -293,7 +290,7 @@
<h2 class=" ">Running</h2>
<p>Molpro is compiled for parallel execution using MPI and OpenMP. By default, Molpro reads the number of allocated nodes from PBS and launches a data server on one node. On the remaining allocated nodes, compute processes are launched, one process per node, each with 16 threads. You can modify this behavior by using -n, -t and helper-server options. Please refer to the <a class="external-link" href="http://www.molpro.net/info/2010.1/doc/manual/node9.html" target="_self" title="">Molpro documentation</a> for more details. </p>
<p class="exclamation">The OpenMP parallelization in Molpro is limited and has been observed to produce limited scaling. We therefore recommend to use MPI parallelization only. This can be achieved by passing option <span class="monospace">mpiprocs=16:ompthreads=1</span> to PBS.</p>
-<p>You are advised to use the -d option to point to a directory in <a target="_self" title="" class="internal-link" href="../../storage-1/storage.html">SCRATCH filesystem</a>. Molpro can produce a large amount of temporary data during its run, and it is important that these are placed in the fast scratch filesystem.</p>
+<p>You are advised to use the -d option to point to a directory in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage">SCRATCH filesystem</a>. Molpro can produce a large amount of temporary data during its run, and it is important that these are placed in the fast scratch filesystem.</p>
<h3 class=" ">Example jobscript</h3>
<pre class=" ">#PBS -A IT4I-0-0<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=16:mpiprocs=16:ompthreads=1<br /><br />cd $PBS_O_WORKDIR<br /><br /># load Molpro module<br />module add molpro<br /><br /># create a directory in the SCRATCH filesystem<br />mkdir -p /scratch/$USER/$PBS_JOBID<br /><br /># copy an example input<br />cp /apps/chem/molpro/2010.1/molprop_2010_1_Linux_x86_64_i8/examples/caffeine_opt_diis.com .<br /><br /># run Molpro with default options<br /><span>molpro -d /scratch/$USER/$PBS_JOBID caffeine_opt_diis.com<br /><br /># delete scratch directory<br />rm -rf /scratch/$USER/$PBS_JOBIDÂ </span></pre>
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<span>What's New</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
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- <a title="In this section we provide overview of installed software and its usage.
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-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
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- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
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- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
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- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
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- <a title="Tools for computational chemistry." class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
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- <a title="Molpro is a complete system of ab initio programs for molecular electronic structure calculations." class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="molpro.html">
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<span>Molpro</span>
</a>
@@ -662,7 +659,7 @@
- <a title="High-Performance Computational Chemistry" class="state-published contenttype-document" href="nwchem.html">
+ <a class="state-published contenttype-document" title="High-Performance Computational Chemistry" href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem">
<span>NWChem</span>
</a>
@@ -687,7 +684,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -703,7 +700,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -719,7 +716,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -735,7 +732,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -751,7 +748,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -767,7 +764,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -783,7 +780,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -799,7 +796,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -815,7 +812,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -831,7 +828,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -847,7 +844,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -863,7 +860,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -879,7 +876,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -895,7 +892,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -911,7 +908,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -936,7 +933,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -952,7 +949,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -977,7 +974,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -993,7 +990,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1009,7 +1006,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1098,7 +1095,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.md b/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.md
new file mode 100644
index 0000000000000000000000000000000000000000..73d81b27948e1ab1045bd290d9ef492ac4424827
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.md
@@ -0,0 +1,67 @@
+Molpro
+======
+Molpro is a complete system of ab initio programs for molecular
+electronic structure calculations.
+About Molpro
+------------
+Molpro is a software package used for accurate ab-initio quantum
+chemistry calculations. More information can be found at the [official
+webpage](http://www.molpro.net/).
+License
+-------
+Molpro software package is available only to users that have a valid
+license. Please contact support to enable access to Molpro if you have a
+valid license appropriate for running on our cluster (eg. <span>academic
+research group licence, parallel execution).</span>
+<span>To run Molpro, you need to have a valid license token present in
+"<span class="monospace">$HOME/.molpro/token"</span></span>. You can
+download the token from [Molpro
+website](https://www.molpro.net/licensee/?portal=licensee).
+Installed version
+-----------------
+Currently on Anselm is installed version 2010.1, patch level 45,
+parallel version compiled with Intel compilers and Intel MPI.
+Compilation parameters are default :
+ Parameter Value
+ --- ------
+ <span>max number of atoms</span> 200
+ <span>max number of valence orbitals</span> 300
+ <span>max number of basis functions</span> 4095
+ <span>max number of states per symmmetry</span> 20
+ <span>max number of state symmetries</span> 16
+ <span>max number of records</span> 200
+ <span>max number of primitives</span> <span>maxbfn x [2]</span>
+Â
+Running
+-------
+Molpro is compiled for parallel execution using MPI and OpenMP. By
+default, Molpro reads the number of allocated nodes from PBS and
+launches a data server on one node. On the remaining allocated nodes,
+compute processes are launched, one process per node, each with 16
+threads. You can modify this behavior by using -n, -t and helper-server
+options. Please refer to the [Molpro
+documentation](http://www.molpro.net/info/2010.1/doc/manual/node9.html)
+for more details.Â
+The OpenMP parallelization in Molpro is limited and has been observed to
+produce limited scaling. We therefore recommend to use MPI
+parallelization only. This can be achieved by passing option <span
+class="monospace">mpiprocs=16:ompthreads=1</span> to PBS.
+You are advised to use the -d option to point to a directory in [SCRATCH
+filesystem](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage).
+Molpro can produce a large amount of temporary data during its run, and
+it is important that these are placed in the fast scratch filesystem.
+### Example jobscript
+ #PBS -A IT4I-0-0
+ #PBS -q qprod
+ #PBS -l select=1:ncpus=16:mpiprocs=16:ompthreads=1
+ cd $PBS_O_WORKDIR
+ # load Molpro module
+ module add molpro
+ # create a directory in the SCRATCH filesystem
+ mkdir -p /scratch/$USER/$PBS_JOBID
+ # copy an example input
+ cp /apps/chem/molpro/2010.1/molprop_2010_1_Linux_x86_64_i8/examples/caffeine_opt_diis.com .
+ # run Molpro with default options
+ molpro -d /scratch/$USER/$PBS_JOBID caffeine_opt_diis.com
+ # delete scratch directory
+ rm -rf /scratch/$USER/$PBS_JOBIDÂ
diff --git a/anselm-cluster-documentation/software/chemistry/nwchem.html b/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.html
old mode 100755
new mode 100644
similarity index 63%
rename from anselm-cluster-documentation/software/chemistry/nwchem.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.html
index efdbb602fdda328553e89024be4fec8fb12b8e32..d6c198e1c1ddb3cfec51b5222b3647f267ade2f8
--- a/anselm-cluster-documentation/software/chemistry/nwchem.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:37 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem" /><!--[if lt IE 7]></base><![endif]-->
<meta content="High-Performance Computational Chemistry" name="description" />
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>NWChem — IT4I Docs</title>
- <link rel="canonical" href="nwchem.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="nwchem.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="nwchem.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../chemistry.html">Chemistry and Materials science</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">Chemistry and Materials science</a>
<span class="breadcrumbSeparator">
/
@@ -276,7 +273,7 @@
<p>Please refer to <a class="external-link" href="http://www.nwchem-sw.org/index.php/Release62:Top-level" target="_self" title="">the documentation</a>Â and in the input file set the following directives :</p>
<ul>
<li><span>MEMORY : controls the amount of memory NWChem will use</span></li>
-<li><span>SCRATCH_DIR : set this to a directory in <a target="_self" title="" class="internal-link" href="../../storage-1/storage.html#scratch">SCRATCH filesystem</a> (or run the calculation completely in a scratch directory). For certain calculations, it might be advisable to reduce I/O by forcing "direct" mode, eg. "scf direct"</span></li>
+<li><span>SCRATCH_DIR : set this to a directory in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage#scratch">SCRATCH filesystem</a> (or run the calculation completely in a scratch directory). For certain calculations, it might be advisable to reduce I/O by forcing "direct" mode, eg. "scf direct"</span></li>
</ul>
</div>
@@ -353,7 +350,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -369,7 +366,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -385,7 +382,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -401,7 +398,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -417,7 +414,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -433,7 +430,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -449,7 +446,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -465,7 +462,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -481,7 +478,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -497,7 +494,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -513,7 +510,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -529,7 +526,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -545,10 +542,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -564,7 +561,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -580,7 +577,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -596,7 +593,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -612,7 +609,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -628,7 +625,7 @@
- <a title="Molpro is a complete system of ab initio programs for molecular electronic structure calculations." class="state-published contenttype-document" href="molpro.html">
+ <a class="state-published contenttype-document" title="Molpro is a complete system of ab initio programs for molecular electronic structure calculations." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro">
<span>Molpro</span>
</a>
@@ -644,7 +641,7 @@
- <a title="High-Performance Computational Chemistry" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="nwchem.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="High-Performance Computational Chemistry" href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem">
<span>NWChem</span>
</a>
@@ -669,7 +666,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -685,7 +682,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -701,7 +698,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -717,7 +714,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -733,7 +730,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -749,7 +746,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -765,7 +762,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -781,7 +778,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -797,7 +794,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -813,7 +810,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -829,7 +826,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -845,7 +842,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -861,7 +858,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -877,7 +874,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -893,7 +890,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -918,7 +915,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -934,7 +931,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -959,7 +956,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -975,7 +972,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -991,7 +988,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
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+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1080,7 +1077,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md b/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md
new file mode 100644
index 0000000000000000000000000000000000000000..c6626f97404950e2e7e155b71ef5aa19cf3cc284
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md
@@ -0,0 +1,46 @@
+NWChem
+======
+High-Performance Computational Chemistry
+<span>Introduction</span>
+--
+<span>NWChem aims to provide its users with computational chemistry
+tools that are scalable both in their ability to treat large scientific
+computational chemistry problems efficiently, and in their use of
+available parallel computing resources from high-performance parallel
+supercomputers to conventional workstation clusters.</span>
+[Homepage](http://www.nwchem-sw.org/index.php/Main_Page)
+Installed versions
+------------------
+The following versions are currently installed :Â
+- 6.1.1, not recommended, problems have been observed with this
+ version
+- 6.3-rev2-patch1, current release with QMD patch applied. Compiled
+ with Intel compilers, MKL and Intel MPI
+- 6.3-rev2-patch1-openmpi, same as above, but compiled with OpenMPI
+ and NWChem provided BLAS instead of MKL. This version is expected to
+ be slower
+- 6.3-rev2-patch1-venus, this version contains only libraries for
+ VENUS interface linking. Does not provide standalone NWChem
+ executable
+For a current list of installed versions, execute :Â
+ module avail nwchem
+Running
+-------
+NWChem is compiled for parallel MPI execution. Normal procedure for MPI
+jobs applies. Sample jobscript :
+ #PBS -A IT4I-0-0
+ #PBS -q qprod
+ #PBS -l select=1:ncpus=16
+ module add nwchem/6.3-rev2-patch1
+ mpirun -np 16 nwchem h2o.nw
+<span>Options</span>
+--------------------
+Please refer to [the
+documentation](http://www.nwchem-sw.org/index.php/Release62:Top-level)Â and
+in the input file set the following directives :
+- <span>MEMORY controls the amount of memory NWChem will use</span>
+- <span>SCRATCH_DIR set this to a directory in [SCRATCH
+ filesystem](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage#scratch)Â (or
+ run the calculation completely in a scratch directory). For certain
+ calculations, it might be advisable to reduce I/O by forcing
+ "direct" mode, eg. "scf direct"</span>
diff --git a/anselm-cluster-documentation/software/compilers.html b/docs.it4i.cz/anselm-cluster-documentation/software/compilers.html
old mode 100755
new mode 100644
similarity index 66%
rename from anselm-cluster-documentation/software/compilers.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/compilers.html
index 17a89269383bbb6bf9d1e70efb204408d4a9c85f..095fee46c8bebd7504e8295ee2232674d9513208
--- a/anselm-cluster-documentation/software/compilers.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/compilers.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers" /><!--[if lt IE 7]></base><![endif]-->
<meta content="Available compilers, including GNU, INTEL and UPC compilers" name="description" />
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Compilers — IT4I Docs</title>
- <link rel="canonical" href="compilers.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="compilers.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="compilers.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -253,7 +250,7 @@
<p>Â </p>
<p class=" ">The C/C++ and Fortran compilers are divided into two main groups GNU and Intel.</p>
<h2 class=" ">Intel Compilers</h2>
-<p class=" ">For information about the usage of Intel Compilers and other Intel products, please read the <a target="_self" title="" class="internal-link" href="intel-suite.html">Intel Parallel studio</a> page.</p>
+<p class=" ">For information about the usage of Intel Compilers and other Intel products, please read the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">Intel Parallel studio</a> page.</p>
<h2 class=" ">GNU C/C++ and Fortran Compilers</h2>
<p>For compatibility reasons there are still available the original (old 4.4.6-4) versions of GNU compilers as part of the OS. These are accessible in the search path by default.</p>
<p>It is strongly recommended to use the up to date version (4.8.1) which comes with the module gcc:</p>
@@ -293,9 +290,9 @@
<pre class=" ">$ qsub -I -q qprod -A PROJECT_ID -l select=2:ncpus=16 <br />$ module add bupc<br />$ upcrun -n 32 ./hello.upc.x</pre>
<p class=" ">Â For more informations see the man pages.</p>
<h2 class=" ">Java</h2>
-<p>For information how to use Java (runtime and/or compiler), please read the <a target="_self" title="" class="internal-link" href="java.html">Java page</a>.</p>
+<p>For information how to use Java (runtime and/or compiler), please read the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">Java page</a>.</p>
<h2 class=" ">nVidia CUDA</h2>
-<p>For information how to work with nVidia CUDA, please read the <a target="_self" title="" class="internal-link" href="nvidia-cuda.html">nVidia CUDA page</a>.</p>
+<p>For information how to work with nVidia CUDA, please read the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">nVidia CUDA page</a>.</p>
</div>
@@ -371,7 +368,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -387,7 +384,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -403,7 +400,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -419,7 +416,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -435,7 +432,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -451,7 +448,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -467,7 +464,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -483,7 +480,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -499,7 +496,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -515,7 +512,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -531,7 +528,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -547,7 +544,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -563,10 +560,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -582,7 +579,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -598,7 +595,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -614,7 +611,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -630,7 +627,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -646,7 +643,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -662,7 +659,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -678,7 +675,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -694,7 +691,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -710,7 +707,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -726,7 +723,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="compilers.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -742,7 +739,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -758,7 +755,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -774,7 +771,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -790,7 +787,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -806,7 +803,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -822,7 +819,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -838,7 +835,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -854,7 +851,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -870,7 +867,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -895,7 +892,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -911,7 +908,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -936,7 +933,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -952,7 +949,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -968,7 +965,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1007,14 +1004,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -1036,12 +1033,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1057,7 +1054,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/compilers by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:52 GMT -->
</html>
diff --git a/anselm-cluster-documentation/software/compilers.md b/docs.it4i.cz/anselm-cluster-documentation/software/compilers.md
similarity index 52%
rename from anselm-cluster-documentation/software/compilers.md
rename to docs.it4i.cz/anselm-cluster-documentation/software/compilers.md
index 1d2a290b80a3dfa09b0cbe0faa0cd4d43393347e..f3f1272e9af9b3bb42921eefd97ddf9c6e4acceb 100644
--- a/anselm-cluster-documentation/software/compilers.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/compilers.md
@@ -1,8 +1,9 @@
+Compilers
+=========
Available compilers, including GNU, INTEL and UPC compilers
-
-
+
Currently there are several compilers for different programming
-languages available on the Anselm cluster
+languages available on the Anselm cluster:
- C/C++
- Fortran 77/90/95
- Unified Parallel C
@@ -15,21 +16,22 @@ Intel Compilers
---------------
For information about the usage of Intel Compilers and other Intel
products, please read the [Intel Parallel
-studio](intel-suite.html) page.
+studio](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite)
+page.
GNU C/C++ and Fortran Compilers
--------------------------------
+--------
For compatibility reasons there are still available the original (old
4.4.6-4) versions of GNU compilers as part of the OS. These are
accessible in the search path by default.
It is strongly recommended to use the up to date version (4.8.1) which
-comes with the module gcc
+comes with the module gcc:
$ module load gcc
$ gcc -v
$ g++ -v
$ gfortran -v
With the module loaded two environment variables are predefined. One for
maximum optimizations on the Anselm cluster architecture, and the other
-for debugging purposes
+for debugging purposes:
$ echo $OPTFLAGS
-O3 -march=corei7-avx
$ echo $DEBUGFLAGS
@@ -38,7 +40,7 @@ For more informations about the possibilities of the compilers, please
see the man pages.
Unified Parallel C
------------------
-UPC is supported by two compiler/runtime implementations
+UPC is supported by two compiler/runtime implementations:
- GNU - SMP/multi-threading support only
- Berkley - multi-node support as well as SMP/multi-threading support
### GNU UPC Compiler
@@ -50,8 +52,8 @@ gupc
Simple program to test the compiler
$ cat count.upc
/* hello.upc - a simple UPC example */
- #include
- #include
+ #include <upc.h>
+ #include <stdio.h>
int main() {
 if (MYTHREAD == 0) {
   printf("Welcome to GNU UPC!!!n");
@@ -77,11 +79,11 @@ implementation of UPC network "ibv". For testing/debugging using
multiple nodes, the "mpi" UPC network is recommended. Please note, that
**the selection of the network is done at the compile time** and not at
runtime (as expected)!
-Example UPC code
+Example UPC code:
$ cat hello.upc
/* hello.upc - a simple UPC example */
- #include
- #include
+ #include <upc.h>
+ #include <stdio.h>
int main() {
 if (MYTHREAD == 0) {
   printf("Welcome to Berkeley UPC!!!n");
@@ -96,78 +98,17 @@ To run the example with 5 threads issue
$ upcrun -n 5 ./hello.upc.x
To run the example on two compute nodes using all 32 cores, with 32
threads, issue
- $ qsub -I -q qprod -A PROJECT_ID -l select=2ncpus=16
+ $ qsub -I -q qprod -A PROJECT_ID -l select=2:ncpus=16
$ module add bupc
$ upcrun -n 32 ./hello.upc.x
 For more informations see the man pages.
Java
----
For information how to use Java (runtime and/or compiler), please read
-the [Java page](java.html).
+the [Java
+page](https://docs.it4i.cz/anselm-cluster-documentation/software/java).
nVidia CUDA
-----------
For information how to work with nVidia CUDA, please read the [nVidia
-CUDA page](nvidia-cuda.html).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage-1.html)
-
- - [Network](../network.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](virtualization.html)
-
+CUDA
+page](https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda).
diff --git a/anselm-cluster-documentation/software/comsol.html b/docs.it4i.cz/anselm-cluster-documentation/software/comsol.html
old mode 100755
new mode 100644
similarity index 69%
rename from anselm-cluster-documentation/software/comsol.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/comsol.html
index f33c64dbc0fcb2ec86ddb6b09582ead334b63906..6e5cd5408bce0fdb5ad3e750f58757016d34d3f4
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<div id="parent-fieldname-text-2aad5f03c8db4ea2bac6df527ebbed80" class="">
<h2 class=" "><span><span>Introduction<br /></span></span></h2>
-<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/" target="_self" title="">COMSOL</a></span></span><span><span> is a powerful environment for modelling and solving various engineering and scientific problems based on partial differential equations. COMSOL is designed to solve coupled or multiphysics phenomena. For many standard engineering problems COMSOL provides add-on products such as electrical, mechanical, fluid flow, and chemical applications.</span></span></p>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com" target="_self" title="">COMSOL</a></span></span><span><span> is a powerful environment for modelling and solving various engineering and scientific problems based on partial differential equations. COMSOL is designed to solve coupled or multiphysics phenomena. For many standard engineering problems COMSOL provides add-on products such as electrical, mechanical, fluid flow, and chemical applications.</span></span></p>
<ul>
<li>
<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/structural-mechanics-module" target="_self" title="">Structural Mechanics Module</a>, </span></span></p>
@@ -274,14 +271,14 @@
<pre class="prettyprint lang-sh"><span><span>$ module load comsol</span></span></pre>
<p align="JUSTIFY"><span><span>By default the </span></span><span><span><b>EDU variant</b></span></span><span><span> will be loaded. If user needs other version or variant, load the particular version. To obtain the list of available versions use</span></span></p>
<pre class="prettyprint lang-sh"><span><span>$ module avail comsol</span></span></pre>
-<p align="JUSTIFY"><span><span>If user needs to prepare COMSOL jobs in the interactive mode it is recommend to use COMSOL on the compute nodes via PBS Pro scheduler. In order run the COMSOL Desktop GUI on Windows is recommended to use the <a target="_self" title="" class="internal-link" href="comsol/resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html">Virtual Network Computing (VNC)</a>.</span></span></p>
+<p align="JUSTIFY"><span><span>If user needs to prepare COMSOL jobs in the interactive mode it is recommend to use COMSOL on the compute nodes via PBS Pro scheduler. In order run the COMSOL Desktop GUI on Windows is recommended to use the <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">Virtual Network Computing (VNC)</a>.</span></span></p>
<pre class="prettyprint lang-sh"><span><span><span>$ xhost +<br />$ qsub -I -X</span></span></span><span><span><span><span> </span></span></span></span><span><span><span>-A</span></span></span><span><span> </span></span><span><span><span><span>PROJECT_ID </span></span></span></span><span><span><span>-q </span></span></span><span><span><span><span>qprod</span></span></span></span><span><span><span> -l </span></span></span><span><span><span><span>select=1:ncpus=16</span><br />$ module load </span></span></span><span><span>comsol<span><br />$ </span></span></span><span><span>comsol<br /></span></span></pre>
<p align="JUSTIFY"><span><span>To run COMSOL in batch mode, without the COMSOL Desktop GUI environment, user can utilized the default (comsol.pbs) job script and execute it via the qsub command.</span></span></p>
<pre class="prettyprint lang-sh"><span><span>#!/bin/bash<br />#PBS -l select=3:ncpus=16<br />#PBS -q qprod<br />#PBS -N JOB_NAME<br />#PBS -A PROJECT_ID<br /><br />cd /scratch/$USER/ || exit<br /><br />echo Time is `date`<br />echo Directory is `pwd`<br />echo '***PBS_NODEFILE***START*******'<br />cat $PBS_NODEFILE<br />echo '***PBS_NODEFILE***END*********'<br /><br />text_nodes < cat $PBS_NODEFILE<br /><br />module load comsol<br /># module load comsol/43b-COM<br /><br />ntask=$(wc -l $PBS_NODEFILE)<br /><br />comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log<br /><br /></span></span></pre>
<p align="JUSTIFY"><span><span>Working directory has to be created before sending the (comsol.pbs) job script into the queue. Input file (name_input_f.mph) has to be in working directory or full path to input file has to be specified. The appropriate path to the temp directory of the job has to be set by command option (-tmpdir).</span></span></p>
<h2 class=" ">LiveLink™<i> </i>for MATLAB<sup>®</sup></h2>
<p align="JUSTIFY"><span><span>COMSOL is the software package for the numerical solution of the partial differential equations. LiveLink for MATLAB allows connection to the COMSOL</span></span><span><span><sup><span><span><span><span><span><span><span><b>®</b></span></span></span></span></span></span></span></sup></span></span><span><span> API (Application Programming Interface) with the benefits of the programming language and computing environment of the MATLAB. </span></span></p>
-<p align="JUSTIFY"><span><span>LiveLink for MATLAB is available in both </span></span><span><span><b>EDU</b></span></span><span><span> and </span></span><span><span><b>COM</b></span></span><span><span> </span></span><span><span><b>variant</b></span></span><span><span> of the COMSOL release. On Anselm 1 commercial (</span></span><span><span><b>COM</b></span></span><span><span>) license and the 5 educational (</span></span><span><span><b>EDU</b></span></span><span><span>) licenses of LiveLink for MATLAB (please see the <a target="_self" title="" class="internal-link" href="isv_licenses.html">ISV Licenses</a>) are available. Following example shows how to start COMSOL model from MATLAB via LiveLink in the interactive mode.</span></span></p>
+<p align="JUSTIFY"><span><span>LiveLink for MATLAB is available in both </span></span><span><span><b>EDU</b></span></span><span><span> and </span></span><span><span><b>COM</b></span></span><span><span> </span></span><span><span><b>variant</b></span></span><span><span> of the COMSOL release. On Anselm 1 commercial (</span></span><span><span><b>COM</b></span></span><span><span>) license and the 5 educational (</span></span><span><span><b>EDU</b></span></span><span><span>) licenses of LiveLink for MATLAB (please see the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">ISV Licenses</a>) are available. Following example shows how to start COMSOL model from MATLAB via LiveLink in the interactive mode.</span></span></p>
<pre class="prettyprint lang-sh">$ xhost +<br />$ qsub -I -X -A PROJECT_ID -q qexp -l select=1:ncpus=16<br />$ module load matlab<br />$ module load comsol<br />$ comsol server matlab</pre>
<p align="JUSTIFY"><span><span>At the first time to launch the LiveLink for MATLAB (client-MATLAB/server-COMSOL connection) the login and password is requested and this information is not requested again.</span></span></p>
<p align="JUSTIFY"><span><span>To run LiveLink for MATLAB in batch mode with (comsol_matlab.pbs) job script you can utilize/modify the following script and execute it via the qsub command.</span></span></p>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
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+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
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+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
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+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
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@@ -653,7 +650,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
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+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
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@@ -717,7 +714,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
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@@ -733,7 +730,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
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@@ -749,7 +746,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
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+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
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+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
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+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -829,7 +826,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -845,7 +842,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -861,7 +858,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -886,7 +883,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -902,7 +899,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -927,7 +924,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -943,7 +940,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -959,7 +956,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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<div id="portal-footer">
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/comsol.md b/docs.it4i.cz/anselm-cluster-documentation/software/comsol.md
new file mode 100644
index 0000000000000000000000000000000000000000..7364eb191f81b7cebaf64e46bd505365a8842ca6
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/comsol.md
@@ -0,0 +1,162 @@
+COMSOL Multiphysics®
+====================
+
+<span><span>Introduction
+</span></span>
+--
+<span><span>[COMSOL](http://www.comsol.com)</span></span><span><span>
+is a powerful environment for modelling and solving various engineering
+and scientific problems based on partial differential equations. COMSOL
+is designed to solve coupled or multiphysics phenomena. For many
+standard engineering problems COMSOL provides add-on products such as
+electrical, mechanical, fluid flow, and chemical
+applications.</span></span>
+- <span><span>[Structural Mechanics
+ Module](http://www.comsol.com/structural-mechanics-module),
+ </span></span>
+- <span><span>[Heat Transfer
+ Module](http://www.comsol.com/heat-transfer-module),
+ </span></span>
+- <span><span>[CFD
+ Module](http://www.comsol.com/cfd-module),
+ </span></span>
+- <span><span>[Acoustics
+ Module](http://www.comsol.com/acoustics-module),
+ </span></span>
+- <span><span>and [many
+ others](http://www.comsol.com/products)</span></span>
+<span><span>COMSOL also allows an
+</span></span><span><span><span><span>interface support for
+equation-based modelling of
+</span></span></span></span><span><span>partial differential
+equations.</span></span>
+<span><span>Execution
+</span></span>
+----------------------
+<span><span>On the Anselm cluster COMSOL is available in the latest
+stable version. There are two variants of the release:</span></span>
+- <span><span>**Non commercial**</span></span><span><span> or so
+ called </span></span><span><span>**EDU
+ variant**</span></span><span><span>, which can be used for research
+ and educational purposes.</span></span>
+- <span><span>**Commercial**</span></span><span><span> or so called
+ </span></span><span><span>**COM variant**</span></span><span><span>,
+ which can used also for commercial activities.
+ </span></span><span><span>**COM variant**</span></span><span><span>
+ has only subset of features compared to the
+ </span></span><span><span>**EDU
+ variant**</span></span><span><span> available. <span
+ class="internal-link"><span id="result_box" class="short_text"><span
+ class="hps">More</span> <span class="hps">about
+ licensing</span> will be posted <span class="hps">here
+ soon</span>.</span></span>
+ </span></span>
+<span><span>To load the of COMSOL load the module</span></span>
+``` {.prettyprint .lang-sh}
+$ module load comsol
+```
+<span><span>By default the </span></span><span><span>**EDU
+variant**</span></span><span><span> will be loaded. If user needs other
+version or variant, load the particular version. To obtain the list of
+available versions use</span></span>
+``` {.prettyprint .lang-sh}
+$ module avail comsol
+```
+<span><span>If user needs to prepare COMSOL jobs in the interactive mode
+it is recommend to use COMSOL on the compute nodes via PBS Pro
+scheduler. In order run the COMSOL Desktop GUI on Windows is recommended
+to use the [Virtual Network Computing
+(VNC)](resolveuid/11e53ad0d2fd4c5187537f4baeedff33).</span></span>
+``` {.prettyprint .lang-sh}
+$ xhost +
+$ qsub -I -X -A PROJECT_ID -q qprod -l select=1:ncpus=16
+$ module load comsol
+$ comsol
+```
+<span><span>To run COMSOL in batch mode, without the COMSOL Desktop GUI
+environment, user can utilized the default (comsol.pbs) job script and
+execute it via the qsub command.</span></span>
+``` {.prettyprint .lang-sh}
+#!/bin/bash
+#PBS -l select=3:ncpus=16
+#PBS -q qprod
+#PBS -N JOB_NAME
+#PBS -AÂ PROJECT_ID
+cd /scratch/$USER/ || exit
+echo Time is `date`
+echo Directory is `pwd`
+echo '***PBS_NODEFILE***START*******'
+cat $PBS_NODEFILE
+echo '***PBS_NODEFILE***END*********'
+text_nodes < cat $PBS_NODEFILE
+module load comsol
+# module load comsol/43b-COM
+ntask=$(wc -l $PBS_NODEFILE)
+comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log
+```
+<span><span>Working directory has to be created before sending the
+(comsol.pbs) job script into the queue. Input file (name_input_f.mph)
+has to be in working directory or full path to input file has to be
+specified. The appropriate path to the temp directory of the job has to
+be set by command option (-tmpdir).</span></span>
+LiveLink™* *for MATLAB^®^
+--
+<span><span>COMSOL is the software package for the numerical solution of
+the partial differential equations. LiveLink for MATLAB allows
+connection to the
+COMSOL</span></span><span><span>^<span><span><span><span><span><span><span>**®**</span></span></span></span></span></span></span>^</span></span><span><span>
+API (Application Programming Interface) with the benefits of the
+programming language and computing environment of the MATLAB.
+</span></span>
+<span><span>LiveLink for MATLAB is available in both
+</span></span><span><span>**EDU**</span></span><span><span> and
+</span></span><span><span>**COM**</span></span><span><span>
+</span></span><span><span>**variant**</span></span><span><span> of the
+COMSOL release. On Anselm 1 commercial
+(</span></span><span><span>**COM**</span></span><span><span>) license
+and the 5 educational
+(</span></span><span><span>**EDU**</span></span><span><span>) licenses
+of LiveLink for MATLAB (please see the [ISV
+Licenses](https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses))
+are available. Following example shows how to start COMSOL model from
+MATLAB via LiveLink in the interactive mode.</span></span>
+``` {.prettyprint .lang-sh}
+$ xhost +
+$ qsub -I -X -A PROJECT_ID -q qexp -l select=1:ncpus=16
+$ module load matlab
+$ module load comsol
+$ comsol server matlab
+```
+<span><span>At the first time to launch the LiveLink for MATLAB
+(client-MATLAB/server-COMSOL connection) the login and password is
+requested and this information is not requested again.</span></span>
+<span><span>To run LiveLink for MATLAB in batch mode with
+(comsol_matlab.pbs) job script you can utilize/modify the following
+script and execute it via the qsub command.</span></span>
+``` {.prettyprint .lang-sh}
+#!/bin/bash
+#PBS -l select=3:ncpus=16
+#PBS -q qprod
+#PBS -N JOB_NAME
+#PBS -AÂ PROJECT_ID
+cd /scratch/$USER || exit
+echo Time is `date`
+echo Directory is `pwd`
+echo '***PBS_NODEFILE***START*******'
+cat $PBS_NODEFILE
+echo '***PBS_NODEFILE***END*********'
+text_nodes < cat $PBS_NODEFILE
+module load matlab
+module load comsol/43b-EDU
+ntask=$(wc -l $PBS_NODEFILE)
+comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/$USER &
+cd /apps/engineering/comsol/comsol43b/mli
+matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/$USER; test_job"
+```
+This example shows how to run Livelink for MATLAB with following
+configuration3 nodes and 16 cores per node. Working directory has to
+be created before submitting (comsol_matlab.pbs) job script into the
+queue. Input file (test_job.m) has to be in working directory or full
+path to input file has to be specified. The Matlab command option (-r
+”mphstart”) created a connection with a COMSOL server using the default
+port number.
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.html b/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.html
new file mode 100644
index 0000000000000000000000000000000000000000..a689cf2e77703675f66679e1e55a8322607d28f7
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.html
@@ -0,0 +1,1049 @@
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+ <div id="content-core">
+
+
+
+ <div id="parent-fieldname-text-2aad5f03c8db4ea2bac6df527ebbed80" class="">
+ <h2 class=" "><span><span>Introduction<br /></span></span></h2>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com" target="_self" title="">COMSOL</a></span></span><span><span> is a powerful environment for modelling and solving various engineering and scientific problems based on partial differential equations. COMSOL is designed to solve coupled or multiphysics phenomena. For many standard engineering problems COMSOL provides add-on products such as electrical, mechanical, fluid flow, and chemical applications.</span></span></p>
+<ul>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/structural-mechanics-module" target="_self" title="">Structural Mechanics Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/heat-transfer-module" target="_self" title="">Heat Transfer Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/cfd-module" target="_self" title="">CFD Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/acoustics-module" target="_self" title="">Acoustics Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span>and <a class="external-link" href="http://www.comsol.com/products" target="_self" title="">many others</a></span></span></p>
+</li>
+</ul>
+<p align="JUSTIFY"><span><span>COMSOL also allows an </span></span><span><span><span><span>interface support for equation-based modelling of </span></span></span></span><span><span>partial differential equations.</span></span></p>
+<h2 class=" "><span><span>Execution<br /></span></span></h2>
+<p align="JUSTIFY"><span><span>On the Anselm cluster COMSOL is available in the latest stable version. There are two variants of the release:</span></span></p>
+<ul>
+<li>
+<p align="JUSTIFY"><span><span><b>Non commercial</b></span></span><span><span> or so called </span></span><span><span><b>EDU variant</b></span></span><span><span>, which can be used for research and educational purposes.</span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><b>Commercial</b></span></span><span><span> or so called </span></span><span><span><b>COM variant</b></span></span><span><span>, which can used also for commercial activities. </span></span><span><span><b>COM variant</b></span></span><span><span> has only subset of features compared to the </span></span><span><span><b>EDU variant</b></span></span><span><span> available. <span class="internal-link"><span class="short_text" id="result_box"><span class="hps">More</span> <span class="hps">about licensing</span> will be posted <span class="hps">here soon</span>.</span></span><br /></span></span></p>
+</li>
+</ul>
+<p align="JUSTIFY"><span><span>To load the of COMSOL load the module</span></span></p>
+<pre class="prettyprint lang-sh"><span><span>$ module load comsol</span></span></pre>
+<p align="JUSTIFY"><span><span>By default the </span></span><span><span><b>EDU variant</b></span></span><span><span> will be loaded. If user needs other version or variant, load the particular version. To obtain the list of available versions use</span></span></p>
+<pre class="prettyprint lang-sh"><span><span>$ module avail comsol</span></span></pre>
+<p align="JUSTIFY"><span><span>If user needs to prepare COMSOL jobs in the interactive mode it is recommend to use COMSOL on the compute nodes via PBS Pro scheduler. In order run the COMSOL Desktop GUI on Windows is recommended to use the <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">Virtual Network Computing (VNC)</a>.</span></span></p>
+<pre class="prettyprint lang-sh"><span><span><span>$ xhost +<br />$ qsub -I -X</span></span></span><span><span><span><span> </span></span></span></span><span><span><span>-A</span></span></span><span><span> </span></span><span><span><span><span>PROJECT_ID </span></span></span></span><span><span><span>-q </span></span></span><span><span><span><span>qprod</span></span></span></span><span><span><span> -l </span></span></span><span><span><span><span>select=1:ncpus=16</span><br />$ module load </span></span></span><span><span>comsol<span><br />$ </span></span></span><span><span>comsol<br /></span></span></pre>
+<p align="JUSTIFY"><span><span>To run COMSOL in batch mode, without the COMSOL Desktop GUI environment, user can utilized the default (comsol.pbs) job script and execute it via the qsub command.</span></span></p>
+<pre class="prettyprint lang-sh"><span><span>#!/bin/bash<br />#PBS -l select=3:ncpus=16<br />#PBS -q qprod<br />#PBS -N JOB_NAME<br />#PBS -A PROJECT_ID<br /><br />cd /scratch/$USER/ || exit<br /><br />echo Time is `date`<br />echo Directory is `pwd`<br />echo '***PBS_NODEFILE***START*******'<br />cat $PBS_NODEFILE<br />echo '***PBS_NODEFILE***END*********'<br /><br />text_nodes < cat $PBS_NODEFILE<br /><br />module load comsol<br /># module load comsol/43b-COM<br /><br />ntask=$(wc -l $PBS_NODEFILE)<br /><br />comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log<br /><br /></span></span></pre>
+<p align="JUSTIFY"><span><span>Working directory has to be created before sending the (comsol.pbs) job script into the queue. Input file (name_input_f.mph) has to be in working directory or full path to input file has to be specified. The appropriate path to the temp directory of the job has to be set by command option (-tmpdir).</span></span></p>
+<h2 class=" ">LiveLink™<i> </i>for MATLAB<sup>®</sup></h2>
+<p align="JUSTIFY"><span><span>COMSOL is the software package for the numerical solution of the partial differential equations. LiveLink for MATLAB allows connection to the COMSOL</span></span><span><span><sup><span><span><span><span><span><span><span><b>®</b></span></span></span></span></span></span></span></sup></span></span><span><span> API (Application Programming Interface) with the benefits of the programming language and computing environment of the MATLAB. </span></span></p>
+<p align="JUSTIFY"><span><span>LiveLink for MATLAB is available in both </span></span><span><span><b>EDU</b></span></span><span><span> and </span></span><span><span><b>COM</b></span></span><span><span> </span></span><span><span><b>variant</b></span></span><span><span> of the COMSOL release. On Anselm 1 commercial (</span></span><span><span><b>COM</b></span></span><span><span>) license and the 5 educational (</span></span><span><span><b>EDU</b></span></span><span><span>) licenses of LiveLink for MATLAB (please see the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">ISV Licenses</a>) are available. Following example shows how to start COMSOL model from MATLAB via LiveLink in the interactive mode.</span></span></p>
+<pre class="prettyprint lang-sh">$ xhost +<br />$ qsub -I -X -A PROJECT_ID -q qexp -l select=1:ncpus=16<br />$ module load matlab<br />$ module load comsol<br />$ comsol server matlab</pre>
+<p align="JUSTIFY"><span><span>At the first time to launch the LiveLink for MATLAB (client-MATLAB/server-COMSOL connection) the login and password is requested and this information is not requested again.</span></span></p>
+<p align="JUSTIFY"><span><span>To run LiveLink for MATLAB in batch mode with (comsol_matlab.pbs) job script you can utilize/modify the following script and execute it via the qsub command.</span></span></p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -l select=3:ncpus=16<br />#PBS -q qprod<br />#PBS -N JOB_NAME<br />#PBS -AÂ PROJECT_ID<br /><br />cd /scratch/$USER || exit<br /><br />echo Time is `date`<br />echo Directory is `pwd`<br />echo '***PBS_NODEFILE***START*******'<br />cat $PBS_NODEFILE<br />echo '***PBS_NODEFILE***END*********'<br /><br />text_nodes < cat $PBS_NODEFILE<br /><br />module load matlab<br />module load comsol/43b-EDU<br /><br />ntask=$(wc -l $PBS_NODEFILE)<br /><br />comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/$USER &<br />cd /apps/engineering/comsol/comsol43b/mli<br />matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/$USER; test_job"</pre>
+<p>This example shows how to run Livelink for MATLAB with following configuration: 3 nodes and 16 cores per node. Working directory has to be created before submitting (comsol_matlab.pbs) job script into the queue. Input file (test_job.m) has to be in working directory or full path to input file has to be specified. The Matlab command option (-r ”mphstart”) created a connection with a COMSOL server using the default port number.<br /><br /></p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md b/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md
new file mode 100644
index 0000000000000000000000000000000000000000..7364eb191f81b7cebaf64e46bd505365a8842ca6
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md
@@ -0,0 +1,162 @@
+COMSOL Multiphysics®
+====================
+
+<span><span>Introduction
+</span></span>
+--
+<span><span>[COMSOL](http://www.comsol.com)</span></span><span><span>
+is a powerful environment for modelling and solving various engineering
+and scientific problems based on partial differential equations. COMSOL
+is designed to solve coupled or multiphysics phenomena. For many
+standard engineering problems COMSOL provides add-on products such as
+electrical, mechanical, fluid flow, and chemical
+applications.</span></span>
+- <span><span>[Structural Mechanics
+ Module](http://www.comsol.com/structural-mechanics-module),
+ </span></span>
+- <span><span>[Heat Transfer
+ Module](http://www.comsol.com/heat-transfer-module),
+ </span></span>
+- <span><span>[CFD
+ Module](http://www.comsol.com/cfd-module),
+ </span></span>
+- <span><span>[Acoustics
+ Module](http://www.comsol.com/acoustics-module),
+ </span></span>
+- <span><span>and [many
+ others](http://www.comsol.com/products)</span></span>
+<span><span>COMSOL also allows an
+</span></span><span><span><span><span>interface support for
+equation-based modelling of
+</span></span></span></span><span><span>partial differential
+equations.</span></span>
+<span><span>Execution
+</span></span>
+----------------------
+<span><span>On the Anselm cluster COMSOL is available in the latest
+stable version. There are two variants of the release:</span></span>
+- <span><span>**Non commercial**</span></span><span><span> or so
+ called </span></span><span><span>**EDU
+ variant**</span></span><span><span>, which can be used for research
+ and educational purposes.</span></span>
+- <span><span>**Commercial**</span></span><span><span> or so called
+ </span></span><span><span>**COM variant**</span></span><span><span>,
+ which can used also for commercial activities.
+ </span></span><span><span>**COM variant**</span></span><span><span>
+ has only subset of features compared to the
+ </span></span><span><span>**EDU
+ variant**</span></span><span><span> available. <span
+ class="internal-link"><span id="result_box" class="short_text"><span
+ class="hps">More</span> <span class="hps">about
+ licensing</span> will be posted <span class="hps">here
+ soon</span>.</span></span>
+ </span></span>
+<span><span>To load the of COMSOL load the module</span></span>
+``` {.prettyprint .lang-sh}
+$ module load comsol
+```
+<span><span>By default the </span></span><span><span>**EDU
+variant**</span></span><span><span> will be loaded. If user needs other
+version or variant, load the particular version. To obtain the list of
+available versions use</span></span>
+``` {.prettyprint .lang-sh}
+$ module avail comsol
+```
+<span><span>If user needs to prepare COMSOL jobs in the interactive mode
+it is recommend to use COMSOL on the compute nodes via PBS Pro
+scheduler. In order run the COMSOL Desktop GUI on Windows is recommended
+to use the [Virtual Network Computing
+(VNC)](resolveuid/11e53ad0d2fd4c5187537f4baeedff33).</span></span>
+``` {.prettyprint .lang-sh}
+$ xhost +
+$ qsub -I -X -A PROJECT_ID -q qprod -l select=1:ncpus=16
+$ module load comsol
+$ comsol
+```
+<span><span>To run COMSOL in batch mode, without the COMSOL Desktop GUI
+environment, user can utilized the default (comsol.pbs) job script and
+execute it via the qsub command.</span></span>
+``` {.prettyprint .lang-sh}
+#!/bin/bash
+#PBS -l select=3:ncpus=16
+#PBS -q qprod
+#PBS -N JOB_NAME
+#PBS -AÂ PROJECT_ID
+cd /scratch/$USER/ || exit
+echo Time is `date`
+echo Directory is `pwd`
+echo '***PBS_NODEFILE***START*******'
+cat $PBS_NODEFILE
+echo '***PBS_NODEFILE***END*********'
+text_nodes < cat $PBS_NODEFILE
+module load comsol
+# module load comsol/43b-COM
+ntask=$(wc -l $PBS_NODEFILE)
+comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log
+```
+<span><span>Working directory has to be created before sending the
+(comsol.pbs) job script into the queue. Input file (name_input_f.mph)
+has to be in working directory or full path to input file has to be
+specified. The appropriate path to the temp directory of the job has to
+be set by command option (-tmpdir).</span></span>
+LiveLink™* *for MATLAB^®^
+--
+<span><span>COMSOL is the software package for the numerical solution of
+the partial differential equations. LiveLink for MATLAB allows
+connection to the
+COMSOL</span></span><span><span>^<span><span><span><span><span><span><span>**®**</span></span></span></span></span></span></span>^</span></span><span><span>
+API (Application Programming Interface) with the benefits of the
+programming language and computing environment of the MATLAB.
+</span></span>
+<span><span>LiveLink for MATLAB is available in both
+</span></span><span><span>**EDU**</span></span><span><span> and
+</span></span><span><span>**COM**</span></span><span><span>
+</span></span><span><span>**variant**</span></span><span><span> of the
+COMSOL release. On Anselm 1 commercial
+(</span></span><span><span>**COM**</span></span><span><span>) license
+and the 5 educational
+(</span></span><span><span>**EDU**</span></span><span><span>) licenses
+of LiveLink for MATLAB (please see the [ISV
+Licenses](https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses))
+are available. Following example shows how to start COMSOL model from
+MATLAB via LiveLink in the interactive mode.</span></span>
+``` {.prettyprint .lang-sh}
+$ xhost +
+$ qsub -I -X -A PROJECT_ID -q qexp -l select=1:ncpus=16
+$ module load matlab
+$ module load comsol
+$ comsol server matlab
+```
+<span><span>At the first time to launch the LiveLink for MATLAB
+(client-MATLAB/server-COMSOL connection) the login and password is
+requested and this information is not requested again.</span></span>
+<span><span>To run LiveLink for MATLAB in batch mode with
+(comsol_matlab.pbs) job script you can utilize/modify the following
+script and execute it via the qsub command.</span></span>
+``` {.prettyprint .lang-sh}
+#!/bin/bash
+#PBS -l select=3:ncpus=16
+#PBS -q qprod
+#PBS -N JOB_NAME
+#PBS -AÂ PROJECT_ID
+cd /scratch/$USER || exit
+echo Time is `date`
+echo Directory is `pwd`
+echo '***PBS_NODEFILE***START*******'
+cat $PBS_NODEFILE
+echo '***PBS_NODEFILE***END*********'
+text_nodes < cat $PBS_NODEFILE
+module load matlab
+module load comsol/43b-EDU
+ntask=$(wc -l $PBS_NODEFILE)
+comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/$USER &
+cd /apps/engineering/comsol/comsol43b/mli
+matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/$USER; test_job"
+```
+This example shows how to run Livelink for MATLAB with following
+configuration3 nodes and 16 cores per node. Working directory has to
+be created before submitting (comsol_matlab.pbs) job script into the
+queue. Input file (test_job.m) has to be in working directory or full
+path to input file has to be specified. The Matlab command option (-r
+”mphstart”) created a connection with a COMSOL server using the default
+port number.
diff --git a/anselm-cluster-documentation/software/debuggers.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.1.html
old mode 100755
new mode 100644
similarity index 61%
rename from anselm-cluster-documentation/software/debuggers.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/debuggers.1.html
index 17335fff229e783916af6bbb44ae694bac11647e..9d47b244414ab076a179fca71c6061fe01ba8835
--- a/anselm-cluster-documentation/software/debuggers.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.1.html
@@ -10,45 +10,42 @@
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Debuggers and profilers summary — IT4I Docs</title>
- <link rel="canonical" href="debuggers.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="debuggers.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="debuggers.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
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/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
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@@ -243,25 +240,25 @@
<h2 class=" ">Introduction</h2>
<p>We provide state of the art programms and tools to develop, profile and debug HPC codes at IT4Innovations.<br />On these pages, we provide an overview of the profiling and debugging tools available on Anslem at IT4I.</p>
<h2 class=" ">Intel debugger</h2>
-<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a target="_self" title="" class="internal-link" href="debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html">X display</a> for running the GUI.</p>
+<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">X display</a> for running the GUI.</p>
<pre class=" ">$ module load intel<br />$ idb</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="intel-suite/intel-debugger.html">Intel Debugger</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger">Intel Debugger</a> page.</p>
<h2 class=" ">Allinea Forge (DDT/MAP)</h2>
<p>Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel Xeon Phi accelerators. DDT provides all the standard debugging features (stack trace, breakpoints, watches, view variables, threads etc.) for every thread running as part of your program, or for every process - even if these processes are distributed across a cluster using an MPI implementation.</p>
<pre class=" ">$ module load Forge<br />$ forge</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="debuggers/allinea-ddt.html">Allinea DDT</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt">Allinea DDT</a> page.</p>
<h2 class=" ">Allinea Performance Reports</h2>
<p>Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs. Our license is limited to 64 MPI processes.</p>
<pre class=" ">$ module load PerformanceReports/6.0 <br />$ perf-report mpirun -n 64 ./my_application argument01 argument02</pre>
-<p class=" ">Read more at the <a target="_self" title="" class="internal-link" href="debuggers/allinea-performance-reports.html">Allinea Performance Reports</a> page.</p>
+<p class=" ">Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports">Allinea Performance Reports</a> page.</p>
<h2 class=" ">RougeWave Totalview</h2>
<p>TotalView is a source- and machine-level debugger for multi-process, multi-threaded programs. Its wide range of tools provides ways to analyze, organize, and test programs, making it easy to isolate and identify problems in individual threads and processes in programs of great complexity.</p>
<pre class=" ">$ module load totalview<br />$ totalview</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="debuggers/total-view.html">Totalview</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view">Totalview</a> page.</p>
<h2 class=" ">Vampir trace analyzer</h2>
<p>Vampir is a GUI trace analyzer for traces in OTF format.</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="../../salomon/software/debuggers/vampir.html">Vampir</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">Vampir</a> page.</p>
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@@ -337,7 +334,7 @@
<dt class="portletHeader hiddenStructure">
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@@ -353,7 +350,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
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@@ -369,7 +366,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
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</a>
@@ -385,7 +382,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
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</a>
@@ -401,7 +398,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
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@@ -417,7 +414,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
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</a>
@@ -433,7 +430,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -449,7 +446,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -465,7 +462,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -481,7 +478,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -497,7 +494,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -513,7 +510,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -529,10 +526,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -548,7 +545,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -564,7 +561,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -580,7 +577,7 @@
- <a title="A collection of development tools" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -596,7 +593,7 @@
- <a title="" class="state-published contenttype-document" href="debuggers/allinea-ddt.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
@@ -612,7 +609,7 @@
- <a title="quick application profiling" class="state-published contenttype-document" href="debuggers/allinea-performance-reports.html">
+ <a class="state-published contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -628,7 +625,7 @@
- <a title="" class="state-published contenttype-document" href="debuggers/cube.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube">
<span>CUBE</span>
</a>
@@ -644,7 +641,7 @@
- <a title="" class="state-published contenttype-document" href="debuggers/intel-performance-counter-monitor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor">
<span>Intel Performance Counter Monitor</span>
</a>
@@ -660,7 +657,7 @@
- <a title="" class="state-published contenttype-document" href="debuggers/intel-vtune-amplifier.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier</span>
</a>
@@ -676,7 +673,7 @@
- <a title="" class="state-published contenttype-document" href="debuggers/papi.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi">
<span>PAPI</span>
</a>
@@ -692,7 +689,7 @@
- <a title="" class="state-published contenttype-document" href="debuggers/scalasca.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca">
<span>Scalasca</span>
</a>
@@ -708,7 +705,7 @@
- <a title="" class="state-published contenttype-document" href="debuggers/score-p.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p">
<span>Score-P</span>
</a>
@@ -724,7 +721,7 @@
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published contenttype-document" href="debuggers/total-view.html">
+ <a class="state-published contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -740,7 +737,7 @@
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="debuggers/valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -756,7 +753,7 @@
- <a title="" class="state-published contenttype-document" href="debuggers/vampir.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -781,7 +778,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -797,7 +794,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -813,7 +810,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -829,7 +826,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -845,7 +842,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -861,7 +858,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -877,7 +874,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -893,7 +890,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -909,7 +906,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -925,7 +922,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -941,7 +938,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -957,7 +954,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -973,7 +970,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -989,7 +986,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1005,7 +1002,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1021,7 +1018,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1046,7 +1043,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1062,7 +1059,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1087,7 +1084,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1103,7 +1100,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1119,7 +1116,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1158,14 +1155,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1187,12 +1184,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1208,7 +1205,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/debuggers by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:44 GMT -->
</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.1.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.1.md
new file mode 100644
index 0000000000000000000000000000000000000000..07f6e5ff872baf1df1c5ad1d4ae89a44a0080de5
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.1.md
@@ -0,0 +1,67 @@
+Debuggers and profilers summary
+===============================
+
+Introduction
+------------
+We provide state of the art programms and tools to develop, profile and
+debug HPC codes at IT4Innovations.
+On these pages, we provide an overview of the profiling and debugging
+tools available on Anslem at IT4I.
+Intel debugger
+--------------
+The intel debugger version 13.0 is available, via module intel. The
+debugger works for applications compiled with C and C++ compiler and the
+ifort fortran 77/90/95 compiler. The debugger provides java GUI
+environment. Use [X
+display](resolveuid/11e53ad0d2fd4c5187537f4baeedff33)
+for running the GUI.
+ $ module load intel
+ $ idb
+Read more at the [Intel
+Debugger](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger)
+page.
+Allinea Forge (DDT/MAP)
+Allinea DDT, is a commercial debugger primarily for debugging parallel
+MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel
+Xeon Phi accelerators. DDT provides all the standard debugging features
+(stack trace, breakpoints, watches, view variables, threads etc.) for
+every thread running as part of your program, or for every process -
+even if these processes are distributed across a cluster using an MPI
+implementation.
+ $ module load Forge
+ $ forge
+Read more at the [Allinea
+DDT](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt)
+page.
+Allinea Performance Reports
+----
+Allinea Performance Reports characterize the performance of HPC
+application runs. After executing your application through the tool, a
+synthetic HTML report is generated automatically, containing information
+about several metrics along with clear behavior statements and hints to
+help you improve the efficiency of your runs. Our license is limited to
+64 MPI processes.
+ $ module load PerformanceReports/6.0
+ $ perf-report mpirun -n 64 ./my_application argument01 argument02
+Read more at the [Allinea Performance
+Reports](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports)
+page.
+RougeWave Totalview
+-------------------
+TotalView is a source- and machine-level debugger for multi-process,
+multi-threaded programs. Its wide range of tools provides ways to
+analyze, organize, and test programs, making it easy to isolate and
+identify problems in individual threads and processes in programs of
+great complexity.
+ $ module load totalview
+ $ totalview
+Read more at the
+[Totalview](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view)
+page.
+Vampir trace analyzer
+---------------------
+Vampir is a GUI trace analyzer for traces in OTF format.
+ $ module load Vampir/8.5.0
+ $ vampir
+Read more at
+the [Vampir](https://docs.it4i.cz/salomon/software/debuggers/vampir) page.
diff --git a/anselm-cluster-documentation/software/debuggers/Snimek obrazovky 2014-12-04 v 12.56.36.png b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/Snmekobrazovky20141204v12.56.36.png
old mode 100755
new mode 100644
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rename from anselm-cluster-documentation/software/debuggers/Snimek obrazovky 2014-12-04 v 12.56.36.png
rename to docs.it4i.cz/anselm-cluster-documentation/software/debuggers/Snmekobrazovky20141204v12.56.36.png
diff --git a/anselm-cluster-documentation/software/debuggers/allinea-ddt.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.html
old mode 100755
new mode 100644
similarity index 64%
rename from anselm-cluster-documentation/software/debuggers/allinea-ddt.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.html
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--- a/anselm-cluster-documentation/software/debuggers/allinea-ddt.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.html
@@ -10,45 +10,42 @@
-
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt" /><!--[if lt IE 7]></base><![endif]-->
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<title>Allinea Forge (DDT,MAP) — IT4I Docs</title>
- <link rel="canonical" href="allinea-ddt.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="allinea-ddt.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="allinea-ddt.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
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</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
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- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../debuggers.html">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">Debuggers and profilers</a>
<span class="breadcrumbSeparator">
/
@@ -280,13 +277,13 @@
<h2 class=" ">Starting a Job with DDT</h2>
<p class=" ">Be sure to log in with an <span class="internal-link">X window forwarding</span> enabled. This could mean using the -X in the ssh: Â </p>
<pre class=" ">$ ssh -X username@anselm.it4i.cz </pre>
-<p class=" ">Other options is to access login node using VNC. Please see the detailed information on how to <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html">use graphic user interface on Anselm</a><span class="internal-link"></span>.</p>
+<p class=" ">Other options is to access login node using VNC. Please see the detailed information on how to <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">use graphic user interface on Anselm</a><span class="internal-link"></span>.</p>
<p class=" ">From the login node an interactive session <strong>with X windows forwarding</strong> (-X option) can be started by following command:Â </p>
<pre class=" ">$ qsub -I -X -A NONE-0-0 -q qexp -lselect=1:ncpus=16:mpiprocs=16,walltime=01:00:00Â </pre>
<p class=" ">Then launch the debugger with the ddt command followed by the name of the executable to debug:</p>
<pre class=" ">$ ddt test_debug</pre>
<p class=" ">A<span style="text-align: start; "> submission window that appears have a prefilled path to the executable to debug. You can select the number of MPI processors and/or OpenMP threads on which to run and press run. Command line arguments to a program can be entered to the</span> "Arguments<span class="Apple-converted-space">" </span><span style="text-align: start; ">box.</span></p>
-<p class=" "><img width="451" height="513" alt="" class="image-inline" title="" src="ddt1.png" />Â </p>
+<p class=" "><img class="image-inline" src="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/ddt1.png" alt="" width="451" title="" height="513" />Â </p>
<p class=" ">To start the debugging directly without the submission window, user can specify the debugging and execution parameters from the command line. For example the number of MPI processes is set by option "-np 4". Skipping the dialog is done by "-start" option. To see the list of the "ddt" command line parameters, run "ddt --help". Â </p>
<pre class=" ">ddt -start -np 4 ./hello_debug_impi</pre>
<p class=" ">Â </p>
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<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
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-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
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- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
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- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -615,7 +612,7 @@
- <a title="A collection of development tools" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
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- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="allinea-ddt.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
@@ -647,7 +644,7 @@
- <a title="quick application profiling" class="state-published contenttype-document" href="allinea-performance-reports.html">
+ <a class="state-published contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -663,7 +660,7 @@
- <a title="" class="state-published contenttype-document" href="cube.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube">
<span>CUBE</span>
</a>
@@ -679,7 +676,7 @@
- <a title="" class="state-published contenttype-document" href="intel-performance-counter-monitor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor">
<span>Intel Performance Counter Monitor</span>
</a>
@@ -695,7 +692,7 @@
- <a title="" class="state-published contenttype-document" href="intel-vtune-amplifier.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier</span>
</a>
@@ -711,7 +708,7 @@
- <a title="" class="state-published contenttype-document" href="papi.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi">
<span>PAPI</span>
</a>
@@ -727,7 +724,7 @@
- <a title="" class="state-published contenttype-document" href="scalasca.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca">
<span>Scalasca</span>
</a>
@@ -743,7 +740,7 @@
- <a title="" class="state-published contenttype-document" href="score-p.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p">
<span>Score-P</span>
</a>
@@ -759,7 +756,7 @@
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published contenttype-document" href="total-view.html">
+ <a class="state-published contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -775,7 +772,7 @@
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -791,7 +788,7 @@
- <a title="" class="state-published contenttype-document" href="vampir.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -816,7 +813,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -832,7 +829,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -848,7 +845,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -864,7 +861,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -880,7 +877,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -896,7 +893,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -912,7 +909,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -928,7 +925,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -944,7 +941,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -960,7 +957,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -976,7 +973,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -992,7 +989,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -1008,7 +1005,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -1024,7 +1021,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1040,7 +1037,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1056,7 +1053,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1081,7 +1078,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1097,7 +1094,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1122,7 +1119,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1138,7 +1135,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1154,7 +1151,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['setTrackerUrl', u+'piwik.php']);
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var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
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<div id="portal-footer">
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
new file mode 100644
index 0000000000000000000000000000000000000000..e36f9ca3e98e9a56193cec41fd8dce738d94d3da
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
@@ -0,0 +1,84 @@
+Allinea Forge (DDT,MAP)
+=======================
+
+Allinea Forge consist of two tools - debugger DDT and profiler MAP.
+Allinea DDT, is a commercial debugger primarily for debugging parallel
+MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel
+Xeon Phi accelerators. DDT provides all the standard debugging features
+(stack trace, breakpoints, watches, view variables, threads etc.) for
+every thread running as part of your program, or for every process -
+even if these processes are distributed across a cluster using an MPI
+implementation.
+Allinea MAP is a profiler for C/C++/Fortran HPC codes. It is designed
+for profiling parallel code, which uses pthreads, OpenMP or MPI.
+License and Limitations for Anselm Users
+-----------------
+On Anselm users can debug OpenMP or MPI code that runs up to 64 parallel
+processes. In case of debugging GPU or Xeon Phi accelerated codes the
+limit is 8 accelerators. These limitation means that:
+- 1 user can debug up 64 processes, or
+- 32 users can debug 2 processes, etc.
+In case of debugging on accelerators:
+- 1 user can debug on up to 8 accelerators, orÂ
+- 8 users can debug on single accelerator.Â
+Compiling Code to run with DDT
+-------
+### Modules
+Load all necessary modules to compile the code. For example:Â
+ $ module load intel
+ $ module load impi ... or ... module load openmpi/X.X.X-icc
+Load the Allinea DDT module:
+ $ module load Forge
+Compile the code:
+``` {.code-basic style="text-alignstart; "}
+$ mpicc -g -O0 -o test_debug test.c
+$ mpif90 -g -O0 -o test_debug test.f
+```
+Â
+### Compiler flags
+Before debugging, you need to compile your code with theses flags:
+**-g** Generates extra debugging information usable by GDB. -g3
+includes even more debugging information. This option is available for
+GNU and INTEL C/C++ and Fortran compilers.
+**-O0** Suppress all optimizations.
+Â
+Starting a Job with DDT
+Be sure to log in with an <span class="internal-link">X window
+forwarding</span> enabled. This could mean using the -X in the sshÂ
+ $ ssh -X username@anselm.it4i.cz
+Other options is to access login node using VNC. Please see the detailed
+information on how to [use graphic user interface on
+Anselm](resolveuid/11e53ad0d2fd4c5187537f4baeedff33)<span
+class="internal-link"></span>.
+From the login node an interactive session **with X windows forwarding**
+(-X option) can be started by following command:Â
+ $ qsub -I -X -A NONE-0-0 -q qexp -lselect=1:ncpus=16:mpiprocs=16,walltime=01:00:00Â
+Then launch the debugger with the ddt command followed by the name of
+the executable to debug:
+ $ ddt test_debug
+A<span style="text-alignstart; "> submission window that appears have
+a prefilled path to the executable to debug. You can select the number
+of MPI processors and/or OpenMP threads on which to run and press run.
+Command line arguments to a program can be entered to the</span>
+"Arguments<span class="Apple-converted-space">" </span><span
+style="text-alignstart; ">box.</span>
+{.image-inline
+width="451" height="513"}Â
+To start the debugging directly without the submission window, user can
+specify the debugging and execution parameters from the command line.
+For example the number of MPI processes is set by option "-np 4".
+Skipping the dialog is done by "-start" option. To see the list of the
+"ddt" command line parameters, run "ddt --help". Â
+ ddt -start -np 4 ./hello_debug_impi
+Â
+Documentation
+-------------
+Users can find original User Guide after loading the DDT module:Â
+ $DDTPATH/doc/userguide.pdf
+Â
+Â
+Â [1] Discipline, Magic, Inspiration and ScienceBest Practice
+Debugging with Allinea DDT, Workshop conducted at LLNL by Allinea on May
+10, 2013,
+[link](https://computing.llnl.gov/tutorials/allineaDDT/index.html)
+Â
diff --git a/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.html
old mode 100755
new mode 100644
similarity index 61%
rename from anselm-cluster-documentation/software/debuggers/allinea-performance-reports.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.html
index 422bc40f2ef6f07639286606680a5400f1ac18aa..6c9d0826f0bfcab2291e453d59448a35ecdb496b
--- a/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:05 GMT -->
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<meta content="quick application profiling" name="description" />
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<title>Allinea Performance Reports — IT4I Docs</title>
- <link rel="canonical" href="allinea-performance-reports.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports" />
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@@ -87,9 +84,9 @@
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<p class="hiddenStructure">
- <a accesskey="2" href="allinea-performance-reports.html#content">PĹ™ejĂt na obsah</a> |
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- <a accesskey="6" href="allinea-performance-reports.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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<div id="portal-advanced-search" class="hiddenStructure">
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+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
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@@ -153,7 +150,7 @@
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<span id="breadcrumbs-1" dir="ltr">
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
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@@ -163,7 +160,7 @@
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<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
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@@ -173,7 +170,7 @@
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<span id="breadcrumbs-3" dir="ltr">
- <a href="../debuggers.html">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">Debuggers and profilers</a>
<span class="breadcrumbSeparator">
/
@@ -262,9 +259,9 @@
<p class=" ">The module sets up environment variables, required for using the Allinea Performance Reports. This particular command loads the default module, which is performance reports version 4.2.</p>
<h2 class=" ">Usage</h2>
<p class="callout">Use the the perf-report wrapper on your (MPI) program.</p>
-<p>Instead of <a target="_self" title="" class="internal-link" href="../mpi-1.html">running your MPI program the usual way</a>, use the the perf report wrapper:</p>
+<p>Instead of <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">running your MPI program the usual way</a>, use the the perf report wrapper:</p>
<pre class=" ">$ perf-report mpirun ./mympiprog.x</pre>
-<p class=" ">The mpi program will run as usual. The perf-report creates two additional files, in *.txt and *.html format, containing the performance report. Note that <a target="_self" title="" class="internal-link" href="../../resource-allocation-and-job-execution/job-submission-and-execution.html">demanding MPI codes should be run within the queue system</a>.</p>
+<p class=" ">The mpi program will run as usual. The perf-report creates two additional files, in *.txt and *.html format, containing the performance report. Note that <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">demanding MPI codes should be run within the queue system</a>.</p>
<h2 class=" ">Example</h2>
<p class=" ">In this example, we will be profiling the mympiprog.x MPI program, using Allinea performance reports. Assume that the code is compiled with intel compilers and linked against intel MPI library:</p>
<p class=" ">First, we allocate some nodes via the express queue:</p>
@@ -273,7 +270,7 @@
<pre class=" ">$ module load intel impi allinea-perf-report/4.2<br />$ mpirun ./mympiprog.x</pre>
<p class=" ">Now lets profile the code:</p>
<pre class=" ">$ perf-report mpirun ./mympiprog.x</pre>
-<p class=" ">Performance report files <a target="_self" title="" class="internal-link" href="mympiprog_32p_2014-10-15_16-56.txt">mympiprog_32p*.txt</a> and <a target="_self" title="" class="internal-link" href="mympiprog_32p_2014-10-15_16-56.html">mympiprog_32p*.html</a> were created. We can see that the code is very efficient on MPI and is CPU bounded.</p>
+<p class=" ">Performance report files <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/mympiprog_32p_2014-10-15_16-56.txt">mympiprog_32p*.txt</a> and <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/mympiprog_32p_2014-10-15_16-56.html">mympiprog_32p*.html</a> were created. We can see that the code is very efficient on MPI and is CPU bounded.</p>
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@@ -349,7 +346,7 @@
<dt class="portletHeader hiddenStructure">
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
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</a>
@@ -381,7 +378,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -397,7 +394,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -413,7 +410,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -429,7 +426,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
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</a>
@@ -445,7 +442,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -461,7 +458,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -477,7 +474,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -493,7 +490,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -509,7 +506,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -525,7 +522,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -541,10 +538,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -560,7 +557,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -576,7 +573,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -592,7 +589,7 @@
- <a title="A collection of development tools" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -608,7 +605,7 @@
- <a title="" class="state-published contenttype-document" href="allinea-ddt.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
@@ -624,7 +621,7 @@
- <a title="quick application profiling" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="allinea-performance-reports.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -640,7 +637,7 @@
- <a title="" class="state-published contenttype-document" href="cube.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube">
<span>CUBE</span>
</a>
@@ -656,7 +653,7 @@
- <a title="" class="state-published contenttype-document" href="intel-performance-counter-monitor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor">
<span>Intel Performance Counter Monitor</span>
</a>
@@ -672,7 +669,7 @@
- <a title="" class="state-published contenttype-document" href="intel-vtune-amplifier.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier</span>
</a>
@@ -688,7 +685,7 @@
- <a title="" class="state-published contenttype-document" href="papi.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi">
<span>PAPI</span>
</a>
@@ -704,7 +701,7 @@
- <a title="" class="state-published contenttype-document" href="scalasca.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca">
<span>Scalasca</span>
</a>
@@ -720,7 +717,7 @@
- <a title="" class="state-published contenttype-document" href="score-p.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p">
<span>Score-P</span>
</a>
@@ -736,7 +733,7 @@
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published contenttype-document" href="total-view.html">
+ <a class="state-published contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -752,7 +749,7 @@
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -768,7 +765,7 @@
- <a title="" class="state-published contenttype-document" href="vampir.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -793,7 +790,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -809,7 +806,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -825,7 +822,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -841,7 +838,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -857,7 +854,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -873,7 +870,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -889,7 +886,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -905,7 +902,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -921,7 +918,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -937,7 +934,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -953,7 +950,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -969,7 +966,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -985,7 +982,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -1001,7 +998,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1017,7 +1014,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1033,7 +1030,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1058,7 +1055,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1074,7 +1071,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1099,7 +1096,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1115,7 +1112,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1131,7 +1128,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -1199,12 +1196,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1220,7 +1217,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
new file mode 100644
index 0000000000000000000000000000000000000000..bdae63a557958b04aa504e2feca9db309b7c0558
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
@@ -0,0 +1,53 @@
+Allinea Performance Reports
+===========================
+quick application profiling
+
+Introduction
+------------
+Allinea Performance Reports characterize the performance of HPC
+application runs. After executing your application through the tool, a
+synthetic HTML report is generated automatically, containing information
+about several metrics along with clear behavior statements and hints to
+help you improve the efficiency of your runs.
+The Allinea Performance Reports is most useful in profiling MPI
+programs.
+Our license is limited to 64 MPI processes.
+Modules
+-------
+Allinea Performance Reports version 6.0 is available
+ $ module load PerformanceReports/6.0
+The module sets up environment variables, required for using the Allinea
+Performance Reports. This particular command loads the default module,
+which is performance reports version 4.2.
+Usage
+-----
+Use the the perf-report wrapper on your (MPI) program.
+Instead of [running your MPI program the usual
+way](https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1),
+use the the perf report wrapper:
+ $ perf-report mpirun ./mympiprog.x
+The mpi program will run as usual. The perf-report creates two
+additional files, in *.txt and *.html format, containing the
+performance report. Note that [demanding MPI codes should be run within
+the queue
+system](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution).
+Example
+-------
+In this example, we will be profiling the mympiprog.x MPI program, using
+Allinea performance reports. Assume that the code is compiled with intel
+compilers and linked against intel MPI library:
+First, we allocate some nodes via the express queue:
+ $ qsub -q qexp -l select=2:ncpus=16:mpiprocs=16:ompthreads=1 -I
+ qsubwaiting for job 262197.dm2 to start
+ qsubjob 262197.dm2 ready
+Then we load the modules and run the program the usual way:
+ $ module load intel impi allinea-perf-report/4.2
+ $ mpirun ./mympiprog.x
+Now lets profile the code:
+ $ perf-report mpirun ./mympiprog.x
+Performance report files
+[mympiprog_32p*.txt](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/mympiprog_32p_2014-10-15_16-56.txt)
+and
+[mympiprog_32p*.html](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/mympiprog_32p_2014-10-15_16-56.html)
+were created. We can see that the code is very efficient on MPI and is
+CPU bounded.
diff --git a/anselm-cluster-documentation/software/debuggers/cube.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube.html
old mode 100755
new mode 100644
similarity index 62%
rename from anselm-cluster-documentation/software/debuggers/cube.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube.html
index 06d25b46b6c7dfef7c183ec1737680365e05aaa7..97070781cddbcda3c7b8d8e4659ef74591465662
--- a/anselm-cluster-documentation/software/debuggers/cube.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:07 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<![endif]-->
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>CUBE — IT4I Docs</title>
- <link rel="canonical" href="cube.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="cube.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="cube.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../debuggers.html">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">Debuggers and profilers</a>
<span class="breadcrumbSeparator">
/
@@ -255,11 +252,11 @@
</ul>
<div>Each dimension is organized in a tree, for example the time performance metric is divided into Execution time and Overhead time, call path dimension is organized by files and routines in your source code etc.</div>
<div></div>
-<div><img title="CUBE Screenshot" class="image-inline" alt="CUBE Screenshot" src="Snimek%20obrazovky%202014-12-04%20v%2012.56.36.png" /></div>
+<div><img alt="CUBE Screenshot" class="image-inline" title="CUBE Screenshot" src="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/Snmekobrazovky20141204v12.56.36.png" /></div>
<p class=" " style="text-align: center; "><em>Figure 1. Screenshot of CUBE displaying data from Scalasca.</em></p>
<p class=" " style="text-align: left; "><em><br /></em>Each node in the tree is colored by severity (the color scheme is displayed at the bottom of the window, ranging from the least severe blue to the most severe being red). For example in Figure 1, we can see that most of the point-to-point MPI communication happens in routine exch_qbc, colored red.</p>
<h2 class=" ">Installed versions</h2>
-<p>Currently, there are two versions of CUBE 4.2.3 available as <a target="_self" title="" class="internal-link" href="../../environment-and-modules.html">modules</a> :</p>
+<p>Currently, there are two versions of CUBE 4.2.3 available as <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">modules</a> :</p>
<ul>
<li>
<p class="p1"><span class="s1"><span class="monospace">cube/4.2.3-gcc</span>, compiled with GCC</span></p>
@@ -269,7 +266,7 @@
</li>
</ul>
<h2 class=" ">Usage</h2>
-<p>CUBE is a graphical application. Refer to <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html">Graphical User Interface documentation</a> for a list of methods to launch graphical applications on Anselm.</p>
+<p>CUBE is a graphical application. Refer to <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">Graphical User Interface documentation</a> for a list of methods to launch graphical applications on Anselm.</p>
<p class="exclamation">Analyzing large data sets can consume large amount of CPU and RAM. Do not perform large analysis on login nodes.</p>
<p class=" ">After loading the apropriate module, simply launch <span class="monospace">cube</span> command, or alternatively you can use <span class="monospace">scalasca -examine</span> command to launch the GUI. Note that for Scalasca datasets, if you do not analyze the data with <span><span class="monospace">scalasca -examine </span></span>before to opening them with CUBE, not all performance data will be available.</p>
<p class=" ">Â <span>References</span></p>
@@ -351,7 +348,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -367,7 +364,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -383,7 +380,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -399,7 +396,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -415,7 +412,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -431,7 +428,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -447,7 +444,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -463,7 +460,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -479,7 +476,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -495,7 +492,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -511,7 +508,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -527,7 +524,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -543,10 +540,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -562,7 +559,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -578,7 +575,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -594,7 +591,7 @@
- <a title="A collection of development tools" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -610,7 +607,7 @@
- <a title="" class="state-published contenttype-document" href="allinea-ddt.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
@@ -626,7 +623,7 @@
- <a title="quick application profiling" class="state-published contenttype-document" href="allinea-performance-reports.html">
+ <a class="state-published contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -642,7 +639,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="cube.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube">
<span>CUBE</span>
</a>
@@ -658,7 +655,7 @@
- <a title="" class="state-published contenttype-document" href="intel-performance-counter-monitor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor">
<span>Intel Performance Counter Monitor</span>
</a>
@@ -674,7 +671,7 @@
- <a title="" class="state-published contenttype-document" href="intel-vtune-amplifier.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier</span>
</a>
@@ -690,7 +687,7 @@
- <a title="" class="state-published contenttype-document" href="papi.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi">
<span>PAPI</span>
</a>
@@ -706,7 +703,7 @@
- <a title="" class="state-published contenttype-document" href="scalasca.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca">
<span>Scalasca</span>
</a>
@@ -722,7 +719,7 @@
- <a title="" class="state-published contenttype-document" href="score-p.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p">
<span>Score-P</span>
</a>
@@ -738,7 +735,7 @@
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published contenttype-document" href="total-view.html">
+ <a class="state-published contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -754,7 +751,7 @@
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -770,7 +767,7 @@
- <a title="" class="state-published contenttype-document" href="vampir.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -795,7 +792,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -811,7 +808,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -827,7 +824,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -843,7 +840,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -859,7 +856,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -875,7 +872,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -891,7 +888,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -907,7 +904,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -923,7 +920,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -939,7 +936,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -955,7 +952,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -971,7 +968,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -987,7 +984,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -1003,7 +1000,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1019,7 +1016,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1035,7 +1032,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1060,7 +1057,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1076,7 +1073,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1101,7 +1098,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1117,7 +1114,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1133,7 +1130,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1172,14 +1169,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -1201,12 +1198,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1222,7 +1219,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:07 GMT -->
</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube.md
new file mode 100644
index 0000000000000000000000000000000000000000..e8cf30ee351e3d1ff66f7be6fae69f97b7f3b087
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube.md
@@ -0,0 +1,49 @@
+CUBE
+====
+Introduction
+------------
+CUBE is a graphical performance report explorer for displaying data from
+Score-P and Scalasca (and other compatible tools). The name comes from
+the fact that it displays performance data in a three-dimensions :
+- **performance metric**, where a number of metrics are available,
+ such as communication time or cache misses,
+- **call path**, which contains the call tree of your program
+- s**ystem resource**, which contains system's nodes, processes and
+ threads, depending on the parallel programming model.
+Each dimension is organized in a tree, for example the time performance
+metric is divided into Execution time and Overhead time, call path
+dimension is organized by files and routines in your source code etc.
+
+*Figure 1. Screenshot of CUBE displaying data from Scalasca.*
+*
+*Each node in the tree is colored by severity (the color scheme is
+displayed at the bottom of the window, ranging from the least severe
+blue to the most severe being red). For example in Figure 1, we can see
+that most of the point-to-point MPI communication happens in routine
+exch_qbc, colored red.
+Installed versions
+------------------
+Currently, there are two versions of CUBE 4.2.3 available as
+[modules](https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules)
+:
+- <span class="s1"><span class="monospace">cube/4.2.3-gcc</span>,
+ compiled with GCC</span>
+- <span class="s1"><span class="monospace">cube/4.2.3-icc</span>,
+ compiled with Intel compiler</span>
+Usage
+-----
+CUBE is a graphical application. Refer to [Graphical User Interface
+documentation](resolveuid/11e53ad0d2fd4c5187537f4baeedff33)
+for a list of methods to launch graphical applications on Anselm.
+Analyzing large data sets can consume large amount of CPU and RAM. Do
+not perform large analysis on login nodes.
+After loading the apropriate module, simply launch <span
+class="monospace">cube</span> command, or alternatively you can use
+<span class="monospace">scalasca -examine</span> command to launch the
+GUI. Note that for Scalasca datasets, if you do not analyze the data
+with <span><span class="monospace">scalasca
+-examine </span></span>before to opening them with CUBE, not all
+performance data will be available.
+Â <span>References</span>
+1. <http://www.scalasca.org/software/cube-4.x/download.html>
diff --git a/anselm-cluster-documentation/software/debuggers/ddt1.png b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/ddt1.png
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/software/debuggers/ddt1.png
rename to docs.it4i.cz/anselm-cluster-documentation/software/debuggers/ddt1.png
diff --git a/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.html
old mode 100755
new mode 100644
similarity index 72%
rename from anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.html
index 7e6a74ca9a5935206c4e84f0aa2c7d4f27894d30..1f0396041de67d4a18755f7cdd2b9a8d26d5b888
--- a/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.html
@@ -10,45 +10,42 @@
-
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<title>Intel Performance Counter Monitor — IT4I Docs</title>
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- <a accesskey="6" href="intel-performance-counter-monitor.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor#portal-globalnav">PĹ™ejĂt na navigaci</a>
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+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
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<span id="breadcrumbs-1" dir="ltr">
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<span id="breadcrumbs-2" dir="ltr">
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<span id="breadcrumbs-3" dir="ltr">
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<div id="parent-fieldname-text-b34df797f1cc4fbd8022b96c8658078c" class="">
<h2 class=" ">Introduction</h2>
-<p>Intel PCM (Performance Counter Monitor) is a tool to monitor performance hardware counters on Intel<span>®</span> processors, similar to <a target="_self" title="" class="internal-link" href="papi.html">PAPI</a>. The difference between PCM and PAPI is that PCM supports only Intel hardware, but PCM can monitor also uncore metrics, like memory controllers and <span>QuickPath Interconnect links.</span></p>
+<p>Intel PCM (Performance Counter Monitor) is a tool to monitor performance hardware counters on Intel<span>®</span> processors, similar to <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi">PAPI</a>. The difference between PCM and PAPI is that PCM supports only Intel hardware, but PCM can monitor also uncore metrics, like memory controllers and <span>QuickPath Interconnect links.</span></p>
<h2 class=" "><span>Installed version</span></h2>
-<p>Currently installed version 2.6. To load the <a target="_self" title="" class="internal-link" href="../../environment-and-modules.html">module</a>, issue :</p>
+<p>Currently installed version 2.6. To load the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">module</a>, issue :</p>
<pre class=" ">$ module load intelpcm</pre>
<h2 class=" ">Command line tools</h2>
<p>PCM provides a set of tools to monitor system/or application. </p>
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- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
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- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
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- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -1125,7 +1122,7 @@ Instructions per clock:1.7<br />L3 cache hit ratio:1.0<br />Bytes read:12513408<
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -1141,7 +1138,7 @@ Instructions per clock:1.7<br />L3 cache hit ratio:1.0<br />Bytes read:12513408<
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -1157,7 +1154,7 @@ Instructions per clock:1.7<br />L3 cache hit ratio:1.0<br />Bytes read:12513408<
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -1173,7 +1170,7 @@ Instructions per clock:1.7<br />L3 cache hit ratio:1.0<br />Bytes read:12513408<
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -1189,7 +1186,7 @@ Instructions per clock:1.7<br />L3 cache hit ratio:1.0<br />Bytes read:12513408<
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -1205,7 +1202,7 @@ Instructions per clock:1.7<br />L3 cache hit ratio:1.0<br />Bytes read:12513408<
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1221,7 +1218,7 @@ Instructions per clock:1.7<br />L3 cache hit ratio:1.0<br />Bytes read:12513408<
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1237,7 +1234,7 @@ Instructions per clock:1.7<br />L3 cache hit ratio:1.0<br />Bytes read:12513408<
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1262,7 +1259,7 @@ Instructions per clock:1.7<br />L3 cache hit ratio:1.0<br />Bytes read:12513408<
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1278,7 +1275,7 @@ Instructions per clock:1.7<br />L3 cache hit ratio:1.0<br />Bytes read:12513408<
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1303,7 +1300,7 @@ Instructions per clock:1.7<br />L3 cache hit ratio:1.0<br />Bytes read:12513408<
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1319,7 +1316,7 @@ Instructions per clock:1.7<br />L3 cache hit ratio:1.0<br />Bytes read:12513408<
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1335,7 +1332,7 @@ Instructions per clock:1.7<br />L3 cache hit ratio:1.0<br />Bytes read:12513408<
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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(function() {
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
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})();
</script>
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+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
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+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
new file mode 100644
index 0000000000000000000000000000000000000000..57d8f1b4065ce3a983da772618cef9c1eb4614ef
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
@@ -0,0 +1,230 @@
+Intel Performance Counter Monitor
+=================================
+Introduction
+------------
+Intel PCM (Performance Counter Monitor) is a tool to monitor performance
+hardware counters on Intel<span>®</span> processors, similar to
+[PAPI](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi).
+The difference between PCM and PAPI is that PCM supports only Intel
+hardware, but PCM can monitor also uncore metrics, like memory
+controllers and <span>QuickPath Interconnect links.</span>
+<span>Installed version</span>
+-------
+Currently installed version 2.6. To load the
+[module](https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules),
+issue :
+ $ module load intelpcm
+Command line tools
+------------------
+PCM provides a set of tools to monitor system/or application.Â
+### pcm-memory
+Measures memory bandwidth of your application or the whole system.
+Usage:
+ $ pcm-memory.x <delay>|[external_program parameters]
+Specify either a delay of updates in seconds or an external program to
+monitor. If you get an error about PMU in use, respond "y" and relaunch
+the program.
+Sample output:
+ ----------------||----------------
+ -- Socket 0 --||-- Socket 1 --
+ ----------------||----------------
+ ----------------||----------------
+ ----------------||----------------
+ -- Memory Performance Monitoring --||-- Memory Performance Monitoring --
+ ----------------||----------------
+ -- Mem Ch 0Reads (MB/s) 2.44 --||-- Mem Ch 0Reads (MB/s) 0.26 --
+ -- Writes(MB/s) 2.16 --||-- Writes(MB/s) 0.08 --
+ -- Mem Ch 1Reads (MB/s) 0.35 --||-- Mem Ch 1Reads (MB/s) 0.78 --
+ -- Writes(MB/s) 0.13 --||-- Writes(MB/s) 0.65 --
+ -- Mem Ch 2Reads (MB/s) 0.32 --||-- Mem Ch 2Reads (MB/s) 0.21 --
+ -- Writes(MB/s) 0.12 --||-- Writes(MB/s) 0.07 --
+ -- Mem Ch 3Reads (MB/s) 0.36 --||-- Mem Ch 3Reads (MB/s) 0.20 --
+ -- Writes(MB/s) 0.13 --||-- Writes(MB/s) 0.07 --
+ -- NODE0 Mem Read (MB/s) 3.47 --||-- NODE1 Mem Read (MB/s) 1.45 --
+ -- NODE0 Mem Write (MB/s) 2.55 --||-- NODE1 Mem Write (MB/s) 0.88 --
+ -- NODE0 P. Write (T/s) 31506 --||-- NODE1 P. Write (T/s) 9099 --
+ -- NODE0 Memory (MB/s) 6.02 --||-- NODE1 Memory (MB/s) 2.33 --
+ ----------------||----------------
+ -- System Read Throughput(MB/s) 4.93 --
+ -- System Write Throughput(MB/s) 3.43 --
+ -- System Memory Throughput(MB/s) 8.35 --
+ ----------------||----------------Â
+### pcm-msr
+Command <span class="monospace">pcm-msr.x</span> can be used to
+read/write model specific registers of the CPU.
+### pcm-numa
+NUMA monitoring utility does not work on Anselm.
+### pcm-pcie
+Can be used to monitor PCI Express bandwith. Usage<span
+class="monospace">pcm-pcie.x <delay></span>
+### pcm-power
+Displays energy usage and thermal headroom for CPU and DRAM sockets.
+Usage:Â <span>Â </span><span class="monospace">pcm-power.x <delay> |
+<external program></span>
+### pcm
+This command provides an overview of performance counters and memory
+usage. <span>Usage: </span><span> </span><span class="monospace">pcm.x
+<delay> | <external program></span>
+Sample output :
+ $ pcm.x ./matrix
+ Intel(r) Performance Counter Monitor V2.6 (2013-11-04 13:43:31 +0100 ID=db05e43)
+ Copyright (c) 2009-2013 Intel Corporation
+ Number of physical cores16
+ Number of logical cores16
+ Threads (logical cores) per physical core1
+ Num sockets2
+ Core PMU (perfmon) version3
+ Number of core PMU generic (programmable) counters8
+ Width of generic (programmable) counters48 bits
+ Number of core PMU fixed counters3
+ Width of fixed counters48 bits
+ Nominal core frequency2400000000 Hz
+ Package thermal spec power115 Watt; Package minimum power51 Watt; Package maximum power180 Watt;
+ Socket 01 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
+ Socket 11 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
+ Number of PCM instances2
+ Max QPI link speed16.0 GBytes/second (8.0 GT/second)
+ Detected Intel(R) Xeon(R) CPU E5-2665 0 @ 2.40GHz "Intel(r) microarchitecture codename Sandy Bridge-EP/Jaketown"
+ Executing "./matrix" command:
+ Exit code0
+ EXEC instructions per nominal CPU cycle
+ IPC instructions per CPU cycle
+ FREQ relation to nominal CPU frequency='unhalted clock ticks'/'invariant timer ticks' (includes Intel Turbo Boost)
+ AFREQ relation to nominal CPU frequency while in active state (not in power-saving C state)='unhalted clock ticks'/'invariant timer ticks while in C0-state' (includes Intel Turbo Boost)
+ L3MISSL3 cache misses
+ L2MISSL2 cache misses (including other core's L2 cache *hits*)
+ L3HIT L3 cache hit ratio (0.00-1.00)
+ L2HIT L2 cache hit ratio (0.00-1.00)
+ L3CLK ratio of CPU cycles lost due to L3 cache misses (0.00-1.00), in some cases could be >1.0 due to a higher memory latency
+ L2CLK ratio of CPU cycles lost due to missing L2 cache but still hitting L3 cache (0.00-1.00)
+ READ bytes read from memory controller (in GBytes)
+ WRITE bytes written to memory controller (in GBytes)
+ TEMP Temperature reading in 1 degree Celsius relative to the TjMax temperature (thermal headroom)0 corresponds to the max temperature
+ Core (SKT) | EXEC | IPC | FREQ | AFREQ | L3MISS | L2MISS | L3HIT | L2HIT | L3CLK | L2CLK | READ | WRITE | TEMP
+ 0 0 0.00 0.64 0.01 0.80 5592 11 K 0.49 0.13 0.32 0.06 N/A N/A 67
+ 1 0 0.00 0.18 0.00 0.69 3086 5552 0.44 0.07 0.48 0.08 N/A N/A 68
+ 2 0 0.00 0.23 0.00 0.81 300 562 0.47 0.06 0.43 0.08 N/A N/A 67
+ 3 0 0.00 0.21 0.00 0.99 437 862 0.49 0.06 0.44 0.09 N/A N/A 73
+ 4 0 0.00 0.23 0.00 0.93 293 559 0.48 0.07 0.42 0.09 N/A N/A 73
+ 5 0 0.00 0.21 0.00 1.00 423 849 0.50 0.06 0.43 0.10 N/A N/A 69
+ 6 0 0.00 0.23 0.00 0.94 285 558 0.49 0.06 0.41 0.09 N/A N/A 71
+ 7 0 0.00 0.18 0.00 0.81 674 1130 0.40 0.05 0.53 0.08 N/A N/A 65
+ 8 1 0.00 0.47 0.01 1.26 6371 13 K 0.51 0.35 0.31 0.07 N/A N/A 64
+ 9 1 2.30 1.80 1.28 1.29 179 K 15 M 0.99 0.59 0.04 0.71 N/A N/A 60
+ 10 1 0.00 0.22 0.00 1.26 315 570 0.45 0.06 0.43 0.08 N/A N/A 67
+ 11 1 0.00 0.23 0.00 0.74 321 579 0.45 0.05 0.45 0.07 N/A N/A 66
+ 12 1 0.00 0.22 0.00 1.25 305 570 0.46 0.05 0.42 0.07 N/A N/A 68
+ 13 1 0.00 0.22 0.00 1.26 336 581 0.42 0.04 0.44 0.06 N/A N/A 69
+ 14 1 0.00 0.22 0.00 1.25 314 565 0.44 0.06 0.43 0.07 N/A N/A 69
+ 15 1 0.00 0.29 0.00 1.19 2815 6926 0.59 0.39 0.29 0.08 N/A N/A 69
+
+ SKT 0 0.00 0.46 0.00 0.79 11 K 21 K 0.47 0.10 0.38 0.07 0.00 0.00 65
+ SKT 1 0.29 1.79 0.16 1.29 190 K 15 M 0.99 0.59 0.05 0.70 0.01 0.01 61
+
+ TOTAL * 0.14 1.78 0.08 1.28 201 K 15 M 0.99 0.59 0.05 0.70 0.01 0.01 N/A
+ Instructions retired1345 M ; Active cycles 755 M ; Time (TSC) 582 Mticks ; C0 (active,non-halted) core residency6.30 %
+ C1 core residency0.14 %; C3 core residency0.20 %; C6 core residency0.00 %; C7 core residency93.36 %;
+ C2 package residency48.81 %; C3 package residency0.00 %; C6 package residency0.00 %; C7 package residency0.00 %;
+ PHYSICAL CORE IPC 1.78 => corresponds to 44.50 % utilization for cores in active state
+ Instructions per nominal CPU cycle0.14 => corresponds to 3.60 % core utilization over time interval
+ Intel(r) QPI data traffic estimation in bytes (data traffic coming to CPU/socket through QPI links):
+ QPI0 QPI1 | QPI0 QPI1
+ --
+ SKT 0 0 0 | 0% 0%
+ SKT 1 0 0 | 0% 0%
+ --
+ Total QPI incoming data traffic 0 QPI data traffic/Memory controller traffic0.00
+ Intel(r) QPI traffic estimation in bytes (data and non-data traffic outgoing from CPU/socket through QPI links):
+ QPI0 QPI1 | QPI0 QPI1
+ --
+ SKT 0 0 0 | 0% 0%
+ SKT 1 0 0 | 0% 0%
+ --
+ Total QPI outgoing data and non-data traffic 0
+ --
+ SKT 0 package consumed 4.06 Joules
+ SKT 1 package consumed 9.40 Joules
+ --
+ TOTAL 13.46 Joules
+ --
+ SKT 0 DIMMs consumed 4.18 Joules
+ SKT 1 DIMMs consumed 4.28 Joules
+ --
+ TOTAL 8.47 Joules
+ Cleaning up
+Â
+### pcm-sensor
+Can be used as a sensor for ksysguard GUI, which is currently not
+installed on Anselm.Â
+API
+---
+In a similar fashion to PAPI, PCM provides a C++ API to access the
+performance counter from within your application. Refer to the [doxygen
+documentation](http://intel-pcm-api-documentation.github.io/classPCM.html)
+for details of the API.
+Due to security limitations, using PCM API to monitor your applications
+is currently not possible on Anselm. (The application must be run as
+root user)
+Sample program using the API :
+ #include <stdlib.h>
+ #include <stdio.h>
+ #include "cpucounters.h"
+ #define SIZE 1000
+ using namespace std;
+ int main(int argc, char **argv) {
+ float matrixa[SIZE][SIZE], matrixb[SIZE][SIZE], mresult[SIZE][SIZE];
+ float real_time, proc_time, mflops;
+ long long flpins;
+ int retval;
+ int i,j,k;
+ PCM * m = PCM::getInstance();
+ if (m->program() != PCM::Success) return 1;
+ SystemCounterState before_sstate = getSystemCounterState();
+ /* Initialize the Matrix arrays */
+ for ( i=0; i<SIZE*SIZE; i++ ){
+ mresult[0][i] = 0.0;
+ matrixa[0][i] = matrixb[0][i] = rand()*(float)1.1; }
+ /* A naive Matrix-Matrix multiplication */
+ for (i=0;i<SIZE;i++)
+ for(j=0;j<SIZE;j++)
+ for(k=0;k<SIZE;k++)
+ mresult[i][j]=mresult[i][j] + matrixa[i][k]*matrixb[k][j];
+ SystemCounterState after_sstate = getSystemCounterState();
+ cout << "Instructions per clock:" << getIPC(before_sstate,after_sstate)
+ << "L3 cache hit ratio:" << getL3CacheHitRatio(before_sstate,after_sstate)
+ << "Bytes read:" << getBytesReadFromMC(before_sstate,after_sstate);
+ for (i=0; i<SIZE;i++)
+ for (j=0; j<SIZE; j++)
+ if (mresult[i][j] == -1) printf("x");
+ return 0;
+ }
+Compile it with :
+ $ icc matrix.cpp -o matrix -lpthread -lpcm
+Sample output :Â
+ $ ./matrix
+ Number of physical cores16
+ Number of logical cores16
+ Threads (logical cores) per physical core1
+ Num sockets2
+ Core PMU (perfmon) version3
+ Number of core PMU generic (programmable) counters8
+ Width of generic (programmable) counters48 bits
+ Number of core PMU fixed counters3
+ Width of fixed counters48 bits
+ Nominal core frequency2400000000 Hz
+ Package thermal spec power115 Watt; Package minimum power51 Watt; Package maximum power180 Watt;
+ Socket 01 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
+ Socket 11 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
+ Number of PCM instances2
+ Max QPI link speed16.0 GBytes/second (8.0 GT/second)
+ Instructions per clock:1.7
+ L3 cache hit ratio:1.0
+ Bytes read:12513408
+References
+----------
+1. <https://software.intel.com/en-us/articles/intel-performance-counter-monitor-a-better-way-to-measure-cpu-utilization>
+2. <https://software.intel.com/sites/default/files/m/3/2/2/xeon-e5-2600-uncore-guide.pdf> Intel®
+ Xeon® Processor E5-2600 Product Family Uncore Performance
+ Monitoring Guide.
+3. <http://intel-pcm-api-documentation.github.io/classPCM.html>Â API
+ Documentation
diff --git a/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.html
old mode 100755
new mode 100644
similarity index 65%
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rename to docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.html
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<title>Intel VTune Amplifier — IT4I Docs</title>
- <link rel="canonical" href="intel-vtune-amplifier.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
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@@ -64,7 +61,7 @@
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="intel-vtune-amplifier.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="intel-vtune-amplifier.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../debuggers.html">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">Debuggers and profilers</a>
<span class="breadcrumbSeparator">
/
@@ -259,13 +256,13 @@
<li>Power usage analysis - frequency and sleep states.</li>
</ul>
<div></div>
-<div><img title="VTune Amplifier" class="image-inline" alt="screenshot" src="vtune-amplifier/%40%40images/3d4533af-8ce5-4aed-9bac-09fbbcd2650a.png" /></div>
+<div><img alt="screenshot" class="image-inline" title="VTune Amplifier" src="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vtune-amplifier/@@images/3d4533af-8ce5-4aed-9bac-09fbbcd2650a.png" /></div>
<h2 class=" ">Usage</h2>
<p>To launch the GUI, first load the module:</p>
<pre class=" "><span class="s1">$ module add VTune/2016_update1</span></pre>
<p class=" "><span class="s1">and launch the GUI :</span></p>
<pre class=" "><span class="s1">$Â </span><span>amplxe-gui</span></pre>
-<p class="exclamation"><span>To profile an application with VTune Amplifier, special kernel modules need to be loaded. The modules are not loaded on Anselm login nodes, thus direct profiling on login nodes is not possible. Use VTune on compute nodes and refer to the documentation on <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html">using GUI applications</a>.</span></p>
+<p class="exclamation"><span>To profile an application with VTune Amplifier, special kernel modules need to be loaded. The modules are not loaded on Anselm login nodes, thus direct profiling on login nodes is not possible. Use VTune on compute nodes and refer to the documentation on <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">using GUI applications</a>.</span></p>
<p class=" "><span>The GUI will open in new window. Click on "<em>New Project...</em>" to create a new project. After clicking <em>OK</em>, a new window with project properties will appear. Â At "<em>Application:</em>", select the bath to your binary you want to profile (the binary should be compiled with -g flag). Some additional options such as command line arguments can be selected. At "<em>Managed code profiling mode:</em>" select "<em>Native</em>" (unless you want to profile managed mode .NET/Mono applications). After clicking <em>OK</em>, your project is created.</span></p>
<p class=" ">To run a new analysis, click "<em>New analysis...</em>". You will see a list of possible analysis. Some of them will not be possible on the current CPU (eg. Intel Atom analysis is not possible on Sandy Bridge CPU), the GUI will show an error box if you select the wrong analysis. For example, select "<em>Advanced Hotspots</em>". Clicking on <em>Start </em>will start profiling of the application.</p>
<h2 class=" ">Remote Analysis</h2>
@@ -278,7 +275,7 @@
<p>It is possible to analyze both native and offload Xeon Phi applications. For offload mode, just specify the path to the binary. For native mode, you need to specify in project properties:</p>
<p>Application: <span class="monospace">ssh</span></p>
<p>Application parameters: <span class="monospace">mic0 source ~/.profile && /path/to/your/bin</span></p>
-<p class=" ">Note that we include <span class="monospace">source ~/.profile </span>in the command to setup environment paths <a target="_self" title="" class="internal-link" href="../intel-xeon-phi.html">as described here</a>. </p>
+<p class=" ">Note that we include <span class="monospace">source ~/.profile </span>in the command to setup environment paths <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">as described here</a>. </p>
<p class="exclamation">If the analysis is interrupted or aborted, further analysis on the card might be impossible and you will get errors like "ERROR connecting to MIC card". In this case please contact our support to reboot the MIC card.</p>
<p class=" ">You may also use remote analysis to collect data from the MIC and then analyze it in the GUI later :</p>
<pre class=" ">$ amplxe-cl -collect knc-hotspots -no-auto-finalize -- ssh mic0<br />"export LD_LIBRARY_PATH=/apps/intel/composer_xe_2015.2.164/compiler/lib/mic/:/apps/intel/composer_xe_2015.2.164/mkl/lib/mic/; export KMP_AFFINITY=compact; /tmp/app.mic"</pre>
@@ -361,7 +358,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
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@@ -377,7 +374,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -393,7 +390,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -425,7 +422,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -441,7 +438,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -457,7 +454,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -473,7 +470,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -489,7 +486,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -505,7 +502,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -521,7 +518,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -537,7 +534,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -553,10 +550,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -572,7 +569,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -588,7 +585,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -604,7 +601,7 @@
- <a title="A collection of development tools" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -620,7 +617,7 @@
- <a title="" class="state-published contenttype-document" href="allinea-ddt.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
@@ -636,7 +633,7 @@
- <a title="quick application profiling" class="state-published contenttype-document" href="allinea-performance-reports.html">
+ <a class="state-published contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -652,7 +649,7 @@
- <a title="" class="state-published contenttype-document" href="cube.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube">
<span>CUBE</span>
</a>
@@ -668,7 +665,7 @@
- <a title="" class="state-published contenttype-document" href="intel-performance-counter-monitor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor">
<span>Intel Performance Counter Monitor</span>
</a>
@@ -684,7 +681,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="intel-vtune-amplifier.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier</span>
</a>
@@ -700,7 +697,7 @@
- <a title="" class="state-published contenttype-document" href="papi.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi">
<span>PAPI</span>
</a>
@@ -716,7 +713,7 @@
- <a title="" class="state-published contenttype-document" href="scalasca.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca">
<span>Scalasca</span>
</a>
@@ -732,7 +729,7 @@
- <a title="" class="state-published contenttype-document" href="score-p.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p">
<span>Score-P</span>
</a>
@@ -748,7 +745,7 @@
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published contenttype-document" href="total-view.html">
+ <a class="state-published contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -764,7 +761,7 @@
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -780,7 +777,7 @@
- <a title="" class="state-published contenttype-document" href="vampir.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -805,7 +802,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -821,7 +818,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -837,7 +834,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -853,7 +850,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -869,7 +866,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -885,7 +882,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -901,7 +898,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -917,7 +914,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -933,7 +930,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -949,7 +946,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -965,7 +962,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -981,7 +978,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -997,7 +994,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -1013,7 +1010,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1029,7 +1026,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1045,7 +1042,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1070,7 +1067,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1086,7 +1083,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1111,7 +1108,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1127,7 +1124,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1143,7 +1140,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
new file mode 100644
index 0000000000000000000000000000000000000000..d52a512bd6d478fc366ede166a30384c72db5443
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
@@ -0,0 +1,79 @@
+Intel VTune Amplifier
+=====================
+
+Introduction
+------------
+Intel*® *VTune™ <span>Amplifier, part of Intel Parallel studio, is a GUI
+profiling tool designed for Intel processors. It offers a graphical
+performance analysis of single core and multithreaded applications. A
+highlight of the features:</span>
+- Hotspot analysis
+- Locks and waits analysis
+- Low level specific counters, such as branch analysis and memory
+ bandwidth
+- Power usage analysis - frequency and sleep states.
+
+Usage
+-----
+To launch the GUI, first load the module:
+ $ module add VTune/2016_update1
+<span class="s1">and launch the GUI :</span>
+ $Â amplxe-gui
+<span>To profile an application with VTune Amplifier, special kernel
+modules need to be loaded. The modules are not loaded on Anselm login
+nodes, thus direct profiling on login nodes is not possible. Use VTune
+on compute nodes and refer to the documentation on [using GUI
+applications](resolveuid/11e53ad0d2fd4c5187537f4baeedff33).</span>
+<span>The GUI will open in new window. Click on "*New Project...*" to
+create a new project. After clicking *OK*, a new window with project
+properties will appear. Â At "*Application:*", select the bath to your
+binary you want to profile (the binary should be compiled with -g flag).
+Some additional options such as command line arguments can be selected.
+At "*Managed code profiling mode:*" select "*Native*" (unless you want
+to profile managed mode .NET/Mono applications). After clicking *OK*,
+your project is created.</span>
+To run a new analysis, click "*New analysis...*". You will see a list of
+possible analysis. Some of them will not be possible on the current CPU
+(eg. Intel Atom analysis is not possible on Sandy Bridge CPU), the GUI
+will show an error box if you select the wrong analysis. For example,
+select "*Advanced Hotspots*". Clicking on *Start *will start profiling
+of the application.
+Remote Analysis
+---------------
+VTune Amplifier also allows a form of remote analysis. In this mode,
+data for analysis is collected from the command line without GUI, and
+the results are then loaded to GUI on another machine. This allows
+profiling without interactive graphical jobs. To perform a remote
+analysis, launch a GUI somewhere, open the new analysis window and then
+click the button "*Command line*" in bottom right corner. It will show
+the command line needed to perform the selected analysis.
+The command line will look like this:
+ /apps/all/VTune/2016_update1/vtune_amplifier_xe_2016.1.1.434111/bin64/amplxe-cl -collect advanced-hotspots -knob collection-detail=stack-and-callcount -mrte-mode=native -target-duration-type=veryshort -app-working-dir /home/sta545/test -- /home/sta545/test_pgsesv
+Copy the line to clipboard and then you can paste it in your jobscript
+or in command line. After the collection is run, open the GUI once
+again, click the menu button in the upper right corner, and select
+"*Open > Result...*". The GUI will load the results from the run.
+Xeon Phi
+--------
+This section is outdated. It will be updated with new information soon.
+It is possible to analyze both native and offload Xeon Phi applications.
+For offload mode, just specify the path to the binary. For native mode,
+you need to specify in project properties:
+Application<span class="monospace">ssh</span>
+Application parameters<span class="monospace">mic0 source ~/.profile
+&& /path/to/your/bin</span>
+Note that we include <span class="monospace">source ~/.profile
+</span>in the command to setup environment paths [as described
+here](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi).Â
+If the analysis is interrupted or aborted, further analysis on the card
+might be impossible and you will get errors like "ERROR connecting to
+MIC card". In this case please contact our support to reboot the MIC
+card.
+You may also use remote analysis to collect data from the MIC and then
+analyze it in the GUI later :
+ $ amplxe-cl -collect knc-hotspots -no-auto-finalize -- ssh mic0
+ "export LD_LIBRARY_PATH=/apps/intel/composer_xe_2015.2.164/compiler/lib/mic/:/apps/intel/composer_xe_2015.2.164/mkl/lib/mic/; export KMP_AFFINITY=compact; /tmp/app.mic"
+References
+----------
+1. <span><https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf>Â Performance
+ Tuning for Intel® Xeon Phi™ Coprocessors</span>
diff --git a/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/mympiprog_32p_2014-10-15_16-56.html
old mode 100755
new mode 100644
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--- a/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.html
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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</html>
diff --git a/anselm-cluster-documentation/software/omics-master-1/images/fig6.png/image_view_fullscreen.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/mympiprog_32p_2014-10-15_16-56.md
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diff --git a/anselm-cluster-documentation/software/debuggers/papi.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.html
old mode 100755
new mode 100644
similarity index 70%
rename from anselm-cluster-documentation/software/debuggers/papi.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.html
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<title>PAPI — IT4I Docs</title>
- <link rel="canonical" href="papi.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="papi.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="papi.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
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@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
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@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../debuggers.html">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">Debuggers and profilers</a>
<span class="breadcrumbSeparator">
/
@@ -255,7 +252,7 @@
<p class=" "><span>PAPI provides two levels of interface - a simpler, high level interface and more detailed low level interface.</span></p>
<p class=" "><span>PAPI can be used with parallel as well as serial programs.</span></p>
<h2 class=" ">Usage</h2>
-<p>To use PAPI, load <a target="_self" title="" class="internal-link" href="../../environment-and-modules.html">module</a> <span class="monospace">papi</span> :</p>
+<p>To use PAPI, load <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">module</a> <span class="monospace">papi</span> :</p>
<pre class=" ">$ module load papi</pre>
<p class=" ">This will load the default version. Execute <span class="monospace">module avail papi</span> for a list of installed versions.</p>
<h2 class=" ">Utilites</h2>
@@ -306,7 +303,7 @@
<pre class=" ">$ gcc -O3 matrix.c -o matrix -lpapi<br />$ ./matrix<br /><span>Real_time: 8.795956<br /></span><span>Proc_time: 8.790000<br /></span><span>Total flpins: 18700983160<br /></span><span>MFLOPS: 2127.529297</span><span>Â </span></pre>
<h3 class=" ">Intel Xeon Phi</h3>
<p class="exclamation">PAPI currently supports only a subset of counters on the Intel Xeon Phi processor compared to Intel Xeon, for example the floating point operations counter is missing.</p>
-<p>To use PAPI in <a target="_self" title="" class="internal-link" href="../intel-xeon-phi.html">Intel Xeon Phi</a> native applications, you need to load module with "<span class="monospace">-mic</span>" suffix, for example "<span class="monospace">papi/5.3.2-mic</span>" :</p>
+<p>To use PAPI in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">Intel Xeon Phi</a> native applications, you need to load module with "<span class="monospace">-mic</span>" suffix, for example "<span class="monospace">papi/5.3.2-mic</span>" :</p>
<pre class=" ">$ module load papi/5.3.2-mic</pre>
<p class=" ">Then, compile your application in the following way:</p>
<pre class=" "><span class="s1">$ module load intel<br />$ icc -mmic -Wl,-rpath,/apps/intel/composer_xe_2013.5.192/compiler/lib/mic matrix-mic.c -o matrix-mic -lpapi -lpfm</span></pre>
@@ -398,7 +395,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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@@ -414,7 +411,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -430,7 +427,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -446,7 +443,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -462,7 +459,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -478,7 +475,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -494,7 +491,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -510,7 +507,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -526,7 +523,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -542,7 +539,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -558,7 +555,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -574,7 +571,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -590,10 +587,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -609,7 +606,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -625,7 +622,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -641,7 +638,7 @@
- <a title="A collection of development tools" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -657,7 +654,7 @@
- <a title="" class="state-published contenttype-document" href="allinea-ddt.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
@@ -673,7 +670,7 @@
- <a title="quick application profiling" class="state-published contenttype-document" href="allinea-performance-reports.html">
+ <a class="state-published contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -689,7 +686,7 @@
- <a title="" class="state-published contenttype-document" href="cube.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube">
<span>CUBE</span>
</a>
@@ -705,7 +702,7 @@
- <a title="" class="state-published contenttype-document" href="intel-performance-counter-monitor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor">
<span>Intel Performance Counter Monitor</span>
</a>
@@ -721,7 +718,7 @@
- <a title="" class="state-published contenttype-document" href="intel-vtune-amplifier.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier</span>
</a>
@@ -737,7 +734,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="papi.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi">
<span>PAPI</span>
</a>
@@ -753,7 +750,7 @@
- <a title="" class="state-published contenttype-document" href="scalasca.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca">
<span>Scalasca</span>
</a>
@@ -769,7 +766,7 @@
- <a title="" class="state-published contenttype-document" href="score-p.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p">
<span>Score-P</span>
</a>
@@ -785,7 +782,7 @@
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published contenttype-document" href="total-view.html">
+ <a class="state-published contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -801,7 +798,7 @@
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -817,7 +814,7 @@
- <a title="" class="state-published contenttype-document" href="vampir.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -842,7 +839,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -858,7 +855,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -874,7 +871,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -890,7 +887,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -906,7 +903,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -922,7 +919,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -938,7 +935,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -954,7 +951,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -970,7 +967,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -986,7 +983,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -1002,7 +999,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -1018,7 +1015,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -1034,7 +1031,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -1050,7 +1047,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1066,7 +1063,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1082,7 +1079,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1107,7 +1104,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1123,7 +1120,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1148,7 +1145,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1164,7 +1161,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1180,7 +1177,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1219,14 +1216,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1248,12 +1245,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1269,7 +1266,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:07 GMT -->
</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.md
new file mode 100644
index 0000000000000000000000000000000000000000..a7dd24df39c17f5cba66da984927f6d19501e837
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.md
@@ -0,0 +1,203 @@
+PAPI
+====
+
+Introduction
+------------
+<span dir="auto">Performance Application Programming
+Interface </span><span>(PAPI)  is a portable interface to access
+hardware performance counters (such as instruction counts and cache
+misses) found in most modern architectures. With the new component
+framework, PAPI is not limited only to CPU counters, but offers also
+components for CUDA, network, Infiniband etc.</span>
+<span>PAPI provides two levels of interface - a simpler, high level
+interface and more detailed low level interface.</span>
+<span>PAPI can be used with parallel as well as serial programs.</span>
+Usage
+-----
+To use PAPI, load
+[module](https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules)
+<span class="monospace">papi</span> :
+ $ module load papi
+This will load the default version. Execute <span
+class="monospace">module avail papi</span> for a list of installed
+versions.
+Utilites
+--------
+The <span class="monospace">bin</span> directory of PAPI (which is
+automatically added to <span class="monospace">$PATH</span> upon
+loading the module) contains various utilites.
+### papi_avail
+Prints which preset events are available on the current CPU. The third
+column indicated whether the preset event is available on the current
+CPU.
+ $ papi_avail
+ Available events and hardware information.
+ -----------
+ PAPI Version 5.3.2.0
+ Vendor string and code GenuineIntel (1)
+ Model string and code Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz (45)
+ CPU Revision 7.000000
+ CPUID Info Family6 Model45 Stepping7
+ CPU Max Megahertz 2601
+ CPU Min Megahertz 1200
+ Hdw Threads per core 1
+ Cores per Socket 8
+ Sockets 2
+ NUMA Nodes 2
+ CPUs per Node 8
+ Total CPUs 16
+ Running in a VM no
+ Number Hardware Counters 11
+ Max Multiplex Counters 32
+ -----------
+ Name Code Avail Deriv Description (Note)
+ PAPI_L1_DCM 0x80000000 Yes No Level 1 data cache misses
+ PAPI_L1_ICM 0x80000001 Yes No Level 1 instruction cache misses
+ PAPI_L2_DCM 0x80000002 Yes Yes Level 2 data cache misses
+ PAPI_L2_ICM 0x80000003 Yes No Level 2 instruction cache misses
+ PAPI_L3_DCM 0x80000004 No No Level 3 data cache misses
+ PAPI_L3_ICM 0x80000005 No No Level 3 instruction cache misses
+ PAPI_L1_TCM 0x80000006 Yes Yes Level 1 cache misses
+ PAPI_L2_TCM 0x80000007 Yes No Level 2 cache misses
+ PAPI_L3_TCM 0x80000008 Yes No Level 3 cache misses
+ ....Â
+### papi_native_avail
+<span>Prints which native events are available on the current
+CPU.</span>
+### <span class="s1">papi_cost</span>
+<span>Measures the cost (in cycles) of basic PAPI operations.</span>
+### <span>papi_mem_info</span>
+<span>Prints information about the memory architecture of the current
+CPU.</span>
+PAPI API
+--------
+PAPI provides two kinds of events:Â
+- **Preset events** is a set of predefined common CPU events,
+ <span>standardized</span>Â across platforms.
+- **Native events **is a set of all events supported by the
+ current hardware. This is a larger set of features than preset. For
+ other components than CPU, only native events are usually available.
+To use PAPI in your application, you need to link the appropriate
+include file.
+- <span class="monospace">papi.h</span> for C
+- <span class="monospace">f77papi.h</span> for Fortran 77
+- <span class="monospace">f90papi.h</span> for Fortran 90
+- <span class="monospace">fpapi.h</span> for Fortran with preprocessor
+The include path is automatically added by papi module to <span
+class="monospace">$INCLUDE</span>.
+### High level API
+Please refer
+to <http://icl.cs.utk.edu/projects/papi/wiki/PAPIC:High_Level> for a
+description of the High level API.
+### Low level API
+Please refer
+to <http://icl.cs.utk.edu/projects/papi/wiki/PAPIC:Low_Level> for a
+description of the Low level API.
+### Timers
+PAPI provides the most accurate timers the platform can support.
+See <http://icl.cs.utk.edu/projects/papi/wiki/PAPIC:Timers>
+### System information
+PAPI can be used to query some system infromation, such as CPU name and
+MHz.
+See <http://icl.cs.utk.edu/projects/papi/wiki/PAPIC:System_Information>
+Example
+-------
+The following example prints MFLOPS rate of a naive matrix-matrix
+multiplication :
+ #include <stdlib.h>
+ #include <stdio.h>
+ #include "papi.h"
+ #define SIZE 1000
+ int main(int argc, char **argv) {
+ float matrixa[SIZE][SIZE], matrixb[SIZE][SIZE], mresult[SIZE][SIZE];
+ float real_time, proc_time, mflops;
+ long long flpins;
+ int retval;
+ int i,j,k;
+ /* Initialize the Matrix arrays */
+ for ( i=0; i<SIZE*SIZE; i++ ){
+ mresult[0][i] = 0.0;
+ matrixa[0][i] = matrixb[0][i] = rand()*(float)1.1;Â
+ }
+ Â
+ /* Setup PAPI library and begin collecting data from the counters */
+ if((retval=PAPI_flops( &real_time, &proc_time, &flpins, &mflops))<PAPI_OK)
+ printf("Error!");
+ /* A naive Matrix-Matrix multiplication */
+ for (i=0;i<SIZE;i++)
+ for(j=0;j<SIZE;j++)
+ for(k=0;k<SIZE;k++)
+ mresult[i][j]=mresult[i][j] + matrixa[i][k]*matrixb[k][j];
+ /* Collect the data into the variables passed in */
+ if((retval=PAPI_flops( &real_time, &proc_time, &flpins, &mflops))<PAPI_OK)
+ printf("Error!");
+
+ printf("Real_time:t%fnProc_time:t%fnTotal flpins:t%lldnMFLOPS:tt%fn", real_time, proc_time, flpins, mflops);
+ PAPI_shutdown();
+ return 0;
+ }
+Â Now compile and run the example :
+ $ gcc matrix.c -o matrix -lpapi
+ $ ./matrix
+ Real_time8.852785
+ Proc_time8.850000
+ Total flpins6012390908
+ MFLOPS679.366211Â
+Let's try with optimizations enabled :
+ $ gcc -O3 matrix.c -o matrix -lpapi
+ $ ./matrix
+ Real_time0.000020
+ Proc_time0.000000
+ Total flpins6
+ MFLOPSinf
+Now we see a seemingly strange result - the multiplication took no time
+and only 6 floating point instructions were issued. This is because the
+compiler optimizations have completely removed the multiplication loop,
+as the result is actually not used anywhere in the program. We can fix
+this by adding some "dummy" code at the end of the Matrix-Matrix
+multiplication routine :
+ for (i=0; i<SIZE;i++)
+ for (j=0; j<SIZE; j++)
+ if (mresult[i][j] == -1.0) printf("x");
+Now the compiler won't remove the multiplication loop. (However it is
+still not that smart to see that the result won't ever be negative). Now
+run the code again:
+ $ gcc -O3 matrix.c -o matrix -lpapi
+ $ ./matrix
+ Real_time8.795956
+ Proc_time8.790000
+ Total flpins18700983160
+ MFLOPS2127.529297Â
+### Intel Xeon Phi
+PAPI currently supports only a subset of counters on the Intel Xeon Phi
+processor compared to Intel Xeon, for example the floating point
+operations counter is missing.
+To use PAPI in [Intel Xeon
+Phi](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi)Â native
+applications, you need to load module with "<span
+class="monospace">-mic</span>" suffix, for example "<span
+class="monospace">papi/5.3.2-mic</span>" :
+ $ module load papi/5.3.2-mic
+Then, compile your application in the following way:
+ $ module load intel
+ $ icc -mmic -Wl,-rpath,/apps/intel/composer_xe_2013.5.192/compiler/lib/mic matrix-mic.c -o matrix-mic -lpapi -lpfm
+To execute the application on MIC, you need to manually set <span
+class="monospace">LD_LIBRARY_PATH :</span>
+ $Â qsub -q qmic -A NONE-0-0 -I
+ $ ssh mic0
+ $ export LD_LIBRARY_PATH=/apps/tools/papi/5.4.0-mic/lib/Â
+ $ ./matrix-micÂ
+Alternatively, you can link PAPI statically (<span
+class="monospace">-static</span> flag), then <span
+class="monospace">LD_LIBRARY_PATH</span> does not need to be set.
+You can also execute the PAPI tools on MIC :
+ $ /apps/tools/papi/5.4.0-mic/bin/papi_native_avail
+To use PAPI in offload mode, you need to provide both host and MIC
+versions of PAPI:
+ $ module load papi/5.4.0
+ $ icc matrix-offload.c -o matrix-offload -offload-option,mic,compiler,"-L$PAPI_HOME-mic/lib -lpapi" -lpapi
+References
+----------
+1. <http://icl.cs.utk.edu/papi/>Â Main project page
+2. <http://icl.cs.utk.edu/projects/papi/wiki/Main_Page>Â Wiki
+3. <http://icl.cs.utk.edu/papi/docs/> API Documentation
diff --git a/anselm-cluster-documentation/software/debuggers/scalasca.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.html
old mode 100755
new mode 100644
similarity index 60%
rename from anselm-cluster-documentation/software/debuggers/scalasca.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.html
index 0f2b89f298fc8c5fef598ff6df6d03c014b8ae84..83517e664509ef473cf6a1a1d0022eb9f3197ed9
--- a/anselm-cluster-documentation/software/debuggers/scalasca.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.html
@@ -10,45 +10,42 @@
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<title>Scalasca — IT4I Docs</title>
- <link rel="canonical" href="scalasca.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
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+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
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@@ -64,7 +61,7 @@
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="scalasca.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="scalasca.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
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<div id="portal-advanced-search" class="hiddenStructure">
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+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
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@@ -153,7 +150,7 @@
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<span id="breadcrumbs-1" dir="ltr">
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
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@@ -163,7 +160,7 @@
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<span id="breadcrumbs-2" dir="ltr">
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@@ -173,7 +170,7 @@
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<span id="breadcrumbs-3" dir="ltr">
- <a href="../debuggers.html">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">Debuggers and profilers</a>
<span class="breadcrumbSeparator">
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@@ -250,13 +247,13 @@
<p><a class="external-link" href="http://www.scalasca.org/" target="_self" title="">Scalasca</a> is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks – in particular those concerning communication and synchronization – and offers guidance in exploring their causes.</p>
<p>Scalasca supports profiling of MPI, OpenMP and hybrid MPI+OpenMP applications.</p>
<h2 class=" ">Installed versions</h2>
-<p>There are currently two versions of Scalasca 2.0 <a target="_self" title="" class="internal-link" href="../../environment-and-modules.html">modules</a> installed on Anselm:</p>
+<p>There are currently two versions of Scalasca 2.0 <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">modules</a> installed on Anselm:</p>
<ul>
<li>
-<p class="p1"><span class="s1"><span class="monospace">scalasca2/2.0-gcc-openmpi</span>, for usage with <a target="_self" title="" class="internal-link" href="../compilers.html">GNU Compiler</a> and <a target="_self" title="" class="internal-link" href="../mpi-1/Running_OpenMPI.html">OpenMPI</a>,</span></p>
+<p class="p1"><span class="s1"><span class="monospace">scalasca2/2.0-gcc-openmpi</span>, for usage with <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">GNU Compiler</a> and <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI">OpenMPI</a>,</span></p>
</li>
<li>
-<p class="p1"><span class="s1"><span class="monospace">scalasca2/2.0-icc-impi</span>, for usage with <a target="_self" title="" class="internal-link" href="../compilers.html">Intel Compiler</a> and <a target="_self" title="" class="internal-link" href="../mpi-1/running-mpich2.html">Intel MPI</a>.</span></p>
+<p class="p1"><span class="s1"><span class="monospace">scalasca2/2.0-icc-impi</span>, for usage with <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">Intel Compiler</a> and <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2">Intel MPI</a>.</span></p>
</li>
</ul>
<h2 class=" ">Usage</h2>
@@ -267,7 +264,7 @@
<li>Analysis of reports</li>
</ol>
<h3 class=" ">Instrumentation</h3>
-<p>Instrumentation via "<span class="monospace">scalasca -instrument</span>" is discouraged. Use <a target="_self" title="" class="internal-link" href="score-p.html">Score-P instrumentation</a>.</p>
+<p>Instrumentation via "<span class="monospace">scalasca -instrument</span>" is discouraged. Use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p">Score-P instrumentation</a>.</p>
<h3 class=" ">Runtime measurement</h3>
<p>After the application is instrumented, runtime measurement can be performed with the "<span class="monospace">scalasca -analyze</span>" command. The syntax is :</p>
<p><span class="monospace">scalasca -analyze [scalasca options] [launcher] [launcher options] [program] [program options]</span></p>
@@ -275,15 +272,15 @@
<pre class=" ">$ <span class="monospace">scalasca -analyze mpirun -np 4 ./mympiprogram</span></pre>
<p class=" ">Some notable Scalsca options are:</p>
<dl><dt>-t Enable trace data collection. By default, only summary data are collected.</dt><dt>-e <directory> Specify a directory to save the collected data to. By default, Scalasca saves the data to a directory with prefix <span>scorep_, followed by name of the executable and launch configuration.</span></dt><dt><span><br /></span></dt></dl>
-<p class="exclamation">Scalasca can generate a huge amount of data, especially if tracing is enabled. Please consider saving the data to a <a target="_self" title="" class="internal-link" href="../../storage-1/storage.html">scratch directory</a>.</p>
+<p class="exclamation">Scalasca can generate a huge amount of data, especially if tracing is enabled. Please consider saving the data to a <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage">scratch directory</a>.</p>
<h3 class=" ">Analysis of reports</h3>
-<p>For the analysis, you must have <a target="_self" title="" class="internal-link" href="score-p.html">Score-P</a> and <a target="_self" title="" class="internal-link" href="cube.html">CUBE</a> modules loaded. The analysis is done in two steps, first, the data is preprocessed and then CUBE GUI tool is launched.</p>
+<p>For the analysis, you must have <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p">Score-P</a> and <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube">CUBE</a> modules loaded. The analysis is done in two steps, first, the data is preprocessed and then CUBE GUI tool is launched.</p>
<p>To launch the analysis, run :</p>
<pre class="fragment">scalasca -examine [options] <experiment_directory></pre>
<p class=" ">If you do not wish to launch the GUI tool, use the "-s" option :</p>
<pre class="fragment">scalasca -examine -s <experiment_directory></pre>
<p class=" ">Alternatively you can open CUBE and load the data directly from here. Keep in mind that in that case the preprocessing is not done and not all metrics will be shown in the viewer.</p>
-<p class=" ">Refer to <a target="_self" title="" class="internal-link" href="cube.html">CUBE documentation</a>Â on usage of the GUI viewer.</p>
+<p class=" ">Refer to <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube">CUBE documentation</a>Â on usage of the GUI viewer.</p>
<h2 class=" ">References</h2>
<ol>
<li><a class="external-link" href="http://www.scalasca.org/" target="_self" title="">http://www.scalasca.org/</a></li>
@@ -363,7 +360,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
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@@ -379,7 +376,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -395,7 +392,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -411,7 +408,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -427,7 +424,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -443,7 +440,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -459,7 +456,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -475,7 +472,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -491,7 +488,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -507,7 +504,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -523,7 +520,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -539,7 +536,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -555,10 +552,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -574,7 +571,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -590,7 +587,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -606,7 +603,7 @@
- <a title="A collection of development tools" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -622,7 +619,7 @@
- <a title="" class="state-published contenttype-document" href="allinea-ddt.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
@@ -638,7 +635,7 @@
- <a title="quick application profiling" class="state-published contenttype-document" href="allinea-performance-reports.html">
+ <a class="state-published contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -654,7 +651,7 @@
- <a title="" class="state-published contenttype-document" href="cube.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube">
<span>CUBE</span>
</a>
@@ -670,7 +667,7 @@
- <a title="" class="state-published contenttype-document" href="intel-performance-counter-monitor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor">
<span>Intel Performance Counter Monitor</span>
</a>
@@ -686,7 +683,7 @@
- <a title="" class="state-published contenttype-document" href="intel-vtune-amplifier.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier</span>
</a>
@@ -702,7 +699,7 @@
- <a title="" class="state-published contenttype-document" href="papi.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi">
<span>PAPI</span>
</a>
@@ -718,7 +715,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="scalasca.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca">
<span>Scalasca</span>
</a>
@@ -734,7 +731,7 @@
- <a title="" class="state-published contenttype-document" href="score-p.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p">
<span>Score-P</span>
</a>
@@ -750,7 +747,7 @@
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published contenttype-document" href="total-view.html">
+ <a class="state-published contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -766,7 +763,7 @@
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -782,7 +779,7 @@
- <a title="" class="state-published contenttype-document" href="vampir.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -807,7 +804,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -823,7 +820,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -839,7 +836,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -855,7 +852,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -871,7 +868,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -887,7 +884,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -903,7 +900,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -919,7 +916,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -935,7 +932,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -951,7 +948,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -967,7 +964,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -983,7 +980,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -999,7 +996,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -1015,7 +1012,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1031,7 +1028,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1047,7 +1044,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1072,7 +1069,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1088,7 +1085,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1113,7 +1110,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1129,7 +1126,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1145,7 +1142,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1184,14 +1181,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -1213,12 +1210,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1234,7 +1231,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.md
new file mode 100644
index 0000000000000000000000000000000000000000..b9db567ced9160a5fe4ed7c16b113eb13bbcfe97
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.md
@@ -0,0 +1,85 @@
+Scalasca
+========
+<span>Introduction</span>
+--
+[Scalasca](http://www.scalasca.org/) is a software tool
+that supports the performance optimization of parallel programs by
+measuring and analyzing their runtime behavior. The analysis identifies
+potential performance bottlenecks – in particular those concerning
+communication and synchronization – and offers guidance in exploring
+their causes.
+Scalasca supports profiling of MPI, OpenMP and hybrid MPI+OpenMP
+applications.
+Installed versions
+------------------
+There are currently two versions of Scalasca 2.0
+[modules](https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules)
+installed on Anselm:
+- <span class="s1"><span
+ class="monospace">scalasca2/2.0-gcc-openmpi</span>, for usage with
+ [GNU
+ Compiler](https://docs.it4i.cz/anselm-cluster-documentation/software/compilers)
+ and
+ [OpenMPI](https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI),</span>
+- <span class="s1"><span
+ class="monospace">scalasca2/2.0-icc-impi</span>, for usage with
+ [Intel
+ Compiler](https://docs.it4i.cz/anselm-cluster-documentation/software/compilers)
+ and [Intel
+ MPI](https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2).</span>
+Usage
+-----
+Profiling a parallel application with Scalasca consists of three steps:
+1. Instrumentation, compiling the application such way, that the
+ profiling data can be generated.
+2. Runtime measurement, running the application with the Scalasca
+ profiler to collect performance data.
+3. Analysis of reports
+### Instrumentation
+Instrumentation via "<span class="monospace">scalasca
+-instrument</span>" is discouraged. Use [Score-P
+instrumentation](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p).
+### Runtime measurement
+After the application is instrumented, runtime measurement can be
+performed with the "<span class="monospace">scalasca -analyze</span>"
+command. The syntax is :
+<span class="monospace">scalasca -analyze [scalasca options]
+[launcher] [launcher options] [program] [program options]</span>
+An example :
+ $ scalasca -analyze mpirun -np 4 ./mympiprogram
+Some notable Scalsca options are:
+-t Enable trace data collection. By default, only summary data are
+collected.
+-e <directory> Specify a directory to save the collected data to.
+By default, Scalasca saves the data to a directory with
+prefix <span>scorep_, followed by name of the executable and launch
+configuration.</span>
+<span>
+</span>
+Scalasca can generate a huge amount of data, especially if tracing is
+enabled. Please consider saving the data to a [scratch
+directory](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage).
+### Analysis of reports
+For the analysis, you must have
+[Score-P](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p)
+and
+[CUBE](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube)
+modules loaded. The analysis is done in two steps, first, the data is
+preprocessed and then CUBE GUI tool is launched.
+To launch the analysis, run :
+``` {.fragment}
+scalasca -examine [options] <experiment_directory>
+```
+If you do not wish to launch the GUI tool, use the "-s" option :
+``` {.fragment}
+scalasca -examine -s <experiment_directory>
+```
+Alternatively you can open CUBE and load the data directly from here.
+Keep in mind that in that case the preprocessing is not done and not all
+metrics will be shown in the viewer.
+Refer to [CUBE
+documentation](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube)Â on
+usage of the GUI viewer.
+References
+----------
+1. <http://www.scalasca.org/>
diff --git a/anselm-cluster-documentation/software/debuggers/score-p.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.html
old mode 100755
new mode 100644
similarity index 63%
rename from anselm-cluster-documentation/software/debuggers/score-p.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.html
index 884dd52333ac7345de6c9c3254e2443c1f583f58..b81f37572292a240eb2e94ce8823ade26a26045b
--- a/anselm-cluster-documentation/software/debuggers/score-p.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.html
@@ -10,45 +10,42 @@
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-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:07 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p" /><!--[if lt IE 7]></base><![endif]-->
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Score-P — IT4I Docs</title>
- <link rel="canonical" href="score-p.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="score-p.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="score-p.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
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@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../debuggers.html">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">Debuggers and profilers</a>
<span class="breadcrumbSeparator">
/
@@ -248,15 +245,15 @@
<div id="parent-fieldname-text-74be0676bd924e95a27a82a3c3cfe3e8" class="">
<h2 class=" ">Introduction</h2>
<p>The <a class="external-link" href="http://www.vi-hps.org/projects/score-p/" target="_self" title="">Score-P measurement infrastructure</a> is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications. </p>
-<p>Score-P can be used as an instrumentation tool for <a target="_self" title="" class="internal-link" href="scalasca.html">Scalasca</a>.</p>
+<p>Score-P can be used as an instrumentation tool for <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca">Scalasca</a>.</p>
<h2 class=" ">Installed versions</h2>
-<p>There are currently two versions of Score-P version 1.2.6 <a target="_self" title="" class="internal-link" href="../../environment-and-modules.html">modules</a>Â installed on Anselm :</p>
+<p>There are currently two versions of Score-P version 1.2.6 <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">modules</a>Â installed on Anselm :</p>
<ul>
<li>
-<p class="p1"><span class="s1">scorep/1.2.3-gcc-openmpi<span>, for usage with </span><a target="_self" title="" class="internal-link" href="../compilers.html">GNU Compiler</a><span> and </span><a target="_self" title="" class="internal-link" href="../mpi-1/Running_OpenMPI.html">OpenMPI</a><span>,</span></span></p>
+<p class="p1"><span class="s1">scorep/1.2.3-gcc-openmpi<span>, for usage with </span><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">GNU Compiler</a><span> and </span><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI">OpenMPI</a><span>,</span></span></p>
</li>
<li>
-<p class="p1"><span class="s1">scorep/1.2.3-icc-impi<span>, for usage with </span><a target="_self" title="" class="internal-link" href="../compilers.html">Intel Compiler</a><span> and </span><a target="_self" title="" class="internal-link" href="../mpi-1/running-mpich2.html">Intel MPI</a><span>.</span></span></p>
+<p class="p1"><span class="s1">scorep/1.2.3-icc-impi<span>, for usage with </span><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">Intel Compiler</a><span> and </span><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2">Intel MPI</a><span>.</span></span></p>
</li>
</ul>
<h2 class=" ">Instrumentation</h2>
@@ -366,7 +363,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -382,7 +379,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -398,7 +395,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -414,7 +411,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -430,7 +427,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -446,7 +443,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -462,7 +459,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -478,7 +475,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -494,7 +491,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -510,7 +507,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -526,7 +523,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -542,7 +539,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -558,10 +555,10 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -577,7 +574,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -593,7 +590,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -609,7 +606,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="A collection of development tools" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -625,7 +622,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published contenttype-document" href="allinea-ddt.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
@@ -641,7 +638,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="quick application profiling" class="state-published contenttype-document" href="allinea-performance-reports.html">
+ <a class="state-published contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -657,7 +654,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published contenttype-document" href="cube.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube">
<span>CUBE</span>
</a>
@@ -673,7 +670,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published contenttype-document" href="intel-performance-counter-monitor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor">
<span>Intel Performance Counter Monitor</span>
</a>
@@ -689,7 +686,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published contenttype-document" href="intel-vtune-amplifier.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier</span>
</a>
@@ -705,7 +702,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published contenttype-document" href="papi.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi">
<span>PAPI</span>
</a>
@@ -721,7 +718,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published contenttype-document" href="scalasca.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca">
<span>Scalasca</span>
</a>
@@ -737,7 +734,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="score-p.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p">
<span>Score-P</span>
</a>
@@ -753,7 +750,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published contenttype-document" href="total-view.html">
+ <a class="state-published contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -769,7 +766,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -785,7 +782,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published contenttype-document" href="vampir.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -810,7 +807,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -826,7 +823,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -842,7 +839,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -858,7 +855,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -874,7 +871,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -890,7 +887,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -906,7 +903,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -922,7 +919,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -938,7 +935,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -954,7 +951,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -970,7 +967,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -986,7 +983,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -1002,7 +999,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -1018,7 +1015,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1034,7 +1031,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1050,7 +1047,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1075,7 +1072,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1091,7 +1088,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1116,7 +1113,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1132,7 +1129,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1148,7 +1145,7 @@ $ scorep mpif90 -o myapp foo.o bar.o</pre>
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1187,14 +1184,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1216,12 +1213,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1237,7 +1234,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.md
new file mode 100644
index 0000000000000000000000000000000000000000..c9a5716413433d3d73384855fd9a738c3771528d
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.md
@@ -0,0 +1,116 @@
+Score-P
+=======
+Introduction
+------------
+The [Score-P measurement
+infrastructure](http://www.vi-hps.org/projects/score-p/)
+is a highly scalable and easy-to-use tool suite for profiling, event
+tracing, and online analysis of HPC applications.Â
+Score-P can be used as an instrumentation tool for
+[Scalasca](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca).
+Installed versions
+------------------
+There are currently two versions of Score-P version 1.2.6
+[modules](https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules)Â installed
+on Anselm :
+- <span class="s1">scorep/1.2.3-gcc-openmpi<span>, for usage
+ with </span>[GNU
+ Compiler](https://docs.it4i.cz/anselm-cluster-documentation/software/compilers)<span> and </span>[OpenMPI](https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI)<span>,</span></span>
+- <span class="s1">scorep/1.2.3-icc-impi<span>, for usage
+ with </span>[Intel
+ Compiler](https://docs.it4i.cz/anselm-cluster-documentation/software/compilers)<span> and </span>[Intel
+ MPI](https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2)<span>.</span></span>
+Instrumentation
+---------------
+<span>There are three ways to instrument your parallel applications in
+order to enable performance data collection :</span>
+1. <span>Automated instrumentation using compiler</span>
+2. <span>Manual instrumentation using API calls</span>
+3. <span>Manual instrumentation using directives</span>
+### Automated instrumentation
+is the easiest method. Score-P will automatically add instrumentation to
+every routine entry and exit using compiler hooks, and will intercept
+MPI calls and OpenMP regions. This method might, however, produce a
+large number of data. If you want to focus on profiler a specific
+regions of your code, consider using the manual instrumentation methods.
+To use automated instrumentation, simply prepend <span
+class="monospace">scorep</span> to your compilation command. For
+example, replace :Â
+``` {.fragment}
+$ mpif90 -c foo.f90
+$ mpif90 -c bar.f90
+$ mpif90 -o myapp foo.o bar.o
+```
+with :
+``` {.fragment}
+$ scorep mpif90 -c foo.f90
+$ scorep mpif90 -c bar.f90
+$ scorep mpif90 -o myapp foo.o bar.o
+```
+Usually your program is compiled using a Makefile or similar script, so
+it advisable to add the <span class="monospace">scorep</span> command to
+your definition of variables <span class="monospace">CC</span>, <span
+class="monospace">CXX</span>, <span class="monospace">FCC</span> etc.
+It is important that <span class="monospace">scorep</span> is prepended
+also to the linking command, in order to link with Score-P
+instrumentation libraries.
+### <span>Manual instrumentation using API calls</span>
+To use this kind of instrumentation, use <span
+class="monospace">scorep</span> with switch <span
+class="monospace">--user</span>. You will then mark regions to be
+instrumented by inserting API calls.
+An example in C/C++ :
+ #include <scorep/SCOREP_User.h>
+ void foo()
+ {
+ SCOREP_USER_REGION_DEFINE( my_region_handle )
+ // more declarations
+ SCOREP_USER_REGION_BEGIN( my_region_handle, "foo", SCOREP_USER_REGION_TYPE_COMMON )
+ // do something
+ SCOREP_USER_REGION_END( my_region_handle )
+ }
+Â and Fortran :
+ #include "scorep/SCOREP_User.inc"
+ subroutine foo
+ SCOREP_USER_REGION_DEFINE( my_region_handle )
+ ! more declarations
+ SCOREP_USER_REGION_BEGIN( my_region_handle, "foo", SCOREP_USER_REGION_TYPE_COMMON )
+ ! do something
+ SCOREP_USER_REGION_END( my_region_handle )
+ end subroutine foo
+Please refer to the [documentation for description of the
+API](https://silc.zih.tu-dresden.de/scorep-current/pdf/scorep.pdf).
+### <span>Manual instrumentation using directives</span>
+This method uses POMP2 directives to mark regions to be instrumented. To
+use this method, use command <span class="monospace">scorep
+--pomp.</span>
+Example directives in C/C++ :
+ void foo(...)
+ {
+ /* declarations */
+ #pragma pomp inst begin(foo)
+ ...
+ if (<condition>)
+ {
+ #pragma pomp inst altend(foo)
+ return;
+ }
+ ...
+ #pragma pomp inst end(foo)
+ }
+<span>and in Fortran :</span>
+ subroutine foo(...)
+ !declarations
+ !POMP$ INST BEGIN(foo)
+ ...
+ if (<condition>) then
+ !POMP$ INST ALTEND(foo)
+ return
+ end if
+ ...
+ !POMP$ INST END(foo)
+ end subroutine foo
+The directives are ignored if the program is compiled without Score-P.
+Again, please refer to the
+[documentation](https://silc.zih.tu-dresden.de/scorep-current/pdf/scorep.pdf)
+for a more elaborate description.
diff --git a/anselm-cluster-documentation/software/debuggers/summary.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary.html
old mode 100755
new mode 100644
similarity index 61%
rename from anselm-cluster-documentation/software/debuggers/summary.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary.html
index 4069c5b3f2cdc3ee1d4267d575f423112da0cae9..ba3e600c1425bd084a2881b5f562af7eb02a55e2
--- a/anselm-cluster-documentation/software/debuggers/summary.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:57 GMT -->
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<title>Debuggers and profilers summary — IT4I Docs</title>
- <link rel="canonical" href="../debuggers.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="summary.html#content">PĹ™ejĂt na obsah</a> |
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- <a accesskey="6" href="summary.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
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<div id="portal-advanced-search" class="hiddenStructure">
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+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
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@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
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@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -243,25 +240,25 @@
<h2 class=" ">Introduction</h2>
<p>We provide state of the art programms and tools to develop, profile and debug HPC codes at IT4Innovations.<br />On these pages, we provide an overview of the profiling and debugging tools available on Anslem at IT4I.</p>
<h2 class=" ">Intel debugger</h2>
-<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html">X display</a> for running the GUI.</p>
+<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">X display</a> for running the GUI.</p>
<pre class=" ">$ module load intel<br />$ idb</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="../intel-suite/intel-debugger.html">Intel Debugger</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger">Intel Debugger</a> page.</p>
<h2 class=" ">Allinea Forge (DDT/MAP)</h2>
<p>Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel Xeon Phi accelerators. DDT provides all the standard debugging features (stack trace, breakpoints, watches, view variables, threads etc.) for every thread running as part of your program, or for every process - even if these processes are distributed across a cluster using an MPI implementation.</p>
<pre class=" ">$ module load Forge<br />$ forge</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="allinea-ddt.html">Allinea DDT</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt">Allinea DDT</a> page.</p>
<h2 class=" ">Allinea Performance Reports</h2>
<p>Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs. Our license is limited to 64 MPI processes.</p>
<pre class=" ">$ module load PerformanceReports/6.0 <br />$ perf-report mpirun -n 64 ./my_application argument01 argument02</pre>
-<p class=" ">Read more at the <a target="_self" title="" class="internal-link" href="allinea-performance-reports.html">Allinea Performance Reports</a> page.</p>
+<p class=" ">Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports">Allinea Performance Reports</a> page.</p>
<h2 class=" ">RougeWave Totalview</h2>
<p>TotalView is a source- and machine-level debugger for multi-process, multi-threaded programs. Its wide range of tools provides ways to analyze, organize, and test programs, making it easy to isolate and identify problems in individual threads and processes in programs of great complexity.</p>
<pre class=" ">$ module load totalview<br />$ totalview</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="total-view.html">Totalview</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view">Totalview</a> page.</p>
<h2 class=" ">Vampir trace analyzer</h2>
<p>Vampir is a GUI trace analyzer for traces in OTF format.</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="../../../salomon/software/debuggers/vampir.html">Vampir</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">Vampir</a> page.</p>
</div>
@@ -337,7 +334,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
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@@ -353,7 +350,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -369,7 +366,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -385,7 +382,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -401,7 +398,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -417,7 +414,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -433,7 +430,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -449,7 +446,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -465,7 +462,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -481,7 +478,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -497,7 +494,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -513,7 +510,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -529,10 +526,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -548,7 +545,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -564,7 +561,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -580,7 +577,7 @@
- <a title="A collection of development tools" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -596,7 +593,7 @@
- <a title="" class="state-published contenttype-document" href="allinea-ddt.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
@@ -612,7 +609,7 @@
- <a title="quick application profiling" class="state-published contenttype-document" href="allinea-performance-reports.html">
+ <a class="state-published contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -628,7 +625,7 @@
- <a title="" class="state-published contenttype-document" href="cube.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube">
<span>CUBE</span>
</a>
@@ -644,7 +641,7 @@
- <a title="" class="state-published contenttype-document" href="intel-performance-counter-monitor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor">
<span>Intel Performance Counter Monitor</span>
</a>
@@ -660,7 +657,7 @@
- <a title="" class="state-published contenttype-document" href="intel-vtune-amplifier.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier</span>
</a>
@@ -676,7 +673,7 @@
- <a title="" class="state-published contenttype-document" href="papi.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi">
<span>PAPI</span>
</a>
@@ -692,7 +689,7 @@
- <a title="" class="state-published contenttype-document" href="scalasca.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca">
<span>Scalasca</span>
</a>
@@ -708,7 +705,7 @@
- <a title="" class="state-published contenttype-document" href="score-p.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p">
<span>Score-P</span>
</a>
@@ -724,7 +721,7 @@
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published contenttype-document" href="total-view.html">
+ <a class="state-published contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -740,7 +737,7 @@
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -756,7 +753,7 @@
- <a title="" class="state-published contenttype-document" href="vampir.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -781,7 +778,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -797,7 +794,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -813,7 +810,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -829,7 +826,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -845,7 +842,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -861,7 +858,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -877,7 +874,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -893,7 +890,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -909,7 +906,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -925,7 +922,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -941,7 +938,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -957,7 +954,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -973,7 +970,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -989,7 +986,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1005,7 +1002,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1021,7 +1018,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1046,7 +1043,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1062,7 +1059,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1087,7 +1084,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1103,7 +1100,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1119,7 +1116,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1158,14 +1155,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -1187,12 +1184,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1208,7 +1205,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary.md
new file mode 100644
index 0000000000000000000000000000000000000000..07f6e5ff872baf1df1c5ad1d4ae89a44a0080de5
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary.md
@@ -0,0 +1,67 @@
+Debuggers and profilers summary
+===============================
+
+Introduction
+------------
+We provide state of the art programms and tools to develop, profile and
+debug HPC codes at IT4Innovations.
+On these pages, we provide an overview of the profiling and debugging
+tools available on Anslem at IT4I.
+Intel debugger
+--------------
+The intel debugger version 13.0 is available, via module intel. The
+debugger works for applications compiled with C and C++ compiler and the
+ifort fortran 77/90/95 compiler. The debugger provides java GUI
+environment. Use [X
+display](resolveuid/11e53ad0d2fd4c5187537f4baeedff33)
+for running the GUI.
+ $ module load intel
+ $ idb
+Read more at the [Intel
+Debugger](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger)
+page.
+Allinea Forge (DDT/MAP)
+Allinea DDT, is a commercial debugger primarily for debugging parallel
+MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel
+Xeon Phi accelerators. DDT provides all the standard debugging features
+(stack trace, breakpoints, watches, view variables, threads etc.) for
+every thread running as part of your program, or for every process -
+even if these processes are distributed across a cluster using an MPI
+implementation.
+ $ module load Forge
+ $ forge
+Read more at the [Allinea
+DDT](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt)
+page.
+Allinea Performance Reports
+----
+Allinea Performance Reports characterize the performance of HPC
+application runs. After executing your application through the tool, a
+synthetic HTML report is generated automatically, containing information
+about several metrics along with clear behavior statements and hints to
+help you improve the efficiency of your runs. Our license is limited to
+64 MPI processes.
+ $ module load PerformanceReports/6.0
+ $ perf-report mpirun -n 64 ./my_application argument01 argument02
+Read more at the [Allinea Performance
+Reports](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports)
+page.
+RougeWave Totalview
+-------------------
+TotalView is a source- and machine-level debugger for multi-process,
+multi-threaded programs. Its wide range of tools provides ways to
+analyze, organize, and test programs, making it easy to isolate and
+identify problems in individual threads and processes in programs of
+great complexity.
+ $ module load totalview
+ $ totalview
+Read more at the
+[Totalview](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view)
+page.
+Vampir trace analyzer
+---------------------
+Vampir is a GUI trace analyzer for traces in OTF format.
+ $ module load Vampir/8.5.0
+ $ vampir
+Read more at
+the [Vampir](https://docs.it4i.cz/salomon/software/debuggers/vampir) page.
diff --git a/anselm-cluster-documentation/software/debuggers/total-view.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.html
old mode 100755
new mode 100644
similarity index 66%
rename from anselm-cluster-documentation/software/debuggers/total-view.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.html
index da3e4a809d5f63b8de768e1604bd23c56db464bc..11711c144d3607b11c739c047210b509bf601f3c
--- a/anselm-cluster-documentation/software/debuggers/total-view.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view" /><!--[if lt IE 7]></base><![endif]-->
<meta content="TotalView is a GUI-based source code multi-process, multi-thread debugger. " name="description" />
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Total View — IT4I Docs</title>
- <link rel="canonical" href="total-view.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="total-view.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="total-view.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../debuggers.html">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">Debuggers and profilers</a>
<span class="breadcrumbSeparator">
/
@@ -267,7 +264,7 @@
<h2 class=" ">Starting a Job with TotalView</h2>
<p>Be sure to log in with an X window forwarding enabled. This could mean using the -X in the ssh:Â </p>
<pre class=" ">ssh -X username@anselm.it4i.cz </pre>
-<p>Other options is to access login node using VNC. Please see the detailed information on how to use graphic user interface on Anselm <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html#VNC">here</a>.</p>
+<p>Other options is to access login node using VNC. Please see the detailed information on how to use graphic user interface on Anselm <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33#VNC">here</a>.</p>
<p>From the login node an interactive session with X windows forwarding (-X option) can be started by following command:</p>
<pre class=" ">qsub -I -X -A NONE-0-0 -q qexp -lselect=1:ncpus=16:mpiprocs=16,walltime=01:00:00 </pre>
<p>Then launch the debugger with the totalview command followed by the name of the executable to debug.</p>
@@ -285,9 +282,9 @@
<p>Now you can run the parallel debugger using:</p>
<pre class=" ">mpirun -tv -n 5 ./test_debug</pre>
<p>When following dialog appears click on "Yes"</p>
-<p><img title="" class="image-inline" alt="" src="totalview1.png" /></p>
+<p><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/totalview1.png" /></p>
<p>At this point the main TotalView GUI window will appear and you can insert the breakpoints and start debugging:</p>
-<p><img title="" class="image-inline" alt="" src="totalview2.png" /></p>
+<p><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/totalview2.png" /></p>
<h3 class=" ">Debugging a parallel code - option 2</h3>
<p>Other option to start new parallel debugging session from a command line is to let TotalView to execute mpirun by itself. In this case user has to specify a MPI implementation used to compile the source code. </p>
<p>The following example shows how to start debugging session with Intel MPI:</p>
@@ -371,7 +368,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -387,7 +384,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -403,7 +400,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -419,7 +416,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -435,7 +432,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -451,7 +448,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -467,7 +464,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -483,7 +480,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -499,7 +496,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -515,7 +512,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -531,7 +528,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -547,7 +544,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -563,10 +560,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -582,7 +579,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -598,7 +595,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -614,7 +611,7 @@
- <a title="A collection of development tools" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -630,7 +627,7 @@
- <a title="" class="state-published contenttype-document" href="allinea-ddt.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
@@ -646,7 +643,7 @@
- <a title="quick application profiling" class="state-published contenttype-document" href="allinea-performance-reports.html">
+ <a class="state-published contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -662,7 +659,7 @@
- <a title="" class="state-published contenttype-document" href="cube.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube">
<span>CUBE</span>
</a>
@@ -678,7 +675,7 @@
- <a title="" class="state-published contenttype-document" href="intel-performance-counter-monitor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor">
<span>Intel Performance Counter Monitor</span>
</a>
@@ -694,7 +691,7 @@
- <a title="" class="state-published contenttype-document" href="intel-vtune-amplifier.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier</span>
</a>
@@ -710,7 +707,7 @@
- <a title="" class="state-published contenttype-document" href="papi.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi">
<span>PAPI</span>
</a>
@@ -726,7 +723,7 @@
- <a title="" class="state-published contenttype-document" href="scalasca.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca">
<span>Scalasca</span>
</a>
@@ -742,7 +739,7 @@
- <a title="" class="state-published contenttype-document" href="score-p.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p">
<span>Score-P</span>
</a>
@@ -758,7 +755,7 @@
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="total-view.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -774,7 +771,7 @@
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -790,7 +787,7 @@
- <a title="" class="state-published contenttype-document" href="vampir.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -815,7 +812,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -831,7 +828,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -847,7 +844,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -863,7 +860,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -879,7 +876,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -895,7 +892,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -911,7 +908,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -927,7 +924,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -943,7 +940,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -959,7 +956,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -975,7 +972,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -991,7 +988,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -1007,7 +1004,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -1023,7 +1020,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1039,7 +1036,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1055,7 +1052,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1080,7 +1077,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1096,7 +1093,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1121,7 +1118,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1137,7 +1134,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1153,7 +1150,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1192,14 +1189,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1221,12 +1218,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1242,7 +1239,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:07 GMT -->
</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.md
new file mode 100644
index 0000000000000000000000000000000000000000..2ca6487cfa891f3bc61b145d79cc2b462d60c6f6
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.md
@@ -0,0 +1,105 @@
+Total View
+==========
+TotalView is a GUI-based source code multi-process, multi-thread
+debugger.
+License and Limitations for Anselm Users
+-----------------
+On Anselm users can debug OpenMP or MPI code that runs up to 64 parallel
+processes. These limitation means that:
+Â Â Â 1 user can debug up 64 processes, or
+Â Â Â 32 users can debug 2 processes, etc.
+Debugging of GPU accelerated codes is also supported.
+You can check the status of the licenses here:
+ cat /apps/user/licenses/totalview_features_state.txt
+ # totalview
+ # ---
+ # FEATUREÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â TOTALÂ Â USEDÂ AVAIL
+ # ---
+ TotalView_Team                    64     0    64
+ Replay                            64     0    64
+ CUDAÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â 64Â Â Â Â Â 0Â Â Â Â 64
+Compiling Code to run with TotalView
+-------------
+### Modules
+Load all necessary modules to compile the code. For example:
+ module load intel
+ module load impi  ... or ... module load openmpi/X.X.X-icc
+Load the TotalView module:
+ module load totalview/8.12
+Compile the code:
+ mpicc -g -O0 -o test_debug test.c
+ mpif90 -g -O0 -o test_debug test.f
+### Compiler flags
+Before debugging, you need to compile your code with theses flags:
+**-g** Generates extra debugging information usable by GDB. -g3
+includes even more debugging information. This option is available for
+GNU and INTEL C/C++ and Fortran compilers.
+**-O0** Suppress all optimizations.
+Starting a Job with TotalView
+------
+Be sure to log in with an X window forwarding enabled. This could mean
+using the -X in the ssh:Â
+ ssh -X username@anselm.it4i.cz
+Other options is to access login node using VNC. Please see the detailed
+information on how to use graphic user interface on Anselm
+[here](resolveuid/11e53ad0d2fd4c5187537f4baeedff33#VNC).
+From the login node an interactive session with X windows forwarding (-X
+option) can be started by following command:
+ qsub -I -X -A NONE-0-0 -q qexp -lselect=1:ncpus=16:mpiprocs=16,walltime=01:00:00
+Then launch the debugger with the totalview command followed by the name
+of the executable to debug.
+### Debugging a serial code
+To debug a serial code use:
+ totalview test_debug
+### Debugging a parallel code - option 1
+To debug a parallel code compiled with <span>**OpenMPI**</span> you need
+to setup your TotalView environment:Â
+**Please note:** To be able to run parallel debugging procedure from the
+command line without stopping the debugger in the mpiexec source code
+you have to add the following function to your **~/.tvdrc** file:
+ proc mpi_auto_run_starter {loaded_id} {
+ Â Â Â set starter_programs {mpirun mpiexec orterun}
+ Â Â Â set executable_name [TV::symbol get $loaded_id full_pathname]
+ Â Â Â set file_component [file tail $executable_name]
+ Â Â Â if {[lsearch -exact $starter_programs $file_component] != -1} {
+ Â Â Â Â Â Â Â puts "**************************************"
+ Â Â Â Â Â Â Â puts "Automatically starting $file_component"
+ Â Â Â Â Â Â Â puts "**************************************"
+ Â Â Â Â Â Â Â dgo
+ Â Â Â }
+ }
+ # Append this function to TotalView's image load callbacks so that
+ # TotalView run this program automatically.
+ dlappend TV::image_load_callbacks mpi_auto_run_starter
+The source code of this function can be also found in
+ /apps/mpi/openmpi/intel/1.6.5/etc/openmpi-totalview.tcl
+You can also add only following line to you ~/.tvdrc file instead of
+the entire function:
+**source /apps/mpi/openmpi/intel/1.6.5/etc/openmpi-totalview.tcl**
+You need to do this step only once.
+Now you can run the parallel debugger using:
+ mpirun -tv -n 5 ./test_debug
+When following dialog appears click on "Yes"
+
+At this point the main TotalView GUI window will appear and you can
+insert the breakpoints and start debugging:
+
+### Debugging a parallel code - option 2
+Other option to start new parallel debugging session from a command line
+is to let TotalView to execute mpirun by itself. In this case user has
+to specify a MPI implementation used to compile the source code.Â
+The following example shows how to start debugging session with Intel
+MPI:
+ module load intel/13.5.192 impi/4.1.1.036 totalview/8/13
+ totalview -mpi "Intel MPI-Hydra" -np 8 ./hello_debug_impi
+After running previous command you will see the same window as shown in
+the screenshot above.
+More information regarding the command line parameters of the TotalView
+can be found TotalView Reference Guide, Chapter 7TotalView Command
+Syntax. Â
+Documentation
+-------------
+[1] The [TotalView
+documentation](http://www.roguewave.com/support/product-documentation/totalview-family.aspx#totalview)
+web page is a good resource for learning more about some of the advanced
+TotalView features.
diff --git a/anselm-cluster-documentation/software/debuggers/totalview1.png b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/totalview1.png
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/software/debuggers/totalview1.png
rename to docs.it4i.cz/anselm-cluster-documentation/software/debuggers/totalview1.png
diff --git a/anselm-cluster-documentation/software/debuggers/totalview2.png b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/totalview2.png
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/software/debuggers/totalview2.png
rename to docs.it4i.cz/anselm-cluster-documentation/software/debuggers/totalview2.png
diff --git a/anselm-cluster-documentation/software/debuggers/valgrind.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.html
old mode 100755
new mode 100644
similarity index 72%
rename from anselm-cluster-documentation/software/debuggers/valgrind.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.html
index 635694944d92b4d1d29b380a8d66ed0348e3da75..32b7e84b6d15f5c66f0f53836e0d2416257f4dd0
--- a/anselm-cluster-documentation/software/debuggers/valgrind.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:07 GMT -->
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<meta content="Valgrind is a tool for memory debugging and profiling." name="description" />
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<title>Valgrind — IT4I Docs</title>
- <link rel="canonical" href="valgrind.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
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@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="valgrind.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="valgrind.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
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@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
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@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
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@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../debuggers.html">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">Debuggers and profilers</a>
<span class="breadcrumbSeparator">
/
@@ -264,7 +261,7 @@
<p>There are two versions of Valgrind available on Anselm.</p>
<ul>
<li><span>Version 3.6.0, installed by operating system vendor in </span><span class="monospace">/usr/bin/valgrind. </span><span>This version is available by default, without the need to load any module. This version however does not provide additional MPI support.</span></li>
-<li><span><span>Version 3.9.0 with support for Intel MPI, available in <a target="_self" title="" class="internal-link" href="../../environment-and-modules.html">module</a>Â </span></span><span class="monospace">valgrind/3.9.0-impi. </span>After loading the module, this version replaces the default valgrind.</li>
+<li><span><span>Version 3.9.0 with support for Intel MPI, available in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">module</a>Â </span></span><span class="monospace">valgrind/3.9.0-impi. </span>After loading the module, this version replaces the default valgrind.</li>
</ul>
<h2 class=" ">Usage</h2>
<p>Compile the application which you want to debug as usual. It is advisable to add compilation flags <span class="monospace">-g </span>(to add debugging information to the binary so that you will see original source code lines in the output) and <span class="monospace">-O0</span> (to disable compiler optimizations). </p>
@@ -367,7 +364,7 @@
<dt class="portletHeader hiddenStructure">
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+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
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@@ -383,7 +380,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -399,7 +396,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -415,7 +412,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -431,7 +428,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -447,7 +444,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -463,7 +460,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -479,7 +476,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -495,7 +492,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -511,7 +508,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -527,7 +524,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -543,7 +540,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -559,10 +556,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -578,7 +575,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -594,7 +591,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -610,7 +607,7 @@
- <a title="A collection of development tools" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -626,7 +623,7 @@
- <a title="" class="state-published contenttype-document" href="allinea-ddt.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
@@ -642,7 +639,7 @@
- <a title="quick application profiling" class="state-published contenttype-document" href="allinea-performance-reports.html">
+ <a class="state-published contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -658,7 +655,7 @@
- <a title="" class="state-published contenttype-document" href="cube.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube">
<span>CUBE</span>
</a>
@@ -674,7 +671,7 @@
- <a title="" class="state-published contenttype-document" href="intel-performance-counter-monitor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor">
<span>Intel Performance Counter Monitor</span>
</a>
@@ -690,7 +687,7 @@
- <a title="" class="state-published contenttype-document" href="intel-vtune-amplifier.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier</span>
</a>
@@ -706,7 +703,7 @@
- <a title="" class="state-published contenttype-document" href="papi.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi">
<span>PAPI</span>
</a>
@@ -722,7 +719,7 @@
- <a title="" class="state-published contenttype-document" href="scalasca.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca">
<span>Scalasca</span>
</a>
@@ -738,7 +735,7 @@
- <a title="" class="state-published contenttype-document" href="score-p.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p">
<span>Score-P</span>
</a>
@@ -754,7 +751,7 @@
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published contenttype-document" href="total-view.html">
+ <a class="state-published contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -770,7 +767,7 @@
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="valgrind.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -786,7 +783,7 @@
- <a title="" class="state-published contenttype-document" href="vampir.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -811,7 +808,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -827,7 +824,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -843,7 +840,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -859,7 +856,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -875,7 +872,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -891,7 +888,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -907,7 +904,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -923,7 +920,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -939,7 +936,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -955,7 +952,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -971,7 +968,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -987,7 +984,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -1003,7 +1000,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -1019,7 +1016,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1035,7 +1032,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1051,7 +1048,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1076,7 +1073,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1092,7 +1089,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1117,7 +1114,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1133,7 +1130,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1149,7 +1146,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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<div id="portal-footer">
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.md
new file mode 100644
index 0000000000000000000000000000000000000000..b0e22272d083cd2fd93a7cf41bc3e094162918cc
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.md
@@ -0,0 +1,251 @@
+Valgrind
+========
+Valgrind is a tool for memory debugging and profiling.
+About Valgrind
+--------------
+Valgrind is an open-source tool, used mainly for debuggig memory-related
+problems, such as memory leaks, use of uninitalized memory etc. in C/C++
+applications. The toolchain was however extended over time with more
+functionality, such as debugging of threaded applications, cache
+profiling, not limited only to C/C++.
+Valgind is an extremely useful tool for debugging memory errors such as
+[off-by-one](http://en.wikipedia.org/wiki/Off-by-one_error).
+Valgrind uses a virtual machine and dynamic recompilation of binary
+code, because of that, you can expect that programs being debugged by
+Valgrind run 5-100 times slower.
+The main tools available in Valgrind are :
+- **Memcheck**, the original, must used and default tool. Verifies
+ memory access in you program and can detect use of unitialized
+ memory, out of bounds memory access, memory leaks, double free, etc.
+- **Massif**, a heap profiler.
+- **Hellgrind** and **DRD** can detect race conditions in
+ multi-threaded applications.
+- **Cachegrind**, a cache profiler.
+- **Callgrind**, a callgraph analyzer.
+- For a full list and detailed documentation, please refer to the
+ [official Valgrind
+ documentation](http://valgrind.org/docs/).
+Installed versions
+------------------
+There are two versions of Valgrind available on Anselm.
+- <span>Version 3.6.0, installed by operating system vendor
+ in </span><span class="monospace">/usr/bin/valgrind.
+ </span><span>This version is available by default, without the need
+ to load any module. This version however does not provide additional
+ MPI support.</span>
+- <span><span>Version 3.9.0 with support for Intel MPI, available in
+ [module](https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules)Â </span></span><span
+ class="monospace">valgrind/3.9.0-impi. </span>After loading the
+ module, this version replaces the default valgrind.
+Usage
+-----
+Compile the application which you want to debug as usual. It is
+advisable to add compilation flags <span class="monospace">-g </span>(to
+add debugging information to the binary so that you will see original
+source code lines in the output) and <span class="monospace">-O0</span>
+(to disable compiler optimizations).Â
+For example, lets look at this C code, which has two problems :
+ #include <stdlib.h>
+ void f(void)
+ {
+ int* x = malloc(10 * sizeof(int));
+ x[10] = 0; // problem 1heap block overrun
+ } // problem 2memory leak -- x not freed
+ int main(void)
+ {
+ f();
+ return 0;
+ }
+Now, compile it with Intel compiler :
+ $ module add intel
+ $ icc -g valgrind-example.c -o valgrind-exampleÂ
+Now, lets run it with Valgrind. The syntax is :
+<span class="monospace">valgrind [valgrind options] <your program
+binary> [your program options]</span>
+If no Valgrind options are specified, Valgrind defaults to running
+Memcheck tool. Please refer to the Valgrind documentation for a full
+description of command line options.
+ $ valgrind ./valgrind-example
+ ==12652== Memcheck, a memory error detector
+ ==12652== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
+ ==12652== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info
+ ==12652== Command./valgrind-example
+ ==12652==
+ ==12652== Invalid write of size 4
+ ==12652== at 0x40053Ef (valgrind-example.c:6)
+ ==12652== by 0x40054Emain (valgrind-example.c:11)
+ ==12652== Address 0x5861068 is 0 bytes after a block of size 40 alloc'd
+ ==12652== at 0x4C27AAAmalloc (vg_replace_malloc.c:291)
+ ==12652== by 0x400528f (valgrind-example.c:5)
+ ==12652== by 0x40054Emain (valgrind-example.c:11)
+ ==12652==
+ ==12652==
+ ==12652== HEAP SUMMARY:
+ ==12652== in use at exit40 bytes in 1 blocks
+ ==12652== total heap usage1 allocs, 0 frees, 40 bytes allocated
+ ==12652==
+ ==12652== LEAK SUMMARY:
+ ==12652== definitely lost40 bytes in 1 blocks
+ ==12652== indirectly lost0 bytes in 0 blocks
+ ==12652== possibly lost0 bytes in 0 blocks
+ ==12652== still reachable0 bytes in 0 blocks
+ ==12652== suppressed0 bytes in 0 blocks
+ ==12652== Rerun with --leak-check=full to see details of leaked memory
+ ==12652==
+ ==12652== For counts of detected and suppressed errors, rerun with-v
+ ==12652== ERROR SUMMARY1 errors from 1 contexts (suppressed6 from 6)
+In the output we can see that Valgrind has detected both errors - the
+off-by-one memory access at line 5 and a memory leak of 40 bytes. If we
+want a detailed analysis of the memory leak, we need to run Valgrind
+with <span class="monospace">--leak-check=full</span> option :
+ $ valgrind --leak-check=full ./valgrind-example
+ ==23856== Memcheck, a memory error detector
+ ==23856== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.
+ ==23856== Using Valgrind-3.6.0 and LibVEX; rerun with -h for copyright info
+ ==23856== Command./valgrind-example
+ ==23856==
+ ==23856== Invalid write of size 4
+ ==23856== at 0x40067Ef (valgrind-example.c:6)
+ ==23856== by 0x40068Emain (valgrind-example.c:11)
+ ==23856== Address 0x66e7068 is 0 bytes after a block of size 40 alloc'd
+ ==23856== at 0x4C26FDEmalloc (vg_replace_malloc.c:236)
+ ==23856== by 0x400668f (valgrind-example.c:5)
+ ==23856== by 0x40068Emain (valgrind-example.c:11)
+ ==23856==
+ ==23856==
+ ==23856== HEAP SUMMARY:
+ ==23856== in use at exit40 bytes in 1 blocks
+ ==23856== total heap usage1 allocs, 0 frees, 40 bytes allocated
+ ==23856==
+ ==23856== 40 bytes in 1 blocks are definitely lost in loss record 1 of 1
+ ==23856== at 0x4C26FDEmalloc (vg_replace_malloc.c:236)
+ ==23856== by 0x400668f (valgrind-example.c:5)
+ ==23856== by 0x40068Emain (valgrind-example.c:11)
+ ==23856==
+ ==23856== LEAK SUMMARY:
+ ==23856== definitely lost40 bytes in 1 blocks
+ ==23856== indirectly lost0 bytes in 0 blocks
+ ==23856== possibly lost0 bytes in 0 blocks
+ ==23856== still reachable0 bytes in 0 blocks
+ ==23856== suppressed0 bytes in 0 blocks
+ ==23856==
+ ==23856== For counts of detected and suppressed errors, rerun with-v
+ ==23856== ERROR SUMMARY2 errors from 2 contexts (suppressed6 from 6)
+Now we can see that the memory leak is due to the <span
+class="monospace">malloc()</span> at line 6.
+<span>Usage with MPI</span>
+----
+Although Valgrind is not primarily a parallel debugger, it can be used
+to debug parallel applications as well. When launching your parallel
+applications, prepend the valgrind command. For example :
+ $ mpirun -np 4 valgrind myapplication
+The default version without MPI support will however report a large
+number of false errors in the MPI library, such as :
+ ==30166== Conditional jump or move depends on uninitialised value(s)
+ ==30166== at 0x4C287E8strlen (mc_replace_strmem.c:282)
+ ==30166== by 0x55443BDI_MPI_Processor_model_number (init_interface.c:427)
+ ==30166== by 0x55439E0I_MPI_Processor_arch_code (init_interface.c:171)
+ ==30166== by 0x558D5AEMPID_nem_impi_init_shm_configuration (mpid_nem_impi_extensions.c:1091)
+ ==30166== by 0x5598F4CMPID_nem_init_ckpt (mpid_nem_init.c:566)
+ ==30166== by 0x5598B65MPID_nem_init (mpid_nem_init.c:489)
+ ==30166== by 0x539BD75MPIDI_CH3_Init (ch3_init.c:64)
+ ==30166== by 0x5578743MPID_Init (mpid_init.c:193)
+ ==30166== by 0x554650AMPIR_Init_thread (initthread.c:539)
+ ==30166== by 0x553369FPMPI_Init (init.c:195)
+ ==30166== by 0x4008BDmain (valgrind-example-mpi.c:18)
+so it is better to use the MPI-enabled valgrind from module. The MPI
+version requires library <span
+class="monospace">/apps/tools/valgrind/3.9.0/impi/lib/valgrind/libmpiwrap-amd64-linux.so</span>,
+which must be included in the<span class="monospace"> LD_PRELOAD
+</span>environment variable.
+Lets look at this MPI example :
+ #include <stdlib.h>
+ #include <mpi.h>Â
+ int main(int argc, char *argv[])
+ {
+ Â Â Â Â Â int *data = malloc(sizeof(int)*99);
+ Â Â Â Â Â MPI_Init(&argc, &argv);
+ Â Â Â Â MPI_Bcast(data, 100, MPI_INT, 0, MPI_COMM_WORLD);
+ Â Â Â Â Â MPI_Finalize();Â
+ Â Â Â Â Â Â Â return 0;
+ }
+There are two errors - use of uninitialized memory and invalid length of
+the buffer. Lets debug it with valgrind :
+ $ module add intel impi
+ $ mpicc -g valgrind-example-mpi.c -o valgrind-example-mpi
+ $ module add valgrind/3.9.0-impi
+ $ mpirun -np 2 -env LD_PRELOAD /apps/tools/valgrind/3.9.0/impi/lib/valgrind/libmpiwrap-amd64-linux.so valgrind ./valgrind-example-mpi
+Prints this output (note that there is output printed for every
+launched MPI process)
+ ==31318== Memcheck, a memory error detector
+ ==31318== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
+ ==31318== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info
+ ==31318== Command./valgrind-example-mpi
+ ==31318==
+ ==31319== Memcheck, a memory error detector
+ ==31319== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
+ ==31319== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info
+ ==31319== Command./valgrind-example-mpi
+ ==31319==
+ valgrind MPI wrappers 31319Active for pid 31319
+ valgrind MPI wrappers 31319Try MPIWRAP_DEBUG=help for possible options
+ valgrind MPI wrappers 31318Active for pid 31318
+ valgrind MPI wrappers 31318Try MPIWRAP_DEBUG=help for possible options
+ ==31319== Unaddressable byte(s) found during client check request
+ ==31319== at 0x4E35974check_mem_is_addressable_untyped (libmpiwrap.c:960)
+ ==31319== by 0x4E5D0FEPMPI_Bcast (libmpiwrap.c:908)
+ ==31319== by 0x400911main (valgrind-example-mpi.c:20)
+ ==31319== Address 0x69291cc is 0 bytes after a block of size 396 alloc'd
+ ==31319== at 0x4C27AAAmalloc (vg_replace_malloc.c:291)
+ ==31319== by 0x4007BCmain (valgrind-example-mpi.c:8)
+ ==31319==
+ ==31318== Uninitialised byte(s) found during client check request
+ ==31318== at 0x4E3591Dcheck_mem_is_defined_untyped (libmpiwrap.c:952)
+ ==31318== by 0x4E5D06DPMPI_Bcast (libmpiwrap.c:908)
+ ==31318== by 0x400911main (valgrind-example-mpi.c:20)
+ ==31318== Address 0x6929040 is 0 bytes inside a block of size 396 alloc'd
+ ==31318== at 0x4C27AAAmalloc (vg_replace_malloc.c:291)
+ ==31318== by 0x4007BCmain (valgrind-example-mpi.c:8)
+ ==31318==
+ ==31318== Unaddressable byte(s) found during client check request
+ ==31318== at 0x4E3591Dcheck_mem_is_defined_untyped (libmpiwrap.c:952)
+ ==31318== by 0x4E5D06DPMPI_Bcast (libmpiwrap.c:908)
+ ==31318== by 0x400911main (valgrind-example-mpi.c:20)
+ ==31318== Address 0x69291cc is 0 bytes after a block of size 396 alloc'd
+ ==31318== at 0x4C27AAAmalloc (vg_replace_malloc.c:291)
+ ==31318== by 0x4007BCmain (valgrind-example-mpi.c:8)
+ ==31318==
+ ==31318==
+ ==31318== HEAP SUMMARY:
+ ==31318== in use at exit3,172 bytes in 67 blocks
+ ==31318== total heap usage191 allocs, 124 frees, 81,203 bytes allocated
+ ==31318==
+ ==31319==
+ ==31319== HEAP SUMMARY:
+ ==31319== in use at exit3,172 bytes in 67 blocks
+ ==31319== total heap usage175 allocs, 108 frees, 48,435 bytes allocated
+ ==31319==
+ ==31318== LEAK SUMMARY:
+ ==31318== definitely lost408 bytes in 3 blocks
+ ==31318== indirectly lost256 bytes in 1 blocks
+ ==31318== possibly lost0 bytes in 0 blocks
+ ==31318== still reachable2,508 bytes in 63 blocks
+ ==31318== suppressed0 bytes in 0 blocks
+ ==31318== Rerun with --leak-check=full to see details of leaked memory
+ ==31318==
+ ==31318== For counts of detected and suppressed errors, rerun with-v
+ ==31318== Use --track-origins=yes to see where uninitialised values come from
+ ==31318== ERROR SUMMARY2 errors from 2 contexts (suppressed4 from 4)
+ ==31319== LEAK SUMMARY:
+ ==31319== definitely lost408 bytes in 3 blocks
+ ==31319== indirectly lost256 bytes in 1 blocks
+ ==31319== possibly lost0 bytes in 0 blocks
+ ==31319== still reachable2,508 bytes in 63 blocks
+ ==31319== suppressed0 bytes in 0 blocks
+ ==31319== Rerun with --leak-check=full to see details of leaked memory
+ ==31319==
+ ==31319== For counts of detected and suppressed errors, rerun with-v
+ ==31319== ERROR SUMMARY1 errors from 1 contexts (suppressed4 from 4)
+We can see that Valgrind has reported use of unitialised memory on the
+master process (which reads the array to be broadcasted) and use of
+unaddresable memory on both processes.
diff --git a/anselm-cluster-documentation/software/debuggers/vampir.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.html
old mode 100755
new mode 100644
similarity index 60%
rename from anselm-cluster-documentation/software/debuggers/vampir.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.html
index 11715e4d49add8b37c2d17caea6e35ad151da85e..d7e62bf19fb85b7624e4d9bf66b99c4b560df86e
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Vampir — IT4I Docs</title>
- <link rel="canonical" href="vampir.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="vampir.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="vampir.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../debuggers.html">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">Debuggers and profilers</a>
<span class="breadcrumbSeparator">
/
@@ -246,8 +243,8 @@
<div id="parent-fieldname-text-f6e25102d1244fb4ab355175867747b5" class="">
- <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a target="_self" title="" class="internal-link" href="../../../acl_users/credentials_cookie_auth/require_loginc71d.html">Score-P</a>) first to collect the traces.</p>
-<h2 class=" "><img title="Vampir screenshot" class="image-inline" alt="Vampir screenshot" src="../../../salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/%40%40images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
+ <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
+<h2 class=" "><img alt="Vampir screenshot" class="image-inline" title="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
<h2 class=" ">Installed versions</h2>
<p>Version 8.5.0 is currently installed as module <span class="monospace">Vampir/8.5.0</span> :</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir &</pre>
@@ -255,7 +252,7 @@
<p>You can find the detailed user manual in PDF format in <span class="monospace">$EBROOTVAMPIR/doc/vampir-manual.pdf</span></p>
<h2>References</h2>
<ol>
-<li><a class="external-link" href="https://www.vampir.eu/" target="_self" title="">https://www.vampir.eu</a></li>
+<li><a class="external-link" href="https://www.vampir.eu" target="_self" title="">https://www.vampir.eu</a></li>
</ol>
</div>
@@ -332,7 +329,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -348,7 +345,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
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-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
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- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
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- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -575,7 +572,7 @@
- <a title="A collection of development tools" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
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- <a title="" class="state-published contenttype-document" href="allinea-ddt.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
@@ -607,7 +604,7 @@
- <a title="quick application profiling" class="state-published contenttype-document" href="allinea-performance-reports.html">
+ <a class="state-published contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -623,7 +620,7 @@
- <a title="" class="state-published contenttype-document" href="cube.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube">
<span>CUBE</span>
</a>
@@ -639,7 +636,7 @@
- <a title="" class="state-published contenttype-document" href="intel-performance-counter-monitor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor">
<span>Intel Performance Counter Monitor</span>
</a>
@@ -655,7 +652,7 @@
- <a title="" class="state-published contenttype-document" href="intel-vtune-amplifier.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier</span>
</a>
@@ -671,7 +668,7 @@
- <a title="" class="state-published contenttype-document" href="papi.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi">
<span>PAPI</span>
</a>
@@ -687,7 +684,7 @@
- <a title="" class="state-published contenttype-document" href="scalasca.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca">
<span>Scalasca</span>
</a>
@@ -703,7 +700,7 @@
- <a title="" class="state-published contenttype-document" href="score-p.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p">
<span>Score-P</span>
</a>
@@ -719,7 +716,7 @@
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published contenttype-document" href="total-view.html">
+ <a class="state-published contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -735,7 +732,7 @@
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -751,7 +748,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="vampir.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -776,7 +773,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -792,7 +789,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -808,7 +805,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -824,7 +821,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -840,7 +837,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -856,7 +853,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -872,7 +869,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -888,7 +885,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -904,7 +901,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -920,7 +917,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -936,7 +933,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -952,7 +949,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -968,7 +965,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -984,7 +981,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1000,7 +997,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1016,7 +1013,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1041,7 +1038,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1057,7 +1054,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1082,7 +1079,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1098,7 +1095,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1114,7 +1111,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1203,7 +1200,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.md
new file mode 100644
index 0000000000000000000000000000000000000000..15d35afbb16fa342102847726baf14e7d1dd8f70
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.md
@@ -0,0 +1,23 @@
+Vampir
+======
+Vampir is a commercial trace analysis and visualisation tool. It can
+work with traces in OTF and OTF2 formats. It does not have the
+functionality to collect traces, you need to use a trace collection tool
+(such
+as [Score-P](https://docs.it4i.cz/salomon/software/debuggers/score-p))
+first to collect the traces.
+
+------
+Installed versions
+------------------
+Version 8.5.0 is currently installed as module <span
+class="monospace">Vampir/8.5.0</span>Â :
+ $ module load Vampir/8.5.0
+ $ vampir &
+User manual
+-----------
+You can find the detailed user manual in PDF format in <span
+class="monospace">$EBROOTVAMPIR/doc/vampir-manual.pdf</span>
+References
+----------
+1. <https://www.vampir.eu>
diff --git a/anselm-cluster-documentation/software/debuggers/vtune-amplifier/@@images/3d4533af-8ce5-4aed-9bac-09fbbcd2650a.png b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vtune-amplifier/@@images/3d4533af-8ce5-4aed-9bac-09fbbcd2650a.png
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rename from anselm-cluster-documentation/software/debuggers/vtune-amplifier/@@images/3d4533af-8ce5-4aed-9bac-09fbbcd2650a.png
rename to docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vtune-amplifier/@@images/3d4533af-8ce5-4aed-9bac-09fbbcd2650a.png
diff --git a/anselm-cluster-documentation/software/gpi2.html b/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.html
old mode 100755
new mode 100644
similarity index 69%
rename from anselm-cluster-documentation/software/gpi2.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/gpi2.html
index f51216bc575abe5a51f95a2fa0a355092aa56cfc..2579135b1faae5403455dbce3cc2bc14068c3c51
--- a/anselm-cluster-documentation/software/gpi2.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.html
@@ -10,45 +10,42 @@
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2" /><!--[if lt IE 7]></base><![endif]-->
<meta content="A library that implements the GASPI specification" name="description" />
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>GPI-2 — IT4I Docs</title>
- <link rel="canonical" href="gpi2.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="gpi2.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="gpi2.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -361,7 +358,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -377,7 +374,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -393,7 +390,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -409,7 +406,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -425,7 +422,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -441,7 +438,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -457,7 +454,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -473,7 +470,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -489,7 +486,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -505,7 +502,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -521,7 +518,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -537,7 +534,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -553,10 +550,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -572,7 +569,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -588,7 +585,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -604,7 +601,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -620,7 +617,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -636,7 +633,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -652,7 +649,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -668,7 +665,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -684,7 +681,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -700,7 +697,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -716,7 +713,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -732,7 +729,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -748,7 +745,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -764,7 +761,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -780,7 +777,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -796,7 +793,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -812,7 +809,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -828,7 +825,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -844,7 +841,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -860,7 +857,7 @@
- <a title="A library that implements the GASPI specification" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="gpi2.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -885,7 +882,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -901,7 +898,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -926,7 +923,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -942,7 +939,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -958,7 +955,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
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var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
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<!-- nagios_check_http_expect_string -->
@@ -1026,12 +1023,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
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<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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@@ -1047,7 +1044,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/anselm-cluster-documentation/software/gpi2.md b/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.md
similarity index 53%
rename from anselm-cluster-documentation/software/gpi2.md
rename to docs.it4i.cz/anselm-cluster-documentation/software/gpi2.md
index 9727c418dbc3d716712841571ac0ea0cf656197f..e4992de3684e26e66ead401dc1f46793f45441ad 100644
--- a/anselm-cluster-documentation/software/gpi2.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.md
@@ -1,23 +1,24 @@
+GPI-2
+=====
A library that implements the GASPI specification
-
-
+
Introduction
------------
-Programming Next Generation Supercomputers GPI-2 is an API library for
+Programming Next Generation SupercomputersGPI-2 is an API library for
asynchronous interprocess, cross-node communication. It provides a
flexible, scalable and fault tolerant interface for parallel
applications.
The GPI-2 library
-([www.gpi-site.com/gpi2/](http//www.gpi-site.com/gpi2/))
+([www.gpi-site.com/gpi2/](http://www.gpi-site.com/gpi2/))
implements the GASPI specification (Global Address Space Programming
Interface,
-[www.gaspi.de](http//www.gaspi.de/en/project.html)).
-GASPI is a Partitioned Global Address Space (PGAS) API. It aims at
+[www.gaspi.de](http://www.gaspi.de/en/project.html)).
+<span>GASPI is a Partitioned Global Address Space (PGAS) API. It aims at
scalable, flexible and failure tolerant computing in massively parallel
-environments.
+environments.</span>
Modules
-------
-The GPI-2, version 1.0.2 is available on Anselm via module gpi2
+The GPI-2, version 1.0.2 is available on Anselm via module gpi2:
$ module load gpi2
The module sets up environment variables, required for linking and
running GPI-2 enabled applications. This particular command loads the
@@ -37,22 +38,21 @@ infinband communication library ibverbs.
$ module load gpi2
$ gcc myprog.c -o myprog.x -Wl,-rpath=$LIBRARY_PATH -lGPI2 -libverbs
Running the GPI-2 codes
------------------------
-gaspi_run
+<span>gaspi_run</span>
gaspi_run starts the GPI-2 application
-The gaspi_run utility is used to start and run GPI-2 applications
+The gaspi_run utility is used to start and run GPI-2 applications:
$ gaspi_run -m machinefile ./myprog.x
A machine file (**machinefile**) with the hostnames of nodes where the
application will run, must be provided. The**** machinefile lists all
nodes on which to run, one entry per node per process. This file may be
-hand created or obtained from standard $PBS_NODEFILE
+hand created or obtained from standard $PBS_NODEFILE:
$ cut -f1 -d"." $PBS_NODEFILE > machinefile
-machinefile
+machinefile:
cn79
cn80
This machinefile will run 2 GPI-2 processes, one on node cn79 other on
node cn80.
-machinefle
+machinefle:
cn79
cn79
cn80
@@ -61,8 +61,8 @@ This machinefile will run 4 GPI-2 processes, 2 on node cn79 o 2 on node
cn80.
Use the **mpiprocs** to control how many GPI-2 processes will run per
node
-Example
- $ qsub -A OPEN-0-0 -q qexp -l select=2ncpus=16mpiprocs=16 -I
+Example:
+ $ qsub -A OPEN-0-0 -q qexp -l select=2:ncpus=16:mpiprocs=16 -I
This example will produce $PBS_NODEFILE with 16 entries per node.
### gaspi_logger
gaspi_logger views the output form GPI-2 application ranks
@@ -74,15 +74,15 @@ gaspi_printf(), will be redirected to the gaspi_logger. Other I/O
routines (e.g. printf) will not.
Example
-------
-Following is an example GPI-2 enabled code
- #include
- #include
+Following is an example GPI-2 enabled code:
+ #include <GASPI.h>
+ #include <stdlib.h>
void success_or_exit ( const char* file, const int line, const int ec)
{
if (ec != GASPI_SUCCESS)
{
- gaspi_printf ("Assertion failed in %s[%i]%dn", file, line, ec);
+ gaspi_printf ("Assertion failed in %s[%i]:%dn", file, line, ec);
exit (1);
}
}
@@ -109,88 +109,25 @@ Following is an example GPI-2 enabled code
return 0;
}
-Load modules and compile
+Load modules and compile:
$ module load gcc gpi2
$ gcc helloworld_gpi.c -o helloworld_gpi.x -Wl,-rpath=$LIBRARY_PATH -lGPI2 -libverbs
Submit the job and run the GPI-2 application
- $ qsub -q qexp -l select=2ncpus=1mpiprocs=1,place=scatter,walltime=000500 -I
- qsub waiting for job 171247.dm2 to start
- qsub job 171247.dm2 ready
+ $ qsub -q qexp -l select=2:ncpus=1:mpiprocs=1,place=scatter,walltime=00:05:00 -I
+ qsubwaiting for job 171247.dm2 to start
+ qsubjob 171247.dm2 ready
cn79 $ module load gpi2
cn79 $ cut -f1 -d"." $PBS_NODEFILE > machinefile
cn79 $ gaspi_run -m machinefile ./helloworld_gpi.x
Hello from rank 0 of 2
-At the same time, in another session, you may start the gaspi logger
+At the same time, in another session, you may start the gaspi logger:
$ ssh cn79
cn79 $ gaspi_logger
GASPI Logger (v1.1)
- [cn800] Hello from rank 1 of 2
+ [cn80:0] Hello from rank 1 of 2
In this example, we compile the helloworld_gpi.c code using the **gnu
compiler**Â (gcc) and link it to the GPI-2 and ibverbs library. The
library search path is compiled in. For execution, we use the qexp
queue, 2 nodes 1 core each. The GPI module must be loaded on the master
compute node (in this example the cn79), gaspi_logger is used from
different session to view the output of the second process.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
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- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
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- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
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-
- - [Network](../network.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
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-
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diff --git a/anselm-cluster-documentation/software/intel-suite.html b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite.html
old mode 100755
new mode 100644
similarity index 62%
rename from anselm-cluster-documentation/software/intel-suite.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/intel-suite.html
index 5752d9c3b6d2f46bc0a659be4ae4a59a6fa854e3..6329c24ae90c449b0f1ac7f140b39ff6d4f2f573
--- a/anselm-cluster-documentation/software/intel-suite.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite.html
@@ -10,45 +10,42 @@
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Intel Parallel Studio — IT4I Docs</title>
- <link rel="canonical" href="intel-suite.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="intel-suite.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="intel-suite.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -264,23 +261,23 @@
<h2 class=" ">Intel compilers</h2>
<p>The Intel compilers version 13.1.3 are available, via module intel. The compilers include the icc C and C++ compiler and the ifort fortran 77/90/95 compiler.</p>
<pre class=" ">$ module load intel<br />$ icc -v<br />$ ifort -v</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="intel-suite/intel-compilers.html">Intel Compilers</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers">Intel Compilers</a> page.</p>
<h2 class=" ">Intel debugger</h2>
-<p>Â The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a target="_self" title="" class="internal-link" href="intel-suite/resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html">X display</a> for running the GUI.</p>
+<p>Â The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">X display</a> for running the GUI.</p>
<pre class=" ">$ module load intel<br />$ idb</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="intel-suite/intel-debugger.html">Intel Debugger</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger">Intel Debugger</a> page.</p>
<h2 class=" ">Intel Math Kernel Library</h2>
<p>Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, extensively threaded and optimized for maximum performance. Intel MKL unites and provides these basic components: BLAS, LAPACK, ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and many more.</p>
<pre class=" ">$ module load mkl</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="intel-suite/intel-mkl.html">Intel MKL</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl">Intel MKL</a> page.</p>
<h2 class=" ">Intel Integrated Performance Primitives</h2>
<p>Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is available, via module ipp. The IPP is a library of highly optimized algorithmic building blocks for media and data applications. This includes signal, image and frame processing algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many more.</p>
<pre class=" ">$ module load ipp</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="intel-suite/intel-integrated-performance-primitives.html">Intel IPP</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives">Intel IPP</a> page.</p>
<h2 class=" ">Intel Threading Building Blocks</h2>
<p>Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. It is designed to promote scalable data parallel programming. Additionally, it fully supports nested parallelism, so you can build larger parallel components from smaller parallel components. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner.</p>
<pre class=" ">$ module load tbb</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="intel-suite/intel-tbb.html">Intel TBB</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb">Intel TBB</a> page.</p>
</div>
@@ -356,7 +353,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
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@@ -372,7 +369,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
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</a>
@@ -388,7 +385,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -404,7 +401,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
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</a>
@@ -420,7 +417,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -436,7 +433,7 @@
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<span>Hardware Overview</span>
</a>
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<span>Accessing the Cluster</span>
</a>
@@ -468,7 +465,7 @@
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<span>Environment and Modules</span>
</a>
@@ -484,7 +481,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -500,7 +497,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -516,7 +513,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -532,7 +529,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -548,10 +545,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -567,7 +564,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -583,7 +580,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -599,7 +596,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -615,7 +612,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -631,7 +628,7 @@
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+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -647,7 +644,7 @@
- <a title="" class="state-published contenttype-document" href="intel-suite/intel-compilers.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers">
<span>Intel Compilers</span>
</a>
@@ -663,7 +660,7 @@
- <a title="" class="state-published contenttype-document" href="intel-suite/intel-debugger.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger">
<span>Intel Debugger</span>
</a>
@@ -679,7 +676,7 @@
- <a title="" class="state-published contenttype-document" href="intel-suite/intel-mkl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl">
<span>Intel MKL</span>
</a>
@@ -695,7 +692,7 @@
- <a title="" class="state-published contenttype-document" href="intel-suite/intel-integrated-performance-primitives.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives">
<span>Intel IPP</span>
</a>
@@ -711,7 +708,7 @@
- <a title="" class="state-published contenttype-document" href="intel-suite/intel-tbb.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb">
<span>Intel TBB</span>
</a>
@@ -736,7 +733,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -752,7 +749,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -768,7 +765,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -784,7 +781,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -800,7 +797,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -816,7 +813,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -832,7 +829,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -848,7 +845,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -864,7 +861,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -880,7 +877,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -896,7 +893,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -912,7 +909,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -928,7 +925,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -944,7 +941,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -969,7 +966,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -985,7 +982,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1010,7 +1007,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1026,7 +1023,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1042,7 +1039,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
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})();
</script>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</div>
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-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/intel-suite by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:47 GMT -->
</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite.md b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite.md
new file mode 100644
index 0000000000000000000000000000000000000000..e387bae02e0c30aae5145d01995cb806bbeffb10
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite.md
@@ -0,0 +1,73 @@
+Intel Parallel Studio
+=====================
+
+The Anselm cluster provides following elements of the Intel Parallel
+Studio XE
+ Intel Parallel Studio XE
+ ---
+ Intel Compilers
+ Intel Debugger
+ Intel MKL Library
+ Intel Integrated Performance Primitives Library
+ Intel Threading Building Blocks Library
+Intel compilers
+---------------
+The Intel compilers version 13.1.3 are available, via module intel. The
+compilers include the icc C and C++ compiler and the ifort fortran
+77/90/95 compiler.
+ $ module load intel
+ $ icc -v
+ $ ifort -v
+Read more at the [Intel
+Compilers](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers)
+page.
+Intel debugger
+--------------
+Â The intel debugger version 13.0 is available, via module intel. The
+debugger works for applications compiled with C and C++ compiler and the
+ifort fortran 77/90/95 compiler. The debugger provides java GUI
+environment. Use [X
+display](resolveuid/11e53ad0d2fd4c5187537f4baeedff33)
+for running the GUI.
+ $ module load intel
+ $ idb
+Read more at the [Intel
+Debugger](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger)
+page.
+Intel Math Kernel Library
+--
+Intel Math Kernel Library (Intel MKL) is a library of math kernel
+subroutines, extensively threaded and optimized for maximum performance.
+Intel MKL unites and provides these basic componentsBLAS, LAPACK,
+ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and
+many more.
+ $ module load mkl
+Read more at the [Intel
+MKL](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl)
+page.
+Intel Integrated Performance Primitives
+----------------
+Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX
+is available, via module ipp. The IPP is a library of highly optimized
+algorithmic building blocks for media and data applications. This
+includes signal, image and frame processing algorithms, such as FFT,
+FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many
+more.
+ $ module load ipp
+Read more at the [Intel
+IPP](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives)
+page.
+Intel Threading Building Blocks
+--------
+Intel Threading Building Blocks (Intel TBB) is a library that supports
+scalable parallel programming using standard ISO C++ code. It does not
+require special languages or compilers. It is designed to promote
+scalable data parallel programming. Additionally, it fully supports
+nested parallelism, so you can build larger parallel components from
+smaller parallel components. To use the library, you specify tasks, not
+threads, and let the library map tasks onto threads in an efficient
+manner.
+ $ module load tbb
+Read more at the [Intel
+TBB](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb)
+page.
diff --git a/anselm-cluster-documentation/software/intel-suite/intel-compilers.html b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.html
old mode 100755
new mode 100644
similarity index 65%
rename from anselm-cluster-documentation/software/intel-suite/intel-compilers.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.html
index 61e0c7ec79f487e76310f69d8a07fff41a3ae55b..f58520b6571953090f46ef7e1a626769b180ed8f
--- a/anselm-cluster-documentation/software/intel-suite/intel-compilers.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.html
@@ -10,45 +10,42 @@
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<title>Intel Compilers — IT4I Docs</title>
- <link rel="canonical" href="intel-compilers.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers" />
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- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="intel-compilers.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="intel-compilers.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../intel-suite.html">Intel Parallel studio</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">Intel Parallel studio</a>
<span class="breadcrumbSeparator">
/
@@ -340,7 +337,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -356,7 +353,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -420,7 +417,7 @@
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<span>Hardware Overview</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -452,7 +449,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -468,7 +465,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -484,7 +481,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -500,7 +497,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -516,7 +513,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -532,10 +529,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -551,7 +548,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -567,7 +564,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -583,7 +580,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -599,7 +596,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -615,7 +612,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -631,7 +628,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="intel-compilers.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers">
<span>Intel Compilers</span>
</a>
@@ -647,7 +644,7 @@
- <a title="" class="state-published contenttype-document" href="intel-debugger.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger">
<span>Intel Debugger</span>
</a>
@@ -663,7 +660,7 @@
- <a title="" class="state-published contenttype-document" href="intel-mkl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl">
<span>Intel MKL</span>
</a>
@@ -679,7 +676,7 @@
- <a title="" class="state-published contenttype-document" href="intel-integrated-performance-primitives.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives">
<span>Intel IPP</span>
</a>
@@ -695,7 +692,7 @@
- <a title="" class="state-published contenttype-document" href="intel-tbb.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb">
<span>Intel TBB</span>
</a>
@@ -720,7 +717,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -736,7 +733,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -752,7 +749,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -768,7 +765,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -784,7 +781,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -800,7 +797,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -816,7 +813,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -832,7 +829,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -848,7 +845,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -864,7 +861,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -880,7 +877,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -896,7 +893,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -912,7 +909,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -928,7 +925,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -953,7 +950,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -969,7 +966,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -994,7 +991,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1010,7 +1007,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1026,7 +1023,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
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})();
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.md b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.md
new file mode 100644
index 0000000000000000000000000000000000000000..67e32b6aaa6cf13e77d66f70e8f5ddd31aa92714
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.md
@@ -0,0 +1,52 @@
+Intel Compilers
+===============
+
+The Intel compilers version 13.1.1 are available, via module intel. The
+compilers include the icc C and C++ compiler and the ifort fortran
+77/90/95 compiler.
+ $ module load intel
+ $ icc -v
+ $ ifort -v
+The intel compilers provide for vectorization of the code, via the AVX
+instructions and support threading parallelization via OpenMP
+For maximum performance on the Anselm cluster, compile your programs
+using the AVX instructions, with reporting where the vectorization was
+used. We recommend following compilation options for high performance
+ $ icc -ipo -O3 -vec -xAVX -vec-report1 myprog.c mysubroutines.c -o myprog.x
+ $ ifort -ipo -O3 -vec -xAVX -vec-report1 myprog.f mysubroutines.f -o myprog.x
+In this example, we compile the program enabling interprocedural
+optimizations between source files (-ipo), aggresive loop optimizations
+(-O3) and vectorization (-vec -xAVX)
+The compiler recognizes the omp, simd, vector and ivdep pragmas for
+OpenMP parallelization and AVX vectorization. Enable the OpenMP
+parallelization by the **-openmp** compiler switch.
+ $ icc -ipo -O3 -vec -xAVX -vec-report1 -openmp myprog.c mysubroutines.c -o myprog.x
+ $ ifort -ipo -O3 -vec -xAVX -vec-report1 -openmp myprog.f mysubroutines.f -o myprog.x
+Read more at
+<http://software.intel.com/sites/products/documentation/doclib/stdxe/2013/composerxe/compiler/cpp-lin/index.htm>
+Sandy Bridge/Haswell binary compatibility
+------------------
+Anselm nodes are currently equipped with Sandy Bridge CPUs, while
+Salomon will use Haswell architecture. <span>The new processors are
+backward compatible with the Sandy Bridge nodes, so all programs that
+ran on the Sandy Bridge processors, should also run on the new Haswell
+nodes. </span><span>To get optimal performance out of the Haswell
+processors a program should make use of the special </span><span>AVX2
+instructions for this processor. One can do this by recompiling codes
+with the compiler flags </span><span>designated to invoke these
+instructions. For the Intel compiler suite, there are two ways of
+doing </span><span>this:</span>
+- <span>Using compiler flag (both for Fortran and C)<span
+ class="monospace">-xCORE-AVX2</span>. This will create a
+ binary </span><span class="s1">with AVX2 instructions, specifically
+ for the Haswell processors. Note that the
+ executable </span><span>will not run on Sandy Bridge nodes.</span>
+- <span>Using compiler flags (both for Fortran and C)<span
+ class="monospace">-xAVX -axCORE-AVX2</span>. This
+ will </span><span>generate multiple, feature specific auto-dispatch
+ code paths for Intel® processors, if there is </span><span>a
+ performance benefit. So this binary will run both on Sandy Bridge
+ and Haswell </span><span>processors. During runtime it will be
+ decided which path to follow, dependent on
+ which </span><span>processor you are running on. In general this
+ will result in larger binaries.</span>
diff --git a/anselm-cluster-documentation/software/intel-suite/intel-debugger.html b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger.html
old mode 100755
new mode 100644
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--- a/anselm-cluster-documentation/software/intel-suite/intel-debugger.html
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@@ -10,45 +10,42 @@
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<title>Intel Debugger — IT4I Docs</title>
- <link rel="canonical" href="intel-debugger.html" />
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- <a accesskey="2" href="intel-debugger.html#content">PĹ™ejĂt na obsah</a> |
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- <a accesskey="6" href="intel-debugger.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
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@@ -153,7 +150,7 @@
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">Intel Parallel studio</a>
<span class="breadcrumbSeparator">
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@@ -251,18 +248,18 @@
<div id="parent-fieldname-text-7bdfe159cf0b4b6891af3f8a7f2585c5" class="">
<h2 class=" ">Debugging serial applications</h2>
-<p>Â The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html">X display</a> for running the GUI.</p>
+<p>Â The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">X display</a> for running the GUI.</p>
<pre class=" ">$ module load intel<br />$ idb</pre>
<p>The debugger may run in text mode. To debug in text mode, use</p>
<pre class=" ">$ idbc</pre>
-<p>To debug on the compute nodes, module intel must be loaded. <br />The GUI on compute nodes may be accessed using the same way as in <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html">the GUI section </a></p>
+<p>To debug on the compute nodes, module intel must be loaded. <br />The GUI on compute nodes may be accessed using the same way as in <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">the GUI section </a></p>
<p>Example:</p>
<pre class=" ">$ qsub -q qexp -l select=1:ncpus=16 -X -I<br />qsub: waiting for job 19654.srv11 to start<br />qsub: job 19654.srv11 ready<br /><br />$ module load intel<br />$ module load java<br />$ icc -O0 -g myprog.c -o myprog.x<br />$ idb ./myprog.x</pre>
<p>In this example, we allocate 1 full compute node, compile program myprog.c with debugging options -O0 -g and run the idb debugger interactively on the myprog.x executable. The GUI access is via X11 port forwarding provided by the PBS workload manager.</p>
<h2 class=" ">Debugging parallel applications</h2>
<p>Intel debugger is capable of debugging multithreaded and MPI parallel programs as well.</p>
<h3 class=" ">Small number of MPI ranks</h3>
-<p>For debugging small number of MPI ranks, you may execute and debug each rank in separate xterm terminal (do not forget the <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html">X display</a>). Using Intel MPI, this may be done in following way:</p>
+<p>For debugging small number of MPI ranks, you may execute and debug each rank in separate xterm terminal (do not forget the <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">X display</a>). Using Intel MPI, this may be done in following way:</p>
<pre class=" ">$ qsub -q qexp -l select=2:ncpus=16 -X -I<br />qsub: waiting for job 19654.srv11 to start<br />qsub: job 19655.srv11 ready<br /><br />$ module load intel impi<br />$ mpirun -ppn 1 -hostfile $PBS_NODEFILE --enable-x xterm -e idbc ./mympiprog.x</pre>
<p>In this example, we allocate 2 full compute node, run xterm on each node and start idb debugger in command line mode, debugging two ranks of mympiprog.x application. The xterm will pop up for each rank, with idb prompt ready. The example is not limited to use of Intel MPI</p>
<h3 class=" ">Large number of MPI ranks</h3>
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<dt class="portletHeader hiddenStructure">
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+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
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</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
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</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
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-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
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- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
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- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
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- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
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- <a title="The Intel Parallel Studio XE" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
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- <a title="" class="state-published contenttype-document" href="intel-compilers.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers">
<span>Intel Compilers</span>
</a>
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- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="intel-debugger.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger">
<span>Intel Debugger</span>
</a>
@@ -670,7 +667,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl">
<span>Intel MKL</span>
</a>
@@ -686,7 +683,7 @@
- <a title="" class="state-published contenttype-document" href="intel-integrated-performance-primitives.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives">
<span>Intel IPP</span>
</a>
@@ -702,7 +699,7 @@
- <a title="" class="state-published contenttype-document" href="intel-tbb.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb">
<span>Intel TBB</span>
</a>
@@ -727,7 +724,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -743,7 +740,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -759,7 +756,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -775,7 +772,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -791,7 +788,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -807,7 +804,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -823,7 +820,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -839,7 +836,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -855,7 +852,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -871,7 +868,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -887,7 +884,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -903,7 +900,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -919,7 +916,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -935,7 +932,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -960,7 +957,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -976,7 +973,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1001,7 +998,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1017,7 +1014,7 @@
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+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1033,7 +1030,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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})();
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-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger.md b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger.md
new file mode 100644
index 0000000000000000000000000000000000000000..ce6bd5acf2a3efc049b1336fc2e191e7f5815e49
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger.md
@@ -0,0 +1,70 @@
+Intel Debugger
+==============
+
+Debugging serial applications
+------
+Â The intel debugger version 13.0 is available, via module intel. The
+debugger works for applications compiled with C and C++ compiler and the
+ifort fortran 77/90/95 compiler. The debugger provides java GUI
+environment. Use [X
+display](resolveuid/11e53ad0d2fd4c5187537f4baeedff33)
+for running the GUI.
+ $ module load intel
+ $ idb
+The debugger may run in text mode. To debug in text mode, use
+ $ idbc
+To debug on the compute nodes, module intel must be loaded.
+The GUI on compute nodes may be accessed using the same way as in [the
+GUI
+section](resolveuid/11e53ad0d2fd4c5187537f4baeedff33)
+Example:
+ $ qsub -q qexp -l select=1:ncpus=16 -X -I
+ qsubwaiting for job 19654.srv11 to start
+ qsubjob 19654.srv11 ready
+ $ module load intel
+ $ module load java
+ $ icc -O0 -g myprog.c -o myprog.x
+ $ idb ./myprog.x
+In this example, we allocate 1 full compute node, compile program
+myprog.c with debugging options -O0 -g and run the idb debugger
+interactively on the myprog.x executable. The GUI access is via X11 port
+forwarding provided by the PBS workload manager.
+Debugging parallel applications
+--------
+Intel debugger is capable of debugging multithreaded and MPI parallel
+programs as well.
+### Small number of MPI ranks
+For debugging small number of MPI ranks, you may execute and debug each
+rank in separate xterm terminal (do not forget the [X
+display](resolveuid/11e53ad0d2fd4c5187537f4baeedff33)).
+Using Intel MPI, this may be done in following way:
+ $ qsub -q qexp -l select=2:ncpus=16 -X -I
+ qsubwaiting for job 19654.srv11 to start
+ qsubjob 19655.srv11 ready
+ $ module load intel impi
+ $ mpirun -ppn 1 -hostfile $PBS_NODEFILE --enable-x xterm -e idbc ./mympiprog.x
+In this example, we allocate 2 full compute node, run xterm on each node
+and start idb debugger in command line mode, debugging two ranks of
+mympiprog.x application. The xterm will pop up for each rank, with idb
+prompt ready. The example is not limited to use of Intel MPI
+### Large number of MPI ranks
+Run the idb debugger from within the MPI debug option. This will cause
+the debugger to bind to all ranks and provide aggregated outputs across
+the ranks, pausing execution automatically just after startup. You may
+then set break points and step the execution manually. Using Intel MPI:
+ $ qsub -q qexp -l select=2:ncpus=16 -X -I
+ qsubwaiting for job 19654.srv11 to start
+ qsubjob 19655.srv11 ready
+ $ module load intel impi
+ $ mpirun -n 32 -idb ./mympiprog.x
+### Debugging multithreaded application
+Run the idb debugger in GUI mode. The menu Parallel contains number of
+tools for debugging multiple threads. One of the most useful tools is
+the **Serialize Execution** tool, which serializes execution of
+concurrent threads for easy orientation and identification of
+concurrency related bugs.
+Further information
+-------------------
+Exhaustive manual on idb features and usage is published at Intel
+website,
+<http://software.intel.com/sites/products/documentation/doclib/stdxe/2013/composerxe/debugger/user_guide/index.htm>
diff --git a/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.html b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.html
old mode 100755
new mode 100644
similarity index 66%
rename from anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.html
index a6b60e77b224a659ccefa5e36abbbbe6deba3605..a44c826f5c2f455a7ff6a75238b7d84e1579f761
--- a/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.html
@@ -10,45 +10,42 @@
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives" /><!--[if lt IE 7]></base><![endif]-->
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<title>Intel IPP — IT4I Docs</title>
- <link rel="canonical" href="intel-integrated-performance-primitives.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="intel-integrated-performance-primitives.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="intel-integrated-performance-primitives.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
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- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../intel-suite.html">Intel Parallel studio</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">Intel Parallel studio</a>
<span class="breadcrumbSeparator">
/
@@ -339,7 +336,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -355,7 +352,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -387,7 +384,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -403,7 +400,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -419,7 +416,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -435,7 +432,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -451,7 +448,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -467,7 +464,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -483,7 +480,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
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- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -550,7 +547,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -566,7 +563,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -582,7 +579,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -598,7 +595,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -614,7 +611,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -630,7 +627,7 @@
- <a title="" class="state-published contenttype-document" href="intel-compilers.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers">
<span>Intel Compilers</span>
</a>
@@ -646,7 +643,7 @@
- <a title="" class="state-published contenttype-document" href="intel-debugger.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger">
<span>Intel Debugger</span>
</a>
@@ -662,7 +659,7 @@
- <a title="" class="state-published contenttype-document" href="intel-mkl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl">
<span>Intel MKL</span>
</a>
@@ -678,7 +675,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="intel-integrated-performance-primitives.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives">
<span>Intel IPP</span>
</a>
@@ -694,7 +691,7 @@
- <a title="" class="state-published contenttype-document" href="intel-tbb.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb">
<span>Intel TBB</span>
</a>
@@ -719,7 +716,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -735,7 +732,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -751,7 +748,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -767,7 +764,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -783,7 +780,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -799,7 +796,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -815,7 +812,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -831,7 +828,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -847,7 +844,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -863,7 +860,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -879,7 +876,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -895,7 +892,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -911,7 +908,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -927,7 +924,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -952,7 +949,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -968,7 +965,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -993,7 +990,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1009,7 +1006,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1025,7 +1022,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
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-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</div>
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-
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
new file mode 100644
index 0000000000000000000000000000000000000000..4f2eeb0c93cb6fb9b81311703649b2f3c7f0ede8
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
@@ -0,0 +1,72 @@
+Intel IPP
+=========
+
+Intel Integrated Performance Primitives
+----------------
+Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX
+vector instructions is available, via module ipp. The IPP is a very rich
+library of highly optimized algorithmic building blocks for media and
+data applications. This includes signal, image and frame processing
+algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough
+transform, Sum, MinMax, as well as cryptographic functions, linear
+algebra functions and many more.
+Check out IPP before implementing own math functions for data
+processing, it is likely already there.
+ $ module load ipp
+The module sets up environment variables, required for linking and
+running ipp enabled applications.
+IPP example
+-----------
+ #include "ipp.h"
+ #include <stdio.h>
+ int main(int argc, char* argv[])
+ {
+ const IppLibraryVersion *lib;
+ Ipp64u fm;
+ IppStatus status;
+ status= ippInit(); //IPP initialization with the best optimization layer
+ if( status != ippStsNoErr ) {
+ printf("IppInit() Error:n");
+ printf("%sn", ippGetStatusString(status) );
+ return -1;
+ }
+ //Get version info
+ lib = ippiGetLibVersion();
+ printf("%s %sn", lib->Name, lib->Version);
+ //Get CPU features enabled with selected library level
+ fm=ippGetEnabledCpuFeatures();
+ printf("SSE :%cn",(fm>>1)&1?'Y':'N');
+ printf("SSE2 :%cn",(fm>>2)&1?'Y':'N');
+ printf("SSE3 :%cn",(fm>>3)&1?'Y':'N');
+ printf("SSSE3 :%cn",(fm>>4)&1?'Y':'N');
+ printf("SSE41 :%cn",(fm>>6)&1?'Y':'N');
+ printf("SSE42 :%cn",(fm>>7)&1?'Y':'N');
+ printf("AVX :%cn",(fm>>8)&1 ?'Y':'N');
+ printf("AVX2 :%cn", (fm>>15)&1 ?'Y':'N' );
+ printf("----------n");
+ printf("OS Enabled AVX :%cn", (fm>>9)&1 ?'Y':'N');
+ printf("AES :%cn", (fm>>10)&1?'Y':'N');
+ printf("CLMUL :%cn", (fm>>11)&1?'Y':'N');
+ printf("RDRAND :%cn", (fm>>13)&1?'Y':'N');
+ printf("F16C :%cn", (fm>>14)&1?'Y':'N');
+ return 0;
+ }
+Â Compile above example, using any compiler and the ipp module.
+ $ module load intel
+ $ module load ipp
+ $ icc testipp.c -o testipp.x -lippi -lipps -lippcore
+You will need the ipp module loaded to run the ipp enabled executable.
+This may be avoided, by compiling library search paths into the
+executable
+ $ module load intel
+ $ module load ipp
+ $ icc testipp.c -o testipp.x -Wl,-rpath=$LIBRARY_PATH -lippi -lipps -lippcore
+Code samples and documentation
+-------
+Intel provides number of [Code Samples for
+IPP](https://software.intel.com/en-us/articles/code-samples-for-intel-integrated-performance-primitives-library),
+illustrating use of IPP.
+Read full documentation on IPP [on Intel
+website,](http://software.intel.com/sites/products/search/search.php?q=&x=15&y=6&product=ipp&version=7.1&docos=lin)
+in particular the [IPP Reference
+manual.](http://software.intel.com/sites/products/documentation/doclib/ipp_sa/71/ipp_manual/index.htm)
diff --git a/anselm-cluster-documentation/software/intel-suite/intel-mkl.html b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.html
old mode 100755
new mode 100644
similarity index 68%
rename from anselm-cluster-documentation/software/intel-suite/intel-mkl.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.html
index 429bdbce8bb94e4a6aa9f5e654b16c32d853b14f..18453cf153735c0ce6af2663362c9aba8b9adb86
--- a/anselm-cluster-documentation/software/intel-suite/intel-mkl.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.html
@@ -10,45 +10,42 @@
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl" /><!--[if lt IE 7]></base><![endif]-->
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<title>Intel MKL — IT4I Docs</title>
- <link rel="canonical" href="intel-mkl.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="intel-mkl.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="intel-mkl.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
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@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
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@@ -163,7 +160,7 @@
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<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
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@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../intel-suite.html">Intel Parallel studio</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">Intel Parallel studio</a>
<span class="breadcrumbSeparator">
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@@ -308,7 +305,7 @@
<pre class=" ">$ module load gcc<br />$ module load mkl<br />$ cp -a $MKL_EXAMPLES/cblas /tmp/<br />$ cd /tmp/cblas<br /> <br />$ gcc -w source/cblas_dgemmx.c source/common_func.c -o cblas_dgemmx.x \<br />-lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lm<br /><br />$ ./cblas_dgemmx.x data/cblas_dgemmx.d</pre>
<p>In this example, we compile, link and run the cblas_dgemm example, using LP64 interface to threaded MKL and gnu OMP threads implementation.</p>
<h2 class=" ">MKL and MIC accelerators</h2>
-<p>The MKL is capable to automatically offload the computations o the MIC accelerator. See section <a target="_self" title="" class="internal-link" href="../intel-xeon-phi.html">Intel Xeon Phi</a> for details.</p>
+<p>The MKL is capable to automatically offload the computations o the MIC accelerator. See section <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">Intel Xeon Phi</a> for details.</p>
<h2 class=" ">Further reading</h2>
<p>Read more on <a class="external-link" href="http://software.intel.com/en-us/intel-mkl" target="_self" title="">Intel website</a>, in particular the <a class="external-link" href="https://software.intel.com/en-us/intel-mkl/documentation/linux" target="_self" title="">MKL users guide</a>.</p>
@@ -386,7 +383,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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@@ -402,7 +399,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
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</a>
@@ -418,7 +415,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -434,7 +431,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -450,7 +447,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
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</a>
@@ -466,7 +463,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -482,7 +479,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -498,7 +495,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -514,7 +511,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -530,7 +527,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -546,7 +543,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -562,7 +559,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -578,10 +575,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -597,7 +594,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -613,7 +610,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -629,7 +626,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -645,7 +642,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -661,7 +658,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -677,7 +674,7 @@
- <a title="" class="state-published contenttype-document" href="intel-compilers.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers">
<span>Intel Compilers</span>
</a>
@@ -693,7 +690,7 @@
- <a title="" class="state-published contenttype-document" href="intel-debugger.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger">
<span>Intel Debugger</span>
</a>
@@ -709,7 +706,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="intel-mkl.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl">
<span>Intel MKL</span>
</a>
@@ -725,7 +722,7 @@
- <a title="" class="state-published contenttype-document" href="intel-integrated-performance-primitives.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives">
<span>Intel IPP</span>
</a>
@@ -741,7 +738,7 @@
- <a title="" class="state-published contenttype-document" href="intel-tbb.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb">
<span>Intel TBB</span>
</a>
@@ -766,7 +763,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -782,7 +779,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -798,7 +795,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -814,7 +811,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -830,7 +827,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -846,7 +843,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -862,7 +859,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -878,7 +875,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -894,7 +891,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -910,7 +907,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -926,7 +923,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -942,7 +939,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -958,7 +955,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -974,7 +971,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -999,7 +996,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1015,7 +1012,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1040,7 +1037,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1056,7 +1053,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1072,7 +1069,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1111,14 +1108,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1140,12 +1137,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1161,7 +1158,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:37 GMT -->
</html>
diff --git a/anselm-cluster-documentation/software/intel-suite/intel-mkl.md b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.md
similarity index 57%
rename from anselm-cluster-documentation/software/intel-suite/intel-mkl.md
rename to docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.md
index d0f4f8142bafc7b75e3f93bccc070fc7d2f65123..ea084f26977a515c746dd04567da9540d28d6c6d 100644
--- a/anselm-cluster-documentation/software/intel-suite/intel-mkl.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.md
@@ -1,45 +1,44 @@
Intel MKL
=========
-
-
+
Intel Math Kernel Library
--------------------------
+--
Intel Math Kernel Library (Intel MKL) is a library of math kernel
subroutines, extensively threaded and optimized for maximum performance.
-Intel MKL provides these basic math kernels
+Intel MKL provides these basic math kernels:
[]()
--
+- <div id="d4841e18">
[]()BLAS (level 1, 2, and 3) and LAPACK linear algebra routines,
offering vector, vector-matrix, and matrix-matrix operations.
--
+- <div id="d4841e21">
[]()The PARDISO direct sparse solver, an iterative sparse solver,
and supporting sparse BLAS (level 1, 2, and 3) routines for solving
sparse systems of equations.
--
+- <div id="d4841e24">
[]()ScaLAPACK distributed processing linear algebra routines for
Linux* and Windows* operating systems, as well as the Basic Linear
Algebra Communications Subprograms (BLACS) and the Parallel Basic
Linear Algebra Subprograms (PBLAS).
--
+- <div id="d4841e27">
[]()Fast Fourier transform (FFT) functions in one, two, or three
dimensions with support for mixed radices (not limited to sizes that
are powers of 2), as well as distributed versions of
these functions.
--
+- <div id="d4841e30">
[]()Vector Math Library (VML) routines for optimized mathematical
operations on vectors.
--
+- <div id="d4841e34">
[]()Vector Statistical Library (VSL) routines, which offer
high-performance vectorized random number generators (RNG) for
several probability distributions, convolution and correlation
routines, and summary statistics functions.
--
+- <div id="d4841e37">
[]()Data Fitting Library, which provides capabilities for
spline-based approximation of functions, derivatives and integrals
@@ -47,7 +46,7 @@ Intel MKL provides these basic math kernels
- Extended Eigensolver, a shared memory version of an eigensolver
based on the Feast Eigenvalue Solver.
For details see the [Intel MKL Reference
-Manual](http//software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mklman/index.htm).
+Manual](http://software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mklman/index.htm).
Intel MKL version 13.5.192 is available on Anselm
$ module load mkl
The module sets up environment variables, required for linking and
@@ -62,16 +61,16 @@ type (necessary for indexing large arrays, with more than 2^31^-1
elements), whereas the LP64 libraries index arrays with the 32-bit
integer type.
Interface Integer type
- ----------- -----------------------------------------------
+ ----------- -
LP64 32-bit, int, integer(kind=4), MPI_INT
ILP64 64-bit, long int, integer(kind=8), MPI_INT64
### Linking
Linking MKL libraries may be complex. Intel [mkl link line
-advisor](http//software.intel.com/en-us/articles/intel-mkl-link-line-advisor)
+advisor](http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor)
helps. See also [examples](#examples) below.
You will need the mkl module loaded to run the mkl enabled executable.
This may be avoided, by compiling library search paths into the
-executable. Include rpath on the compile line
+executable. Include rpath on the compile line:
$ icc .... -Wl,-rpath=$LIBRARY_PATH ...
### Threading
Advantage in using the MKL library is that it brings threaded
@@ -98,7 +97,7 @@ program for multi-threaded matrix multiplication.
$ make sointel64 function=cblas_dgemm
In this example, we compile, link and run the cblas_dgemm example,
demonstrating use of MKL example suite installed on Anselm.
-### Example MKL and Intel compiler
+### ExampleMKL and Intel compiler
$ module load intel
$ module load mkl
$ cp -a $MKL_EXAMPLES/cblas /tmp/
@@ -108,12 +107,12 @@ demonstrating use of MKL example suite installed on Anselm.
$ ./cblas_dgemmx.x data/cblas_dgemmx.d
In this example, we compile, link and run the cblas_dgemm example,
demonstrating use of MKL with icc -mkl option. Using the -mkl option is
-equivalent to
+equivalent to:
$ icc -w source/cblas_dgemmx.c source/common_func.c -o cblas_dgemmx.x
-I$MKL_INC_DIR -L$MKL_LIB_DIR -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5
In this example, we compile and link the cblas_dgemm example, using
LP64 interface to threaded MKL and Intel OMP threads implementation.
-### Example MKL and GNU compiler
+### ExampleMKL and GNU compiler
$ module load gcc
$ module load mkl
$ cp -a $MKL_EXAMPLES/cblas /tmp/
@@ -125,93 +124,14 @@ LP64 interface to threaded MKL and Intel OMP threads implementation.
In this example, we compile, link and run the cblas_dgemm example,
using LP64 interface to threaded MKL and gnu OMP threads implementation.
MKL and MIC accelerators
-------------------------
+-
The MKL is capable to automatically offload the computations o the MIC
accelerator. See section [Intel Xeon
-Phi](../intel-xeon-phi.html) for details.
+Phi](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi)
+for details.
Further reading
---------------
Read more on [Intel
-website](http//software.intel.com/en-us/intel-mkl), in
+website](http://software.intel.com/en-us/intel-mkl), in
particular the [MKL users
-guide](https//software.intel.com/en-us/intel-mkl/documentation/linux).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
- .navTreeFolderish
- .contenttype-folder}
- - [Intel
- Compilers](intel-compilers.html)
-
- - [Intel
- Debugger](intel-debugger.html)
-
- - [Intel
- MKL](intel-mkl.html)
-
-
- - [Intel
- IPP](intel-integrated-performance-primitives.html)
-
- - [Intel
- TBB](intel-tbb.html)
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
+guide](https://software.intel.com/en-us/intel-mkl/documentation/linux).
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.html b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.html
new file mode 100644
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--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.html
@@ -0,0 +1,1132 @@
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+
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+ <p>The Anselm cluster provides following elements of the Intel Parallel Studio XE</p>
+<table class="listing">
+<tbody>
+<tr><th>Intel Parallel Studio XE</th></tr>
+<tr class="even">
+<td>Intel Compilers</td>
+</tr>
+<tr class="odd">
+<td>Intel Debugger</td>
+</tr>
+<tr class="even">
+<td>Intel MKL Library</td>
+</tr>
+<tr class="odd">
+<td>Intel Integrated Performance Primitives Library</td>
+</tr>
+<tr class="even">
+<td>Intel Threading Building Blocks Library</td>
+</tr>
+</tbody>
+</table>
+<h2 class=" ">Intel compilers</h2>
+<p>The Intel compilers version 13.1.3 are available, via module intel. The compilers include the icc C and C++ compiler and the ifort fortran 77/90/95 compiler.</p>
+<pre class=" ">$ module load intel<br />$ icc -v<br />$ ifort -v</pre>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers">Intel Compilers</a> page.</p>
+<h2 class=" ">Intel debugger</h2>
+<p>Â The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">X display</a> for running the GUI.</p>
+<pre class=" ">$ module load intel<br />$ idb</pre>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger">Intel Debugger</a> page.</p>
+<h2 class=" ">Intel Math Kernel Library</h2>
+<p>Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, extensively threaded and optimized for maximum performance. Intel MKL unites and provides these basic components: BLAS, LAPACK, ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and many more.</p>
+<pre class=" ">$ module load mkl</pre>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl">Intel MKL</a> page.</p>
+<h2 class=" ">Intel Integrated Performance Primitives</h2>
+<p>Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is available, via module ipp. The IPP is a library of highly optimized algorithmic building blocks for media and data applications. This includes signal, image and frame processing algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many more.</p>
+<pre class=" ">$ module load ipp</pre>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives">Intel IPP</a> page.</p>
+<h2 class=" ">Intel Threading Building Blocks</h2>
+<p>Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. It is designed to promote scalable data parallel programming. Additionally, it fully supports nested parallelism, so you can build larger parallel components from smaller parallel components. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner.</p>
+<pre class=" ">$ module load tbb</pre>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb">Intel TBB</a> page.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.md b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.md
new file mode 100644
index 0000000000000000000000000000000000000000..e387bae02e0c30aae5145d01995cb806bbeffb10
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.md
@@ -0,0 +1,73 @@
+Intel Parallel Studio
+=====================
+
+The Anselm cluster provides following elements of the Intel Parallel
+Studio XE
+ Intel Parallel Studio XE
+ ---
+ Intel Compilers
+ Intel Debugger
+ Intel MKL Library
+ Intel Integrated Performance Primitives Library
+ Intel Threading Building Blocks Library
+Intel compilers
+---------------
+The Intel compilers version 13.1.3 are available, via module intel. The
+compilers include the icc C and C++ compiler and the ifort fortran
+77/90/95 compiler.
+ $ module load intel
+ $ icc -v
+ $ ifort -v
+Read more at the [Intel
+Compilers](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers)
+page.
+Intel debugger
+--------------
+Â The intel debugger version 13.0 is available, via module intel. The
+debugger works for applications compiled with C and C++ compiler and the
+ifort fortran 77/90/95 compiler. The debugger provides java GUI
+environment. Use [X
+display](resolveuid/11e53ad0d2fd4c5187537f4baeedff33)
+for running the GUI.
+ $ module load intel
+ $ idb
+Read more at the [Intel
+Debugger](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger)
+page.
+Intel Math Kernel Library
+--
+Intel Math Kernel Library (Intel MKL) is a library of math kernel
+subroutines, extensively threaded and optimized for maximum performance.
+Intel MKL unites and provides these basic componentsBLAS, LAPACK,
+ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and
+many more.
+ $ module load mkl
+Read more at the [Intel
+MKL](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl)
+page.
+Intel Integrated Performance Primitives
+----------------
+Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX
+is available, via module ipp. The IPP is a library of highly optimized
+algorithmic building blocks for media and data applications. This
+includes signal, image and frame processing algorithms, such as FFT,
+FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many
+more.
+ $ module load ipp
+Read more at the [Intel
+IPP](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives)
+page.
+Intel Threading Building Blocks
+--------
+Intel Threading Building Blocks (Intel TBB) is a library that supports
+scalable parallel programming using standard ISO C++ code. It does not
+require special languages or compilers. It is designed to promote
+scalable data parallel programming. Additionally, it fully supports
+nested parallelism, so you can build larger parallel components from
+smaller parallel components. To use the library, you specify tasks, not
+threads, and let the library map tasks onto threads in an efficient
+manner.
+ $ module load tbb
+Read more at the [Intel
+TBB](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb)
+page.
diff --git a/anselm-cluster-documentation/software/intel-suite/intel-tbb.html b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb.html
old mode 100755
new mode 100644
similarity index 63%
rename from anselm-cluster-documentation/software/intel-suite/intel-tbb.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb.html
index b719d75e88b74086e24e335b3276e57880ba1ad7..51704cd9eb50e5fed3ab44f47a6e63cc99a02856
--- a/anselm-cluster-documentation/software/intel-suite/intel-tbb.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:37 GMT -->
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<title>Intel TBB — IT4I Docs</title>
- <link rel="canonical" href="intel-tbb.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
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+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
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@@ -64,7 +61,7 @@
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="intel-tbb.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="intel-tbb.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
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- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
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@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
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@@ -163,7 +160,7 @@
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
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@@ -173,7 +170,7 @@
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">Intel Parallel studio</a>
<span class="breadcrumbSeparator">
/
@@ -251,7 +248,7 @@
<div id="parent-fieldname-text-142d2895eb3b49e8bb0eb68c9b274ef6" class="">
<h2 class=" ">Intel Threading Building Blocks</h2>
-<p>Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner. The tasks are executed by a runtime scheduler and may be offloaded to <a target="_self" title="" class="internal-link" href="../intel-xeon-phi.html">MIC accelerator</a>.</p>
+<p>Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner. The tasks are executed by a runtime scheduler and may be offloaded to <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">MIC accelerator</a>.</p>
<p>Intel TBB version 4.1 is available on Anselm</p>
<pre class=" ">$ module load tbb</pre>
<p>The module sets up environment variables, required for linking and running tbb enabled applications.</p>
@@ -339,7 +336,7 @@
<dt class="portletHeader hiddenStructure">
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+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
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@@ -355,7 +352,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
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@@ -371,7 +368,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
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@@ -387,7 +384,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
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</a>
@@ -403,7 +400,7 @@
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+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -419,7 +416,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
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<span>Hardware Overview</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
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<span>Environment and Modules</span>
</a>
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<span>Resource Allocation and Job Execution</span>
</a>
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<span>Compute Nodes</span>
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<span>Storage</span>
</a>
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<span>Network</span>
</a>
@@ -531,10 +528,10 @@
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-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -550,7 +547,7 @@
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<span>ANSYS</span>
</a>
@@ -566,7 +563,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -582,7 +579,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -598,7 +595,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -614,7 +611,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -630,7 +627,7 @@
- <a title="" class="state-published contenttype-document" href="intel-compilers.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers">
<span>Intel Compilers</span>
</a>
@@ -646,7 +643,7 @@
- <a title="" class="state-published contenttype-document" href="intel-debugger.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger">
<span>Intel Debugger</span>
</a>
@@ -662,7 +659,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl">
<span>Intel MKL</span>
</a>
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- <a title="" class="state-published contenttype-document" href="intel-integrated-performance-primitives.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives">
<span>Intel IPP</span>
</a>
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<span>Intel TBB</span>
</a>
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- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
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- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
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- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -767,7 +764,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -783,7 +780,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -799,7 +796,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -815,7 +812,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -831,7 +828,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -847,7 +844,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -863,7 +860,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -879,7 +876,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -895,7 +892,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -911,7 +908,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -927,7 +924,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -952,7 +949,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -968,7 +965,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -993,7 +990,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1009,7 +1006,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb.md b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb.md
new file mode 100644
index 0000000000000000000000000000000000000000..093b2b3e1a0af3377b99051bf8d4c0a708beb2f6
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb.md
@@ -0,0 +1,38 @@
+Intel TBB
+=========
+
+Intel Threading Building Blocks
+--------
+Intel Threading Building Blocks (Intel TBB) is a library that supports
+scalable parallel programming using standard ISO C++ code. It does not
+require special languages or compilers. To use the library, you specify
+tasks, not threads, and let the library map tasks onto threads in an
+efficient manner. The tasks are executed by a runtime scheduler and may
+be offloaded to [MIC
+accelerator](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi).
+Intel TBB version 4.1 is available on Anselm
+ $ module load tbb
+The module sets up environment variables, required for linking and
+running tbb enabled applications.
+Link the tbb library, using -ltbb
+Examples
+--------
+Number of examples, demonstrating use of TBB and its built-in schedulerÂ
+is available on Anselm, in the $TBB_EXAMPLES directory.
+ $ module load intel
+ $ module load tbb
+ $ cp -a $TBB_EXAMPLES/common $TBB_EXAMPLES/parallel_reduce /tmp/
+ $ cd /tmp/parallel_reduce/primes
+ $ icc -O2 -DNDEBUG -o primes.x main.cpp primes.cpp -ltbb
+ $ ./primes.x
+In this example, we compile, link and run the primes example,
+demonstrating use of parallel task-based reduce in computation of prime
+numbers.
+You will need the tbb module loaded to run the tbb enabled executable.
+This may be avoided, by compiling library search paths into the
+executable.
+ $ icc -O2 -o primes.x main.cpp primes.cpp -Wl,-rpath=$LIBRARY_PATH -ltbb
+Further reading
+---------------
+Read more on Intel website,
+<http://software.intel.com/sites/products/documentation/doclib/tbb_sa/help/index.htm>
diff --git a/anselm-cluster-documentation/software/intel-xeon-phi.html b/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.html
old mode 100755
new mode 100644
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<title>Intel Xeon Phi — IT4I Docs</title>
- <link rel="canonical" href="intel-xeon-phi.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi" />
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+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
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@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="intel-xeon-phi.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="intel-xeon-phi.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -509,7 +506,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -525,7 +522,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -541,7 +538,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -557,7 +554,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -573,7 +570,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -589,7 +586,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -605,7 +602,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -621,7 +618,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -637,7 +634,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -653,7 +650,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -669,7 +666,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -685,7 +682,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -701,10 +698,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -720,7 +717,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -736,7 +733,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -752,7 +749,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -768,7 +765,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -784,7 +781,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -800,7 +797,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -816,7 +813,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -832,7 +829,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -848,7 +845,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -864,7 +861,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -880,7 +877,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -896,7 +893,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -912,7 +909,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -928,7 +925,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -944,7 +941,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -960,7 +957,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -976,7 +973,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -992,7 +989,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1008,7 +1005,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1033,7 +1030,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1049,7 +1046,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1074,7 +1071,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1090,7 +1087,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1106,7 +1103,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1145,14 +1142,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1174,12 +1171,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1195,7 +1192,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:52 GMT -->
</html>
diff --git a/anselm-cluster-documentation/software/intel-xeon-phi.md b/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.md
similarity index 69%
rename from anselm-cluster-documentation/software/intel-xeon-phi.md
rename to docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.md
index a8f2879b499da505a6f27ace5f6a1e4da0fef2b7..74fa9d5388346178c96416d70733c8aa0aecb733 100644
--- a/anselm-cluster-documentation/software/intel-xeon-phi.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.md
@@ -1,11 +1,12 @@
+Intel Xeon Phi
+==============
A guide to Intel Xeon Phi usage
-
-
+
Intel Xeon Phi can be programmed in several modes. The default mode on
Anselm is offload mode, but all modes described in this document are
supported.
Intel Utilities for Xeon Phi
-----------------------------
+-----
To get access to a compute node with Intel Xeon Phi accelerator, use the
PBS interactive session
$ qsub -I -q qmic -A NONE-0-0
@@ -15,59 +16,59 @@ Information about the hardware can be obtained by running
the micinfo program on the host.
$ /usr/bin/micinfo
The output of the "micinfo" utility executed on one of the Anselm node
-is as follows. (note to get PCIe related details the command has to be
+is as follows. (noteto get PCIe related details the command has to be
run with root privileges)
MicInfo Utility Log
- Created Mon Jul 22 002350 2013
+ Created Mon Jul 22 00:23:50 2013
       System Info
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â HOST OSÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Linux
-                OS Version             2.6.32-279.5.2.bl6.Bull.33.x86_64
-                Driver Version         6720-15
-                MPSS Version           2.1.6720-15
-                Host Physical Memory   98843 MB
- Device No 0, Device Name mic0
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â HOST OSÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Linux
+                OS Version             2.6.32-279.5.2.bl6.Bull.33.x86_64
+                Driver Version         6720-15
+                MPSS Version           2.1.6720-15
+                Host Physical Memory   98843 MB
+ Device No0, Device Namemic0
       Version
-                Flash Version           2.1.03.0386
-                SMC Firmware Version    1.15.4830
-                SMC Boot Loader Version 1.8.4326
-                uOS Version             2.6.38.8-g2593b11
-                Device Serial Number    ADKC30102482
+                Flash Version           2.1.03.0386
+                SMC Firmware Version    1.15.4830
+                SMC Boot Loader Version 1.8.4326
+                uOS Version             2.6.38.8-g2593b11
+                Device Serial Number    ADKC30102482
       Board
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Vendor IDÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â 0x8086
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Device IDÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â 0x2250
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Subsystem IDÂ Â Â Â Â Â Â Â Â Â Â Â 0x2500
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Coprocessor Stepping IDÂ 3
-                PCIe Width              x16
-                PCIe Speed              5 GT/s
-                PCIe Max payload size   256 bytes
-                PCIe Max read req size  512 bytes
-                Coprocessor Model       0x01
-                Coprocessor Model Ext   0x00
-                Coprocessor Type        0x00
-                Coprocessor Family      0x0b
-                Coprocessor Family Ext  0x00
-                Coprocessor Stepping    B1
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Board SKUÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â B1PRQ-5110P/5120D
-                ECC Mode                Enabled
-                SMC HW Revision         Product 225W Passive CS
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Vendor IDÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â 0x8086
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Device IDÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â 0x2250
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Subsystem IDÂ Â Â Â Â Â Â Â Â Â Â Â 0x2500
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Coprocessor Stepping IDÂ 3
+                PCIe Width              x16
+                PCIe Speed              5 GT/s
+                PCIe Max payload size   256 bytes
+                PCIe Max read req size  512 bytes
+                Coprocessor Model       0x01
+                Coprocessor Model Ext   0x00
+                Coprocessor Type        0x00
+                Coprocessor Family      0x0b
+                Coprocessor Family Ext  0x00
+                Coprocessor Stepping    B1
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Board SKUÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â B1PRQ-5110P/5120D
+                ECC Mode                Enabled
+                SMC HW Revision         Product 225W Passive CS
       Cores
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Total No of Active Cores 60
-                Voltage                 1032000 uV
-                Frequency               1052631 kHz
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Total No of Active Cores 60
+                Voltage                 1032000 uV
+                Frequency               1052631 kHz
       Thermal
-                Fan Speed Control       N/A
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Fan RPMÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â N/A
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Fan PWMÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â N/A
-                Die Temp                49 C
+                Fan Speed Control       N/A
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Fan RPMÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â N/A
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Fan PWMÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â N/A
+                Die Temp                49 C
       GDDR
-                GDDR Vendor             Elpida
-                GDDR Version            0x1
-                GDDR Density            2048 Mb
-                GDDR Size               7936 MB
-                GDDR Technology         GDDR5
-                GDDR Speed              5.000000 GT/s
-                GDDR Frequency          2500000 kHz
-                GDDR Voltage            1501000 uV
+                GDDR Vendor             Elpida
+                GDDR Version            0x1
+                GDDR Density            2048 Mb
+                GDDR Size               7936 MB
+                GDDR Technology         GDDR5
+                GDDR Speed              5.000000 GT/s
+                GDDR Frequency          2500000 kHz
+                GDDR Voltage            1501000 uV
Offload Mode
------------
To compile a code for Intel Xeon Phi a MPSS stack has to be installed on
@@ -83,7 +84,7 @@ A very basic example of code that employs offload programming technique
is shown in the next listing. Please note that this code is sequential
and utilizes only single core of the accelerator.
$ vim source-offload.cpp
- #include
+ #include <iostream>
int main(int argc, char* argv[])
{
   const int niter = 100000;
@@ -94,7 +95,7 @@ and utilizes only single core of the accelerator.
       result += 4.0 / (t * t + 1.0);
   }
   result /= niter;
- Â Â Â stdcout << "Pi ~ " << result << 'n';
+ Â Â Â std::cout << "Pi ~ " << result << 'n';
}
To compile a code using Intel compiler run
$ icc source-offload.cpp -o bin-offload
@@ -105,7 +106,7 @@ One way of paralelization a code for Xeon Phi is using OpenMP
directives. The following example shows code for parallel vector
addition.Â
$ vim ./vect-add
- #include
+ #include <stdio.h>
typedef int T;
#define SIZE 1000
#pragma offload_attribute(push, target(mic))
@@ -169,50 +170,49 @@ vectorized in both host and accelerator. This can be enabled with
compiler option "-vec-report2". To compile and execute the code run
$ icc vect-add.c -openmp_report2 -vec-report2 -o vect-add
$ ./vect-add
-Some interesting compiler flags useful not only for code debugging are
+Some interesting compiler flags useful not only for code debugging are:
Debugging
 openmp_report[0|1|2] - controls the compiler based vectorization
diagnostic level
 vec-report[0|1|2] - controls the OpenMP parallelizer diagnostic
level
-
Performance ooptimization
 xhost - FOR HOST ONLY - to generate AVX (Advanced Vector Extensions)
instructions.
Automatic Offload using Intel MKL Library
------------------------------------------
+------------------
Intel MKL includes an Automatic Offload (AO) feature that enables
computationally intensive MKL functions called in user code to benefit
from attached Intel Xeon Phi coprocessors automatically and
transparently.
Behavioral of automatic offload mode is controlled by functions called
within the program or by environmental variables. Complete list of
-controls is listed [
-class="external-link">here](http//software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mkl_userguide_lnx/GUID-3DC4FC7D-A1E4-423D-9C0C-06AB265FFA86.htm).
+controls is listed [<span
+class="external-link">here</span>](http://software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mkl_userguide_lnx/GUID-3DC4FC7D-A1E4-423D-9C0C-06AB265FFA86.htm).
The Automatic Offload may be enabled by either an MKL function call
-within the code
+within the code:
mkl_mic_enable();
or by setting environment variable
$ export MKL_MIC_ENABLE=1
To get more information about automatic offload please refer to "[Using
Intel® MKL Automatic Offload on Intel ® Xeon Phi™
-Coprocessors](http//software.intel.com/sites/default/files/11MIC42_How_to_Use_MKL_Automatic_Offload_0.pdf)"
-white paper or [Intel MKL
-documentation](https//software.intel.com/en-us/articles/intel-math-kernel-library-documentation).
+Coprocessors](http://software.intel.com/sites/default/files/11MIC42_How_to_Use_MKL_Automatic_Offload_0.pdf)"
+white paper or [<span class="external-link">Intel MKL
+documentation</span>](https://software.intel.com/en-us/articles/intel-math-kernel-library-documentation).
### Automatic offload example
At first get an interactive PBS session on a node with MIC accelerator
and load "intel" module that automatically loads "mkl" module as well.
- $ qsub -I -q qmic -A OPEN-0-0 -l select=1ncpus=16
+ $ qsub -I -q qmic -A OPEN-0-0 -l select=1:ncpus=16
$ module load intel
Following example show how to automatically offload an SGEMM (single
-precision - general matrix multiply) function to
+precision - g<span dir="auto">eneral matrix multiply</span>) function to
MIC coprocessor. The code can be copied to a file and compiled without
any necessary modification.Â
$ vim sgemm-ao-short.c
- #include
- #include
- #include
- #include
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <malloc.h>
+ #include <stdint.h>
#include "mkl.h"
int main(int argc, char **argv)
{
@@ -239,7 +239,7 @@ any necessary modification.Â
       mkl_mic_enable();
      Â
       int ndevices = mkl_mic_get_device_count(); /* Number of MIC devices */
-        printf("Automatic Offload enabled %d MIC devices presentn",  ndevices);
+        printf("Automatic Offload enabled%d MIC devices presentn",  ndevices);
       printf("Computing SGEMM with automatic workdivisionn");
       sgemm(&transa, &transb, &N, &N, &N, &alpha, A, &N, B, &N, &beta, C, &N);
       /* Free the matrix memory */
@@ -247,19 +247,19 @@ any necessary modification.Â
       printf("Donen");
   return 0;
}
-Please note This example is simplified version of an example from MKL.
-The expanded version can be found here
+Please noteThis example is simplified version of an example from MKL.
+The expanded version can be found here:
**$MKL_EXAMPLES/mic_ao/blasc/source/sgemm.c**
-To compile a code using Intel compiler use
+To compile a code using Intel compiler use:
$ icc -mkl sgemm-ao-short.c -o sgemm
For debugging purposes enable the offload report to see more information
about automatic offloading.
$ export OFFLOAD_REPORT=2
The output of a code should look similar to following listing, where
-lines starting with [MKL] are generated by offload reporting
+lines starting with [MKL] are generated by offload reporting:
Computing SGEMM on the host
Enabling Automatic Offload
- Automatic Offload enabled 1 MIC devices present
+ Automatic Offload enabled1 MIC devices present
Computing SGEMM with automatic workdivision
[MKL] [MIC --] [AO Function]Â Â Â SGEMM
[MKL] [MIC --] [AO SGEMM Workdivision]Â 0.00 1.00
@@ -276,7 +276,7 @@ without involvement of the host machine. Similarly to offload mode, the
code is compiled on the host computer with Intel compilers.
To compile a code user has to be connected to a compute with MIC and
load Intel compilers module. To get an interactive session on a compute
-node with an Intel Xeon Phi and load the module use following commandsÂ
+node with an Intel Xeon Phi and load the module use following commands:Â
$ qsub -I -q qmic -A NONE-0-0
$ module load intel/13.5.192
Please note that particular version of the Intel module is specified.
@@ -284,147 +284,154 @@ This information is used later to specify the correct library paths.
To produce a binary compatible with Intel Xeon Phi architecture user has
to specify "-mmic" compiler flag. Two compilation examples are shown
below. The first example shows how to compile OpenMP parallel code
-"vect-add.c" for host only
+"vect-add.c" for host only:
$ icc -xhost -no-offload -fopenmp vect-add.c -o vect-add-host
-To run this code on host, use
+To run this code on host, use:
$ ./vect-add-host
The second example shows how to compile the same code for Intel Xeon
-Phi
+Phi:
$ icc -mmic -fopenmp vect-add.c -o vect-add-mic
### Execution of the Program in Native Mode on Intel Xeon Phi
The user access to the Intel Xeon Phi is through the SSH. Since user
home directories are mounted using NFS on the accelerator, users do not
have to copy binary files or libraries between the host and accelerator.
Â
-To connect to the accelerator run
+To connect to the accelerator run:
$ ssh mic0
-If the code is sequential, it can be executed directly
+If the code is sequential, it can be executed directly:
mic0 $ ~/path_to_binary/vect-add-seq-mic
If the code is parallelized using OpenMP a set of additional libraries
is required for execution. To locate these libraries new path has to be
added to the LD_LIBRARY_PATH environment variable prior to the
-execution
- mic0 $ export LD_LIBRARY_PATH=/apps/intel/composer_xe_2013.5.192/compiler/lib/mic$LD_LIBRARY_PATH
+execution:
+ mic0 $ export LD_LIBRARY_PATH=/apps/intel/composer_xe_2013.5.192/compiler/lib/mic:$LD_LIBRARY_PATH
Please note that the path exported in the previous example contains path
to a specific compiler (here the version is 5.192). This version number
has to match with the version number of the Intel compiler module that
was used to compile the code on the host computer.
For your information the list of libraries and their location required
-for execution of an OpenMP parallel code on Intel Xeon Phi is
-class="discreet visualHighlight">
-/apps/intel/composer_xe_2013.5.192/compiler/lib/mic
-
+for execution of an OpenMP parallel code on Intel Xeon Phi is:<span
+class="discreet visualHighlight"></span>
+<span>/apps/intel/composer_xe_2013.5.192/compiler/lib/mic
libiomp5.so
libimf.so
libsvml.so
libirng.so
libintlc.so.5
-Finally, to run the compiled code use
+</span>
+<span>Finally, to run the compiled code use</span>
$ ~/path_to_binary/vect-add-mic
-OpenCL
+<span>OpenCL</span>
-------------------
-OpenCL (Open Computing Language) is an open standard for
+<span>OpenCL (Open Computing Language) is an open standard for
general-purpose parallel programming for diverse mix of multi-core CPUs,
GPU coprocessors, and other parallel processors. OpenCL provides a
flexible execution model and uniform programming environment for
software developers to write portable code for systems running on both
the CPU and graphics processors or accelerators like the Intel® Xeon
-Phi.
-On Anselm OpenCL is installed only on compute nodes with MIC
+Phi.</span>
+<span>On Anselm OpenCL is installed only on compute nodes with MIC
accelerator, therefore OpenCL code can be compiled only on these nodes.
+</span>
module load opencl-sdk opencl-rt
-Always load "opencl-sdk" (providing devel files like headers) and
+<span>Always load "opencl-sdk" (providing devel files like headers) and
"opencl-rt" (providing dynamic library libOpenCL.so) modules to compile
and link OpenCL code. Load "opencl-rt" for running your compiled code.
-There are two basic examples of OpenCL code in the following
-directory
+</span>
+<span>There are two basic examples of OpenCL code in the following
+directory</span>
/apps/intel/opencl-examples/
-First example "CapsBasic" detects OpenCL compatible hardware, here
+<span>First example "CapsBasic" detects OpenCL compatible hardware, here
CPU and MIC, and prints basic information about the capabilities of
it.Â
+</span>
/apps/intel/opencl-examples/CapsBasic/capsbasic
-To compile and run the example copy it to your home directory, get
+<span>To compile and run the example copy it to your home directory, get
a PBS interactive session on of the nodes with MIC and run make for
compilation. Make files are very basic and shows how the OpenCL code can
-be compiled on Anselm.
+be compiled on Anselm. </span>
$ cp /apps/intel/opencl-examples/CapsBasic/* .
$ qsub -I -q qmic -A NONE-0-0
$ make
-The compilation command for this example is
+<span>The compilation command for this example is</span>
$ g++ capsbasic.cpp -lOpenCL -o capsbasic -I/apps/intel/opencl/include/
-After executing the complied binary file, following output should
+<span>After executing the complied binary file, following output should
be displayed.
+</span>
./capsbasic
- Number of available platforms 1
- Platform names
+ Number of available platforms1
+ Platform names:
   [0] Intel(R) OpenCL [Selected]
- Number of devices available for each type
- Â Â Â CL_DEVICE_TYPE_CPU 1
- Â Â Â CL_DEVICE_TYPE_GPU 0
- Â Â Â CL_DEVICE_TYPE_ACCELERATOR 1
+ Number of devices available for each type:
+ Â Â Â CL_DEVICE_TYPE_CPU1
+ Â Â Â CL_DEVICE_TYPE_GPU0
+ Â Â Â CL_DEVICE_TYPE_ACCELERATOR1
*** Detailed information for each device ***
CL_DEVICE_TYPE_CPU[0]
- Â Â Â CL_DEVICE_NAMEÂ Â Â Â Â Â Â Intel(R) Xeon(R) CPU E5-2470 0 @ 2.30GHz
- Â Â Â CL_DEVICE_AVAILABLE 1
+ Â Â Â CL_DEVICE_NAME:Â Â Â Â Â Â Â Intel(R) Xeon(R) CPU E5-2470 0 @ 2.30GHz
+ Â Â Â CL_DEVICE_AVAILABLE1
...
CL_DEVICE_TYPE_ACCELERATOR[0]
- Â Â Â CL_DEVICE_NAME Intel(R) Many Integrated Core Acceleration Card
- Â Â Â CL_DEVICE_AVAILABLE 1
+ Â Â Â CL_DEVICE_NAMEIntel(R) Many Integrated Core Acceleration Card
+ Â Â Â CL_DEVICE_AVAILABLE1
...
-More information about this example can be found on Intel website
-
-The second example that can be found in
-"/apps/intel/opencl-examples" directory is General Matrix
+<span>More information about this example can be found on Intel website:
+<http://software.intel.com/en-us/vcsource/samples/caps-basic/>
+</span>
+<span>The second example that can be found in
+"/apps/intel/opencl-examples" </span><span>directory is General Matrix
Multiply. You can follow the the same procedure to download the example
to your directory and compile it.Â
+</span>
$ cp -r /apps/intel/opencl-examples/* .
$ qsub -I -q qmic -A NONE-0-0
$ cd GEMM
$ make
-The compilation command for this example is
+<span>The compilation command for this example is</span>
$ g++ cmdoptions.cpp gemm.cpp ../common/basic.cpp ../common/cmdparser.cpp ../common/oclobject.cpp -I../common -lOpenCL -o gemm -I/apps/intel/opencl/include/
-To see the performance of Intel Xeon Phi performing the DGEMM run
-the example as follows
+<span>To see the performance of Intel Xeon Phi performing the DGEMM run
+the example as follows</span>
./gemm -d 1
- Platforms (1)
+ Platforms (1):
[0] Intel(R) OpenCL [Selected]
- Devices (2)
+ Devices (2):
[0] Intel(R) Xeon(R) CPU E5-2470 0 @ 2.30GHz
[1] Intel(R) Many Integrated Core Acceleration Card [Selected]
- Build program options "-DT=float -DTILE_SIZE_M=1 -DTILE_GROUP_M=16 -DTILE_SIZE_N=128 -DTILE_GROUP_N=1 -DTILE_SIZE_K=8"
- Running gemm_nn kernel with matrix size 3968x3968
- Memory row stride to ensure necessary alignment 15872 bytes
- Size of memory region for one matrix 62980096 bytes
+ Build program options"-DT=float -DTILE_SIZE_M=1 -DTILE_GROUP_M=16 -DTILE_SIZE_N=128 -DTILE_GROUP_N=1 -DTILE_SIZE_K=8"
+ Running gemm_nn kernel with matrix size3968x3968
+ Memory row stride to ensure necessary alignment15872 bytes
+ Size of memory region for one matrix62980096 bytes
Using alpha = 0.57599 and beta = 0.872412
...
- Host time 0.292953 sec.
- Host perf 426.635 GFLOPS
- Host time 0.293334 sec.
- Host perf 426.081 GFLOPS
+ Host time0.292953 sec.
+ Host perf426.635 GFLOPS
+ Host time0.293334 sec.
+ Host perf426.081 GFLOPS
...
-Please note GNU compiler is used to compile the OpenCL codes for
+<span>Please noteGNU compiler is used to compile the OpenCL codes for
Intel MIC. You do not need to load Intel compiler module.
-MPIÂ
+</span>
+<span>MPIÂ </span>
-----------------
### Environment setup and compilation
Again an MPI code for Intel Xeon Phi has to be compiled on a compute
node with accelerator and MPSS software stack installed. To get to a
-compute node with accelerator use
+compute node with accelerator use:
$ qsub -I -q qmic -A NONE-0-0
The only supported implementation of MPI standard for Intel Xeon Phi is
Intel MPI. To setup a fully functional development environment a
combination of Intel compiler and Intel MPI has to be used. On a host
-load following modules before compilation
+load following modules before compilation:
$ module load intel/13.5.192 impi/4.1.1.036
-To compile an MPI code for host use
+To compile an MPI code for host use:
$ mpiicc -xhost -o mpi-test mpi-test.c
-To compile the same code for Intel Xeon Phi architecture use
+To compile the same code for Intel Xeon Phi architecture use:
$ mpiicc -mmic -o mpi-test-mic mpi-test.c
An example of basic MPI version of "hello-world" example in C language,
that can be executed on both host and Xeon Phi is (can be directly copy
and pasted to a .c file)
- #include
- #include
+ #include <stdio.h>
+ #include <mpi.h>
int main (argc, argv)
    int argc;
    char *argv[];
@@ -441,31 +448,30 @@ and pasted to a .c file)
 return 0;
}
### MPI programming models
-Intel MPI for the Xeon Phi coprocessors offers different MPI
-programming models
+<span>Intel MPI for the Xeon Phi coprocessors offers different MPI
+programming models:</span>
**Host-only model** - all MPI ranks reside on the host. The coprocessors
can be used by using offload pragmas. (Using MPI calls inside offloaded
code is not supported.)**
-
Coprocessor-only model** - all MPI ranks reside only on the
coprocessors.
-
**Symmetric model** - the MPI ranks reside on both the host and the
coprocessor. Most general MPI case.
-### Host-only model
-In this case all environment variables are set by modules,
-so to execute the compiled MPI program on a single node, use
+### <span>Host-only model</span>
+<span></span>In this case all environment variables are set by modules,
+so to execute the compiled MPI program on a single node, use:
$ mpirun -np 4 ./mpi-test
-The output should be similar to
+The output should be similar to:
Hello world from process 1 of 4 on host cn207
Hello world from process 3 of 4 on host cn207
Hello world from process 2 of 4 on host cn207
Hello world from process 0 of 4 on host cn207
### Coprocessor-only model
-There are two ways how to execute an MPI code on a single
-coprocessor 1.) lunch the program using "**mpirun**" from the
+<span>There are two ways how to execute an MPI code on a single
+coprocessor1.) lunch the program using "**mpirun**" from the
coprocessor; or 2.) lunch the task using "**mpiexec.hydra**" from a
host.
+</span>
**Execution on coprocessor**Â
Similarly to execution of OpenMP programs in native mode, since the
environmental module are not supported on MIC, user has to setup paths
@@ -475,27 +481,27 @@ sets up the environment on the MIC automatically once user access to the
accelerator through the SSH.
$ vim ~/.profile
PS1='[u@h W]$ '
- export PATH=/usr/bin/usr/sbin/bin/sbin
+ export PATH=/usr/bin:/usr/sbin:/bin:/sbin
#OpenMP
- export LD_LIBRARY_PATH=/apps/intel/composer_xe_2013.5.192/compiler/lib/mic$LD_LIBRARY_PATH
+ export LD_LIBRARY_PATH=/apps/intel/composer_xe_2013.5.192/compiler/lib/mic:$LD_LIBRARY_PATH
#Intel MPI
- export LD_LIBRARY_PATH=/apps/intel/impi/4.1.1.036/mic/lib/$LD_LIBRARY_PATH
- export PATH=/apps/intel/impi/4.1.1.036/mic/bin/$PATH
-Please note
+ export LD_LIBRARY_PATH=/apps/intel/impi/4.1.1.036/mic/lib/:$LD_LIBRARY_PATH
+ export PATH=/apps/intel/impi/4.1.1.036/mic/bin/:$PATH
+Please note:
 - this file sets up both environmental variable for both MPI and OpenMP
libraries.
 - this file sets up the paths to a particular version of Intel MPI
library and particular version of an Intel compiler. These versions have
to match with loaded modules.
To access a MIC accelerator located on a node that user is currently
-connected to, use
+connected to, use:
$ ssh mic0
-or in case you need specify a MIC accelerator on a particular node, use
+or in case you need specify a MIC accelerator on a particular node, use:
$ ssh cn207-mic0
To run the MPI code in parallel on multiple core of the accelerator,
-use
+use:
$ mpirun -np 4 ./mpi-test-mic
-The output should be similar to
+The output should be similar to:
Hello world from process 1 of 4 on host cn207-mic0
Hello world from process 2 of 4 on host cn207-mic0
Hello world from process 3 of 4 on host cn207-mic0
@@ -510,77 +516,79 @@ user has to specify library paths from the command line when calling
First step is to tell mpiexec that the MPI should be executed on a local
accelerator by setting up the environmental variable "I_MPI_MIC"
$ export I_MPI_MIC=1
-Now the MPI program can be executed as
+Now the MPI program can be executed as:
$ mpiexec.hydra -genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/ -host mic0 -n 4 ~/mpi-test-mic
or using mpirun
$ mpirun -genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/ -host mic0 -n 4 ~/mpi-test-mic
-Please note
-Â - the full path to the binary has to specified (here
-"**~/mpi-test-mic**")
+Please note:
+Â - the full path to the binary has to specified (here:
+"**<span>~/mpi-test-mic</span>**")
 - the LD_LIBRARY_PATH has to match with Intel MPI module used to
compile the MPI code
-The output should be again similar to
+The output should be again similar to:
Hello world from process 1 of 4 on host cn207-mic0
Hello world from process 2 of 4 on host cn207-mic0
Hello world from process 3 of 4 on host cn207-mic0
Hello world from process 0 of 4 on host cn207-mic0
Please note that the "mpiexec.hydra" requires a file
-"**pmi_proxy**" from Intel MPI library to be copied to the
+"**<span>pmi_proxy</span>**" from Intel MPI library to be copied to the
MIC filesystem. If the file is missing please contact the system
administrators. A simple test to see if the file is present is to
-execute
+execute:
  $ ssh mic0 ls /bin/pmi_proxy
 /bin/pmi_proxy
**
**
**Execution on host - MPI processes distributed over multiple
accelerators on multiple nodes**
-To get access to multiple nodes with MIC accelerator, user has to
+<span>To get access to multiple nodes with MIC accelerator, user has to
use PBS to allocate the resources. To start interactive session, that
allocates 2 compute nodes = 2 MIC accelerators run qsub command with
-following parameters
- $ qsub -I -q qmic -A NONE-0-0 -l select=2ncpus=16
+following parameters</span>
+ $ qsub -I -q qmic -A NONE-0-0 -l select=2:ncpus=16
$ module load intel/13.5.192 impi/4.1.1.036
-This command connects user through ssh to one of the nodes
-immediately. To see the other nodes that have been allocated use
+<span>This command connects user through ssh to one of the nodes
+immediately. To see the other nodes that have been allocated use:
+</span>
$ cat $PBS_NODEFILE
-For example
+<span>For example</span>
cn204.bullx
cn205.bullx
-This output means that the PBS allocated nodes cn204 and cn205,
+<span>This output means that the PBS allocated nodes cn204 and cn205,
which means that user has direct access to "**cn204-mic0**" and
-"**cn-205-mic0**" accelerators.
-Please note At this point user can connect to any of the
-allocated nodes or any of the allocated MIC accelerators using ssh
-- to connect to the second node **$ ssh
-cn205**
-- to connect to the accelerator on the first node from the first
-node **$ ssh cn204-mic0** or
-**$ ssh mic0**
+"**cn-205-mic0**" accelerators.</span>
+<span>Please noteAt this point user can connect to any of the
+allocated nodes or any of the allocated MIC accelerators using ssh:
+- to connect to the second node **<span class="monospace">$ ssh
+cn205</span>**
+<span>- to connect to the accelerator on the first node from the first
+node<span class="monospace">**$ ssh cn204-mic0**</span></span> or
+**<span class="monospace">$ ssh mic0</span>**
**-** to connect to the accelerator on the second node from the first
-node **$ ssh cn205-mic0**
-At this point we expect that correct modules are loaded and binary
-is compiled. For parallel execution the mpiexec.hydra is used.
+node<span class="monospace">**$ ssh cn205-mic0**</span>
+</span>
+<span>At this point we expect that correct modules are loaded and binary
+is compiled. For parallel execution the mpiexec.hydra is used.</span>
Again the first step is to tell mpiexec that the MPI can be executed on
MIC accelerators by setting up the environmental variable "I_MPI_MIC"
$ export I_MPI_MIC=1
-The launch the MPI program use
+<span>The launch the MPI program use:</span>
$ mpiexec.hydra -genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/
-genv I_MPI_FABRICS_LIST tcp
- Â -genv I_MPI_FABRICS shmtcp
+ Â -genv I_MPI_FABRICS shm:tcp
 -genv I_MPI_TCP_NETMASK=10.1.0.0/16
-host cn204-mic0 -n 4 ~/mpi-test-mic
- -host cn205-mic0 -n 6 ~/mpi-test-mic
-or using mpirun
+ -host cn205-mic0 -n 6 ~/mpi-test-mic
+or using mpirun:
$ mpirun -genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/
-genv I_MPI_FABRICS_LIST tcp
- Â -genv I_MPI_FABRICS shmtcp
+ Â -genv I_MPI_FABRICS shm:tcp
 -genv I_MPI_TCP_NETMASK=10.1.0.0/16
-host cn204-mic0 -n 4 ~/mpi-test-mic
- -host cn205-mic0 -n 6 ~/mpi-test-mic
+ -host cn205-mic0 -n 6 ~/mpi-test-mic
In this case four MPI processes are executed on accelerator cn204-mic
and six processes are executed on accelerator cn205-mic0. The sample
-output (sorted after execution) is
+output (sorted after execution) is:
Hello world from process 0 of 10 on host cn204-mic0
Hello world from process 1 of 10 on host cn204-mic0
Hello world from process 2 of 10 on host cn204-mic0
@@ -591,50 +599,53 @@ output (sorted after execution) is
Hello world from process 7 of 10 on host cn205-mic0
Hello world from process 8 of 10 on host cn205-mic0
Hello world from process 9 of 10 on host cn205-mic0
-The same way MPI program can be executed on multiple hostsÂ
+The same way MPI program can be executed on multiple hosts:Â
$ mpiexec.hydra -genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/
-genv I_MPI_FABRICS_LIST tcp
- Â -genv I_MPI_FABRICS shmtcp
+ Â -genv I_MPI_FABRICS shm:tcp
 -genv I_MPI_TCP_NETMASK=10.1.0.0/16
-host cn204 -n 4 ~/mpi-test
- -host cn205 -n 6 ~/mpi-test
-### Symmetric model
-In a symmetric mode MPI programs are executed on both host
+ -host cn205 -n 6 ~/mpi-test
+### <span>Symmetric model </span>
+<span>In a symmetric mode MPI programs are executed on both host
computer(s) and MIC accelerator(s). Since MIC has a different
architecture and requires different binary file produced by the Intel
compiler two different files has to be compiled before MPI program is
-executed.
-In the previous section we have compiled two binary files, one for
+executed. </span>
+<span>In the previous section we have compiled two binary files, one for
hosts "**mpi-test**" and one for MIC accelerators "**mpi-test-mic**".
-These two binaries can be executed at once using mpiexec.hydra
+These two binaries can be executed at once using mpiexec.hydra:
+</span>
$ mpiexec.hydra
-genv I_MPI_FABRICS_LIST tcp
- -genv I_MPI_FABRICS shmtcp
+ -genv I_MPI_FABRICS shm:tcp
 -genv I_MPI_TCP_NETMASK=10.1.0.0/16
-genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/
-host cn205 -n 2 ~/mpi-test
- -host cn205-mic0 -n 2 ~/mpi-test-mic
+ -host cn205-mic0 -n 2 ~/mpi-test-mic
In this example the first two parameters (line 2 and 3) sets up required
environment variables for execution. The third line specifies binary
that is executed on host (here cn205) and the last line specifies the
binary that is execute on the accelerator (here cn205-mic0).
-The output of the program is
+<span>The output of the program is</span>
Hello world from process 0 of 4 on host cn205
Hello world from process 1 of 4 on host cn205
Hello world from process 2 of 4 on host cn205-mic0
Hello world from process 3 of 4 on host cn205-mic0
-The execution procedure can be simplified by using the mpirun
+<span>The execution procedure can be simplified by using the mpirun
command with the machine file a a parameter. Machine file contains list
of all nodes and accelerators that should used to execute MPI processes.
-An example of a machine file that uses 2 hosts (**cn205**
+</span>
+<span>An example of a machine file that uses 2 <span>hosts (**cn205**
and **cn206**) and 2 accelerators **(cn205-mic0** and **cn206-mic0**) to
-run 2 MPI processes on each of them
+run 2 MPI processes on each</span> of them:
+</span>
$ cat hosts_file_mix
- cn2052
- cn205-mic02
- cn2062
- cn206-mic02
-In addition if a naming convention is set in a way that the name
+ cn205:2
+ cn205-mic0:2
+ cn206:2
+ cn206-mic0:2
+<span>In addition if a naming convention is set in a way that the name
of the binary for host is **"bin_name"**Â and the name of the binary
for the accelerator is **"bin_name-mic"** then by setting up the
environment variable **I_MPI_MIC_POSTFIX** to **"-mic"** user do not
@@ -642,19 +653,22 @@ have to specify the names of booth binaries. In this case mpirun needs
just the name of the host binary file (i.e. "mpi-test") and uses the
suffix to get a name of the binary for accelerator (i..e.
"mpi-test-mic").
+</span>
$ export I_MPI_MIC_POSTFIX=-mic
-Â To run the MPI code using mpirun and the machine file
-"hosts_file_mix" use
+Â <span>To run the MPI code using mpirun and the machine file
+"hosts_file_mix" use:
+</span>
$ mpirun
- -genv I_MPI_FABRICS shmtcp
+ -genv I_MPI_FABRICS shm:tcp
-genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/
-genv I_MPI_FABRICS_LIST tcp
- Â -genv I_MPI_FABRICS shmtcp
+ Â -genv I_MPI_FABRICS shm:tcp
 -genv I_MPI_TCP_NETMASK=10.1.0.0/16
-machinefile hosts_file_mix
~/mpi-test
-A possible output of the MPI "hello-world" example executed on two
-hosts and two accelerators is
+<span>A possible output of the MPI "hello-world" example executed on two
+hosts and two accelerators is:
+</span>
Hello world from process 0 of 8 on host cn204
Hello world from process 1 of 8 on host cn204
Hello world from process 2 of 8 on host cn204-mic0
@@ -663,17 +677,17 @@ hosts and two accelerators is
Hello world from process 5 of 8 on host cn205
Hello world from process 6 of 8 on host cn205-mic0
Hello world from process 7 of 8 on host cn205-mic0
-Please note At this point the MPI communication between MIC
+Please noteAt this point the MPI communication between MIC
accelerators on different nodes uses 1Gb Ethernet only.
**Using the PBS automatically generated node-files
**
PBS also generates a set of node-files that can be used instead of
-manually creating a new one every time. Three node-files are genereated
-**Host only node-file**
+manually creating a new one every time. Three node-files are genereated:
+**Host only node-file:**
 - /lscratch/${PBS_JOBID}/nodefile-cn
-**MIC only node-file**
+**MIC only node-file**:
 - /lscratch/${PBS_JOBID}/nodefile-mic
-**Host and MIC node-file**
+**Host and MIC node-file**:
 - /lscratch/${PBS_JOBID}/nodefile-mix
Please note each host or accelerator is listed only per files. User has
to specify how many jobs should be executed per node using "-n"
@@ -682,69 +696,6 @@ Optimization
------------
For more details about optimization techniques please read Intel
document [Optimization and Performance Tuning for Intel® Xeon Phi™
-Coprocessors](http//software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization "http//software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization"){.external
+Coprocessors](http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization "http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization"){.external
.text}.
Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage-1.html)
-
- - [Network](../network.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](virtualization.html)
-
diff --git a/anselm-cluster-documentation/software/isv_licenses.html b/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.html
old mode 100755
new mode 100644
similarity index 69%
rename from anselm-cluster-documentation/software/isv_licenses.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.html
index 82ef01b9d7167a84111876f06884ddd7e4df78e2..011237c9e2cb9f3f5291c5ebf49341f3c8485b94
--- a/anselm-cluster-documentation/software/isv_licenses.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:52 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses" /><!--[if lt IE 7]></base><![endif]-->
<meta content="A guide to managing Independent Software Vendor licences" name="description" />
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>ISV Licenses — IT4I Docs</title>
- <link rel="canonical" href="isv_licenses.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="isv_licenses.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="isv_licenses.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -243,7 +240,7 @@
<div id="parent-fieldname-text-2d8d49e87ab042dab1fba609153dd57f" class="">
<p>On Anselm cluster there are also installed commercial software applications, also known as ISV (Independent Software Vendor), which are subjects to licensing. The licenses are limited and their usage may be restricted only to some users or user groups.</p>
-<p>Currently Flex License Manager based licensing is supported on the cluster for products Ansys, Comsol and Matlab. More information about the applications can be found in the general <a target="_self" title="" class="internal-link" href="../software.html">Software</a> section.</p>
+<p>Currently Flex License Manager based licensing is supported on the cluster for products Ansys, Comsol and Matlab. More information about the applications can be found in the general <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a> section.</p>
<p>If an ISV application was purchased for educational (research) purposes and also for commercial purposes, then there are always two separate versions maintained and suffix "edu" is used in the name of the non-commercial version.</p>
<h2 class=" ">Overview of the licenses usage</h2>
<p class="callout">The overview is generated every minute and is accessible from web or command line interface.</p>
@@ -474,7 +471,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -490,7 +487,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -506,7 +503,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -522,7 +519,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -538,7 +535,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -554,7 +551,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -570,7 +567,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -586,7 +583,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -602,7 +599,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -618,7 +615,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -634,7 +631,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -650,7 +647,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -666,10 +663,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -685,7 +682,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -701,7 +698,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -717,7 +714,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -733,7 +730,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -749,7 +746,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -765,7 +762,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -781,7 +778,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -797,7 +794,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -813,7 +810,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -829,7 +826,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -845,7 +842,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -861,7 +858,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="isv_licenses.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -877,7 +874,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -893,7 +890,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -909,7 +906,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -925,7 +922,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -941,7 +938,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -957,7 +954,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -973,7 +970,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -998,7 +995,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1014,7 +1011,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1039,7 +1036,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1055,7 +1052,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1071,7 +1068,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -1139,12 +1136,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:52 GMT -->
</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md b/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md
new file mode 100644
index 0000000000000000000000000000000000000000..70c075bf959a429b4bd023484ad27dee3ed69a03
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md
@@ -0,0 +1,192 @@
+ISV Licenses
+============
+A guide to managing Independent Software Vendor licences
+
+On Anselm cluster there are also installed commercial software
+applications, also known as ISV (Independent Software Vendor), which are
+subjects to licensing. The licenses are limited and their usage may be
+restricted only to some users or user groups.
+Currently Flex License Manager based licensing is supported on the
+cluster for products Ansys, Comsol and Matlab. More information about
+the applications can be found in the general
+[Software](https://docs.it4i.cz/anselm-cluster-documentation/software)
+section.
+If an ISV application was purchased for educational (research) purposes
+and also for commercial purposes, then there are always two separate
+versions maintained and suffix "edu" is used in the name of the
+non-commercial version.
+Overview of the licenses usage
+-------
+The overview is generated every minute and is accessible from web or
+command line interface.
+### Web interface
+For each license there is a table, which provides the information about
+the name, number of available (purchased/licensed), number of used and
+number of free license features
+<https://extranet.it4i.cz/anselm/licenses>
+### Text interface
+For each license there is a unique text file, which provides the
+information about the name, number of available (purchased/licensed),
+number of used and number of free license features. The text files are
+accessible from the Anselm command prompt.[]()
+ Product File with license state Note
+ ------------ ------- ---------------------
+ ansys /apps/user/licenses/ansys_features_state.txt Commercial
+ comsol /apps/user/licenses/comsol_features_state.txt Commercial
+ comsol-edu /apps/user/licenses/comsol-edu_features_state.txt Non-commercial only
+ matlab /apps/user/licenses/matlab_features_state.txt Commercial
+ matlab-edu /apps/user/licenses/matlab-edu_features_state.txt Non-commercial only
+The file has a header which serves as a legend. All the info in the
+legend starts with a hash (#) so it can be easily filtered when parsing
+the file via a script.
+Example of the Commercial Matlab license state:
+ $ cat /apps/user/licenses/matlab_features_state.txt
+ # matlab
+ # ---
+ # FEATURE TOTAL USED AVAIL
+ # ---
+ MATLAB 1 1 0
+ SIMULINK 1 0 1
+ Curve_Fitting_Toolbox 1 0 1
+ Signal_Blocks 1 0 1
+ GADS_Toolbox 1 0 1
+ Image_Toolbox 1 0 1
+ Compiler 1 0 1
+ Neural_Network_Toolbox 1 0 1
+ Optimization_Toolbox 1 0 1
+ Signal_Toolbox 1 0 1
+ Statistics_Toolbox 1 0 1
+License tracking in PBS Pro scheduler and users usage
+-------
+Each feature of each license is accounted and checked by the scheduler
+of PBS Pro. If you ask for certain licences, the scheduler won't start
+the job until the asked licenses are free (available). This prevents to
+crash batch jobs, just because of <span id="result_box"
+class="short_text"><span class="hps">unavailability</span></span> of the
+needed licenses.
+The general format of the name is:
+**feature__APP__FEATURE**
+Names of applications (APP):
+- ansys
+- comsol
+- comsol-edu
+- matlab
+- matlab-edu
+Â
+To get the FEATUREs of a license take a look into the corresponding
+state file ([see above](#Licence)), or use:
+<table>
+<colgroup>
+<col width="50%" />
+<col width="50%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Application</th>
+<th align="left">List of provided features</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left">ansys</td>
+<td align="left"><pre><code>$ grep -v "#" /apps/user/licenses/ansys_features_state.txt | cut -f1 -d' '</code></pre></td>
+</tr>
+<tr class="even">
+<td align="left">comsol</td>
+<td align="left"><pre><code>$ grep -v "#" /apps/user/licenses/comsol_features_state.txt | cut -f1 -d' '</code></pre></td>
+</tr>
+<tr class="odd">
+<td align="left">comsol-edu</td>
+<td align="left"><pre><code>$ grep -v "#" /apps/user/licenses/comsol-edu_features_state.txt | cut -f1 -d' '</code></pre></td>
+</tr>
+<tr class="even">
+<td align="left">matlab</td>
+<td align="left"><pre><code>$ grep -v "#" /apps/user/licenses/matlab_features_state.txt | cut -f1 -d' '</code></pre></td>
+</tr>
+<tr class="odd">
+<td align="left">matlab-edu</td>
+<td align="left"><pre><code>$ grep -v "#" /apps/user/licenses/matlab-edu_features_state.txt | cut -f1 -d' '</code></pre></td>
+</tr>
+</tbody>
+</table>
+Â
+Example of PBS Pro resource name, based on APP and FEATURE name:
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Application</th>
+<th align="left">Feature</th>
+<th align="left">PBS Pro resource name</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left">ansys</td>
+<td align="left">acfd</td>
+<td align="left">feature__ansys__acfd</td>
+</tr>
+<tr class="even">
+<td align="left">ansys</td>
+<td align="left">aa_r</td>
+<td align="left">feature__ansys__aa_r</td>
+</tr>
+<tr class="odd">
+<td align="left">comsol</td>
+<td align="left">COMSOL</td>
+<td align="left">feature__comsol__COMSOL</td>
+</tr>
+<tr class="even">
+<td align="left">comsol</td>
+<td align="left">HEATTRANSFER</td>
+<td align="left">feature__comsol__HEATTRANSFER</td>
+</tr>
+<tr class="odd">
+<td align="left">comsol-edu</td>
+<td align="left">COMSOLBATCH</td>
+<td align="left">feature__comsol-edu__COMSOLBATCH</td>
+</tr>
+<tr class="even">
+<td align="left">comsol-edu</td>
+<td align="left">STRUCTURALMECHANICS</td>
+<td align="left">feature__comsol-edu__STRUCTURALMECHANICS</td>
+</tr>
+<tr class="odd">
+<td align="left">matlab</td>
+<td align="left">MATLAB</td>
+<td align="left">feature__matlab__MATLAB</td>
+</tr>
+<tr class="even">
+<td align="left">matlab</td>
+<td align="left">Image_Toolbox</td>
+<td align="left">feature__matlab__Image_Toolbox</td>
+</tr>
+<tr class="odd">
+<td align="left">matlab-edu</td>
+<td align="left">MATLAB_Distrib_Comp_Engine</td>
+<td align="left">feature__matlab-edu__MATLAB_Distrib_Comp_Engine</td>
+</tr>
+<tr class="even">
+<td align="left">matlab-edu</td>
+<td align="left">Image_Acquisition_Toolbox</td>
+<td align="left"><p>feature__matlab-edu__Image_Acquisition_Toolbox</p></td>
+</tr>
+</tbody>
+</table>
+**Be aware, that the resource names in PBS Pro are CASE SENSITIVE!**
+### Example of qsub statement
+Run an interactive PBS job with 1 Matlab EDU license, 1 Distributed
+Computing Toolbox and 32 Distributed Computing Engines (running on 32
+cores):
+ $ qsub -I -q qprod -A PROJECT_ID -l select=2:ncpus=16 -l feature__matlab-edu__MATLAB=1 -l feature__matlab-edu__Distrib_Computing_Toolbox=1 -l feature__matlab-edu__MATLAB_Distrib_Comp_Engine=32
+The license is used and accounted only with the real usage of the
+product. So in this example, the general Matlab is used after Matlab is
+run vy the user and not at the time, when the shell of the interactive
+job is started. Also the Distributed Computing licenses are used at the
+time, when the user uses the distributed parallel computation in Matlab
+(e. g. issues pmode start, matlabpool, etc.).
+Â
diff --git a/anselm-cluster-documentation/software/java.html b/docs.it4i.cz/anselm-cluster-documentation/software/java.html
old mode 100755
new mode 100644
similarity index 64%
rename from anselm-cluster-documentation/software/java.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/java.html
index 83435b9e25c0ff098242cf4066489003f8ce4edf..7cc2589c5500cbbdb6b0ef2e5335eed690c81c8d
--- a/anselm-cluster-documentation/software/java.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/java.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/java by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:52 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/java" /><!--[if lt IE 7]></base><![endif]-->
<meta content="Java on ANSELM" name="description" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Java — IT4I Docs</title>
- <link rel="canonical" href="java.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="java.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="java.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
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@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -325,7 +322,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -341,7 +338,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -389,7 +386,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -405,7 +402,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -421,7 +418,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -437,7 +434,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -453,7 +450,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -469,7 +466,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -485,7 +482,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -501,7 +498,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -517,10 +514,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -536,7 +533,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -552,7 +549,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -568,7 +565,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -584,7 +581,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -600,7 +597,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -616,7 +613,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -632,7 +629,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -648,7 +645,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -664,7 +661,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -680,7 +677,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -696,7 +693,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -712,7 +709,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -728,7 +725,7 @@
- <a title="Java on ANSELM" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="java.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -744,7 +741,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -760,7 +757,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -776,7 +773,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -792,7 +789,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -808,7 +805,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -824,7 +821,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -849,7 +846,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -865,7 +862,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -890,7 +887,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -906,7 +903,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -922,7 +919,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -990,12 +987,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1011,7 +1008,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/java by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:52 GMT -->
</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/java.md b/docs.it4i.cz/anselm-cluster-documentation/software/java.md
new file mode 100644
index 0000000000000000000000000000000000000000..88c1c3746d34f2401ce6d816e0a2935f6b50ef63
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/java.md
@@ -0,0 +1,22 @@
+Java
+====
+Java on ANSELM
+
+Java is available on Anselm cluster. Activate java by loading the java
+module
+ $ module load java
+Note that the java module must be loaded on the compute nodes as well,
+in order to run java on compute nodes.
+Check for java version and path
+ $ java -version
+ $ which java
+With the module loaded, not only the runtime environment (JRE), but also
+the development environment (JDK) with the compiler is available.
+ $ javac -version
+ $ which javac
+Java applications may use MPI for interprocess communication, in
+conjunction with OpenMPI. Read more
+on <http://www.open-mpi.org/faq/?category=java>.
+This functionality is currently not supported on Anselm cluster. In case
+you require the java interface to MPI, please contact [Anselm
+support](https://support.it4i.cz/rt/).
diff --git a/anselm-cluster-documentation/software/mpi-1.html b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1.html
old mode 100755
new mode 100644
similarity index 68%
rename from anselm-cluster-documentation/software/mpi-1.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/mpi-1.html
index faea35bf2bb2d992540f643627a0c394beb3d780..8780a53b19b0acc02432118ae3674c3f543ebda4
--- a/anselm-cluster-documentation/software/mpi-1.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>MPI — IT4I Docs</title>
- <link rel="canonical" href="mpi-1.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="mpi-1.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="mpi-1.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -340,10 +337,10 @@
<p>In the previous two cases with one or two MPI processes per node, the operating system might still migrate OpenMP threads between cores. You want to avoid this by setting the KMP_AFFINITY or GOMP_CPU_AFFINITY environment variables.</p>
<p class=" "><strong class=" ">16 MPI</strong> processes per node, using 1 thread each bound to processor core is most suitable for highly scalable applications with low communication demand.</p>
<h3 class=" ">Running OpenMPI</h3>
-<p>The <strong>bullxmpi-1.2.4.1</strong> and <a class="external-link" href="http://www.open-mpi.org/" target="_self" title=""><strong>OpenMPI 1.6.5</strong></a> are both based on OpenMPI. Read more on <a target="_self" title="" class="internal-link" href="mpi-1/Running_OpenMPI.html">how to run OpenMPI</a> based MPI.</p>
+<p>The <strong>bullxmpi-1.2.4.1</strong> and <a class="external-link" href="http://www.open-mpi.org/" target="_self" title=""><strong>OpenMPI 1.6.5</strong></a> are both based on OpenMPI. Read more on <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI">how to run OpenMPI</a> based MPI.</p>
<h3 class=" ">Running MPICH2</h3>
-<p>The <strong>Intel MPI</strong> and <strong>mpich2 1.9</strong> are MPICH2 based implementations. Read more on <a target="_self" title="" class="internal-link" href="mpi-1/running-mpich2.html">how to run MPICH2</a> based MPI.</p>
-<p>The Intel MPI may run on the Intel Xeon Phi accelerators as well. Read more on <a target="_self" title="" class="internal-link" href="intel-xeon-phi.html">how to run Intel MPI on accelerators</a>.</p>
+<p>The <strong>Intel MPI</strong> and <strong>mpich2 1.9</strong> are MPICH2 based implementations. Read more on <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2">how to run MPICH2</a> based MPI.</p>
+<p>The Intel MPI may run on the Intel Xeon Phi accelerators as well. Read more on <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">how to run Intel MPI on accelerators</a>.</p>
</div>
@@ -419,7 +416,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -435,7 +432,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -451,7 +448,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -467,7 +464,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -483,7 +480,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -499,7 +496,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -515,7 +512,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -531,7 +528,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -547,7 +544,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -563,7 +560,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -579,7 +576,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -595,7 +592,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -611,10 +608,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -630,7 +627,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -646,7 +643,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -662,7 +659,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -678,7 +675,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -694,7 +691,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -710,7 +707,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -726,7 +723,7 @@
- <a title="" class="state-published contenttype-document" href="mpi-1/Running_OpenMPI.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI">
<span>Running OpenMPI</span>
</a>
@@ -742,7 +739,7 @@
- <a title="" class="state-published contenttype-document" href="mpi-1/running-mpich2.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2">
<span>Running MPICH2</span>
</a>
@@ -758,7 +755,7 @@
- <a title="OpenMPI interface to Python" class="state-published contenttype-document" href="mpi-1/mpi4py-mpi-for-python.html">
+ <a class="state-published contenttype-document" title="OpenMPI interface to Python" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python">
<span>MPI4Py (MPI for Python)</span>
</a>
@@ -783,7 +780,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -799,7 +796,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -815,7 +812,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -831,7 +828,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -847,7 +844,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -863,7 +860,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -879,7 +876,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -895,7 +892,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -911,7 +908,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -927,7 +924,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -943,7 +940,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -959,7 +956,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -975,7 +972,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1000,7 +997,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1016,7 +1013,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1041,7 +1038,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1057,7 +1054,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1073,7 +1070,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1112,14 +1109,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1141,12 +1138,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1162,7 +1159,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/mpi-1 by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:48 GMT -->
</html>
diff --git a/anselm-cluster-documentation/software/mpi-1.md b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1.md
similarity index 55%
rename from anselm-cluster-documentation/software/mpi-1.md
rename to docs.it4i.cz/anselm-cluster-documentation/software/mpi-1.md
index ab6ae9a1ec6e69720524db1336b7b5c5f81ff617..f44150a184df1262a5ddaf82e065dca4a97df385 100644
--- a/anselm-cluster-documentation/software/mpi-1.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1.md
@@ -1,24 +1,47 @@
-
-
+MPI
+===
+
Setting up MPI Environment
---------------------------
-The Anselm cluster provides several implementations of the MPI library
-MPI Library
-Thread support
-The highly optimized and stable bullxmpi 1.2.4.1
-Partial thread support up to MPI_THREAD_SERIALIZED
-The Intel MPI 4.1
-Full thread support up to MPI_THREAD_MULTIPLE
-The OpenMPI 1.6.5
-Full thread support up to MPI_THREAD_MULTIPLE, BLCR c/r support
-The OpenMPI 1.8.1
-Full thread support up to MPI_THREAD_MULTIPLE, MPI-3.0 support
-The mpich2 1.9
-Full thread support up to MPI_THREAD_MULTIPLE, BLCR c/r support
+---
+The Anselm cluster provides several implementations of the MPI library:
+<table>
+<colgroup>
+<col width="50%" />
+<col width="50%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">MPI Library</th>
+<th align="left">Thread support</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><p>The highly optimized and stable <strong>bullxmpi 1.2.4.1</strong></p></td>
+<td align="left"><strong></strong>Partial thread support up to MPI_THREAD_SERIALIZED</td>
+</tr>
+<tr class="even">
+<td align="left">The <strong>Intel MPI 4.1</strong></td>
+<td align="left">Full thread support up to MPI_THREAD_MULTIPLE</td>
+</tr>
+<tr class="odd">
+<td align="left">The <a href="http://www.open-mpi.org/" class="external-link"><strong>OpenMPI 1.6.5</strong></a></td>
+<td align="left">Full thread support up to MPI_THREAD_MULTIPLE, BLCR c/r support</td>
+</tr>
+<tr class="even">
+<td align="left">The OpenMPI 1.8.1</td>
+<td align="left">Full thread support up to MPI_THREAD_MULTIPLE, MPI-3.0 support</td>
+</tr>
+<tr class="odd">
+<td align="left">The <strong><strong>mpich2 1.9</strong></strong></td>
+<td align="left">Full thread support up to <strong></strong> MPI_THREAD_MULTIPLE, BLCR c/r support</td>
+</tr>
+</tbody>
+</table>
MPI libraries are activated via the environment modules.
Look up section modulefiles/mpi in module avail
$ module avail
- ------------------------- /opt/modules/modulefiles/mpi -------------------------
+ -- /opt/modules/modulefiles/mpi --
bullxmpi/bullxmpi-1.2.4.1 mvapich2/1.9-icc
impi/4.0.3.008 openmpi/1.6.5-gcc(default)
impi/4.1.0.024 openmpi/1.6.5-gcc46
@@ -32,7 +55,7 @@ implementation. The defaults may be changed, the MPI libraries may be
used in conjunction with any compiler.
The defaults are selected via the modules in following way
Module MPI Compiler suite
- -------------- ------------------ --------------------------------------------------------------------------------
+ -------------- ------------------ -----------
PrgEnv-gnu bullxmpi-1.2.4.1 bullx GNU 4.4.6
PrgEnv-intel Intel MPI 4.1.1 Intel 13.1.1
bullxmpi bullxmpi-1.2.4.1 none, select via module
@@ -40,7 +63,7 @@ The defaults are selected via the modules in following way
openmpi OpenMPI 1.6.5 GNU compilers 4.8.1, GNU compilers 4.4.6, Intel Compilers
openmpi OpenMPI 1.8.1 GNU compilers 4.8.1, GNU compilers 4.4.6, GNU compilers 4.9.0, Intel Compilers
mvapich2 MPICH2 1.9 GNU compilers 4.8.1, GNU compilers 4.4.6, Intel Compilers
-Examples
+Examples:
$ module load openmpi
In this example, we activate the latest openmpi with latest GNU
compilers
@@ -55,10 +78,10 @@ the mpi wrappers
$ mpicc -v
$ mpif77 -v
$ mpif90 -v
-Example program
+Example program:
// helloworld_mpi.c
- #include
- #include
+ #include <stdio.h>
+ #include<mpi.h>
int main(int argc, char **argv) {
int len;
int rank, size;
@@ -91,7 +114,7 @@ scratch /lscratch filesystem.
### Ways to run MPI programs
Optimal way to run an MPI program depends on its memory requirements,
memory access pattern and communication pattern.
-Consider these ways to run an MPI program
+Consider these ways to run an MPI program:
1. One MPI process per node, 16 threads per process
2. Two MPI processes per node, 8 threads per process
3. 16 MPI processes per node, 1 thread per process.
@@ -116,85 +139,15 @@ core is most suitable for highly scalable applications with low
communication demand.
### Running OpenMPI
The **bullxmpi-1.2.4.1** and [**OpenMPI
-1.6.5**](http//www.open-mpi.org/) are both based on
+1.6.5**](http://www.open-mpi.org/) are both based on
OpenMPI. Read more on [how to run
-OpenMPI](mpi-1/Running_OpenMPI.html) based MPI.
+OpenMPI](https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI)
+based MPI.
### Running MPICH2
The **Intel MPI** and **mpich2 1.9** are MPICH2 based implementations.
Read more on [how to run
-MPICH2](mpi-1/running-mpich2.html) based MPI.
+MPICH2](https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2)
+based MPI.
The Intel MPI may run on the Intel Xeon Phi accelerators as well. Read
more on [how to run Intel MPI on
-accelerators](intel-xeon-phi.html).
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- ") .navTreeFolderish
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- - [ANSYS](ansys.html "An engineering simulation software ")
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-
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- science](chemistry.html "Tools for computational chemistry.")
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-
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-
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- OpenMPI](mpi-1/Running_OpenMPI.html)
-
- - [Running
- MPICH2](mpi-1/running-mpich2.html)
-
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- for Python)](mpi-1/mpi4py-mpi-for-python.html "OpenMPI interface to Python")
-
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-
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-
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+accelerators](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi).
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1035,7 +1032,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
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@@ -1051,7 +1048,7 @@
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@@ -1067,7 +1064,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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diff --git a/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md
similarity index 56%
rename from anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md
rename to docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md
index 074e79fd873ff50e6163db57b0d04382418406b4..e26dc86330c5c1b0b7e313d63791183b5478145f 100644
--- a/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md
@@ -1,18 +1,17 @@
Running OpenMPI
===============
-
-
+
OpenMPI program execution
--------------------------
+--
The OpenMPI programs may be executed only via the PBS Workload manager,
by entering an appropriate queue. On Anselm, the **bullxmpi-1.2.4.1**
and **OpenMPI 1.6.5** are OpenMPI based MPI implementations.
### Basic usage
Use the mpiexec to run the OpenMPI code.
-Example
- $ qsub -q qexp -l select=4ncpus=16 -I
- qsub waiting for job 15210.srv11 to start
- qsub job 15210.srv11 ready
+Example:
+ $ qsub -q qexp -l select=4:ncpus=16 -I
+ qsubwaiting for job 15210.srv11 to start
+ qsubjob 15210.srv11 ready
$ pwd
/home/username
$ module load openmpi
@@ -29,8 +28,8 @@ directive** to run up to 16 MPI tasks per each node.
In this example, we allocate 4 nodes via the express queue
interactively. We set up the openmpi environment and interactively run
the helloworld_mpi.x program.
-Note that the executable
-class="monospace">helloworld_mpi.x must be available within the
+Note that the executable <span
+class="monospace">helloworld_mpi.x</span> must be available within the
same path on all nodes. This is automatically fulfilled on the /home and
/scratch filesystem.
You need to preload the executable, if running on the local scratch
@@ -42,12 +41,12 @@ You need to preload the executable, if running on the local scratch
Hello world! from rank 1 of 4 on host cn108
Hello world! from rank 2 of 4 on host cn109
Hello world! from rank 3 of 4 on host cn110
-In this example, we assume the executable
-class="monospace">helloworld_mpi.x is present on compute node
+In this example, we assume the executable <span
+class="monospace">helloworld_mpi.x</span> is present on compute node
cn17 on local scratch. We call the mpiexec whith the
**--preload-binary** argument (valid for openmpi). The mpiexec will copy
-the executable from cn17 to the
-class="monospace">/lscratch/15210.srv11 directory on cn108, cn109
+the executable from cn17 to the <span
+class="monospace">/lscratch/15210.srv11</span> directory on cn108, cn109
and cn110 and execute the program.
MPI process mapping may be controlled by PBS parameters.
The mpiprocs and ompthreads parameters allow for selection of number of
@@ -56,7 +55,7 @@ MPI process.
### One MPI process per node
Follow this example to run one MPI process per node, 16 threads per
process.Â
- $ qsub -q qexp -l select=4ncpus=16mpiprocs=1ompthreads=16 -I
+ $ qsub -q qexp -l select=4:ncpus=16:mpiprocs=1:ompthreads=16 -I
$ module load openmpi
$ mpiexec --bind-to-none ./helloworld_mpi.x
In this example, we demonstrate recommended way to run an MPI
@@ -65,7 +64,7 @@ on 4 nodes.
### Two MPI processes per node
Follow this example to run two MPI processes per node, 8 threads per
process. Note the options to mpiexec.
- $ qsub -q qexp -l select=4ncpus=16mpiprocs=2ompthreads=8 -I
+ $ qsub -q qexp -l select=4:ncpus=16:mpiprocs=2:ompthreads=8 -I
$ module load openmpi
$ mpiexec -bysocket -bind-to-socket ./helloworld_mpi.x
In this example, we demonstrate recommended way to run an MPI
@@ -75,7 +74,7 @@ node, on 4 nodes
### 16 MPI processes per node
Follow this example to run 16 MPI processes per node, 1 thread per
process. Note the options to mpiexec.
- $ qsub -q qexp -l select=4ncpus=16mpiprocs=16ompthreads=1 -I
+ $ qsub -q qexp -l select=4:ncpus=16:mpiprocs=16:ompthreads=1 -I
$ module load openmpi
$ mpiexec -bycore -bind-to-core ./helloworld_mpi.x
In this example, we demonstrate recommended way to run an MPI
@@ -86,16 +85,16 @@ Important! Bind every OpenMP thread to a core!
In the previous two examples with one or two MPI processes per node, the
operating system might still migrate OpenMP threads between cores. You
might want to avoid this by setting these environment variable for GCC
-OpenMP
+OpenMP:
$ export GOMP_CPU_AFFINITY="0-15"
-or this one for Intel OpenMP
+or this one for Intel OpenMP:
$ export KMP_AFFINITY=granularity=fine,compact,1,0
As of OpenMP 4.0 (supported by GCC 4.9 and later and Intel 14.0 and
-later) the following variables may be used for Intel or GCC
+later) the following variables may be used for Intel or GCC:
$ export OMP_PROC_BIND=true
$ export OMP_PLACES=coresÂ
-OpenMPI Process Mapping and Binding
-------------------------------------------------
+<span>OpenMPI Process Mapping and Binding</span>
+--
The mpiexec allows for precise selection of how the MPI processes will
be mapped to the computational nodes and how these processes will bind
to particular processor sockets and cores.
@@ -122,15 +121,15 @@ Exact control of MPI process placement and resource binding is provided
by specifying a rankfile
Appropriate binding may boost performance of your application.
Example rankfile
- rank 0=cn110.bullx slot=10,1
- rank 1=cn109.bullx slot=0*
- rank 2=cn108.bullx slot=11-2
- rank 3=cn17.bullx slot=01,10-2
- rank 4=cn109.bullx slot=0*,1*
+ rank 0=cn110.bullx slot=1:0,1
+ rank 1=cn109.bullx slot=0:*
+ rank 2=cn108.bullx slot=1:1-2
+ rank 3=cn17.bullx slot=0:1,1:0-2
+ rank 4=cn109.bullx slot=0:*,1:*
This rankfile assumes 5 ranks will be running on 4 nodes and provides
exact mapping and binding of the processes to the processor sockets and
cores
-Explanation
+Explanation:
rank 0 will be bounded to cn110, socket1 core0 and core1
rank 1 will be bounded to cn109, socket0, all cores
rank 2 will be bounded to cn108, socket1, core1 and core2
@@ -138,11 +137,11 @@ rank 3 will be bounded to cn17, socket0 core1, socket1 core0, core1,
core2
rank 4 will be bounded to cn109, all cores on both sockets
$ mpiexec -n 5 -rf rankfile --report-bindings ./helloworld_mpi.x
- [cn1711180] MCW rank 3 bound to socket 0[core 1] socket 1[core 0-2] [. B . . . . . .][B B B . . . . .] (slot list 01,10-2)
- [cn11009928] MCW rank 0 bound to socket 1[core 0-1] [. . . . . . . .][B B . . . . . .] (slot list 10,1)
- [cn10910395] MCW rank 1 bound to socket 0[core 0-7] [B B B B B B B B][. . . . . . . .] (slot list 0*)
- [cn10810406] MCW rank 2 bound to socket 1[core 1-2] [. . . . . . . .][. B B . . . . .] (slot list 11-2)
- [cn10910406] MCW rank 4 bound to socket 0[core 0-7] socket 1[core 0-7] [B B B B B B B B][B B B B B B B B] (slot list 0*,1*)
+ [cn17:11180] MCW rank 3 bound to socket 0[core 1] socket 1[core 0-2][. B . . . . . .][B B B . . . . .] (slot list 0:1,1:0-2)
+ [cn110:09928] MCW rank 0 bound to socket 1[core 0-1][. . . . . . . .][B B . . . . . .] (slot list 1:0,1)
+ [cn109:10395] MCW rank 1 bound to socket 0[core 0-7][B B B B B B B B][. . . . . . . .] (slot list 0:*)
+ [cn108:10406] MCW rank 2 bound to socket 1[core 1-2][. . . . . . . .][. B B . . . . .] (slot list 1:1-2)
+ [cn109:10406] MCW rank 4 bound to socket 0[core 0-7] socket 1[core 0-7][B B B B B B B B][B B B B B B B B] (slot list 0:*,1:*)
Hello world! from rank 3 of 5 on host cn17
Hello world! from rank 1 of 5 on host cn109
Hello world! from rank 0 of 5 on host cn110
@@ -157,98 +156,48 @@ It is users responsibility to provide correct number of ranks, sockets
and cores.
### Bindings verification
In all cases, binding and threading may be verified by executing for
-example
+example:
$ mpiexec -bysocket -bind-to-socket --report-bindings echo
$ mpiexec -bysocket -bind-to-socket numactl --show
$ mpiexec -bysocket -bind-to-socket echo $OMP_NUM_THREADS
Changes in OpenMPI 1.8
----------------------
Some options have changed in OpenMPI version 1.8.
-version 1.6.5
-version 1.8.1
---bind-to-none
---bind-to none
---bind-to-core
---bind-to core
---bind-to-socket
---bind-to socket
--bysocket
---map-by socket
--bycore
---map-by core
--pernode
---map-by ppr1node
-------------------------------------------------------------------------
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+<table>
+<colgroup>
+<col width="50%" />
+<col width="50%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">version 1.6.5</th>
+<th align="left">version 1.8.1</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left">--bind-to-none</td>
+<td align="left">--bind-to none</td>
+</tr>
+<tr class="even">
+<td align="left">--bind-to-core</td>
+<td align="left">--bind-to core</td>
+</tr>
+<tr class="odd">
+<td align="left">--bind-to-socket</td>
+<td align="left">--bind-to socket</td>
+</tr>
+<tr class="even">
+<td align="left">-bysocket</td>
+<td align="left">--map-by socket</td>
+</tr>
+<tr class="odd">
+<td align="left">-bycore</td>
+<td align="left">--map-by core</td>
+</tr>
+<tr class="even">
+<td align="left">-pernode</td>
+<td align="left"><p><span class="s1">--map-by ppr:1:node</span></p></td>
+</tr>
+</tbody>
+</table>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.html b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.html
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+ MPI
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+ <h2 class=" ">Setting up MPI Environment</h2>
+<p>The Anselm cluster provides several implementations of the MPI library:</p>
+<table class="listing">
+<tbody>
+<tr><th>MPI Library</th><th>Thread support</th></tr>
+<tr class="even">
+<td>
+<p>The highly optimized and stable <strong>bullxmpi 1.2.4.1</strong></p>
+</td>
+<td><strong></strong>Partial thread support up to MPI_THREAD_SERIALIZED</td>
+</tr>
+<tr class="odd">
+<td>The<strong> Intel MPI 4.1</strong></td>
+<td>Full thread support up to MPI_THREAD_MULTIPLE</td>
+</tr>
+<tr class="even">
+<td>The <a class="external-link" href="http://www.open-mpi.org/" target="_self" title=""><strong>OpenMPI 1.6.5</strong></a></td>
+<td>Full thread support up to MPI_THREAD_MULTIPLE, BLCR c/r support</td>
+</tr>
+<tr class="even">
+<td>The OpenMPI 1.8.1</td>
+<td>Full thread support up to MPI_THREAD_MULTIPLE, MPI-3.0 support</td>
+</tr>
+<tr class="odd">
+<td>The<strong> <strong>mpich2 1.9</strong></strong></td>
+<td>Full thread support up to<strong> </strong>MPI_THREAD_MULTIPLE, BLCR c/r support</td>
+</tr>
+</tbody>
+</table>
+<ul></ul>
+<p class="callout">MPI libraries are activated via the environment modules.</p>
+<p>Look up section modulefiles/mpi in module avail</p>
+<pre class=" ">$ module avail<br />------------------------- /opt/modules/modulefiles/mpi -------------------------<br />bullxmpi/bullxmpi-1.2.4.1 mvapich2/1.9-icc<br />impi/4.0.3.008 openmpi/1.6.5-gcc(default)<br />impi/4.1.0.024 openmpi/1.6.5-gcc46<br />impi/4.1.0.030 openmpi/1.6.5-icc<br />impi/4.1.1.036(default) openmpi/1.8.1-gcc<br />openmpi/1.8.1-gcc46<br />mvapich2/1.9-gcc(default) openmpi/1.8.1-gcc49<br />mvapich2/1.9-gcc46 openmpi/1.8.1-icc</pre>
+<p>There are default compilers associated with any particular MPI implementation. The defaults may be changed, the MPI libraries may be used in conjunction with any compiler.<br />The defaults are selected via the modules in following way</p>
+<table class="listing" summary="Modules selecting the MPI environment">
+<tbody>
+<tr><th>Module</th><th>MPI</th><th>Compiler suite</th></tr>
+<tr class="even">
+<td>PrgEnv-gnu</td>
+<td>bullxmpi-1.2.4.1</td>
+<td>bullx GNU 4.4.6</td>
+</tr>
+<tr class="odd">
+<td>PrgEnv-intel</td>
+<td>Intel MPI 4.1.1</td>
+<td>Intel 13.1.1</td>
+</tr>
+<tr class="even">
+<td>bullxmpi</td>
+<td>bullxmpi-1.2.4.1</td>
+<td>none, select via module</td>
+</tr>
+<tr class="odd">
+<td>impi</td>
+<td>Intel MPI 4.1.1</td>
+<td>none, select via module</td>
+</tr>
+<tr class="even">
+<td>openmpi</td>
+<td>OpenMPI 1.6.5</td>
+<td>GNU compilers 4.8.1, GNU compilers 4.4.6, Intel Compilers</td>
+</tr>
+<tr class="even">
+<td>openmpi</td>
+<td>OpenMPI 1.8.1</td>
+<td>GNU compilers 4.8.1, GNU compilers 4.4.6, GNU compilers 4.9.0, Intel Compilers</td>
+</tr>
+<tr class="odd">
+<td>mvapich2</td>
+<td>MPICH2 1.9</td>
+<td>GNU compilers 4.8.1, GNU compilers 4.4.6, Intel Compilers</td>
+</tr>
+</tbody>
+</table>
+<p>Examples:</p>
+<pre class=" ">$ module load openmpi</pre>
+<p>In this example, we activate the latest openmpi with latest GNU compilers</p>
+<p>To use openmpi with the intel compiler suite, use</p>
+<pre class=" ">$ module load intel<br />$ module load openmpi/1.6.5-icc</pre>
+<p>In this example, the openmpi 1.6.5 using intel compilers is activated</p>
+<h2 class=" ">Compiling MPI Programs</h2>
+<p class="callout">After setting up your MPI environment, compile your program using one of the mpi wrappers</p>
+<pre class=" ">$ mpicc -v<br />$ mpif77 -v<br />$ mpif90 -v</pre>
+<p>Example program:</p>
+<pre class=" ">// helloworld_mpi.c<br />#include <stdio.h><br /><br />#include<mpi.h><br /><br />int main(int argc, char **argv) {<br /><br />int len;<br />int rank, size;<br />char node[MPI_MAX_PROCESSOR_NAME];<br /><br />// Initiate MPI<br />MPI_Init(&argc, &argv);<br />MPI_Comm_rank(MPI_COMM_WORLD,&rank);<br />MPI_Comm_size(MPI_COMM_WORLD,&size);<br /><br />// Get hostame and print<br />MPI_Get_processor_name(node,&len);<br />printf("Hello world! from rank %d of %d on host %s\n",rank,size,node);<br /><br />// Finalize and exit<br />MPI_Finalize();<br /><br />return 0;<br />}</pre>
+<p>Compile the above example with</p>
+<pre class=" ">$ mpicc helloworld_mpi.c -o helloworld_mpi.x</pre>
+<h2 class=" ">Running MPI Programs</h2>
+<p class="callout">The MPI program executable must be compatible with the loaded MPI module. <br />Always compile and execute using the very same MPI module.</p>
+<p>It is strongly discouraged to mix mpi implementations. Linking an application with one MPI implementation and running mpirun/mpiexec form other implementation may result in unexpected errors.</p>
+<p>The MPI program executable must be available within the same path on all nodes. This is automatically fulfilled on the /home and /scratch filesystem. You need to preload the executable, if running on the local scratch /lscratch filesystem.</p>
+<h3 class=" ">Ways to run MPI programs</h3>
+<p>Optimal way to run an MPI program depends on its memory requirements, memory access pattern and communication pattern.</p>
+<p class="callout">Consider these ways to run an MPI program:<br />1. One MPI process per node, 16 threads per process<br />2. Two MPI processes per node, 8 threads per process<br />3. 16 MPI processes per node, 1 thread per process.</p>
+<p class=" "><strong>One MPI</strong> process per node, using 16 threads, is most useful for memory demanding applications, that make good use of processor cache memory and are not memory bound. This is also a preferred way for communication intensive applications as one process per node enjoys full bandwidth access to the network interface. </p>
+<p class=" "><strong>Two MPI</strong> processes per node, using 8 threads each, bound to processor socket is most useful for memory bandwidth bound applications such as BLAS1 or FFT, with scalable memory demand. However, note that the two processes will share access to the network interface. The 8 threads and socket binding should ensure maximum memory access bandwidth and minimize communication, migration and numa effect overheads.</p>
+<p class="callout">Important! Bind every OpenMP thread to a core!</p>
+<p>In the previous two cases with one or two MPI processes per node, the operating system might still migrate OpenMP threads between cores. You want to avoid this by setting the KMP_AFFINITY or GOMP_CPU_AFFINITY environment variables.</p>
+<p class=" "><strong class=" ">16 MPI</strong> processes per node, using 1 thread each bound to processor core is most suitable for highly scalable applications with low communication demand.</p>
+<h3 class=" ">Running OpenMPI</h3>
+<p>The <strong>bullxmpi-1.2.4.1</strong> and <a class="external-link" href="http://www.open-mpi.org/" target="_self" title=""><strong>OpenMPI 1.6.5</strong></a> are both based on OpenMPI. Read more on <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI">how to run OpenMPI</a> based MPI.</p>
+<h3 class=" ">Running MPICH2</h3>
+<p>The <strong>Intel MPI</strong> and <strong>mpich2 1.9</strong> are MPICH2 based implementations. Read more on <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2">how to run MPICH2</a> based MPI.</p>
+<p>The Intel MPI may run on the Intel Xeon Phi accelerators as well. Read more on <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">how to run Intel MPI on accelerators</a>.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md
new file mode 100644
index 0000000000000000000000000000000000000000..f44150a184df1262a5ddaf82e065dca4a97df385
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md
@@ -0,0 +1,153 @@
+MPI
+===
+
+Setting up MPI Environment
+---
+The Anselm cluster provides several implementations of the MPI library:
+<table>
+<colgroup>
+<col width="50%" />
+<col width="50%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">MPI Library</th>
+<th align="left">Thread support</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><p>The highly optimized and stable <strong>bullxmpi 1.2.4.1</strong></p></td>
+<td align="left"><strong></strong>Partial thread support up to MPI_THREAD_SERIALIZED</td>
+</tr>
+<tr class="even">
+<td align="left">The <strong>Intel MPI 4.1</strong></td>
+<td align="left">Full thread support up to MPI_THREAD_MULTIPLE</td>
+</tr>
+<tr class="odd">
+<td align="left">The <a href="http://www.open-mpi.org/" class="external-link"><strong>OpenMPI 1.6.5</strong></a></td>
+<td align="left">Full thread support up to MPI_THREAD_MULTIPLE, BLCR c/r support</td>
+</tr>
+<tr class="even">
+<td align="left">The OpenMPI 1.8.1</td>
+<td align="left">Full thread support up to MPI_THREAD_MULTIPLE, MPI-3.0 support</td>
+</tr>
+<tr class="odd">
+<td align="left">The <strong><strong>mpich2 1.9</strong></strong></td>
+<td align="left">Full thread support up to <strong></strong> MPI_THREAD_MULTIPLE, BLCR c/r support</td>
+</tr>
+</tbody>
+</table>
+MPI libraries are activated via the environment modules.
+Look up section modulefiles/mpi in module avail
+ $ module avail
+ -- /opt/modules/modulefiles/mpi --
+ bullxmpi/bullxmpi-1.2.4.1 mvapich2/1.9-icc
+ impi/4.0.3.008 openmpi/1.6.5-gcc(default)
+ impi/4.1.0.024 openmpi/1.6.5-gcc46
+ impi/4.1.0.030 openmpi/1.6.5-icc
+ impi/4.1.1.036(default) openmpi/1.8.1-gcc
+ openmpi/1.8.1-gcc46
+ mvapich2/1.9-gcc(default) openmpi/1.8.1-gcc49
+ mvapich2/1.9-gcc46 openmpi/1.8.1-icc
+There are default compilers associated with any particular MPI
+implementation. The defaults may be changed, the MPI libraries may be
+used in conjunction with any compiler.
+The defaults are selected via the modules in following way
+ Module MPI Compiler suite
+ -------------- ------------------ -----------
+ PrgEnv-gnu bullxmpi-1.2.4.1 bullx GNU 4.4.6
+ PrgEnv-intel Intel MPI 4.1.1 Intel 13.1.1
+ bullxmpi bullxmpi-1.2.4.1 none, select via module
+ impi Intel MPI 4.1.1 none, select via module
+ openmpi OpenMPI 1.6.5 GNU compilers 4.8.1, GNU compilers 4.4.6, Intel Compilers
+ openmpi OpenMPI 1.8.1 GNU compilers 4.8.1, GNU compilers 4.4.6, GNU compilers 4.9.0, Intel Compilers
+ mvapich2 MPICH2 1.9 GNU compilers 4.8.1, GNU compilers 4.4.6, Intel Compilers
+Examples:
+ $ module load openmpi
+In this example, we activate the latest openmpi with latest GNU
+compilers
+To use openmpi with the intel compiler suite, use
+ $ module load intel
+ $ module load openmpi/1.6.5-icc
+In this example, the openmpi 1.6.5 using intel compilers is activated
+Compiling MPI Programs
+----------------------
+After setting up your MPI environment, compile your program using one of
+the mpi wrappers
+ $ mpicc -v
+ $ mpif77 -v
+ $ mpif90 -v
+Example program:
+ // helloworld_mpi.c
+ #include <stdio.h>
+ #include<mpi.h>
+ int main(int argc, char **argv) {
+ int len;
+ int rank, size;
+ char node[MPI_MAX_PROCESSOR_NAME];
+ // Initiate MPI
+ MPI_Init(&argc, &argv);
+ MPI_Comm_rank(MPI_COMM_WORLD,&rank);
+ MPI_Comm_size(MPI_COMM_WORLD,&size);
+ // Get hostame and print
+ MPI_Get_processor_name(node,&len);
+ printf("Hello world! from rank %d of %d on host %sn",rank,size,node);
+ // Finalize and exit
+ MPI_Finalize();
+ return 0;
+ }
+Compile the above example with
+ $ mpicc helloworld_mpi.c -o helloworld_mpi.x
+Running MPI Programs
+--------------------
+The MPI program executable must be compatible with the loaded MPI
+module.
+Always compile and execute using the very same MPI module.
+It is strongly discouraged to mix mpi implementations. Linking an
+application with one MPI implementation and running mpirun/mpiexec form
+other implementation may result in unexpected errors.
+The MPI program executable must be available within the same path on all
+nodes. This is automatically fulfilled on the /home and /scratch
+filesystem. You need to preload the executable, if running on the local
+scratch /lscratch filesystem.
+### Ways to run MPI programs
+Optimal way to run an MPI program depends on its memory requirements,
+memory access pattern and communication pattern.
+Consider these ways to run an MPI program:
+1. One MPI process per node, 16 threads per process
+2. Two MPI processes per node, 8 threads per process
+3. 16 MPI processes per node, 1 thread per process.
+**One MPI** process per node, using 16 threads, is most useful for
+memory demanding applications, that make good use of processor cache
+memory and are not memory bound. This is also a preferred way for
+communication intensive applications as one process per node enjoys full
+bandwidth access to the network interface.Â
+**Two MPI** processes per node, using 8 threads each, bound to processor
+socket is most useful for memory bandwidth bound applications such as
+BLAS1 or FFT, with scalable memory demand. However, note that the two
+processes will share access to the network interface. The 8 threads and
+socket binding should ensure maximum memory access bandwidth and
+minimize communication, migration and numa effect overheads.
+Important! Bind every OpenMP thread to a core!
+In the previous two cases with one or two MPI processes per node, the
+operating system might still migrate OpenMP threads between cores. You
+want to avoid this by setting the KMP_AFFINITY or GOMP_CPU_AFFINITY
+environment variables.
+**16 MPI** processes per node, using 1 thread each bound to processor
+core is most suitable for highly scalable applications with low
+communication demand.
+### Running OpenMPI
+The **bullxmpi-1.2.4.1** and [**OpenMPI
+1.6.5**](http://www.open-mpi.org/) are both based on
+OpenMPI. Read more on [how to run
+OpenMPI](https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI)
+based MPI.
+### Running MPICH2
+The **Intel MPI** and **mpich2 1.9** are MPICH2 based implementations.
+Read more on [how to run
+MPICH2](https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2)
+based MPI.
+The Intel MPI may run on the Intel Xeon Phi accelerators as well. Read
+more on [how to run Intel MPI on
+accelerators](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi).
diff --git a/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.html b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.html
old mode 100755
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index e9373400c50121222292a7b0e733c3fa32f5af2c..e78163271f3a92a171fe75c25cd7f831cf9cc0c2
--- a/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.html
@@ -10,45 +10,42 @@
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<title>MPI4Py (MPI for Python) — IT4I Docs</title>
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+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python" />
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<h2 class=" ">Execution</h2>
<p>You need to import MPI to your python program. Include the following line to the python script:</p>
<pre class=" ">from mpi4py import MPI</pre>
-<p>The MPI4Py enabled python programs <a target="_self" title="" class="internal-link" href="Running_OpenMPI.html">execute as any other OpenMPI</a> code.The simpliest way is to run</p>
+<p>The MPI4Py enabled python programs <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI">execute as any other OpenMPI</a> code.The simpliest way is to run</p>
<pre><span>$ mpiexec python <script>.py</span></pre>
<p><span>For example</span></p>
<pre>$ mpiexec python hello_world.py</pre>
@@ -350,7 +347,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
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@@ -382,7 +379,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -398,7 +395,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -414,7 +411,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -430,7 +427,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -446,7 +443,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -462,7 +459,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -478,7 +475,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -494,7 +491,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -510,7 +507,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -526,7 +523,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -542,10 +539,10 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -561,7 +558,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -577,7 +574,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -593,7 +590,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -609,7 +606,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -625,7 +622,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -641,7 +638,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -657,7 +654,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="" class="state-published contenttype-document" href="Running_OpenMPI.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI">
<span>Running OpenMPI</span>
</a>
@@ -673,7 +670,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="" class="state-published contenttype-document" href="running-mpich2.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2">
<span>Running MPICH2</span>
</a>
@@ -689,7 +686,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="OpenMPI interface to Python" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="mpi4py-mpi-for-python.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="OpenMPI interface to Python" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python">
<span>MPI4Py (MPI for Python)</span>
</a>
@@ -714,7 +711,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -730,7 +727,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -746,7 +743,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -762,7 +759,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -778,7 +775,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -794,7 +791,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -810,7 +807,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -826,7 +823,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -842,7 +839,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -858,7 +855,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -874,7 +871,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -890,7 +887,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -906,7 +903,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -931,7 +928,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -947,7 +944,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -972,7 +969,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -988,7 +985,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1004,7 +1001,7 @@ from __future__ import division<br />import numpy as np<br /><br />comm = MPI.CO
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1043,14 +1040,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -1072,12 +1069,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1093,7 +1090,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.md b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.md
new file mode 100644
index 0000000000000000000000000000000000000000..fbc70cadd6edb3b6a71904354cf015f4687ac694
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.md
@@ -0,0 +1,69 @@
+MPI4Py (MPI for Python)
+=======================
+OpenMPI interface to Python
+
+Introduction
+------------
+MPI for Python provides bindings of the Message Passing Interface (MPI)
+standard for the Python programming language, allowing any Python
+program to exploit multiple processors.
+This package is constructed on top of the MPI-1/2 specifications and
+provides an object oriented interface which closely follows MPI-2 C++
+bindings. It supports point-to-point (sends, receives) and collective
+(broadcasts, scatters, gathers) communications of any picklable Python
+object, as well as optimized communications of Python object exposing
+the single-segment buffer interface (NumPy arrays, builtin
+bytes/string/array objects).
+On Anselm MPI4Py is available in standard Python modules.
+Modules
+-------
+MPI4Py is build for OpenMPI. Before you start with MPI4Py you need to
+load Python and OpenMPI modules.
+ $ module load python
+ $ module load openmpi
+Execution
+---------
+You need to import MPI to your python program. Include the following
+line to the python script:
+ from mpi4py import MPI
+The MPI4Py enabled python programs [execute as any other
+OpenMPI](https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI)
+code.The simpliest way is to run
+ $ mpiexec python <script>.py
+<span>For example</span>
+ $ mpiexec python hello_world.py
+Examples
+--------
+### Hello world!
+ from mpi4py import MPI
+ comm = MPI.COMM_WORLD
+ print "Hello! I'm rank %d from %d running in total..." % (comm.rank, comm.size)
+ comm.Barrier() Â # wait for everybody to synchronize
+### <span>Collective Communication with NumPy arrays</span>
+ from mpi4py import MPI
+ from __future__ import division
+ import numpy as np
+ comm = MPI.COMM_WORLD
+ print("-"*78)
+ print(" Running on %d cores" % comm.size)
+ print("-"*78)
+ comm.Barrier()
+ # Prepare a vector of N=5 elements to be broadcasted...
+ N = 5
+ if comm.rank == 0:
+ Â Â A = np.arange(N, dtype=np.float64) Â Â # rank 0 has proper data
+ else:
+ Â Â A = np.empty(N, dtype=np.float64) Â Â # all other just an empty array
+ # Broadcast A from rank 0 to everybody
+ comm.Bcast( [A, MPI.DOUBLE] )
+ # Everybody should now have the same...
+ print "[%02d] %s" % (comm.rank, A)
+Execute the above code as:
+ $ qsub -q qexp -l select=4:ncpus=16:mpiprocs=16:ompthreads=1 -I
+ $ module load python openmpi
+ $ mpiexec -bycore -bind-to-core python hello_world.py
+In this example, we run MPI4Py enabled code on 4 nodes, 16 cores per
+node (total of 64 processes), each python process is bound to a
+different core.
+More examples and documentation can be found on [MPI for Python
+webpage](https://pythonhosted.org/mpi4py/usrman/index.html).
diff --git a/anselm-cluster-documentation/software/mpi-1/running-mpich2.html b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2.html
old mode 100755
new mode 100644
similarity index 69%
rename from anselm-cluster-documentation/software/mpi-1/running-mpich2.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2.html
index a3a3251b1f703d3910299acc9c1d227b6b2dacd4..db067efc7da6e93973ccf6b4016258d5830bcbdf
--- a/anselm-cluster-documentation/software/mpi-1/running-mpich2.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2.html
@@ -10,45 +10,42 @@
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- <base /><!--[if lt IE 7]></base><![endif]-->
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<title>Running MPICH2 — IT4I Docs</title>
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<p>In all cases, binding and threading may be verified by executing</p>
<pre class=" ">$ mpirun -bindto numa numactl --show<br />$ mpirun -bindto numa echo $OMP_NUM_THREADS</pre>
<h2 class=" ">Intel MPI on Xeon Phi</h2>
-<p>The<a target="_self" title="" class="internal-link" href="../intel-xeon-phi.html"> MPI section of Intel Xeon Phi chapter</a> provides details on how to run Intel MPI code on Xeon Phi architecture.</p>
+<p>The<a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi"> MPI section of Intel Xeon Phi chapter</a> provides details on how to run Intel MPI code on Xeon Phi architecture.</p>
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<span>Resource Allocation and Job Execution</span>
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<span>Software</span>
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<span>MPI</span>
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<span>Running OpenMPI</span>
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<span>Running MPICH2</span>
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<span>Numerical Libraries</span>
</a>
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- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
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- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
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- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
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- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
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- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
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- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
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<span>OMICS Master</span>
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+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
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- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
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- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
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- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
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- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
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- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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diff --git a/anselm-cluster-documentation/software/anselm-cluster-documentation/software/mpi-1/running-mpich2.md b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
similarity index 58%
rename from anselm-cluster-documentation/software/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
rename to docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
index af77b753c49011fd6299d2ad4324d0980c63229e..c8d0b2abc90013cd168d0571b9fa0eaaf9d14368 100644
--- a/anselm-cluster-documentation/software/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
@@ -1,19 +1,18 @@
Running MPICH2
==============
-
-
+
MPICH2 program execution
-------------------------
+-
The MPICH2 programs use mpd daemon or ssh connection to spawn processes,
no PBS support is needed. However the PBS allocation is required to
access compute nodes. On Anselm, the **Intel MPI** and **mpich2 1.9**
are MPICH2 based MPI implementations.
### Basic usage
Use the mpirun to execute the MPICH2 code.
-Example
- $ qsub -q qexp -l select=4ncpus=16 -I
- qsub waiting for job 15210.srv11 to start
- qsub job 15210.srv11 ready
+Example:
+ $ qsub -q qexp -l select=4:ncpus=16 -I
+ qsubwaiting for job 15210.srv11 to start
+ qsubjob 15210.srv11 ready
$ module load impi
$ mpirun -ppn 1 -hostfile $PBS_NODEFILE ./helloworld_mpi.x
Hello world! from rank 0 of 4 on host cn17
@@ -49,7 +48,7 @@ MPI process.
### One MPI process per node
Follow this example to run one MPI process per node, 16 threads per
process. Note that no options to mpirun are needed
- $ qsub -q qexp -l select=4ncpus=16mpiprocs=1ompthreads=16 -I
+ $ qsub -q qexp -l select=4:ncpus=16:mpiprocs=1:ompthreads=16 -I
$ module load mvapich2
$ mpirun ./helloworld_mpi.x
In this example, we demonstrate recommended way to run an MPI
@@ -59,7 +58,7 @@ on 4 nodes.
Follow this example to run two MPI processes per node, 8 threads per
process. Note the options to mpirun for mvapich2. No options are needed
for impi.
- $ qsub -q qexp -l select=4ncpus=16mpiprocs=2ompthreads=8 -I
+ $ qsub -q qexp -l select=4:ncpus=16:mpiprocs=2:ompthreads=8 -I
$ module load mvapich2
$ mpirun -bind-to numa ./helloworld_mpi.x
In this example, we demonstrate recommended way to run an MPI
@@ -70,7 +69,7 @@ node, on 4 nodes
Follow this example to run 16 MPI processes per node, 1 thread per
process. Note the options to mpirun for mvapich2. No options are needed
for impi.
- $ qsub -q qexp -l select=4ncpus=16mpiprocs=16ompthreads=1 -I
+ $ qsub -q qexp -l select=4:ncpus=16:mpiprocs=16:ompthreads=1 -I
$ module load mvapich2
$ mpirun -bind-to core ./helloworld_mpi.x
In this example, we demonstrate recommended way to run an MPI
@@ -81,17 +80,17 @@ Important! Bind every OpenMP thread to a core!
In the previous two examples with one or two MPI processes per node, the
operating system might still migrate OpenMP threads between cores. You
might want to avoid this by setting these environment variable for GCC
-OpenMP
+OpenMP:
$ export GOMP_CPU_AFFINITY="0-15"
-or this one for Intel OpenMP
+or this one for Intel OpenMP:
$ export KMP_AFFINITY=granularity=fine,compact,1,0
As of OpenMP 4.0 (supported by GCC 4.9 and later and Intel 14.0 and
-later) the following variables may be used for Intel or GCC
+later) the following variables may be used for Intel or GCC:
$ export OMP_PROC_BIND=true
$ export OMP_PLACES=cores
Â
MPICH2 Process Mapping and Binding
-----------------------------------
+-----------
The mpirun allows for precise selection of how the MPI processes will be
mapped to the computational nodes and how these processes will bind to
particular processor sockets and cores.
@@ -120,7 +119,7 @@ The Intel MPI automatically binds each process and its threads to the
corresponding portion of cores on the processor socket of the node, no
options needed. The binding is primarily controlled by environment
variables. Read more about mpi process binding on [Intel
-website](https//software.intel.com/sites/products/documentation/hpc/ics/impi/41/lin/Reference_Manual/Environment_Variables_Process_Pinning.htm).
+website](https://software.intel.com/sites/products/documentation/hpc/ics/impi/41/lin/Reference_Manual/Environment_Variables_Process_Pinning.htm).
The MPICH2 uses the -bind-to option Use -bind-to numa or -bind-to core
to bind the process on single core or entire socket.
### Bindings verification
@@ -130,79 +129,5 @@ In all cases, binding and threading may be verified by executing
Intel MPI on Xeon Phi
---------------------
The[MPI section of Intel Xeon Phi
-chapter](../../../intel-xeon-phi.html) provides details
-on how to run Intel MPI code on Xeon Phi architecture.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../../sitemap.html)
- - [What's
- New](../../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../../compute-nodes.html)
-
- - [Storage](../../../../storage-1.html)
-
- - [Network](../../../../network.html)
-
- - [Software](../../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../../../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../../../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../../../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../../../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../../../mpi-1.html "Message Passing Interface libraries on ANSELM")
- .navTreeFolderish
- .contenttype-folder}
- - [Running
- OpenMPI](../../../mpi-1/Running_OpenMPI.html)
-
- - [Running
- MPICH2](../../../mpi-1/running-mpich2.html)
-
-
- - [MPI4Py (MPI
- for Python)](../../../mpi-1/mpi4py-mpi-for-python.html "OpenMPI interface to Python")
-
- - [Numerical
- Libraries](../../../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../../../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../../../virtualization.html)
+chapter](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi)
+provides details on how to run Intel MPI code on Xeon Phi architecture.
diff --git a/anselm-cluster-documentation/software/numerical-languages.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages.1.html
old mode 100755
new mode 100644
similarity index 62%
rename from anselm-cluster-documentation/software/numerical-languages.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages.1.html
index 7ac5d4c0db7551f8248908c873a3e3557425fa31..7adca8bfac8c731b70388d4b761f382837075647
--- a/anselm-cluster-documentation/software/numerical-languages.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages.1.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:51 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction" /><!--[if lt IE 7]></base><![endif]-->
<meta content="Interpreted languages for numerical computations and analysis" name="description" />
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- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
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- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Numerical languages — IT4I Docs</title>
- <link rel="canonical" href="numerical-languages.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="numerical-languages.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="numerical-languages.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -247,15 +244,15 @@
<h2 class=" ">Matlab</h2>
<p>MATLAB<sup>®</sup> is a high-level language and interactive environment for numerical computation, visualization, and programming.</p>
<pre class=" ">$ module load MATLAB/2015b-EDU<br />$ matlab</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="numerical-languages/matlab.html">Matlab<span class="internal-link"></span> page</a>.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab">Matlab<span class="internal-link"></span> page</a>.</p>
<h2 class=" ">Octave</h2>
<p>GNU Octave is a high-level interpreted language, primarily intended for numerical computations. The Octave language is quite similar to Matlab so that most programs are easily portable.</p>
<pre class=" ">$ module load Octave<br />$ octave</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="numerical-languages/octave.html">Octave page</a>.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave">Octave page</a>.</p>
<h2 class=" ">R</h2>
<p>The R is an interpreted language and environment for statistical computing and graphics.</p>
<pre class=" ">$ module load R<br />$ R</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="numerical-languages/r.html">R page</a>.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r">R page</a>.</p>
</div>
@@ -331,7 +328,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -347,7 +344,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -363,7 +360,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -379,7 +376,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -395,7 +392,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -411,7 +408,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -427,7 +424,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -443,7 +440,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -459,7 +456,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -475,7 +472,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -491,7 +488,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -507,7 +504,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -523,10 +520,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -542,7 +539,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -558,7 +555,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -574,7 +571,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -590,7 +587,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -606,7 +603,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -622,7 +619,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -638,7 +635,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -654,7 +651,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -670,7 +667,7 @@
- <a title="" class="state-published contenttype-document" href="numerical-languages/copy_of_matlab.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab">
<span>Matlab</span>
</a>
@@ -686,7 +683,7 @@
- <a title="" class="state-published contenttype-document" href="numerical-languages/matlab.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab">
<span>Matlab 2013-2014</span>
</a>
@@ -702,7 +699,7 @@
- <a title="" class="state-published contenttype-document" href="numerical-languages/octave.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave">
<span>Octave</span>
</a>
@@ -718,7 +715,7 @@
- <a title="" class="state-published contenttype-document" href="numerical-languages/r.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r">
<span>R</span>
</a>
@@ -743,7 +740,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -759,7 +756,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -775,7 +772,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -791,7 +788,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -807,7 +804,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -823,7 +820,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -839,7 +836,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -855,7 +852,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -871,7 +868,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -887,7 +884,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -903,7 +900,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -928,7 +925,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -944,7 +941,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -969,7 +966,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -985,7 +982,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1001,7 +998,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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(function() {
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+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</div>
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages.1.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages.1.md
new file mode 100644
index 0000000000000000000000000000000000000000..d21af4a17880d87385405d699e9a2b6f0922528e
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages.1.md
@@ -0,0 +1,33 @@
+Numerical languages
+===================
+Interpreted languages for numerical computations and analysis
+
+Introduction
+------------
+This section contains a collection of high-level interpreted languages,
+primarily intended for numerical computations.
+Matlab
+------
+MATLAB^®^ is a high-level language and interactive environment for
+numerical computation, visualization, and programming.
+ $ module load MATLAB/2015b-EDU
+ $ matlab
+Read more at the [Matlab<span class="internal-link"></span>
+page](https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab).
+Octave
+------
+GNU Octave is a high-level interpreted language, primarily intended for
+numerical computations. The Octave language is quite similar to Matlab
+so that most programs are easily portable.
+ $ module load Octave
+ $ octave
+Read more at the [Octave
+page](https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave).
+R
+-
+The R is an interpreted language and environment for statistical
+computing and graphics.
+ $ module load R
+ $ R
+Read more at the [R
+page](https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r).
diff --git a/anselm-cluster-documentation/software/numerical-languages/Matlab.png b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/Matlab.png
old mode 100755
new mode 100644
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rename from anselm-cluster-documentation/software/numerical-languages/Matlab.png
rename to docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/Matlab.png
diff --git a/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.html
old mode 100755
new mode 100644
similarity index 70%
rename from anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.html
index eea029a53e1f6b7292627288b5d698f79d4c603a..46d98db7c0bc7941bbe66d706d1252ddeb613d9a
--- a/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.html
@@ -10,45 +10,42 @@
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab" /><!--[if lt IE 7]></base><![endif]-->
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Matlab — IT4I Docs</title>
- <link rel="canonical" href="copy_of_matlab.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="copy_of_matlab.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="copy_of_matlab.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../numerical-languages.html">Numerical languages</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">Numerical languages</a>
<span class="breadcrumbSeparator">
/
@@ -262,8 +259,8 @@
<p>By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use</p>
<pre class=" ">$ module avail MATLAB</pre>
<p>If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.</p>
-<p>If you require the Matlab GUI, please follow the general informations about <a target="_self" title="" class="internal-link" href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html">running graphical applications</a>.</p>
-<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a target="_self" title="" class="internal-link" href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html">here</a>) is recommended.</p>
+<p>If you require the Matlab GUI, please follow the general informations about <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">running graphical applications</a>.</p>
+<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">here</a>) is recommended.</p>
<p>To run Matlab with GUI, use</p>
<pre class=" ">$ matlab</pre>
<p>To run Matlab in text mode, without the Matlab Desktop GUI environment, use</p>
@@ -280,7 +277,7 @@
<p class=" ">With the new mode, MATLAB itself launches the workers via PBS, so you can either use interactive mode or a batch mode on one node, but the actual parallel processing will be done in a separate job started by MATLAB itself. Alternatively, you can use "local" mode to run parallel code on just a single node.</p>
<p class="exclamation">The profile is confusingly named Salomon, but you can use it also on Anselm.</p>
<h3 class=" ">Parallel Matlab interactive session</h3>
-<p>Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a target="_self" title="" class="internal-link" href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html">this page</a>.</p>
+<p>Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">this page</a>.</p>
<pre class=" ">$ xhost +<br />$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00 \<br />-l feature__matlab__MATLAB=1 </pre>
<p>This qsub command example shows how to run Matlab on a single node.</p>
<p>The second part of the command shows how to request all necessary licenses. In this case 1 Matlab-EDU license and 48 Distributed Computing Engines licenses.</p>
@@ -358,8 +355,8 @@ whos % T and W are both distributed arrays here.
% shut down parallel pool
delete(pool)</pre>
<h3 class=" ">Non-interactive Session and Licenses</h3>
-<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a target="_self" title="" class="internal-link" href="../isv_licenses.html">look here</a>.</p>
-<p>In case of non-interactive session please read the <a target="_self" title="" class="internal-link" href="../isv_licenses.html">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
+<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">look here</a>.</p>
+<p>In case of non-interactive session please read the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
<h3 class=" ">Matlab Distributed Computing Engines start up time</h3>
<p>Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:</p>
<table class="plain">
@@ -472,7 +469,7 @@ delete(pool)</pre>
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -488,7 +485,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -504,7 +501,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -520,7 +517,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -536,7 +533,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -552,7 +549,7 @@ delete(pool)</pre>
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -568,7 +565,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -584,7 +581,7 @@ delete(pool)</pre>
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -600,7 +597,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -616,7 +613,7 @@ delete(pool)</pre>
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -632,7 +629,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -648,7 +645,7 @@ delete(pool)</pre>
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -664,10 +661,10 @@ delete(pool)</pre>
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -683,7 +680,7 @@ delete(pool)</pre>
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -699,7 +696,7 @@ delete(pool)</pre>
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -715,7 +712,7 @@ delete(pool)</pre>
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -731,7 +728,7 @@ delete(pool)</pre>
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -747,7 +744,7 @@ delete(pool)</pre>
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -763,7 +760,7 @@ delete(pool)</pre>
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -779,7 +776,7 @@ delete(pool)</pre>
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -795,7 +792,7 @@ delete(pool)</pre>
- <a title="Interpreted languages for numerical computations" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -811,7 +808,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="copy_of_matlab.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab">
<span>Matlab</span>
</a>
@@ -827,7 +824,7 @@ delete(pool)</pre>
- <a title="" class="state-published contenttype-document" href="matlab.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab">
<span>Matlab 2013-2014</span>
</a>
@@ -843,7 +840,7 @@ delete(pool)</pre>
- <a title="" class="state-published contenttype-document" href="octave.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave">
<span>Octave</span>
</a>
@@ -859,7 +856,7 @@ delete(pool)</pre>
- <a title="" class="state-published contenttype-document" href="r.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r">
<span>R</span>
</a>
@@ -884,7 +881,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -900,7 +897,7 @@ delete(pool)</pre>
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -916,7 +913,7 @@ delete(pool)</pre>
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -932,7 +929,7 @@ delete(pool)</pre>
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -948,7 +945,7 @@ delete(pool)</pre>
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -964,7 +961,7 @@ delete(pool)</pre>
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -980,7 +977,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -996,7 +993,7 @@ delete(pool)</pre>
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -1012,7 +1009,7 @@ delete(pool)</pre>
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1028,7 +1025,7 @@ delete(pool)</pre>
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1044,7 +1041,7 @@ delete(pool)</pre>
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1069,7 +1066,7 @@ delete(pool)</pre>
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1085,7 +1082,7 @@ delete(pool)</pre>
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1110,7 +1107,7 @@ delete(pool)</pre>
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1126,7 +1123,7 @@ delete(pool)</pre>
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1142,7 +1139,7 @@ delete(pool)</pre>
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1181,14 +1178,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1210,12 +1207,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1231,7 +1228,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:55 GMT -->
</html>
diff --git a/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md
similarity index 67%
rename from anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md
rename to docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md
index 18fef60df1e41cbf964d13b7c94738ffa79799b5..d65abbc583fe9dc933ede89a50d669c7597aa16a 100644
--- a/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md
@@ -1,11 +1,10 @@
Matlab
======
-
-
+
Introduction
------------
Matlab is available in versions R2015a and R2015b. There are always two
-variants of the release
+variants of the release:
- Non commercial or so called EDU variant, which can be used for
common research and educational purposes.
- Commercial or so called COM variant, which can used also for
@@ -24,11 +23,11 @@ can use Matlab directly on the login nodes. But for all computations use
Matlab on the compute nodes via PBS Pro scheduler.
If you require the Matlab GUI, please follow the general informations
about [running graphical
-applications](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+applications](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc).
Matlab GUI is quite slow using the X forwarding built in the PBS (qsub
-X), so using X11 display redirection either via SSH or directly by
xauth (please see the "GUI Applications on Compute Nodes over VNC" part
-[here](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html))
+[here](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc))
is recommended.
To run Matlab with GUI, use
$ matlab
@@ -37,22 +36,22 @@ use
$ matlab -nodesktop -nosplash
plots, images, etc... will be still available.
[]()Running parallel Matlab using Distributed Computing Toolbox / Engine
-------------------------------------------------------------------------
+---
Distributed toolbox is available only for the EDU variant
The MPIEXEC mode available in previous versions is no longer available
in MATLAB 2015. Also, the programming interface has changed. Refer
to [Release
-Notes](http//www.mathworks.com/help/distcomp/release-notes.html#buanp9e-1).
+Notes](http://www.mathworks.com/help/distcomp/release-notes.html#buanp9e-1).
Delete previously used file mpiLibConf.m, we have observed crashes when
using Intel MPI.
To use Distributed Computing, you first need to setup a parallel
profile. We have provided the profile for you, you can either import it
-in MATLAB command line
+in MATLAB command line:
>> parallel.importProfile('/apps/all/MATLAB/2015a-EDU/SalomonPBSPro.settings')
ans =
SalomonPBSProÂ
Or in the GUI, go to tab HOME -> Parallel -> Manage Cluster
-Profiles..., click Import and navigate to
+Profiles..., click Import and navigate to :
/apps/all/MATLAB/2015a-EDU/SalomonPBSPro.settings
With the new mode, MATLAB itself launches the workers via PBS, so you
can either use interactive mode or a batch mode on one node, but the
@@ -65,16 +64,16 @@ Anselm.
Following example shows how to start interactive session with support
for Matlab GUI. For more information about GUI based applications on
Anselm see [this
-page](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+page](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc).
$ xhost +
- $ qsub -I -v DISPLAY=$(uname -n)$(echo $DISPLAY | cut -d '' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=003000
+ $ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00
-l feature__matlab__MATLAB=1
This qsub command example shows how to run Matlab on a single node.
The second part of the command shows how to request all necessary
licenses. In this case 1 Matlab-EDU license and 48 Distributed Computing
Engines licenses.
Once the access to compute nodes is granted by PBS, user can load
-following modules and start MatlabÂ
+following modules and start Matlab:Â
r1i0n17$ module load MATLAB/2015b-EDU
r1i0n17$ matlab &
### []()Parallel Matlab batch job in Local mode
@@ -84,7 +83,7 @@ execute one matlab worker instance per allocated core.
#!/bin/bash
#PBS -A PROJECT ID
#PBS -q qprod
- #PBS -l select=1ncpus=16mpiprocs=16ompthreads=1
+ #PBS -l select=1:ncpus=16:mpiprocs=16:ompthreads=1
# change to shared scratch directory
SCR=/scratch/work/user/$USER/$PBS_JOBID
mkdir -p $SCR ; cd $SCR || exit
@@ -110,7 +109,7 @@ script before Distributed Computing Toolbox is started.
cluster = parcluster('local')
This script creates scheduler object "cluster" of type "local" that
starts workers locally.Â
-Please note Every Matlab script that needs to initialize/use matlabpool
+Please noteEvery Matlab script that needs to initialize/use matlabpool
has to contain these three lines prior to calling parpool(sched, ...)
function.Â
The last step is to start matlabpool with "cluster" object and correct
@@ -130,7 +129,7 @@ local mode is shown here.Â
n=2000;
W = rand(n,n);
W = distributed(W);
- x = (1n)';
+ x = (1:n)';
x = distributed(x);
spmd
[~, name] = system('hostname')
@@ -150,16 +149,16 @@ This mode uses PBS scheduler to launch the parallel pool. It uses the
SalomonPBSPro profile that needs to be imported to Cluster Manager, as
mentioned before. This methodod uses MATLAB's PBS Scheduler interface -
it spawns the workers in a separate job submitted by MATLAB using qsub.
-This is an example of m-script using PBS mode
+This is an example of m-script using PBS mode:
cluster = parcluster('SalomonPBSPro');
set(cluster, 'SubmitArguments', '-A OPEN-0-0');
- set(cluster, 'ResourceTemplate', '-q qprod -l select=10ncpus=16');
+ set(cluster, 'ResourceTemplate', '-q qprod -l select=10:ncpus=16');
set(cluster, 'NumWorkers', 160);
pool = parpool(cluster, 160);
n=2000;
W = rand(n,n);
W = distributed(W);
- x = (1n)';
+ x = (1:n)';
x = distributed(x);
spmd
[~, name] = system('hostname')
@@ -170,7 +169,7 @@ This is an example of m-script using PBS mode
% shut down parallel pool
delete(pool)
Note that we first construct a cluster object using the imported
-profile, then set some important options, namely SubmitArguments,
+profile, then set some important options, namely SubmitArguments,
where you need to specify accounting id, and ResourceTemplate, where you
need to specify number of nodes to run the job.Â
You can start this script using batch mode the same way as in Local mode
@@ -187,7 +186,7 @@ Please note that this method is experimental.
For this method, you need to use SalomonDirect profile, import it
using [the same way as
SalomonPBSPro](#running-parallel-matlab-using-distributed-computing-toolbox---engine)Â
-This is an example of m-script using direct mode
+This is an example of m-script using direct mode:
parallel.importProfile('/apps/all/MATLAB/2015a-EDU/SalomonDirect.settings')
cluster = parcluster('SalomonDirect');
set(cluster, 'NumWorkers', 48);
@@ -195,7 +194,7 @@ This is an example of m-script using direct mode
n=2000;
W = rand(n,n);
W = distributed(W);
- x = (1n)';
+ x = (1:n)';
x = distributed(x);
spmd
[~, name] = system('hostname')
@@ -211,14 +210,14 @@ appropriate license features with the PBS Pro scheduler, at least the "
-l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More
information about how to check the license features states and how to
request them with PBS Pro, please [look
-here](../isv_licenses.html).
+here](https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses).
In case of non-interactive session please read the [following
-information](../isv_licenses.html) on how to modify the
-qsub command to test for available licenses prior getting the resource
-allocation.
+information](https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses)
+on how to modify the qsub command to test for available licenses prior
+getting the resource allocation.
### Matlab Distributed Computing Engines start up time
Starting Matlab workers is an expensive process that requires certain
-amount of time. For your information please see the following table
+amount of time. For your information please see the following table:
compute nodes number of workers start-up time[s]
--------------- ------------------- --------------------
16 384 831
@@ -231,93 +230,20 @@ UV2000 machine available in queue "qfat" can be used for MATLAB
computations. This is a SMP NUMA machine with large amount of RAM, which
can be beneficial for certain types of MATLAB jobs. CPU cores are
allocated in chunks of 8 for this machine.
-You can use MATLAB on UV2000 in two parallel modes
+You can use MATLAB on UV2000 in two parallel modes :
### Threaded mode
Since this is a SMP machine, you can completely avoid using Parallel
Toolbox and use only MATLAB's threading. MATLAB will automatically
-detect the number of cores you have allocated and will setÂ
-class="monospace">maxNumCompThreads accordingly and certain
-operations, such as fft, , eig, svd,
+detect the number of cores you have allocated and will set <span
+class="monospace">maxNumCompThreads </span>accordingly and certain
+operations, such as <span class="monospace">fft, , eig, svd</span>,
etc. will be automatically run in threads. The advantage of this mode is
-that you don't need to modify your existing sequential codes.
+that you don't need to modify your existing sequential codes.<span
class="monospace">
+</span>
### Local cluster mode
You can also use Parallel Toolbox on UV2000. Use l[ocal cluster
mode](#parallel-matlab-batch-job-in-local-mode),
"SalomonPBSPro" profile will not work.
Â
Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
- .navTreeFolderish
- .contenttype-folder}
- - [Matlab](copy_of_matlab.html)
-
-
- - [Matlab
- 2013-2014](matlab.html)
-
- - [Octave](octave.html)
-
- - [R](r.html)
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/numerical-languages/introduction.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.html
old mode 100755
new mode 100644
similarity index 61%
rename from anselm-cluster-documentation/software/numerical-languages/introduction.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.html
index da9cc3a675f984b61df9d9324a4f35ff4a061991..7981d3f3cec08f9b975c71d36f56318fcd6102ac
--- a/anselm-cluster-documentation/software/numerical-languages/introduction.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:57 GMT -->
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction" /><!--[if lt IE 7]></base><![endif]-->
<meta content="Interpreted languages for numerical computations and analysis" name="description" />
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Numerical languages — IT4I Docs</title>
- <link rel="canonical" href="../numerical-languages.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="introduction.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="introduction.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -247,15 +244,15 @@
<h2 class=" ">Matlab</h2>
<p>MATLAB<sup>®</sup> is a high-level language and interactive environment for numerical computation, visualization, and programming.</p>
<pre class=" ">$ module load MATLAB/2015b-EDU<br />$ matlab</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="matlab.html">Matlab<span class="internal-link"></span> page</a>.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab">Matlab<span class="internal-link"></span> page</a>.</p>
<h2 class=" ">Octave</h2>
<p>GNU Octave is a high-level interpreted language, primarily intended for numerical computations. The Octave language is quite similar to Matlab so that most programs are easily portable.</p>
<pre class=" ">$ module load Octave<br />$ octave</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="octave.html">Octave page</a>.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave">Octave page</a>.</p>
<h2 class=" ">R</h2>
<p>The R is an interpreted language and environment for statistical computing and graphics.</p>
<pre class=" ">$ module load R<br />$ R</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="r.html">R page</a>.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r">R page</a>.</p>
</div>
@@ -331,7 +328,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -347,7 +344,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -363,7 +360,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -379,7 +376,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -395,7 +392,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -411,7 +408,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -427,7 +424,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -443,7 +440,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -459,7 +456,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -475,7 +472,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -491,7 +488,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -507,7 +504,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -523,10 +520,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -542,7 +539,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -558,7 +555,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -574,7 +571,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -590,7 +587,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -606,7 +603,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -622,7 +619,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -638,7 +635,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -654,7 +651,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -670,7 +667,7 @@
- <a title="" class="state-published contenttype-document" href="copy_of_matlab.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab">
<span>Matlab</span>
</a>
@@ -686,7 +683,7 @@
- <a title="" class="state-published contenttype-document" href="matlab.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab">
<span>Matlab 2013-2014</span>
</a>
@@ -702,7 +699,7 @@
- <a title="" class="state-published contenttype-document" href="octave.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave">
<span>Octave</span>
</a>
@@ -718,7 +715,7 @@
- <a title="" class="state-published contenttype-document" href="r.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r">
<span>R</span>
</a>
@@ -743,7 +740,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -759,7 +756,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -775,7 +772,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -791,7 +788,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -807,7 +804,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -823,7 +820,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -839,7 +836,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -855,7 +852,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -871,7 +868,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -887,7 +884,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -903,7 +900,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -928,7 +925,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -944,7 +941,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -969,7 +966,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -985,7 +982,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1001,7 +998,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.md
new file mode 100644
index 0000000000000000000000000000000000000000..d21af4a17880d87385405d699e9a2b6f0922528e
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.md
@@ -0,0 +1,33 @@
+Numerical languages
+===================
+Interpreted languages for numerical computations and analysis
+
+Introduction
+------------
+This section contains a collection of high-level interpreted languages,
+primarily intended for numerical computations.
+Matlab
+------
+MATLAB^®^ is a high-level language and interactive environment for
+numerical computation, visualization, and programming.
+ $ module load MATLAB/2015b-EDU
+ $ matlab
+Read more at the [Matlab<span class="internal-link"></span>
+page](https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab).
+Octave
+------
+GNU Octave is a high-level interpreted language, primarily intended for
+numerical computations. The Octave language is quite similar to Matlab
+so that most programs are easily portable.
+ $ module load Octave
+ $ octave
+Read more at the [Octave
+page](https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave).
+R
+-
+The R is an interpreted language and environment for statistical
+computing and graphics.
+ $ module load R
+ $ R
+Read more at the [R
+page](https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r).
diff --git a/anselm-cluster-documentation/software/numerical-languages/matlab.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.html
old mode 100755
new mode 100644
similarity index 68%
rename from anselm-cluster-documentation/software/numerical-languages/matlab.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.html
index 3b5fb2ddd78807ff111e31cc31b3cb29a254e3e8..dc80a126e937cf090f5372b8b93cc770d16d1da6
--- a/anselm-cluster-documentation/software/numerical-languages/matlab.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.html
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab" /><!--[if lt IE 7]></base><![endif]-->
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
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<title>Matlab 2013-2014 — IT4I Docs</title>
- <link rel="canonical" href="matlab.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="matlab.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="matlab.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
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-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../numerical-languages.html">Numerical languages</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">Numerical languages</a>
<span class="breadcrumbSeparator">
/
@@ -251,7 +248,7 @@
<div id="parent-fieldname-text-41bf242708954438ac56e1a431788c0e" class="">
<h2 class=" ">Introduction</h2>
-<p class="exclamation">This document relates to the old versions R2013 and R2014. For MATLAB 2015, please use <a target="_self" title="" class="internal-link" href="copy_of_matlab.html">this documentation instead</a>.</p>
+<p class="exclamation">This document relates to the old versions R2013 and R2014. For MATLAB 2015, please use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab">this documentation instead</a>.</p>
<p>Matlab is available in the latest stable version. There are always two variants of the release:</p>
<ul>
<li>Non commercial or so called EDU variant, which can be used for common research and educational purposes.</li>
@@ -263,8 +260,8 @@
<p>By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use</p>
<pre class=" ">$ module avail matlab</pre>
<p>If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.</p>
-<p>If you require the Matlab GUI, please follow the general informations about <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html">running graphical applications</a>.</p>
-<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html">here</a>) is recommended.</p>
+<p>If you require the Matlab GUI, please follow the general informations about <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">running graphical applications</a>.</p>
+<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">here</a>) is recommended.</p>
<p>To run Matlab with GUI, use</p>
<pre class=" ">$ matlab</pre>
<p>To run Matlab in text mode, without the Matlab Desktop GUI environment, use</p>
@@ -272,14 +269,14 @@
<p>plots, images, etc... will be still available.</p>
<h2 class=" ">Running parallel Matlab using Distributed Computing Toolbox / Engine</h2>
<p>Recommended parallel mode for running parallel Matlab on Anselm is MPIEXEC mode. In this mode user allocates resources through PBS prior to starting Matlab. Once resources are granted the main Matlab instance is started on the first compute node assigned to job by PBS and workers are started on all remaining nodes. User can use both interactive and non-interactive PBS sessions. This mode guarantees that the data processing is not performed on login nodes, but all processing is on compute nodes.</p>
-<p>Â <img title="Parallel Matlab" class="image-inline" alt="Parallel Matlab" src="Matlab.png" /></p>
+<p>Â <img alt="Parallel Matlab" class="image-inline" title="Parallel Matlab" src="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/Matlab.png" /></p>
<p>For the performance reasons Matlab should use system MPI. On Anselm the supported MPI implementation for Matlab is Intel MPI. To switch to system MPI user has to override default Matlab setting by creating new configuration file in its home directory. The path and file name has to be exactly the same as in the following listing:</p>
<pre class=" "><strong>$ vim ~/matlab/mpiLibConf.m </strong></pre>
<pre class=" "><strong>function [lib, extras] = mpiLibConf</strong><br /><strong>%MATLAB MPI Library overloading for Infiniband Networks</strong><br /><br /><strong>mpich = '/opt/intel/impi/4.1.1.036/lib64/';</strong><br /><br /><strong>disp('Using Intel MPI 4.1.1.036 over Infiniband')</strong><br /><br /><strong>lib = strcat(mpich, 'libmpich.so');</strong><br /><strong>mpl = strcat(mpich, 'libmpl.so');</strong><br /><strong>opa = strcat(mpich, 'libopa.so');</strong><br /><br /><strong>extras = {};</strong></pre>
<p>System MPI library allows Matlab to communicate through 40Gbps Infiniband QDR interconnect instead of slower 1Gb ethernet network.</p>
<p class="callout">Please note: The path to MPI library in "mpiLibConf.m" has to match with version of loaded Intel MPI module. In this example the version 4.1.1.036 of Iintel MPI is used by Matlab and therefore module impi/4.1.1.036Â has to be loaded prior to starting Matlab.</p>
<h3 class=" ">Parallel Matlab interactive session</h3>
-<p>Once this file is in place, user can request resources from PBS. Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html">this page</a>.</p>
+<p>Once this file is in place, user can request resources from PBS. Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">this page</a>.</p>
<pre class=" ">$ xhost +<br />$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=4:ncpus=16:mpiprocs=16 -l walltime=00:30:00 \<br />-l feature__matlab__MATLAB=1 </pre>
<p>This qsub command example shows how to run Matlab with 32 workers in following configuration: 2 nodes (use all 16 cores per node) and 16 workers = mpirocs per node (-l select=2:ncpus=16:mpiprocs=16). If user requires to run smaller number of workers per node then the "mpiprocs" parameter has to be changed.</p>
<p>The second part of the command shows how to request all necessary licenses. In this case 1 Matlab-EDU license and 32 Distributed Computing Engines licenses.</p>
@@ -302,8 +299,8 @@
<pre class=" ">sched = findResource('scheduler', 'type', 'mpiexec');<br />set(sched, 'MpiexecFileName', '/apps/intel/impi/4.1.1/bin/mpirun')<br />set(sched, 'EnvironmentSetMethod', 'setenv')<br />set(sched, 'SubmitArguments', '') <br />sched<br /><br />matlabpool(sched,32);<br /><br />n=2000;<br /><br />W = rand(n,n);<br />W = distributed(W);<br />x = (1:n)';<br />x = distributed(x);<br />spmd<br />[~, name] = system('hostname')<br />   <br />   T = W*x; % Calculation performed on labs, in parallel.<br />            % T and W are both codistributed arrays here.<br />end<br />T;<br />whos        % T and W are both distributed arrays here.<br /><br />matlabpool close<br />quit</pre>
<p>You can copy and paste the example in a .m file and execute. Note that the matlabpool size should correspond to <strong>total number of cores</strong> available on allocated nodes.</p>
<h3 class=" ">Non-interactive Session and Licenses</h3>
-<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a target="_self" title="" class="internal-link" href="../isv_licenses.html">look here</a>.</p>
-<p>In case of non-interactive session please read the <a target="_self" title="" class="internal-link" href="../isv_licenses.html">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
+<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">look here</a>.</p>
+<p>In case of non-interactive session please read the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
<h3 class=" ">Matlab Distributed Computing Engines start up time</h3>
<p>Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:</p>
<table class="plain">
@@ -409,7 +406,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -425,7 +422,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -441,7 +438,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -457,7 +454,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -473,7 +470,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -489,7 +486,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -505,7 +502,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -521,7 +518,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -537,7 +534,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -553,7 +550,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -569,7 +566,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -585,7 +582,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -601,10 +598,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -620,7 +617,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -636,7 +633,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -652,7 +649,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -668,7 +665,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -684,7 +681,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -700,7 +697,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -716,7 +713,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -732,7 +729,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -748,7 +745,7 @@
- <a title="" class="state-published contenttype-document" href="copy_of_matlab.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab">
<span>Matlab</span>
</a>
@@ -764,7 +761,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="matlab.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab">
<span>Matlab 2013-2014</span>
</a>
@@ -780,7 +777,7 @@
- <a title="" class="state-published contenttype-document" href="octave.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave">
<span>Octave</span>
</a>
@@ -796,7 +793,7 @@
- <a title="" class="state-published contenttype-document" href="r.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r">
<span>R</span>
</a>
@@ -821,7 +818,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -837,7 +834,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -853,7 +850,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -869,7 +866,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -885,7 +882,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -901,7 +898,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -917,7 +914,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -933,7 +930,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -949,7 +946,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -965,7 +962,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -981,7 +978,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1006,7 +1003,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1022,7 +1019,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1047,7 +1044,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1063,7 +1060,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1079,7 +1076,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1118,14 +1115,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1147,12 +1144,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1168,7 +1165,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:57 GMT -->
</html>
diff --git a/anselm-cluster-documentation/software/numerical-languages/matlab.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.md
similarity index 65%
rename from anselm-cluster-documentation/software/numerical-languages/matlab.md
rename to docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.md
index 172053229b155d9ef26ed68aa5b4e44cccd8f9d6..833a63de9913ede2ed8f5e4109dd6ae0c078b94a 100644
--- a/anselm-cluster-documentation/software/numerical-languages/matlab.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.md
@@ -1,14 +1,13 @@
Matlab 2013-2014
================
-
-
+
Introduction
------------
This document relates to the old versions R2013 and R2014. For MATLAB
2015, please use [this documentation
-instead](copy_of_matlab.html).
+instead](https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab).
Matlab is available in the latest stable version. There are always two
-variants of the release
+variants of the release:
- Non commercial or so called EDU variant, which can be used for
common research and educational purposes.
- Commercial or so called COM variant, which can used also for
@@ -27,12 +26,12 @@ can use Matlab directly on the login nodes. But for all computations use
Matlab on the compute nodes via PBS Pro scheduler.
If you require the Matlab GUI, please follow the general informations
about [running graphical
-applications](resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html).
+applications](resolveuid/11e53ad0d2fd4c5187537f4baeedff33).
Matlab GUI is quite slow using the X forwarding built in the PBS (qsub
-X), so using X11 display redirection either via SSH or directly by
xauth (please see the "GUI Applications on Compute Nodes over VNC" part
-[here](resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html))
-is recommended.
+[here](resolveuid/11e53ad0d2fd4c5187537f4baeedff33)) is
+recommended.
To run Matlab with GUI, use
$ matlab
To run Matlab in text mode, without the Matlab Desktop GUI environment,
@@ -40,7 +39,7 @@ use
$ matlab -nodesktop -nosplash
plots, images, etc... will be still available.
Running parallel Matlab using Distributed Computing Toolbox / Engine
---------------------------------------------------------------------
+----------------------
Recommended parallel mode for running parallel Matlab on Anselm is
MPIEXEC mode. In this mode user allocates resources through PBS prior to
starting Matlab. Once resources are granted the main Matlab instance is
@@ -49,12 +48,13 @@ started on all remaining nodes. User can use both interactive and
non-interactive PBS sessions. This mode guarantees that the data
processing is not performed on login nodes, but all processing is on
compute nodes.
-Â 
+Â 
For the performance reasons Matlab should use system MPI. On Anselm the
supported MPI implementation for Matlab is Intel MPI. To switch to
system MPI user has to override default Matlab setting by creating new
configuration file in its home directory. The path and file name has to
-be exactly the same as in the following listing
+be exactly the same as in the following listing:
$ vim ~/matlab/mpiLibConf.m
function [lib, extras] = mpiLibConf
%MATLAB MPI Library overloading for Infiniband Networks
@@ -66,7 +66,7 @@ be exactly the same as in the following listing
extras = {};
System MPI library allows Matlab to communicate through 40Gbps
Infiniband QDR interconnect instead of slower 1Gb ethernet network.
-Please note The path to MPI library in "mpiLibConf.m" has to match with
+Please noteThe path to MPI library in "mpiLibConf.m" has to match with
version of loaded Intel MPI module. In this example the version
4.1.1.036 of Iintel MPI is used by Matlab and therefore module
impi/4.1.1.036Â has to be loaded prior to starting Matlab.
@@ -75,20 +75,20 @@ Once this file is in place, user can request resources from PBS.
Following example shows how to start interactive session with support
for Matlab GUI. For more information about GUI based applications on
Anselm see [this
-page](resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html).
+page](resolveuid/11e53ad0d2fd4c5187537f4baeedff33).
$ xhost +
- $ qsub -I -v DISPLAY=$(uname -n)$(echo $DISPLAY | cut -d '' -f 2) -A NONE-0-0 -q qexp -l select=4ncpus=16mpiprocs=16 -l walltime=003000
+ $ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=4:ncpus=16:mpiprocs=16 -l walltime=00:30:00
-l feature__matlab__MATLAB=1
This qsub command example shows how to run Matlab with 32 workers in
-following configuration 2 nodes (use all 16 cores per node) and 16
-workers = mpirocs per node (-l select=2ncpus=16mpiprocs=16). If user
+following configuration2 nodes (use all 16 cores per node) and 16
+workers = mpirocs per node (-l select=2:ncpus=16:mpiprocs=16). If user
requires to run smaller number of workers per node then the "mpiprocs"
parameter has to be changed.
The second part of the command shows how to request all necessary
licenses. In this case 1 Matlab-EDU license and 32 Distributed Computing
Engines licenses.
Once the access to compute nodes is granted by PBS, user can load
-following modules and start MatlabÂ
+following modules and start Matlab:Â
cn79$ module load matlab/R2013a-EDU
cn79$ module load impi/4.1.1.036
cn79$ matlab &
@@ -99,7 +99,7 @@ execute one matlab worker instance per allocated core.
#!/bin/bash
#PBS -A PROJECT ID
#PBS -q qprod
- #PBS -l select=2ncpus=16mpiprocs=16ompthreads=1
+ #PBS -l select=2:ncpus=16:mpiprocs=16:ompthreads=1
# change to shared scratch directory
SCR=/scratch/$USER/$PBS_JOBID
mkdir -p $SCR ; cd $SCR || exit
@@ -130,7 +130,7 @@ This script creates scheduler object "sched" of type "mpiexec" that
starts workers using mpirun tool. To use correct version of mpirun, the
second line specifies the path to correct version of system Intel MPI
library.
-Please note Every Matlab script that needs to initialize/use matlabpool
+Please noteEvery Matlab script that needs to initialize/use matlabpool
has to contain these three lines prior to calling matlabpool(sched, ...)
function.Â
The last step is to start matlabpool with "sched" object and correct
@@ -154,7 +154,7 @@ show here.Â
n=2000;
W = rand(n,n);
W = distributed(W);
- x = (1n)';
+ x = (1:n)';
x = distributed(x);
spmd
[~, name] = system('hostname')
@@ -175,14 +175,14 @@ appropriate license features with the PBS Pro scheduler, at least the "
-l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More
information about how to check the license features states and how to
request them with PBS Pro, please [look
-here](../isv_licenses.html).
+here](https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses).
In case of non-interactive session please read the [following
-information](../isv_licenses.html) on how to modify the
-qsub command to test for available licenses prior getting the resource
-allocation.
+information](https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses)
+on how to modify the qsub command to test for available licenses prior
+getting the resource allocation.
### Matlab Distributed Computing Engines start up time
Starting Matlab workers is an expensive process that requires certain
-amount of time. For your information please see the following table
+amount of time. For your information please see the following table:
compute nodes number of workers start-up time[s]
--------------- ------------------- --------------------
16 256 1008
@@ -191,77 +191,3 @@ amount of time. For your information please see the following table
2 32 210
Â
Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
- .navTreeFolderish
- .contenttype-folder}
- - [Matlab](copy_of_matlab.html)
-
- - [Matlab
- 2013-2014](matlab.html)
-
-
- - [Octave](octave.html)
-
- - [R](r.html)
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/numerical-languages/octave.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.html
old mode 100755
new mode 100644
similarity index 66%
rename from anselm-cluster-documentation/software/numerical-languages/octave.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.html
index ab57feab1eacdbfcf49f93e85d056361778394a1..c14bfd1099ef68f50003cebc412e68e8d6c5e3c5
--- a/anselm-cluster-documentation/software/numerical-languages/octave.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:03 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/IEFixes-cachekey-ec9b60024fd235ff2c883b4b54db91cb.css" />
<![endif]-->
- <style type="text/css" media="screen">@import url(../../../portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Octave — IT4I Docs</title>
- <link rel="canonical" href="octave.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="octave.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="octave.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../numerical-languages.html">Numerical languages</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">Numerical languages</a>
<span class="breadcrumbSeparator">
/
@@ -282,14 +279,14 @@
<pre class=" ">$ mkoctfile -v</pre>
<p>Octave may use MPI for interprocess communication<br />This functionality is currently not supported on Anselm cluster. In case you require the octave interface to MPI, please contact <a class="external-link" href="https://support.it4i.cz/rt/" target="_self" title="">Anselm support</a>.</p>
<h2 class=" ">Xeon Phi Support</h2>
-<p>Octave may take advantage of the Xeon Phi accelerators. This will only work on the <a target="_self" title="" class="internal-link" href="../intel-xeon-phi.html">Intel Xeon Phi</a> <a target="_self" title="" class="internal-link" href="../../compute-nodes.html">accelerated nodes</a>.</p>
+<p>Octave may take advantage of the Xeon Phi accelerators. This will only work on the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">Intel Xeon Phi</a> <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">accelerated nodes</a>.</p>
<h3 class=" ">Automatic offload support</h3>
-<p>Octave can accelerate BLAS type operations (in particular the Matrix Matrix multiplications] on the Xeon Phi accelerator, via <a target="_self" title="" class="external-link" href="../intel-xeon-phi.html#section-3">Automatic Offload using the MKL library</a></p>
+<p>Octave can accelerate BLAS type operations (in particular the Matrix Matrix multiplications] on the Xeon Phi accelerator, via <a title="" class="external-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi#section-3">Automatic Offload using the MKL library</a></p>
<p>Example</p>
<pre class=" ">$ export OFFLOAD_REPORT=2<br />$ export MKL_MIC_ENABLE=1<br />$ module load octave<br />$ octave -q<br />octave:1> A=rand(10000); B=rand(10000);<br />octave:2> tic; C=A*B; toc<br />[MKL] [MIC --] [AO Function]Â Â Â DGEMM<br />[MKL] [MIC --] [AO DGEMM Workdivision]Â Â Â 0.32 0.68<br />[MKL] [MIC 00] [AO DGEMM CPU Time]Â Â Â 2.896003 seconds<br />[MKL] [MIC 00] [AO DGEMM MIC Time]Â Â Â 1.967384 seconds<br />[MKL] [MIC 00] [AO DGEMM CPU->MIC Data]Â Â Â 1347200000 bytes<br />[MKL] [MIC 00] [AO DGEMM MIC->CPU Data]Â Â Â 2188800000 bytes<br />Elapsed time is 2.93701 seconds.</pre>
<p>In this example, the calculation was automatically divided among the CPU cores and the Xeon Phi MIC accelerator, reducing the total runtime from 6.3 secs down to 2.9 secs.</p>
<h3 class=" ">Native support</h3>
-<p>A version of <a target="_self" title="" class="external-link" href="../intel-xeon-phi.html#section-4">native</a> Octave is compiled for Xeon Phi accelerators. Some limitations apply for this version:</p>
+<p>A version of <a title="" class="external-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi#section-4">native</a> Octave is compiled for Xeon Phi accelerators. Some limitations apply for this version:</p>
<ul>
<li>Only command line support. GUI, graph plotting etc. is not supported.</li>
<li>Command history in interactive mode is not supported.</li>
@@ -374,7 +371,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -390,7 +387,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -406,7 +403,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -422,7 +419,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -438,7 +435,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -454,7 +451,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -470,7 +467,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -486,7 +483,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -502,7 +499,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -518,7 +515,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -534,7 +531,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -550,7 +547,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -566,10 +563,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -585,7 +582,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -601,7 +598,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -617,7 +614,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -633,7 +630,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -649,7 +646,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -665,7 +662,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -681,7 +678,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -697,7 +694,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -713,7 +710,7 @@
- <a title="" class="state-published contenttype-document" href="copy_of_matlab.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab">
<span>Matlab</span>
</a>
@@ -729,7 +726,7 @@
- <a title="" class="state-published contenttype-document" href="matlab.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab">
<span>Matlab 2013-2014</span>
</a>
@@ -745,7 +742,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="octave.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave">
<span>Octave</span>
</a>
@@ -761,7 +758,7 @@
- <a title="" class="state-published contenttype-document" href="r.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r">
<span>R</span>
</a>
@@ -786,7 +783,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -802,7 +799,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -818,7 +815,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -834,7 +831,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -850,7 +847,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -866,7 +863,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -882,7 +879,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -898,7 +895,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -914,7 +911,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -930,7 +927,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -946,7 +943,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -971,7 +968,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -987,7 +984,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1012,7 +1009,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1028,7 +1025,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1044,7 +1041,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1083,14 +1080,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -1112,12 +1109,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1133,7 +1130,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/anselm-cluster-documentation/software/numerical-languages/octave.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.md
similarity index 53%
rename from anselm-cluster-documentation/software/numerical-languages/octave.md
rename to docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.md
index f62b5081d0ee5b285489f0fb26d5b13f0a5c636f..c14965c877a4019eb8854ed5cda16bc244959710 100644
--- a/anselm-cluster-documentation/software/numerical-languages/octave.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.md
@@ -1,7 +1,6 @@
Octave
======
-
-
+
Introduction
------------
GNU Octave is a high-level interpreted language, primarily intended for
@@ -12,14 +11,14 @@ for data visualization and manipulation. Octave is normally used through
its interactive command line interface, but it can also be used to write
non-interactive programs. The Octave language is quite similar to Matlab
so that most programs are easily portable. Read more on
-****
+<http://www.gnu.org/software/octave/>****
**
**Two versions of octave are available on Anselm, via module
Version module
- ----------------------------------------------------------- ---------------------------
+ ------------- ----
Octave 3.8.2, compiled with GCC and Multithreaded MKL Octave/3.8.2-gimkl-2.11.5
Octave 4.0.1, compiled with GCC and Multithreaded MKL Octave/4.0.1-gimkl-2.11.5
- Octave 4.0.0, compiled with GCC and OpenBLAS Octave/4.0.0-foss-2015g
+ Octave 4.0.0, compiled with <span>GCC and OpenBLAS</span> Octave/4.0.0-foss-2015g
 Modules and execution
----------------------
$ module load Octave
@@ -30,7 +29,7 @@ calculation kernels without any penalty. By default, octave would
parallelize to 16 threads. You may control the threads by setting the
OMP_NUM_THREADS environment variable.
To run octave interactively, log in with ssh -X parameter for X11
-forwarding. Run octave
+forwarding. Run octave:
$ octave
To run octave in batch mode, write an octave script, then write a bash
jobscript and execute via the qsub command. By default, octave will use
@@ -52,7 +51,7 @@ This script may be submitted directly to the PBS workload manager via
the qsub command. The inputs are in octcode.m file, outputs in
output.out file. See the single node jobscript example in the [Job
execution
-section](http//support.it4i.cz/docs/anselm-cluster-documentation/resource-allocation-and-job-execution).
+section](http://support.it4i.cz/docs/anselm-cluster-documentation/resource-allocation-and-job-execution).
The octave c compiler mkoctfile calls the GNU gcc 4.8.1 for compiling
native c code. This is very useful for running native c subroutines in
octave environment.
@@ -60,24 +59,26 @@ octave environment.
Octave may use MPI for interprocess communication
This functionality is currently not supported on Anselm cluster. In case
you require the octave interface to MPI, please contact [Anselm
-support](https//support.it4i.cz/rt/).
+support](https://support.it4i.cz/rt/).
Xeon Phi Support
----------------
Octave may take advantage of the Xeon Phi accelerators. This will only
-work on the [Intel Xeon Phi](../intel-xeon-phi.html)
-[accelerated nodes](../../compute-nodes.html).
+work on the [Intel Xeon
+Phi](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi)
+[accelerated
+nodes](https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes).
### Automatic offload support
Octave can accelerate BLAS type operations (in particular the Matrix
Matrix multiplications] on the Xeon Phi accelerator, via [Automatic
Offload using the MKL
-library](../intel-xeon-phi.html#section-3)
+library](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi#section-3)
Example
$ export OFFLOAD_REPORT=2
$ export MKL_MIC_ENABLE=1
$ module load octave
$ octave -q
- octave1> A=rand(10000); B=rand(10000);
- octave2> tic; C=A*B; toc
+ octave:1> A=rand(10000); B=rand(10000);
+ octave:2> tic; C=A*B; toc
[MKL] [MIC --] [AO Function]Â Â Â DGEMM
[MKL] [MIC --] [AO DGEMM Workdivision]Â Â Â 0.32 0.68
[MKL] [MIC 00] [AO DGEMM CPU Time]Â Â Â 2.896003 seconds
@@ -89,98 +90,25 @@ In this example, the calculation was automatically divided among the CPU
cores and the Xeon Phi MIC accelerator, reducing the total runtime from
6.3 secs down to 2.9 secs.
### Native support
-A version of [native](../intel-xeon-phi.html#section-4)
+A version of
+[native](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi#section-4)
Octave is compiled for Xeon Phi accelerators. Some limitations apply for
-this version
+this version:
- Only command line support. GUI, graph plotting etc. is
not supported.
- Command history in interactive mode is not supported.
Octave is linked with parallel Intel MKL, so it best suited for batch
processing of tasks that utilize BLAS, LAPACK and FFT operations. By
default, number of threads is set to 120, you can control this
-with OMP_NUM_THREADS environment
-variable.
+with <span><span class="monospace">OMP_NUM_THREADS</span> environment
+variable. </span>
Calculations that do not employ parallelism (either by using parallel
-MKL eg. via matrix operations, fork()
+MKL eg. via matrix operations, <span class="monospace">fork()</span>
function, [parallel
-package](http//octave.sourceforge.net/parallel/) or
+package](http://octave.sourceforge.net/parallel/) or
other mechanism) will actually run slower than on host CPU.
-To use Octave on a node with Xeon Phi
+<span>To use Octave on a node with Xeon Phi:</span>
$ ssh mic0 # login to the MIC card
$ source /apps/tools/octave/3.8.2-mic/bin/octave-env.sh # set up environment variables
$ octave -q /apps/tools/octave/3.8.2-mic/example/test0.m # run an exampleÂ
-Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
- .navTreeFolderish
- .contenttype-folder}
- - [Matlab](copy_of_matlab.html)
-
- - [Matlab
- 2013-2014](matlab.html)
-
- - [Octave](octave.html)
-
-
- - [R](r.html)
-
- - [Virtualization](../virtualization.html)
+<span>Â </span>
diff --git a/anselm-cluster-documentation/software/numerical-languages/parallel.pdf b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/package-parallel-vignette
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/software/numerical-languages/parallel.pdf
rename to docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/package-parallel-vignette
diff --git a/anselm-cluster-documentation/software/numerical-languages/r.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.html
old mode 100755
new mode 100644
similarity index 72%
rename from anselm-cluster-documentation/software/numerical-languages/r.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.html
index 493958e0a56e7b2c803c5656671540cfa2ac43bd..ae71f7fbbad3eee77946700dbcc283f1abf809f9
--- a/anselm-cluster-documentation/software/numerical-languages/r.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:03 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>R — IT4I Docs</title>
- <link rel="canonical" href="r.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="r.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="r.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../numerical-languages.html">Numerical languages</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">Numerical languages</a>
<span class="breadcrumbSeparator">
/
@@ -285,7 +282,7 @@
<p>To run R in batch mode, write an R script, then write a bash jobscript and execute via the qsub command. By default, R will use 16 threads when running MKL kernels.</p>
<p>Example jobscript:</p>
<pre class=" ">#!/bin/bash<br /><br /># change to local scratch directory<br />cd /lscratch/$PBS_JOBID || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/rscript.R .<br /><br /># load R module<br />module load R<br /><br /># execute the calculation<br />R CMD BATCH rscript.R routput.out<br /><br /># copy output file to home<br />cp routput.out $PBS_O_WORKDIR/.<br /><br />#exit<br />exit</pre>
-<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs are in rscript.R file, outputs in routput.out file. See the single node jobscript example in the <a target="_self" title="" class="internal-link" href="../../resource-allocation-and-job-execution/job-submission-and-execution.html">Job execution section</a>.</p>
+<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs are in rscript.R file, outputs in routput.out file. See the single node jobscript example in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">Job execution section</a>.</p>
<h2 class=" ">Parallel R</h2>
<p>Parallel execution of R may be achieved in many ways. One approach is the implied parallelization due to linked libraries or specially enabled functions, as <a class="anchor-link" href="#interactive-execution" target="_self" title="">described above</a>. In the following sections, we focus on explicit parallelization, where parallel constructs are directly stated within the R script.</p>
<h2 class=" "><a name="package-parallel"></a>Package parallel</h2>
@@ -294,7 +291,7 @@
<pre class=" ">$ R<br />> library(parallel)</pre>
<p class=" ">More information and examples may be obtained directly by reading the documentation available in R</p>
<pre class=" ">> ?parallel<br />> library(help = "parallel")<br />> <span class="internal-link">vignette("parallel")</span></pre>
-<p class=" ">Download the package <a target="_self" title="" class="internal-link" href="parallel.pdf">parallell</a> vignette.</p>
+<p class=" ">Download the package <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/package-parallel-vignette">parallell</a> vignette.</p>
<p class=" ">The forking is the most simple to use. Forking family of functions provide parallelized, drop in replacement for the serial apply() family of functions.</p>
<p class="callout">Forking via package parallel provides functionality similar to OpenMP construct<br />#omp parallel for <br /><br />Only cores of single node can be utilized this way!</p>
<p class=" ">Forking example:</p>
@@ -304,7 +301,7 @@
<p>Every evaluation of the integrad function runs in parallel on different process.</p>
<h2 class=" ">Package Rmpi</h2>
<p class="callout">package Rmpi provides an interface (wrapper) to MPI APIs.</p>
-<p>It also provides interactive R slave environment. On Anselm, Rmpi provides interface to the <a target="_self" title="" class="internal-link" href="../mpi-1/Running_OpenMPI.html">OpenMPI</a>.</p>
+<p>It also provides interactive R slave environment. On Anselm, Rmpi provides interface to the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI">OpenMPI</a>.</p>
<p>Read more on Rmpi at <a class="external-link" href="http://cran.r-project.org/web/packages/Rmpi/" target="_self" title="">http://cran.r-project.org/web/packages/Rmpi/</a>, reference manual is available at <a class="external-link" href="http://cran.r-project.org/web/packages/Rmpi/Rmpi.pdf" target="_self" title="">http://cran.r-project.org/web/packages/Rmpi/Rmpi.pdf</a></p>
<p>When using package Rmpi, both openmpi and R modules must be loaded</p>
<pre class=" ">$ module load openmpi<br />$ module load R</pre>
@@ -336,7 +333,7 @@
<p>The R parallel jobs are executed via the PBS queue system exactly as any other parallel jobs. User must create an appropriate jobscript and submit via the <strong>qsub</strong></p>
<p>Example jobscript for <a class="anchor-link" href="#static-rmpi" target="_self" title="">static Rmpi</a> parallel R execution, running 1 process per core:</p>
<pre class=" ">#!/bin/bash<br />#PBS -q qprod<br />#PBS -N Rjob<br />#PBS -l select=100:ncpus=16:mpiprocs=16:ompthreads=1<br /><br /># change to scratch directory<span class="pln"><br />SCRDIR</span><span class="pun">=/</span><span class="pln">scratch</span><span class="pun">/</span><span class="pln">$USER</span><span class="pun">/</span><span class="pln">myjob</span><br /><span class="pln">cd $SCRDIR </span><span class="pun">||</span><span class="pln"> exit</span><br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/rscript.R .<br /><br /># load R and openmpi module<br />module load R<br />module load openmpi<br /><br /># execute the calculation<br />mpiexec -bycore -bind-to-core R --slave --no-save --no-restore -f rscript.R<br /><br /># copy output file to home<br />cp routput.out $PBS_O_WORKDIR/.<br /><br />#exit<br />exit</pre>
-For more information about jobscripts and MPI execution refer to the <a target="_self" title="" class="internal-link" href="../../resource-allocation-and-job-execution/job-submission-and-execution.html">Job submission</a> and general <a target="_self" title="" class="internal-link" href="../mpi-1.html">MPI</a> sections.</div>
+For more information about jobscripts and MPI execution refer to the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">Job submission</a> and general <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">MPI</a> sections.</div>
</div>
</div>
@@ -413,7 +410,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -429,7 +426,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -445,7 +442,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -461,7 +458,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -477,7 +474,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -493,7 +490,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -509,7 +506,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -525,7 +522,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -541,7 +538,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -557,7 +554,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -573,7 +570,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -589,7 +586,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -605,10 +602,10 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -624,7 +621,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -640,7 +637,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -656,7 +653,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -672,7 +669,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -688,7 +685,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -704,7 +701,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -720,7 +717,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -736,7 +733,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="Interpreted languages for numerical computations" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -752,7 +749,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published contenttype-document" href="copy_of_matlab.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab">
<span>Matlab</span>
</a>
@@ -768,7 +765,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published contenttype-document" href="matlab.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab">
<span>Matlab 2013-2014</span>
</a>
@@ -784,7 +781,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published contenttype-document" href="octave.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave">
<span>Octave</span>
</a>
@@ -800,7 +797,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="r.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r">
<span>R</span>
</a>
@@ -825,7 +822,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -841,7 +838,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -857,7 +854,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -873,7 +870,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -889,7 +886,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -905,7 +902,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -921,7 +918,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -937,7 +934,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -953,7 +950,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -969,7 +966,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -985,7 +982,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1010,7 +1007,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1026,7 +1023,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1051,7 +1048,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1067,7 +1064,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1083,7 +1080,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1122,14 +1119,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1151,12 +1148,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1172,7 +1169,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:04 GMT -->
</html>
diff --git a/anselm-cluster-documentation/software/numerical-languages/r.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.md
similarity index 70%
rename from anselm-cluster-documentation/software/numerical-languages/r.md
rename to docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.md
index f981dc047b9dd45b3e7e15efd663d82f97e9330c..f7abed65a21defa132f7f5a40afcf21bcd204443 100644
--- a/anselm-cluster-documentation/software/numerical-languages/r.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.md
@@ -1,7 +1,6 @@
R
=
-
-
+
Introduction {#parent-fieldname-title}
------------
The R is a language and environment for statistical computing and
@@ -17,7 +16,8 @@ full control.
Another convenience is the ease with which the C code or third party
libraries may be integrated within R.
Extensive support for parallel computing is available within R.
-Read more on ,
+Read more on <http://www.r-project.org/>,
+<http://cran.r-project.org/doc/manuals/r-release/R-lang.html>
Modules
-------
****The R version 3.0.1 is available on Anselm, along with GUI interface
@@ -37,14 +37,14 @@ parallelize to 16 threads. You may control the threads by setting the
OMP_NUM_THREADS environment variable.
### Interactive execution
To run R interactively, using Rstudio GUI, log in with ssh -X parameter
-for X11 forwarding. Run rstudio
+for X11 forwarding. Run rstudio:
$ module load Rstudio
$ rstudio
### Batch execution
To run R in batch mode, write an R script, then write a bash jobscript
and execute via the qsub command. By default, R will use 16 threads when
running MKL kernels.
-Example jobscript
+Example jobscript:
#!/bin/bash
# change to local scratch directory
cd /lscratch/$PBS_JOBID || exit
@@ -62,7 +62,7 @@ This script may be submitted directly to the PBS workload manager via
the qsub command. The inputs are in rscript.R file, outputs in
routput.out file. See the single node jobscript example in the [Job
execution
-section](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
+section](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution).
Parallel R
----------
Parallel execution of R may be achieved in many ways. One approach is
@@ -75,7 +75,7 @@ parallel constructs are directly stated within the R script.
The package parallel provides support for parallel computation,
including by forking (taken from package multicore), by sockets (taken
from package snow) and random-number generation.
-The package is activated this way
+The package is activated this way:
$ R
> library(parallel)
More information and examples may be obtained directly by reading the
@@ -83,16 +83,17 @@ documentation available in R
> ?parallel
> library(help = "parallel")
> vignette("parallel")
-Download the package [parallell](parallel.pdf) vignette.
+Download the package
+[parallell](https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/package-parallel-vignette)
+vignette.
The forking is the most simple to use. Forking family of functions
provide parallelized, drop in replacement for the serial apply() family
of functions.
Forking via package parallel provides functionality similar to OpenMP
construct
#omp parallel for
-
Only cores of single node can be utilized this way!
-Forking example
+Forking example:
library(parallel)
#integrand function
f <- function(i,h) {
@@ -104,7 +105,7 @@ Forking example
while (TRUE)
{
#read number of intervals
- cat("Enter the number of intervals (0 quits) ")
+ cat("Enter the number of intervals(0 quits) ")
fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)
if(n<=0) break
#run the calculation
@@ -117,7 +118,7 @@ Forking example
}
The above example is the classic parallel example for calculating the
number π. Note the **detectCores()** and **mclapply()** functions.
-Execute the example as
+Execute the example as:
$ R --slave --no-save --no-restore -f pi3p.R
Every evaluation of the integrad function runs in parallel on different
process.
@@ -126,9 +127,10 @@ Package Rmpi
package Rmpi provides an interface (wrapper) to MPI APIs.
It also provides interactive R slave environment. On Anselm, Rmpi
provides interface to the
-[OpenMPI](../mpi-1/Running_OpenMPI.html).
-Read more on Rmpi at ,
+[OpenMPI](https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI).
+Read more on Rmpi at <http://cran.r-project.org/web/packages/Rmpi/>,
reference manual is available at
+<http://cran.r-project.org/web/packages/Rmpi/Rmpi.pdf>
When using package Rmpi, both openmpi and R modules must be loaded
$ module load openmpi
$ module load R
@@ -140,7 +142,7 @@ these concepts.
### []()static Rmpi
Static Rmpi programs are executed via mpiexec, as any other MPI
programs. Number of processes is static - given at the launch time.
-Static Rmpi example
+Static Rmpi example:
library(Rmpi)
#integrand function
f <- function(i,h) {
@@ -156,7 +158,7 @@ Static Rmpi example
{
#read number of intervals
if (rank==0) {
- cat("Enter the number of intervals (0 quits) ")
+ cat("Enter the number of intervals(0 quits) ")
fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)
}
#broadcat the intervals
@@ -174,13 +176,13 @@ Static Rmpi example
mpi.quit()
The above is the static MPI example for calculating the number π. Note
the **library(Rmpi)** and **mpi.comm.dup()** function calls.
-Execute the example as
+Execute the example as:
$ mpiexec R --slave --no-save --no-restore -f pi3.R
### dynamic Rmpi
Dynamic Rmpi programs are executed by calling the R directly. openmpi
module must be still loaded. The R slave processes will be spawned by a
function call within the Rmpi program.
-Dynamic Rmpi example
+Dynamic Rmpi example:
#integrand function
f <- function(i,h) {
x <- h*(i-0.5)
@@ -197,7 +199,7 @@ Dynamic Rmpi example
{
#read number of intervals
if (rank==0) {
- cat("Enter the number of intervals (0 quits) ")
+ cat("Enter the number of intervals(0 quits) ")
fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)
}
#broadcat the intervals
@@ -215,7 +217,7 @@ Dynamic Rmpi example
}
#main
library(Rmpi)
- cat("Enter the number of slaves ")
+ cat("Enter the number of slaves")
fp<-file("stdin"); ns<-scan(fp,nmax=1); close(fp)
mpi.spawn.Rslaves(nslaves=ns)
mpi.bcast.Robj2slave(f)
@@ -227,14 +229,14 @@ The above example is the dynamic MPI example for calculating the number
Ď€. Both master and slave processes carry out the calculation. Note the
**mpi.spawn.Rslaves(), mpi.bcast.Robj2slave()** and the
**mpi.bcast.cmd()** function calls.
-Execute the example as
+Execute the example as:
$ R --slave --no-save --no-restore -f pi3Rslaves.R
### mpi.apply Rmpi
mpi.apply is a specific way of executing Dynamic Rmpi programs.
mpi.apply() family of functions provide MPI parallelized, drop in
replacement for the serial apply() family of functions.
Execution is identical to other dynamic Rmpi programs.
-mpi.apply Rmpi example
+mpi.apply Rmpi example:
#integrand function
f <- function(i,h) {
x <- h*(i-0.5)
@@ -252,7 +254,7 @@ mpi.apply Rmpi example
}
#main
library(Rmpi)
- cat("Enter the number of slaves ")
+ cat("Enter the number of slaves")
fp<-file("stdin"); ns<-scan(fp,nmax=1); close(fp)
mpi.spawn.Rslaves(nslaves=ns)
mpi.bcast.Robj2slave(f)
@@ -260,7 +262,7 @@ mpi.apply Rmpi example
while (TRUE)
{
#read number of intervals
- cat("Enter the number of intervals (0 quits) ")
+ cat("Enter the number of intervals(0 quits) ")
fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)
if(n<=0) break
#run workerpi
@@ -272,15 +274,15 @@ mpi.apply Rmpi example
mpi.quit()
The above is the mpi.apply MPI example for calculating the number π.
Only the slave processes carry out the calculation. Note the
-**mpi.parSapply(), ** function call. The package
+**mpi.parSapply(), ** function call. The package <span
class="anchor-link">parallel
-[example](#package-parallel)[above](#package-parallel)
+[example](#package-parallel)</span>[above](#package-parallel)
may be trivially adapted (for much better performance) to this structure
using the mclapply() in place of mpi.parSapply().
-Execute the example as
+Execute the example as:
$ R --slave --no-save --no-restore -f pi3parSapply.R
Combining parallel and Rmpi
----------------------------
+----
Currently, the two packages can not be combined for hybrid calculations.
Parallel execution
------------------
@@ -288,11 +290,11 @@ The R parallel jobs are executed via the PBS queue system exactly as any
other parallel jobs. User must create an appropriate jobscript and
submit via the **qsub**
Example jobscript for [static Rmpi](#static-rmpi) parallel
-R execution, running 1 process per core
+R execution, running 1 process per core:
#!/bin/bash
#PBS -q qprod
#PBS -N Rjob
- #PBS -l select=100ncpus=16mpiprocs=16ompthreads=1
+ #PBS -l select=100:ncpus=16:mpiprocs=16:ompthreads=1
# change to scratch directory
SCRDIR=/scratch/$USER/myjob
cd $SCRDIR || exit
@@ -309,79 +311,7 @@ R execution, running 1 process per core
exit
For more information about jobscripts and MPI execution refer to the
[Job
-submission](../../resource-allocation-and-job-execution/job-submission-and-execution.html)
-and general [MPI](../mpi-1.html) sections.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
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-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
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-
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-
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-
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-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
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- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
- .navTreeFolderish
- .contenttype-folder}
- - [Matlab](copy_of_matlab.html)
-
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- 2013-2014](matlab.html)
-
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-
- - [R](r.html)
-
-
- - [Virtualization](../virtualization.html)
+submission](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution)
+and general
+[MPI](https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1)
+sections.
diff --git a/anselm-cluster-documentation/software/numerical-libraries.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries.html
old mode 100755
new mode 100644
similarity index 61%
rename from anselm-cluster-documentation/software/numerical-libraries.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries.html
index f74d3724253229f76f5095a897e32a7eb67fd5b0..36e3be39ea8dc9bea37a753d624cb2a448f42e42
--- a/anselm-cluster-documentation/software/numerical-libraries.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries.html
@@ -10,45 +10,42 @@
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-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:48 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/" /><!--[if lt IE 7]></base><![endif]-->
<meta content="Libraries for numerical computations" name="description" />
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Numerical Libraries — IT4I Docs</title>
- <link rel="canonical" href="numerical-libraries.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="numerical-libraries.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="numerical-libraries.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
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-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
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@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
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@@ -262,7 +259,7 @@
<span class="summary">
- <a href="numerical-libraries/intel-numerical-libraries.html" class="contenttype-document state-published url">Intel numerical libraries</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries" class="contenttype-document state-published url">Intel numerical libraries</a>
</span>
<span class="documentByLine">
@@ -288,7 +285,7 @@
<span class="summary">
- <a href="numerical-libraries/gsl.html" class="contenttype-document state-published url">GSL</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl" class="contenttype-document state-published url">GSL</a>
</span>
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@@ -314,7 +311,7 @@
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5" class="contenttype-document state-published url">HDF5</a>
</span>
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@@ -340,7 +337,7 @@
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</span>
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@@ -366,7 +363,7 @@
<span class="summary">
- <a href="numerical-libraries/magma-for-intel-xeon-phi.html" class="contenttype-document state-published url">MAGMA for Intel Xeon Phi</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi" class="contenttype-document state-published url">MAGMA for Intel Xeon Phi</a>
</span>
<span class="documentByLine">
@@ -393,7 +390,7 @@
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@@ -419,7 +416,7 @@
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<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -524,7 +521,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -540,7 +537,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -572,7 +569,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -588,7 +585,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -604,7 +601,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -620,7 +617,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
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<span>Compute Nodes</span>
</a>
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<span>Storage</span>
</a>
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<span>Network</span>
</a>
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<span>Software</span>
</a>
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<span>ANSYS</span>
</a>
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<span>COMSOL</span>
</a>
@@ -751,7 +748,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -767,7 +764,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -783,7 +780,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
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- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
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<span>Numerical Libraries</span>
</a>
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- <a title="Intel libraries for high performance in numerical computing" class="state-published contenttype-document" href="numerical-libraries/intel-numerical-libraries.html">
+ <a class="state-published contenttype-document" title="Intel libraries for high performance in numerical computing" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries">
<span>Intel numerical libraries</span>
</a>
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- <a title="The GNU Scientific Library. Provides a wide range of mathematical routines." class="state-published contenttype-document" href="numerical-libraries/gsl.html">
+ <a class="state-published contenttype-document" title="The GNU Scientific Library. Provides a wide range of mathematical routines." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl">
<span>GSL</span>
</a>
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+ <a class="state-published contenttype-document" title="Hierarchical Data Format library. Serial and MPI parallel version." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5">
<span>HDF5</span>
</a>
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+ <a class="state-published contenttype-document" title="The discrete Fourier transform in one or more dimensions, MPI parallel" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw">
<span>FFTW</span>
</a>
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-" class="state-published contenttype-document" href="numerical-libraries/magma-for-intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="Next generation dense algebra library for heterogeneous systems with accelerators
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi">
<span>MAGMA for Intel Xeon Phi</span>
</a>
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+ <a class="state-published contenttype-document" title="PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc">
<span>PETSc</span>
</a>
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+ <a class="state-published contenttype-document" title=" Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos">
<span>Trilinos</span>
</a>
@@ -953,7 +950,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -969,7 +966,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -985,7 +982,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -1001,7 +998,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -1017,7 +1014,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -1033,7 +1030,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -1049,7 +1046,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -1065,7 +1062,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -1081,7 +1078,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -1097,7 +1094,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1113,7 +1110,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1129,7 +1126,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1154,7 +1151,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1170,7 +1167,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1195,7 +1192,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1211,7 +1208,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1227,7 +1224,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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<title>FFTW — IT4I Docs</title>
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- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="fftw.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="fftw.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../numerical-libraries.html">Numerical Libraries</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">Numerical Libraries</a>
<span class="breadcrumbSeparator">
/
@@ -318,7 +315,7 @@
<pre class=" ">#include <fftw3-mpi.h><br />int main(int argc, char **argv)<br />{<br />Â Â Â const ptrdiff_t N0 = 100, N1 = 1000;<br />Â Â Â fftw_plan plan;<br />Â Â Â fftw_complex *data;<br />Â Â Â ptrdiff_t alloc_local, local_n0, local_0_start, i, j;<br /><br />Â Â Â MPI_Init(&argc, &argv);<br />Â Â Â fftw_mpi_init();<br /><br />Â Â Â /* get local data size and allocate */<br />Â Â Â alloc_local = fftw_mpi_local_size_2d(N0, N1, MPI_COMM_WORLD,<br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â &local_n0, &local_0_start);<br />Â Â Â data = fftw_alloc_complex(alloc_local);<br /><br />Â Â Â /* create plan for in-place forward DFT */<br />Â Â Â plan = fftw_mpi_plan_dft_2d(N0, N1, data, data, MPI_COMM_WORLD,<br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â FFTW_FORWARD, FFTW_ESTIMATE);<br /><br />Â Â Â /* initialize data */<br />Â Â Â for (i = 0; i < local_n0; ++i) for (j = 0; j < N1; ++j)<br />Â Â Â {Â Â data[i*N1 + j][0] = i;<br />Â Â Â Â Â Â Â data[i*N1 + j][1] = j; }<br /><br />Â Â Â /* compute transforms, in-place, as many times as desired */<br />Â Â Â fftw_execute(plan);<br /><br />Â Â Â fftw_destroy_plan(plan);<br /><br />Â Â Â MPI_Finalize();<br />}</pre>
<p>Load modules and compile:</p>
<pre class=" ">$ module load impi intel<br />$ module load fftw3-mpi<br /><br />$ mpicc testfftw3mpi.c -o testfftw3mpi.x -Wl,-rpath=$LIBRARY_PATH -lfftw3_mpi</pre>
-<p class=" "><span class="internal-link">Run the example as <a target="_self" title="" class="internal-link" href="../mpi-1/running-mpich2.html">Intel MPI program</a></span>.</p>
+<p class=" "><span class="internal-link">Run the example as <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2">Intel MPI program</a></span>.</p>
<p class=" ">Read more on FFTW usage on the <a class="external-link" href="http://www.fftw.org/fftw3_doc/" target="_self" title="">FFTW website.</a><br /><br /></p>
</div>
@@ -395,7 +392,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -411,7 +408,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -427,7 +424,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -443,7 +440,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -459,7 +456,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -475,7 +472,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -491,7 +488,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -507,7 +504,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -523,7 +520,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -539,7 +536,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -555,7 +552,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -571,7 +568,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -587,10 +584,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -606,7 +603,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -622,7 +619,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -638,7 +635,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -654,7 +651,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -670,7 +667,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -686,7 +683,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -702,7 +699,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -718,7 +715,7 @@
- <a title="Intel libraries for high performance in numerical computing" class="state-published contenttype-document" href="intel-numerical-libraries.html">
+ <a class="state-published contenttype-document" title="Intel libraries for high performance in numerical computing" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries">
<span>Intel numerical libraries</span>
</a>
@@ -734,7 +731,7 @@
- <a title="The GNU Scientific Library. Provides a wide range of mathematical routines." class="state-published contenttype-document" href="gsl.html">
+ <a class="state-published contenttype-document" title="The GNU Scientific Library. Provides a wide range of mathematical routines." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl">
<span>GSL</span>
</a>
@@ -750,7 +747,7 @@
- <a title="Hierarchical Data Format library. Serial and MPI parallel version." class="state-published contenttype-document" href="hdf5.html">
+ <a class="state-published contenttype-document" title="Hierarchical Data Format library. Serial and MPI parallel version." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5">
<span>HDF5</span>
</a>
@@ -766,7 +763,7 @@
- <a title="The discrete Fourier transform in one or more dimensions, MPI parallel" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="fftw.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="The discrete Fourier transform in one or more dimensions, MPI parallel" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw">
<span>FFTW</span>
</a>
@@ -782,8 +779,8 @@
- <a title="Next generation dense algebra library for heterogeneous systems with accelerators
-" class="state-published contenttype-document" href="magma-for-intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="Next generation dense algebra library for heterogeneous systems with accelerators
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi">
<span>MAGMA for Intel Xeon Phi</span>
</a>
@@ -799,7 +796,7 @@
- <a title="PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism." class="state-published contenttype-document" href="petsc.html">
+ <a class="state-published contenttype-document" title="PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc">
<span>PETSc</span>
</a>
@@ -815,7 +812,7 @@
- <a title=" Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization." class="state-published contenttype-document" href="trilinos.html">
+ <a class="state-published contenttype-document" title=" Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos">
<span>Trilinos</span>
</a>
@@ -840,7 +837,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -856,7 +853,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -872,7 +869,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -888,7 +885,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -904,7 +901,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -920,7 +917,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -936,7 +933,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -952,7 +949,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -968,7 +965,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -984,7 +981,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1000,7 +997,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1016,7 +1013,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1041,7 +1038,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1057,7 +1054,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1082,7 +1079,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1098,7 +1095,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1114,7 +1111,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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(function() {
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md
new file mode 100644
index 0000000000000000000000000000000000000000..3d4d6b8663976cc25fb80bc5624b7feef64efef7
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md
@@ -0,0 +1,131 @@
+FFTW
+====
+The discrete Fourier transform in one or more dimensions, MPI parallel
+
+Â
+FFTW is a C subroutine library for computing the discrete Fourier
+transform in one or more dimensions, of arbitrary input size, and of
+both real and complex data (as well as of even/odd data, i.e. the
+discrete cosine/sine transforms or DCT/DST). The FFTW library allows for
+MPI parallel, in-place discrete Fourier transform, with data distributed
+over number of nodes.****
+**
+**Two versions, **3.3.3** and **2.1.5** of FFTW are available on Anselm,
+each compiled for **Intel MPI** and **OpenMPI** using **intel** and
+**gnu** compilers. These are available via modules:
+<table>
+<colgroup>
+<col width="25%" />
+<col width="25%" />
+<col width="25%" />
+<col width="25%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Version</th>
+<th align="left">Parallelization</th>
+<th align="left">module</th>
+<th align="left">linker options</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left">FFTW3 gcc<br />
+3.3.3</td>
+<td align="left">pthread, OpenMP</td>
+<td align="left">fftw3/3.3.3-gcc</td>
+<td align="left">-lfftw3, -lfftw3_threads<br />
+-lfftw3_omp</td>
+</tr>
+<tr class="even">
+<td align="left"><p>FFTW3 icc<br />
+3.3.3</p></td>
+<td align="left">pthread, OpenMP</td>
+<td align="left">fftw3</td>
+<td align="left">-lfftw3, -lfftw3_threads<br />
+-lfftw3_omp</td>
+</tr>
+<tr class="odd">
+<td align="left"><p>FFTW2 gcc<br />
+2.1.5</p></td>
+<td align="left">pthread</td>
+<td align="left">fftw2/2.1.5-gcc</td>
+<td align="left">-lfftw, -lfftw_threads</td>
+</tr>
+<tr class="even">
+<td align="left">FFTW2 icc<br />
+2.1.5</td>
+<td align="left">pthread</td>
+<td align="left">fftw2</td>
+<td align="left">-lfftw, -lfftw_threads</td>
+</tr>
+<tr class="odd">
+<td align="left">FFTW3 gcc<br />
+3.3.3</td>
+<td align="left">OpenMPI</td>
+<td align="left">fftw-mpi3/3.3.3-gcc</td>
+<td align="left">-lfftw3_mpi</td>
+</tr>
+<tr class="even">
+<td align="left">FFTW3 icc<br />
+3.3.3</td>
+<td align="left">Intel MPI</td>
+<td align="left">fftw3-mpi</td>
+<td align="left">-lfftw3_mpi</td>
+</tr>
+<tr class="odd">
+<td align="left">FFTW2 gcc<br />
+2.1.5</td>
+<td align="left">OpenMPI</td>
+<td align="left">fftw2-mpi/2.1.5-gcc</td>
+<td align="left">-lfftw_mpi</td>
+</tr>
+<tr class="even">
+<td align="left">FFTW2 gcc<br />
+2.1.5</td>
+<td align="left">IntelMPI</td>
+<td align="left">fftw2-mpi/2.1.5-gcc</td>
+<td align="left">-lfftw_mpi</td>
+</tr>
+</tbody>
+</table>
+ $ module load fftw3
+The module sets up environment variables, required for linking and
+running fftw enabled applications. Make sure that the choice of fftw
+module is consistent with your choice of MPI library. Mixing MPI of
+different implementations may have unpredictable results.
+Example
+-------
+ #include <fftw3-mpi.h>
+ int main(int argc, char **argv)
+ {
+ Â Â Â const ptrdiff_t N0 = 100, N1 = 1000;
+ Â Â Â fftw_plan plan;
+ Â Â Â fftw_complex *data;
+ Â Â Â ptrdiff_t alloc_local, local_n0, local_0_start, i, j;
+ Â Â Â MPI_Init(&argc, &argv);
+ Â Â Â fftw_mpi_init();
+ Â Â Â /* get local data size and allocate */
+ Â Â Â alloc_local = fftw_mpi_local_size_2d(N0, N1, MPI_COMM_WORLD,
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â &local_n0, &local_0_start);
+ Â Â Â data = fftw_alloc_complex(alloc_local);
+ Â Â Â /* create plan for in-place forward DFT */
+ Â Â Â plan = fftw_mpi_plan_dft_2d(N0, N1, data, data, MPI_COMM_WORLD,
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â FFTW_FORWARD, FFTW_ESTIMATE);
+ Â Â Â /* initialize data */
+ Â Â Â for (i = 0; i < local_n0; ++i) for (j = 0; j < N1; ++j)
+ Â Â Â {Â Â data[i*N1 + j][0] = i;
+ Â Â Â Â Â Â Â data[i*N1 + j][1] = j; }
+ Â Â Â /* compute transforms, in-place, as many times as desired */
+ Â Â Â fftw_execute(plan);
+ Â Â Â fftw_destroy_plan(plan);
+ Â Â Â MPI_Finalize();
+ }
+Load modules and compile:
+ $ module load impi intel
+ $ module load fftw3-mpi
+ $ mpicc testfftw3mpi.c -o testfftw3mpi.x -Wl,-rpath=$LIBRARY_PATH -lfftw3_mpi
+<span class="internal-link">Run the example as [Intel MPI
+program](https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2)</span>.
+Read more on FFTW usage on the [FFTW
+website.](http://www.fftw.org/fftw3_doc/)
diff --git a/anselm-cluster-documentation/software/numerical-libraries/gsl.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.html
old mode 100755
new mode 100644
similarity index 65%
rename from anselm-cluster-documentation/software/numerical-libraries/gsl.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.html
index 701094e7e6e14983e7dad1a436933740f7aa8fac..10cb995e9ea4a9375555704e0ef0893185869a10
--- a/anselm-cluster-documentation/software/numerical-libraries/gsl.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:37 GMT -->
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl" /><!--[if lt IE 7]></base><![endif]-->
<meta content="The GNU Scientific Library. Provides a wide range of mathematical routines." name="description" />
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>GSL — IT4I Docs</title>
- <link rel="canonical" href="gsl.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="gsl.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="gsl.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
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@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
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@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../numerical-libraries.html">Numerical Libraries</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">Numerical Libraries</a>
<span class="breadcrumbSeparator">
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@@ -448,7 +445,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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@@ -464,7 +461,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
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@@ -480,7 +477,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -496,7 +493,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -512,7 +509,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -528,7 +525,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -544,7 +541,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -560,7 +557,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -576,7 +573,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -592,7 +589,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../network.html">
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<span>Network</span>
</a>
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+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
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<span>ANSYS</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -691,7 +688,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -707,7 +704,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -723,7 +720,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
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- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -755,7 +752,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -771,7 +768,7 @@
- <a title="Intel libraries for high performance in numerical computing" class="state-published contenttype-document" href="intel-numerical-libraries.html">
+ <a class="state-published contenttype-document" title="Intel libraries for high performance in numerical computing" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries">
<span>Intel numerical libraries</span>
</a>
@@ -787,7 +784,7 @@
- <a title="The GNU Scientific Library. Provides a wide range of mathematical routines." class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="gsl.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="The GNU Scientific Library. Provides a wide range of mathematical routines." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl">
<span>GSL</span>
</a>
@@ -803,7 +800,7 @@
- <a title="Hierarchical Data Format library. Serial and MPI parallel version." class="state-published contenttype-document" href="hdf5.html">
+ <a class="state-published contenttype-document" title="Hierarchical Data Format library. Serial and MPI parallel version." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5">
<span>HDF5</span>
</a>
@@ -819,7 +816,7 @@
- <a title="The discrete Fourier transform in one or more dimensions, MPI parallel" class="state-published contenttype-document" href="fftw.html">
+ <a class="state-published contenttype-document" title="The discrete Fourier transform in one or more dimensions, MPI parallel" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw">
<span>FFTW</span>
</a>
@@ -835,8 +832,8 @@
- <a title="Next generation dense algebra library for heterogeneous systems with accelerators
-" class="state-published contenttype-document" href="magma-for-intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="Next generation dense algebra library for heterogeneous systems with accelerators
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi">
<span>MAGMA for Intel Xeon Phi</span>
</a>
@@ -852,7 +849,7 @@
- <a title="PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism." class="state-published contenttype-document" href="petsc.html">
+ <a class="state-published contenttype-document" title="PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc">
<span>PETSc</span>
</a>
@@ -868,7 +865,7 @@
- <a title=" Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization." class="state-published contenttype-document" href="trilinos.html">
+ <a class="state-published contenttype-document" title=" Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos">
<span>Trilinos</span>
</a>
@@ -893,7 +890,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -909,7 +906,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -925,7 +922,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -941,7 +938,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -957,7 +954,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -973,7 +970,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -989,7 +986,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -1005,7 +1002,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -1021,7 +1018,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -1037,7 +1034,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1053,7 +1050,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1069,7 +1066,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1094,7 +1091,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1110,7 +1107,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1135,7 +1132,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1151,7 +1148,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1167,7 +1164,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
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+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1256,7 +1253,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
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</html>
diff --git a/anselm-cluster-documentation/software/numerical-libraries/gsl.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.md
similarity index 50%
rename from anselm-cluster-documentation/software/numerical-libraries/gsl.md
rename to docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.md
index 16b446860a198ce11f7e2d49c32a6d2f48a661de..a0ea6c83b62bd602e811237f32f3b8f6ea4eac4b 100644
--- a/anselm-cluster-documentation/software/numerical-libraries/gsl.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.md
@@ -2,8 +2,7 @@ GSL
===
The GNU Scientific Library. Provides a wide range of mathematical
routines.
-
-
+
Introduction
------------
The GNU Scientific Library (GSL) provides a wide range of mathematical
@@ -13,8 +12,8 @@ routines have been written from scratch in C, and present a modern
Applications Programming Interface (API) for C programmers, allowing
wrappers to be written for very high level languages.
The library covers a wide range of topics in numerical computing.
-Routines are available for the following areas
- ------------------------ ------------------------ ------------------------
+Routines are available for the following areas:
+ - - -
Complex Numbers Roots of Polynomials
Special Functions Vectors and Matrices
Permutations Combinations
@@ -34,13 +33,13 @@ Routines are available for the following areas
Least-Squares Fitting Minimization
IEEE Floating-Point Physical Constants
Basis Splines Wavelets
- ------------------------ ------------------------ ------------------------
+ - - -
Modules
-------
The GSL 1.16 is available on Anselm, compiled for GNU and Intel
-compiler. These variants are available via modules
+compiler. These variants are available via modules:
Module Compiler
- ----------------------- -----------
+ -----------
gsl/1.16-gcc gcc 4.8.6
gsl/1.16-icc(default) icc
 $ module load gsl
@@ -66,11 +65,11 @@ Using the MKL is recommended.
Example
-------
Following is an example of discrete wavelet transform implemented by
-GSL
- #include
- #include
- #include
- #include
+GSL:
+ #include <stdio.h>
+ #include <math.h>
+ #include <gsl/gsl_sort.h>
+ #include <gsl/gsl_wavelet.h>
int
main (int argc, char **argv)
{
@@ -109,92 +108,10 @@ GSL
 free (p);
 return 0;
}
-Load modules and compile
+Load modules and compile:
$ module load intel gsl
icc dwt.c -o dwt.x -Wl,-rpath=$LIBRARY_PATH -mkl -lgsl
In this example, we compile the dwt.c code using the Intel compiler and
link it to the MKL and GSL library, note the -mkl and -lgsl options. The
library search path is compiled in, so that no modules are necessary to
run the code.
-
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../../hardware-overview.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage-1.html)
-
- - [Network](../../network.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](../numerical-libraries.html "Libraries for numerical computations")
- .navTreeFolderish
- .contenttype-folder}
- - [Intel numerical
- libraries](intel-numerical-libraries.html "Intel libraries for high performance in numerical computing")
-
- - [GSL](gsl.html "The GNU Scientific Library. Provides a wide range of mathematical routines.")
-
-
- - [HDF5](hdf5.html "Hierarchical Data Format library. Serial and MPI parallel version.")
-
- - [FFTW](fftw.html "The discrete Fourier transform in one or more dimensions, MPI parallel")
-
- - [MAGMA for Intel Xeon
- Phi](magma-for-intel-xeon-phi.html "Next generation dense algebra library for heterogeneous systems with accelerators
- ")
- - [PETSc](petsc.html "PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism.")
-
- - [Trilinos](trilinos.html " Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization.")
-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
diff --git a/anselm-cluster-documentation/software/numerical-libraries/hdf5.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.html
old mode 100755
new mode 100644
similarity index 67%
rename from anselm-cluster-documentation/software/numerical-libraries/hdf5.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.html
index c1031399840a97aea2ffa9da3263f6c3eab66c62..215a96d85b2819c21e4176c361175b04e13371bc
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+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5" /><!--[if lt IE 7]></base><![endif]-->
<meta content="Hierarchical Data Format library. Serial and MPI parallel version." name="description" />
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>HDF5 — IT4I Docs</title>
- <link rel="canonical" href="hdf5.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="hdf5.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="hdf5.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../numerical-libraries.html">Numerical Libraries</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">Numerical Libraries</a>
<span class="breadcrumbSeparator">
/
@@ -330,7 +327,7 @@
<pre class=" ">#include "hdf5.h"<br />#define FILE "dset.h5"<br /><br />int main() {<br /><br /> hid_t file_id, dataset_id, dataspace_id; /* identifiers */<br /> hsize_t dims[2];<br /> herr_t status;<br /> int i, j, dset_data[4][6];<br /><br /> /* Create a new file using default properties. */<br /> file_id = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);<br /><br /> /* Create the data space for the dataset. */<br /> dims[0] = 4;<br /> dims[1] = 6;<br /> dataspace_id = H5Screate_simple(2, dims, NULL);<br /><br /> /* Initialize the dataset. */<br /> for (i = 0; i < 4; i++)<br /> for (j = 0; j < 6; j++)<br /> dset_data[i][j] = i * 6 + j + 1;<br /><br /><br /> /* Create the dataset. */<br /> dataset_id = H5Dcreate2(file_id, "/dset", H5T_STD_I32BE, dataspace_id,<br /> H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);<br /><br /> /* Write the dataset. */<br /> status = H5Dwrite(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,<br /> dset_data);<br /><br /> status = H5Dread(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,<br /> dset_data);<br /><br /> /* End access to the dataset and release resources used by it. */<br /> status = H5Dclose(dataset_id);<br /><br /> /* Terminate access to the data space. */<br /> status = H5Sclose(dataspace_id);<br /><br /> /* Close the file. */<br /> status = H5Fclose(file_id);<br />}</pre>
<p>Load modules and compile:</p>
<pre class=" ">$ module load intel impi<br />$ module load hdf5-parallel<br /><br />$ mpicc hdf5test.c -o hdf5test.x -Wl,-rpath=$LIBRARY_PATH $HDF5_INC $HDF5_SHLIB</pre>
-<p><span class="internal-link">Run the example as <a target="_self" title="" class="internal-link" href="../anselm-cluster-documentation/software/mpi-1/running-mpich2.html">Intel MPI program</a></span>.</p>
+<p><span class="internal-link">Run the example as <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/anselm-cluster-documentation/software/mpi-1/running-mpich2">Intel MPI program</a></span>.</p>
<p>For further informations, please see the website: <a class="external-link" href="http://www.hdfgroup.org/HDF5/" target="_self" title="">http://www.hdfgroup.org/HDF5/</a></p>
<p>Â </p>
<p>Â </p>
@@ -411,7 +408,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -427,7 +424,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -443,7 +440,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -459,7 +456,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -475,7 +472,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -491,7 +488,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -507,7 +504,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -523,7 +520,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -539,7 +536,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -555,7 +552,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -571,7 +568,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -587,7 +584,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -603,10 +600,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -622,7 +619,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -638,7 +635,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -654,7 +651,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -670,7 +667,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -686,7 +683,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -702,7 +699,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -718,7 +715,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -734,7 +731,7 @@
- <a title="Intel libraries for high performance in numerical computing" class="state-published contenttype-document" href="intel-numerical-libraries.html">
+ <a class="state-published contenttype-document" title="Intel libraries for high performance in numerical computing" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries">
<span>Intel numerical libraries</span>
</a>
@@ -750,7 +747,7 @@
- <a title="The GNU Scientific Library. Provides a wide range of mathematical routines." class="state-published contenttype-document" href="gsl.html">
+ <a class="state-published contenttype-document" title="The GNU Scientific Library. Provides a wide range of mathematical routines." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl">
<span>GSL</span>
</a>
@@ -766,7 +763,7 @@
- <a title="Hierarchical Data Format library. Serial and MPI parallel version." class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="hdf5.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="Hierarchical Data Format library. Serial and MPI parallel version." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5">
<span>HDF5</span>
</a>
@@ -782,7 +779,7 @@
- <a title="The discrete Fourier transform in one or more dimensions, MPI parallel" class="state-published contenttype-document" href="fftw.html">
+ <a class="state-published contenttype-document" title="The discrete Fourier transform in one or more dimensions, MPI parallel" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw">
<span>FFTW</span>
</a>
@@ -798,8 +795,8 @@
- <a title="Next generation dense algebra library for heterogeneous systems with accelerators
-" class="state-published contenttype-document" href="magma-for-intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="Next generation dense algebra library for heterogeneous systems with accelerators
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi">
<span>MAGMA for Intel Xeon Phi</span>
</a>
@@ -815,7 +812,7 @@
- <a title="PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism." class="state-published contenttype-document" href="petsc.html">
+ <a class="state-published contenttype-document" title="PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc">
<span>PETSc</span>
</a>
@@ -831,7 +828,7 @@
- <a title=" Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization." class="state-published contenttype-document" href="trilinos.html">
+ <a class="state-published contenttype-document" title=" Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos">
<span>Trilinos</span>
</a>
@@ -856,7 +853,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -872,7 +869,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -888,7 +885,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -904,7 +901,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -920,7 +917,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -936,7 +933,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -952,7 +949,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -968,7 +965,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -984,7 +981,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -1000,7 +997,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1016,7 +1013,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1032,7 +1029,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1057,7 +1054,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1073,7 +1070,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1098,7 +1095,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1114,7 +1111,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1130,7 +1127,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
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+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
new file mode 100644
index 0000000000000000000000000000000000000000..7b57486f1af1555df1ac4624211638ec6061e051
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
@@ -0,0 +1,161 @@
+HDF5
+====
+Hierarchical Data Format library. Serial and MPI parallel version.
+Â
+[HDF5 (Hierarchical Data Format)](http://www.hdfgroup.org/HDF5/) is a
+general purpose library and file format for storing scientific data.
+HDF5 can store two primary objectsdatasets and groups. A dataset is
+essentially a multidimensional array of data elements, and a group is a
+structure for organizing objects in an HDF5 file. Using these two basic
+objects, one can create and store almost any kind of scientific data
+structure, such as images, arrays of vectors, and structured and
+unstructured grids. You can also mix and match them in HDF5 files
+according to your needs.
+Versions **1.8.11** and **1.8.13** of HDF5 library are available on
+Anselm, compiled for **Intel MPI** and **OpenMPI** using **intel** and
+**gnu** compilers. These are available via modules:
+<table style="width:100%;">
+<colgroup>
+<col width="16%" />
+<col width="16%" />
+<col width="16%" />
+<col width="16%" />
+<col width="16%" />
+<col width="16%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Version</th>
+<th align="left">Parallelization</th>
+<th align="left">module</th>
+<th align="left">C linker options</th>
+<th align="left">C++ linker options</th>
+<th align="left">Fortran linker options</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left">HDF5 icc serial</td>
+<td align="left">pthread</td>
+<td align="left">hdf5/1.8.11</td>
+<td align="left">$HDF5_INC $HDF5_SHLIB</td>
+<td align="left">$HDF5_INC $HDF5_CPP_LIB</td>
+<td align="left">$HDF5_INC $HDF5_F90_LIB</td>
+</tr>
+<tr class="even">
+<td align="left"><p>HDF5 icc parallel MPI</p></td>
+<td align="left">pthread, IntelMPI</td>
+<td align="left">hdf5-parallel/1.8.11</td>
+<td align="left">$HDF5_INC $HDF5_SHLIB</td>
+<td align="left">Not supported</td>
+<td align="left">$HDF5_INC $HDF5_F90_LIB</td>
+</tr>
+<tr class="odd">
+<td align="left">HDF5 icc serial</td>
+<td align="left">pthread</td>
+<td align="left">hdf5/1.8.13</td>
+<td align="left">$HDF5_INC $HDF5_SHLIB</td>
+<td align="left">$HDF5_INC $HDF5_CPP_LIB</td>
+<td align="left">$HDF5_INC $HDF5_F90_LIB</td>
+</tr>
+<tr class="even">
+<td align="left"><p>HDF5 icc parallel MPI</p></td>
+<td align="left">pthread, IntelMPI</td>
+<td align="left">hdf5-parallel/1.8.13</td>
+<td align="left">$HDF5_INC $HDF5_SHLIB</td>
+<td align="left">Not supported</td>
+<td align="left">$HDF5_INC $HDF5_F90_LIB</td>
+</tr>
+<tr class="odd">
+<td align="left"><p>HDF5 gcc parallel MPI</p></td>
+<td align="left">pthread, OpenMPI 1.6.5, gcc 4.8.1</td>
+<td align="left">hdf5-parallel/1.8.11-gcc</td>
+<td align="left">$HDF5_INC $HDF5_SHLIB</td>
+<td align="left">Not supported</td>
+<td align="left">$HDF5_INC $HDF5_F90_LIB</td>
+</tr>
+<tr class="even">
+<td align="left"><p>HDF5 gcc parallel MPI</p></td>
+<td align="left">pthread, OpenMPI 1.6.5, gcc 4.8.1</td>
+<td align="left">hdf5-parallel/1.8.13-gcc</td>
+<td align="left">$HDF5_INC $HDF5_SHLIB</td>
+<td align="left">Not supported</td>
+<td align="left">$HDF5_INC $HDF5_F90_LIB</td>
+</tr>
+<tr class="odd">
+<td align="left"><p>HDF5 gcc parallel MPI</p></td>
+<td align="left">pthread, OpenMPI 1.8.1, gcc 4.9.0</td>
+<td align="left">hdf5-parallel/1.8.13-gcc49</td>
+<td align="left">$HDF5_INC $HDF5_SHLIB</td>
+<td align="left">Not supported</td>
+<td align="left">$HDF5_INC $HDF5_F90_LIB</td>
+</tr>
+</tbody>
+</table>
+Â
+ $ module load hdf5-parallel
+The module sets up environment variables, required for linking and
+running HDF5 enabled applications. Make sure that the choice of HDF5
+module is consistent with your choice of MPI library. Mixing MPI of
+different implementations may have unpredictable results.
+Be aware, that GCC version of **HDF5 1.8.11** has serious performance
+issues, since it's compiled with -O0 optimization flag. This version is
+provided only for testing of code compiled only by GCC and IS NOT
+recommended for production computations. For more informations, please
+see:
+<http://www.hdfgroup.org/ftp/HDF5/prev-releases/ReleaseFiles/release5-1811>
+All GCC versions of **HDF5 1.8.13** are not affected by the bug, are
+compiled with -O3 optimizations and are recommended for production
+computations.
+Example
+-------
+ #include "hdf5.h"
+ #define FILE "dset.h5"
+ int main() {
+ hid_t file_id, dataset_id, dataspace_id; /* identifiers */
+ hsize_t dims[2];
+ herr_t status;
+ int i, j, dset_data[4][6];
+ /* Create a new file using default properties. */
+ file_id = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ /* Create the data space for the dataset. */
+ dims[0] = 4;
+ dims[1] = 6;
+ dataspace_id = H5Screate_simple(2, dims, NULL);
+ /* Initialize the dataset. */
+ for (i = 0; i < 4; i++)
+ for (j = 0; j < 6; j++)
+ dset_data[i][j] = i * 6 + j + 1;
+ /* Create the dataset. */
+ dataset_id = H5Dcreate2(file_id, "/dset", H5T_STD_I32BE, dataspace_id,
+ H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ /* Write the dataset. */
+ status = H5Dwrite(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
+ dset_data);
+ status = H5Dread(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
+ dset_data);
+ /* End access to the dataset and release resources used by it. */
+ status = H5Dclose(dataset_id);
+ /* Terminate access to the data space. */
+ status = H5Sclose(dataspace_id);
+ /* Close the file. */
+ status = H5Fclose(file_id);
+ }
+Load modules and compile:
+ $ module load intel impi
+ $ module load hdf5-parallel
+ $ mpicc hdf5test.c -o hdf5test.x -Wl,-rpath=$LIBRARY_PATH $HDF5_INC $HDF5_SHLIB
+<span class="internal-link">Run the example as [Intel MPI
+program](https://docs.it4i.cz/anselm-cluster-documentation/software/anselm-cluster-documentation/software/mpi-1/running-mpich2)</span>.
+For further informations, please see the website:
+<http://www.hdfgroup.org/HDF5/>
+Â
+Â
+Â
+<span
+class="smarterwiki-popup-bubble smarterwiki-popup-bubble-active smarterwiki-popup-bubble-flipped"><span
+class="smarterwiki-popup-bubble-tip"></span><span
+class="smarterwiki-popup-bubble-body"><span
+class="smarterwiki-popup-bubble-links-container"><span
+class="smarterwiki-popup-bubble-links"><span
+class="smarterwiki-popup-bubble-links-row">[{.smarterwiki-popup-bubble-link-favicon}](http://maps.google.com/maps?q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB "Search Google Maps"){.smarterwiki-popup-bubble-link}[{.smarterwiki-popup-bubble-link-favicon}](http://www.google.com/search?q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB "Search Google"){.smarterwiki-popup-bubble-link}[](http://www.google.com/search?hl=com&btnI=I'm+Feeling+Lucky&q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB+wikipedia "Search Wikipedia"){.smarterwiki-popup-bubble-link}</span></span></span></span></span>
diff --git a/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.html
old mode 100755
new mode 100644
similarity index 60%
rename from anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.html
index 030c7fe3119517a6dcf1e3015a9a57d88264a916..81c753df7b5e85ee8d3b98094ded6007e0f27830
--- a/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:37 GMT -->
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<meta content="Intel libraries for high performance in numerical computing" name="description" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Intel numerical libraries — IT4I Docs</title>
- <link rel="canonical" href="intel-numerical-libraries.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="intel-numerical-libraries.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="intel-numerical-libraries.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../numerical-libraries.html">Numerical Libraries</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">Numerical Libraries</a>
<span class="breadcrumbSeparator">
/
@@ -255,15 +252,15 @@
<h2 class=" ">Intel Math Kernel Library</h2>
<p>Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, extensively threaded and optimized for maximum performance. Intel MKL unites and provides these basic components: BLAS, LAPACK, ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and many more.</p>
<pre class=" ">$ module load mkl</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="../intel-suite/intel-mkl.html">Intel MKL</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl">Intel MKL</a> page.</p>
<h2 class=" ">Intel Integrated Performance Primitives</h2>
<p>Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is available, via module ipp. The IPP is a library of highly optimized algorithmic building blocks for media and data applications. This includes signal, image and frame processing algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many more.</p>
<pre class=" ">$ module load ipp</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="../intel-suite/intel-integrated-performance-primitives.html">Intel IPP</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives">Intel IPP</a> page.</p>
<h2 class=" ">Intel Threading Building Blocks</h2>
<p>Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. It is designed to promote scalable data parallel programming. Additionally, it fully supports nested parallelism, so you can build larger parallel components from smaller parallel components. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner.</p>
<pre class=" ">$ module load tbb</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="../intel-suite/intel-tbb.html">Intel TBB</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb">Intel TBB</a> page.</p>
</div>
@@ -339,7 +336,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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@@ -355,7 +352,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -371,7 +368,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -387,7 +384,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -403,7 +400,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -419,7 +416,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -435,7 +432,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -451,7 +448,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -467,7 +464,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -483,7 +480,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -499,7 +496,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -515,7 +512,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -531,10 +528,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -550,7 +547,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -566,7 +563,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -582,7 +579,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -598,7 +595,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -614,7 +611,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -630,7 +627,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -646,7 +643,7 @@
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<span>Numerical Libraries</span>
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<span>Intel numerical libraries</span>
</a>
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<span>GSL</span>
</a>
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<span>HDF5</span>
</a>
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<span>FFTW</span>
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-" class="state-published contenttype-document" href="magma-for-intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="Next generation dense algebra library for heterogeneous systems with accelerators
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi">
<span>MAGMA for Intel Xeon Phi</span>
</a>
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+ <a class="state-published contenttype-document" title="PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc">
<span>PETSc</span>
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<span>Numerical languages</span>
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<span>Intel Xeon Phi</span>
</a>
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<span>ISV Licenses</span>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
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--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
@@ -0,0 +1,41 @@
+Intel numerical libraries
+=========================
+Intel libraries for high performance in numerical computing
+
+Intel Math Kernel Library
+--
+Intel Math Kernel Library (Intel MKL) is a library of math kernel
+subroutines, extensively threaded and optimized for maximum performance.
+Intel MKL unites and provides these basic componentsBLAS, LAPACK,
+ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and
+many more.
+ $ module load mkl
+Read more at the [Intel
+MKL](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl)
+page.
+Intel Integrated Performance Primitives
+----------------
+Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX
+is available, via module ipp. The IPP is a library of highly optimized
+algorithmic building blocks for media and data applications. This
+includes signal, image and frame processing algorithms, such as FFT,
+FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many
+more.
+ $ module load ipp
+Read more at the [Intel
+IPP](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives)
+page.
+Intel Threading Building Blocks
+--------
+Intel Threading Building Blocks (Intel TBB) is a library that supports
+scalable parallel programming using standard ISO C++ code. It does not
+require special languages or compilers. It is designed to promote
+scalable data parallel programming. Additionally, it fully supports
+nested parallelism, so you can build larger parallel components from
+smaller parallel components. To use the library, you specify tasks, not
+threads, and let the library map tasks onto threads in an efficient
+manner.
+ $ module load tbb
+Read more at the [Intel
+TBB](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb)
+page.
diff --git a/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.html
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<title>MAGMA for Intel Xeon Phi — IT4I Docs</title>
- <link rel="canonical" href="magma-for-intel-xeon-phi.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi" />
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+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="magma-for-intel-xeon-phi.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi#portal-globalnav">PĹ™ejĂt na navigaci</a>
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</a>
@@ -393,7 +390,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -409,7 +406,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -425,7 +422,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -441,7 +438,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -457,7 +454,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -473,7 +470,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -489,7 +486,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -505,7 +502,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -521,7 +518,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -537,10 +534,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -556,7 +553,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -572,7 +569,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -588,7 +585,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -604,7 +601,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -620,7 +617,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -636,7 +633,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -652,7 +649,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -668,7 +665,7 @@
- <a title="Intel libraries for high performance in numerical computing" class="state-published contenttype-document" href="intel-numerical-libraries.html">
+ <a class="state-published contenttype-document" title="Intel libraries for high performance in numerical computing" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries">
<span>Intel numerical libraries</span>
</a>
@@ -684,7 +681,7 @@
- <a title="The GNU Scientific Library. Provides a wide range of mathematical routines." class="state-published contenttype-document" href="gsl.html">
+ <a class="state-published contenttype-document" title="The GNU Scientific Library. Provides a wide range of mathematical routines." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl">
<span>GSL</span>
</a>
@@ -700,7 +697,7 @@
- <a title="Hierarchical Data Format library. Serial and MPI parallel version." class="state-published contenttype-document" href="hdf5.html">
+ <a class="state-published contenttype-document" title="Hierarchical Data Format library. Serial and MPI parallel version." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5">
<span>HDF5</span>
</a>
@@ -716,7 +713,7 @@
- <a title="The discrete Fourier transform in one or more dimensions, MPI parallel" class="state-published contenttype-document" href="fftw.html">
+ <a class="state-published contenttype-document" title="The discrete Fourier transform in one or more dimensions, MPI parallel" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw">
<span>FFTW</span>
</a>
@@ -732,8 +729,8 @@
- <a title="Next generation dense algebra library for heterogeneous systems with accelerators
-" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="magma-for-intel-xeon-phi.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="Next generation dense algebra library for heterogeneous systems with accelerators
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi">
<span>MAGMA for Intel Xeon Phi</span>
</a>
@@ -749,7 +746,7 @@
- <a title="PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism." class="state-published contenttype-document" href="petsc.html">
+ <a class="state-published contenttype-document" title="PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc">
<span>PETSc</span>
</a>
@@ -765,7 +762,7 @@
- <a title=" Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization." class="state-published contenttype-document" href="trilinos.html">
+ <a class="state-published contenttype-document" title=" Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos">
<span>Trilinos</span>
</a>
@@ -790,7 +787,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -806,7 +803,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -822,7 +819,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -838,7 +835,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -854,7 +851,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -870,7 +867,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -886,7 +883,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -902,7 +899,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -918,7 +915,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -934,7 +931,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -950,7 +947,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -966,7 +963,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -991,7 +988,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1007,7 +1004,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1032,7 +1029,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1048,7 +1045,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1064,7 +1061,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
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+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</div>
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
new file mode 100644
index 0000000000000000000000000000000000000000..06461c5f3148945c71063dd0e41f5a9d8e03a4bb
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
@@ -0,0 +1,64 @@
+MAGMA for Intel Xeon Phi
+========================
+Next generation dense algebra library for heterogeneous systems with
+accelerators
+### Compiling and linking with MAGMA
+To be able to compile and link code with MAGMA library user has to load
+following module:
+ $ module load magma/1.3.0-mic
+To make compilation more user friendly module also sets these two
+environment variables:
+MAGMA_INC - contains paths to the MAGMA header files (to be used for
+compilation step)
+MAGMA_LIBS - contains paths to MAGMA libraries (to be used for linking
+step). Â
+Compilation example:
+ $ icc -mkl -O3 -DHAVE_MIC -DADD_ -Wall $MAGMA_INC -c testing_dgetrf_mic.cpp -o testing_dgetrf_mic.o
+ $ icc -mkl -O3 -DHAVE_MIC -DADD_ -Wall -fPIC -Xlinker -zmuldefs -Wall -DNOCHANGE -DHOST testing_dgetrf_mic.o -o testing_dgetrf_mic $MAGMA_LIBS
+Â
+### Running MAGMA code
+MAGMA implementation for Intel MIC requires a MAGMA server running on
+accelerator prior to executing the user application. The server can be
+started and stopped using following scripts:
+To start MAGMA server use:
+**$MAGMAROOT/start_magma_server**
+To stop the server use:
+**$MAGMAROOT/stop_magma_server**
+For deeper understanding how the MAGMA server is started, see the
+following script:
+**$MAGMAROOT/launch_anselm_from_mic.sh**
+To test if the MAGMA server runs properly we can run one of examples
+that are part of the MAGMA installation:
+ [user@cn204 ~]$ $MAGMAROOT/testing/testing_dgetrf_mic
+ [user@cn204 ~]$ export OMP_NUM_THREADS=16
+ [lriha@cn204 ~]$ $MAGMAROOT/testing/testing_dgetrf_mic
+ Usage/apps/libs/magma-mic/magmamic-1.3.0/testing/testing_dgetrf_mic [options] [-h|--help]
+ Â MÂ Â Â Â NÂ Â Â Â CPU GFlop/s (sec)Â Â MAGMA GFlop/s (sec)Â Â ||PA-LU||/(||A||*N)
+ =========================================================================
+ Â 1088Â 1088Â Â Â Â ---Â Â (Â ---Â )Â Â Â Â 13.93 (Â Â 0.06)Â Â Â Â ---
+ Â 2112Â 2112Â Â Â Â ---Â Â (Â ---Â )Â Â Â Â 77.85 (Â Â 0.08)Â Â Â Â ---
+ Â 3136Â 3136Â Â Â Â ---Â Â (Â ---Â )Â Â Â 183.21 (Â Â 0.11)Â Â Â Â ---
+ Â 4160Â 4160Â Â Â Â ---Â Â (Â ---Â )Â Â Â 227.52 (Â Â 0.21)Â Â Â Â ---
+ Â 5184Â 5184Â Â Â Â ---Â Â (Â ---Â )Â Â Â 258.61 (Â Â 0.36)Â Â Â Â ---
+ Â 6208Â 6208Â Â Â Â ---Â Â (Â ---Â )Â Â Â 333.12 (Â Â 0.48)Â Â Â Â ---
+ Â 7232Â 7232Â Â Â Â ---Â Â (Â ---Â )Â Â Â 416.52 (Â Â 0.61)Â Â Â Â ---
+ Â 8256Â 8256Â Â Â Â ---Â Â (Â ---Â )Â Â Â 446.97 (Â Â 0.84)Â Â Â Â ---
+ Â 9280Â 9280Â Â Â Â ---Â Â (Â ---Â )Â Â Â 461.15 (Â Â 1.16)Â Â Â Â ---
+ 10304 10304Â Â Â Â ---Â Â (Â ---Â )Â Â Â 500.70 (Â Â 1.46)Â Â Â Â ---
+Â
+Please noteMAGMA contains several benchmarks and examples that can be
+found in:
+**$MAGMAROOT/testing/**
+MAGMA relies on the performance of all CPU cores as well as on the
+performance of the accelerator. Therefore on Anselm number of CPU OpenMP
+threads has to be set to 16Â **
+export OMP_NUM_THREADS=16**
+Â
+See more details at [MAGMA home
+page](http://icl.cs.utk.edu/magma/).
+References
+----------
+[1] MAGMA MICLinear Algebra Library for Intel Xeon Phi Coprocessors,
+Jack Dongarra et. al,Â
+[http://icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf
+](http://icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf)
diff --git a/anselm-cluster-documentation/software/numerical-libraries/petsc.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.html
old mode 100755
new mode 100644
similarity index 66%
rename from anselm-cluster-documentation/software/numerical-libraries/petsc.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.html
index ed339f0cc2f47fec45a1e0c80680b4e687f6460f..05d4d4d5b2af74b9839b422e35ace982ed6d32d2
--- a/anselm-cluster-documentation/software/numerical-libraries/petsc.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.html
@@ -10,45 +10,42 @@
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc" /><!--[if lt IE 7]></base><![endif]-->
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+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
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<title>PETSc — IT4I Docs</title>
- <link rel="canonical" href="petsc.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="petsc.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="petsc.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../numerical-libraries.html">Numerical Libraries</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">Numerical Libraries</a>
<span class="breadcrumbSeparator">
/
@@ -390,7 +387,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -406,7 +403,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -422,7 +419,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -438,7 +435,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -454,7 +451,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -470,7 +467,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -486,7 +483,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -502,7 +499,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -518,7 +515,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -534,7 +531,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -550,7 +547,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -566,7 +563,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -582,10 +579,10 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -601,7 +598,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -617,7 +614,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -633,7 +630,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -649,7 +646,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -665,7 +662,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -681,7 +678,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -697,7 +694,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="Libraries for numerical computations" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -713,7 +710,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="Intel libraries for high performance in numerical computing" class="state-published contenttype-document" href="intel-numerical-libraries.html">
+ <a class="state-published contenttype-document" title="Intel libraries for high performance in numerical computing" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries">
<span>Intel numerical libraries</span>
</a>
@@ -729,7 +726,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="The GNU Scientific Library. Provides a wide range of mathematical routines." class="state-published contenttype-document" href="gsl.html">
+ <a class="state-published contenttype-document" title="The GNU Scientific Library. Provides a wide range of mathematical routines." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl">
<span>GSL</span>
</a>
@@ -745,7 +742,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="Hierarchical Data Format library. Serial and MPI parallel version." class="state-published contenttype-document" href="hdf5.html">
+ <a class="state-published contenttype-document" title="Hierarchical Data Format library. Serial and MPI parallel version." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5">
<span>HDF5</span>
</a>
@@ -761,7 +758,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="The discrete Fourier transform in one or more dimensions, MPI parallel" class="state-published contenttype-document" href="fftw.html">
+ <a class="state-published contenttype-document" title="The discrete Fourier transform in one or more dimensions, MPI parallel" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw">
<span>FFTW</span>
</a>
@@ -777,8 +774,8 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="Next generation dense algebra library for heterogeneous systems with accelerators
-" class="state-published contenttype-document" href="magma-for-intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="Next generation dense algebra library for heterogeneous systems with accelerators
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi">
<span>MAGMA for Intel Xeon Phi</span>
</a>
@@ -794,7 +791,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism." class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="petsc.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc">
<span>PETSc</span>
</a>
@@ -810,7 +807,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title=" Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization." class="state-published contenttype-document" href="trilinos.html">
+ <a class="state-published contenttype-document" title=" Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos">
<span>Trilinos</span>
</a>
@@ -835,7 +832,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -851,7 +848,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -867,7 +864,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -883,7 +880,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -899,7 +896,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -915,7 +912,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -931,7 +928,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -947,7 +944,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -963,7 +960,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -979,7 +976,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -995,7 +992,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1011,7 +1008,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -1036,7 +1033,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1052,7 +1049,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1077,7 +1074,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1093,7 +1090,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1109,7 +1106,7 @@ Their static or shared program libraries are available in <code>$PETSC_DIR/$PETS
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
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<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.md
new file mode 100644
index 0000000000000000000000000000000000000000..8c2bbdd271f08197dd6eb462706d8e28eaac8850
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.md
@@ -0,0 +1,89 @@
+PETSc
+=====
+PETSc is a suite of building blocks for the scalable solution of
+scientific and engineering applications modelled by partial differential
+equations. It supports MPI, shared memory, and GPUs through CUDA or
+OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism.
+
+Introduction
+------------
+PETSc (Portable, Extensible Toolkit for Scientific Computation) is a
+suite of building blocks (data structures and routines) for the scalable
+solution of scientific and engineering applications modelled by partial
+differential equations. It allows thinking in terms of high-level
+objects (matrices) instead of low-level objects (raw arrays). Written in
+C language but can also be called from FORTRAN, C++, Python and Java
+codes. It supports MPI, shared memory, and GPUs through CUDA or OpenCL,
+as well as hybrid MPI-shared memory or MPI-GPU parallelism.
+Resources
+---------
+- [project webpage](http://www.mcs.anl.gov/petsc/)
+- [documentation](http://www.mcs.anl.gov/petsc/documentation/)
+ - [PETSc Users
+ Manual (PDF)](http://www.mcs.anl.gov/petsc/petsc-current/docs/manual.pdf)
+ - [index of all manual
+ pages](http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/singleindex.html)
+- PRACE Video Tutorial [part
+ 1](http://www.youtube.com/watch?v=asVaFg1NDqY), [part
+ 2](http://www.youtube.com/watch?v=ubp_cSibb9I), [part
+ 3](http://www.youtube.com/watch?v=vJAAAQv-aaw), [part
+ 4](http://www.youtube.com/watch?v=BKVlqWNh8jY), [part
+ 5](http://www.youtube.com/watch?v=iXkbLEBFjlM)
+Modules
+-------
+You can start using PETSc on Anselm by loading the PETSc module. Module
+names obey this pattern:
+ # module load petsc/version-compiler-mpi-blas-variant, e.g.
+ module load petsc/3.4.4-icc-impi-mkl-opt
+where `variant` is replaced by one of
+`{dbg, opt, threads-dbg, threads-opt}`. The `opt` variant is compiled
+without debugging information (no `-g` option) and with aggressive
+compiler optimizations (`-O3 -xAVX`). This variant is suitable for
+performance measurements and production runs. In all other cases use the
+debug (`dbg`) variant, because it contains debugging information,
+performs validations and self-checks, and provides a clear stack trace
+and message in case of an error. The other two variants `threads-dbg`
+and `threads-opt` are `dbg` and `opt`, respectively, built with [OpenMP
+and pthreads threading
+support](http://www.mcs.anl.gov/petsc/features/threads.html).
+External libraries
+------------------
+PETSc needs at least MPI, BLAS and LAPACK. These dependencies are
+currently satisfied with Intel MPI and Intel MKL in Anselm `petsc`
+modules.
+PETSc can be linked with a plethora of [external numerical
+libraries](http://www.mcs.anl.gov/petsc/miscellaneous/external.html),
+extending PETSc functionality, e.g. direct linear system solvers,
+preconditioners or partitioners. See below a list of libraries currently
+included in Anselm `petsc` modules.
+All these libraries can be used also alone, without PETSc. Their static
+or shared program libraries are available in
+`$PETSC_DIR/$PETSC_ARCH/lib` and header files in
+`$PETSC_DIR/$PETSC_ARCH/include`. `PETSC_DIR` and `PETSC_ARCH` are
+environment variables pointing to a specific PETSc instance based on the
+petsc module loaded.
+### Libraries linked to PETSc on Anselm (as of 11 April 2015)
+- dense linear algebra
+ - [Elemental](http://libelemental.org/)
+- sparse linear system solvers
+ - [Intel MKL
+ Pardiso](https://software.intel.com/en-us/node/470282)
+ - [MUMPS](http://mumps.enseeiht.fr/)
+ - [PaStiX](http://pastix.gforge.inria.fr/)
+ - [SuiteSparse](http://faculty.cse.tamu.edu/davis/suitesparse.html)
+ - [SuperLU](http://crd.lbl.gov/~xiaoye/SuperLU/#superlu)
+ - [SuperLU_Dist](http://crd.lbl.gov/~xiaoye/SuperLU/#superlu_dist)
+- input/output
+ - [ExodusII](http://sourceforge.net/projects/exodusii/)
+ - [HDF5](http://www.hdfgroup.org/HDF5/)
+ - [NetCDF](http://www.unidata.ucar.edu/software/netcdf/)
+- partitioning
+ - [Chaco](http://www.cs.sandia.gov/CRF/chac.html)
+ - [METIS](http://glaros.dtc.umn.edu/gkhome/metis/metis/overview)
+ - [ParMETIS](http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview)
+ - [PT-Scotch](http://www.labri.fr/perso/pelegrin/scotch/)
+- preconditioners & multigrid
+ - [Hypre](http://acts.nersc.gov/hypre/)
+ - [Trilinos ML](http://trilinos.sandia.gov/packages/ml/)
+ - [SPAI - Sparse Approximate
+ Inverse](https://bitbucket.org/petsc/pkg-spai)
diff --git a/anselm-cluster-documentation/software/numerical-libraries/trilinos.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.html
old mode 100755
new mode 100644
similarity index 63%
rename from anselm-cluster-documentation/software/numerical-libraries/trilinos.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.html
index c7962ed0f218e5694af706332d68195c80e60b87..a0a700bca76b8b86be11056d28aa3a0b613bff8f
--- a/anselm-cluster-documentation/software/numerical-libraries/trilinos.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.html
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+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos" /><!--[if lt IE 7]></base><![endif]-->
<meta content=" Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization." name="description" />
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<title>Trilinos — IT4I Docs</title>
- <link rel="canonical" href="trilinos.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
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+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
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<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="trilinos.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="trilinos.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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@@ -125,13 +122,13 @@
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
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- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../numerical-libraries.html">Numerical Libraries</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">Numerical Libraries</a>
<span class="breadcrumbSeparator">
/
@@ -261,7 +258,7 @@
<li><strong>IFPACK</strong> - distributed algebraic preconditioner (includes e.g. incomplete LU factorization)</li>
<li><strong>Teuchos</strong> - common tools packages. This package contains classes for memory management, output, performance monitoring, BLAS and LAPACK wrappers etc.</li>
</ul>
-<p>For the full list of Trilinos packages, descriptions of their capabilities, and user manuals see <a class="external-link" href="http://trilinos.sandia.gov/" target="_self" title="">http://trilinos.sandia.gov.</a></p>
+<p>For the full list of Trilinos packages, descriptions of their capabilities, and user manuals see <a class="external-link" href="http://trilinos.sandia.gov" target="_self" title="">http://trilinos.sandia.gov.</a></p>
<h3 class=" ">Installed version</h3>
<p>Currently, Trilinos in version 11.2.3 compiled with Intel Compiler is installed on ANSELM.</p>
<h3 class=" ">Compilling against Trilinos</h3>
@@ -348,7 +345,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -396,7 +393,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -428,7 +425,7 @@
- <a title="" class="state-published contenttype-document" href="../../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -444,7 +441,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -460,7 +457,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -476,7 +473,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -492,7 +489,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -524,7 +521,7 @@
- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -540,10 +537,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -559,7 +556,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -575,7 +572,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -591,7 +588,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -607,7 +604,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -623,7 +620,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -639,7 +636,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -655,7 +652,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -671,7 +668,7 @@
- <a title="Intel libraries for high performance in numerical computing" class="state-published contenttype-document" href="intel-numerical-libraries.html">
+ <a class="state-published contenttype-document" title="Intel libraries for high performance in numerical computing" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries">
<span>Intel numerical libraries</span>
</a>
@@ -687,7 +684,7 @@
- <a title="The GNU Scientific Library. Provides a wide range of mathematical routines." class="state-published contenttype-document" href="gsl.html">
+ <a class="state-published contenttype-document" title="The GNU Scientific Library. Provides a wide range of mathematical routines." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl">
<span>GSL</span>
</a>
@@ -703,7 +700,7 @@
- <a title="Hierarchical Data Format library. Serial and MPI parallel version." class="state-published contenttype-document" href="hdf5.html">
+ <a class="state-published contenttype-document" title="Hierarchical Data Format library. Serial and MPI parallel version." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5">
<span>HDF5</span>
</a>
@@ -719,7 +716,7 @@
- <a title="The discrete Fourier transform in one or more dimensions, MPI parallel" class="state-published contenttype-document" href="fftw.html">
+ <a class="state-published contenttype-document" title="The discrete Fourier transform in one or more dimensions, MPI parallel" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw">
<span>FFTW</span>
</a>
@@ -735,8 +732,8 @@
- <a title="Next generation dense algebra library for heterogeneous systems with accelerators
-" class="state-published contenttype-document" href="magma-for-intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="Next generation dense algebra library for heterogeneous systems with accelerators
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi">
<span>MAGMA for Intel Xeon Phi</span>
</a>
@@ -752,7 +749,7 @@
- <a title="PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism." class="state-published contenttype-document" href="petsc.html">
+ <a class="state-published contenttype-document" title="PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc">
<span>PETSc</span>
</a>
@@ -768,7 +765,7 @@
- <a title=" Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization." class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="trilinos.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title=" Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization." href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos">
<span>Trilinos</span>
</a>
@@ -793,7 +790,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -809,7 +806,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -825,7 +822,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -841,7 +838,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -857,7 +854,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -873,7 +870,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -889,7 +886,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -905,7 +902,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -921,7 +918,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -937,7 +934,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -953,7 +950,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -969,7 +966,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -994,7 +991,7 @@
- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1010,7 +1007,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1035,7 +1032,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1051,7 +1048,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1067,7 +1064,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
new file mode 100644
index 0000000000000000000000000000000000000000..2a043cfd1e6ad269c7c6da495c4f54ec1d42ade9
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
@@ -0,0 +1,55 @@
+Trilinos
+========
+Packages for large scale scientific and engineering problems. Provides
+MPI and hybrid parallelization.
+### Introduction
+Trilinos is a collection of software packages for the numerical solution
+of large scale scientific and engineering problems. It is based on C++
+and feautures modern object-oriented design. Both serial as well as
+parallel computations based on MPI and hybrid parallelization are
+supported within Trilinos packages.
+### Installed packages
+Current Trilinos installation on ANSELM contains (among others) the
+following main packages
+- **Epetra** - core linear algebra package containing classes for
+ manipulation with serial and distributed vectors, matrices,
+ and graphs. Dense linear solvers are supported via interface to BLAS
+ and LAPACK (Intel MKL on ANSELM). Its extension **EpetraExt**
+ contains e.g. methods for matrix-matrix multiplication.
+- **Tpetra** - next-generation linear algebra package. Supports 64bit
+ indexing and arbitrary data type using C++ templates.
+- **Belos** - library of various iterative solvers (CG, block CG,
+ GMRES, block GMRES etc.).
+- **Amesos** - interface to direct sparse solvers.
+- **Anasazi** - framework for large-scale eigenvalue algorithms.
+- **IFPACK** - distributed algebraic preconditioner (includes e.g.
+ incomplete LU factorization)
+- **Teuchos** - common tools packages. This package contains classes
+ for memory management, output, performance monitoring, BLAS and
+ LAPACK wrappers etc.
+For the full list of Trilinos packages, descriptions of their
+capabilities, and user manuals see
+[http://trilinos.sandia.gov.](http://trilinos.sandia.gov)
+### Installed version
+Currently, Trilinos in version 11.2.3 compiled with Intel Compiler is
+installed on ANSELM.
+### Compilling against Trilinos
+First, load the appropriate module:
+ $ module load trilinos
+For the compilation of CMake-aware project, Trilinos provides the
+FIND_PACKAGE( Trilinos ) capability, which makes it easy to build
+against Trilinos, including linking against the correct list of
+libraries. For details, see
+<http://trilinos.sandia.gov/Finding_Trilinos.txt>
+For compiling using simple makefiles, Trilinos provides Makefile.export
+system, which allows users to include important Trilinos variables
+directly into their makefiles. This can be done simply by inserting the
+following line into the makefile:
+ include Makefile.export.Trilinos
+or
+ include Makefile.export.<package>
+if you are interested only in a specific Trilinos package. This will
+give you access to the variables such as Trilinos_CXX_COMPILER,
+Trilinos_INCLUDE_DIRS, Trilinos_LIBRARY_DIRS etc. For the detailed
+description and example makefile see
+<http://trilinos.sandia.gov/Export_Makefile.txt>.
diff --git a/anselm-cluster-documentation/software/nvidia-cuda.html b/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.html
old mode 100755
new mode 100644
similarity index 74%
rename from anselm-cluster-documentation/software/nvidia-cuda.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.html
index fa80daa4c15dd76ac09db5d4672b6285e5c1953b..f940e2a40aaac4b31884a6d44ed2e252a4d56164
--- a/anselm-cluster-documentation/software/nvidia-cuda.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda" /><!--[if lt IE 7]></base><![endif]-->
<meta content="A guide to nVidia CUDA programming and GPU usage" name="description" />
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- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
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<title>nVidia CUDA — IT4I Docs</title>
- <link rel="canonical" href="nvidia-cuda.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="nvidia-cuda.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="nvidia-cuda.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
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+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
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@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
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@@ -163,7 +160,7 @@
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<span id="breadcrumbs-2" dir="ltr">
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
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@@ -353,7 +350,7 @@
<dt class="portletHeader hiddenStructure">
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- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
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@@ -369,7 +366,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
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@@ -385,7 +382,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
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@@ -401,7 +398,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -417,7 +414,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -433,7 +430,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -449,7 +446,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -465,7 +462,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -481,7 +478,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -497,7 +494,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -513,7 +510,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -529,7 +526,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -545,10 +542,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -564,7 +561,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -580,7 +577,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -596,7 +593,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -612,7 +609,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -628,7 +625,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -644,7 +641,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -660,7 +657,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -676,7 +673,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -692,7 +689,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -708,7 +705,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -724,7 +721,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -740,7 +737,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -756,7 +753,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -772,7 +769,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="nvidia-cuda.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -788,7 +785,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -804,7 +801,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -820,7 +817,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -836,7 +833,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -852,7 +849,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -877,7 +874,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -893,7 +890,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -918,7 +915,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -934,7 +931,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -950,7 +947,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -989,14 +986,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1018,12 +1015,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1039,7 +1036,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:52 GMT -->
</html>
diff --git a/anselm-cluster-documentation/software/nvidia-cuda.md b/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.md
similarity index 63%
rename from anselm-cluster-documentation/software/nvidia-cuda.md
rename to docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.md
index e9773d5989cb8608357cf30e56b3843abfe3b5ba..e8f6dc8e2d65fd507e268852d45103f100ae0764 100644
--- a/anselm-cluster-documentation/software/nvidia-cuda.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.md
@@ -1,8 +1,9 @@
+nVidia CUDA
+===========
A guide to nVidia CUDA programming and GPU usage
-
-
+
CUDA Programming on Anselm
---------------------------
+---
The default programming model for GPU accelerators on Anselm is Nvidia
CUDA. To set up the environment for CUDA use
$ module load cuda
@@ -15,9 +16,9 @@ CUDA code can be compiled directly on login1 or login2 nodes. User does
not have to use compute nodes with GPU accelerator for compilation. To
compile a CUDA source code, use nvcc compiler.
$ nvcc --version
-CUDA Toolkit comes with large number of examples, that can be
+<span>CUDA Toolkit comes with large number of examples, that can be
helpful to start with. To compile and test these examples user should
-copy them to its home directoryÂ
+copy them to its home directory </span>
$ cd ~
$ mkdir cuda-samples
$ cp -R /apps/nvidia/cuda/6.5.14/samples/* ~/cuda-samples/
@@ -26,7 +27,7 @@ the example used is deviceQuery) and run "make" to start the compilation
$ cd ~/cuda-samples/1_Utilities/deviceQuery
$ makeÂ
To run the code user can use PBS interactive session to get access to a
-node from qnvidia queue (note use your project name with parameter -A
+node from qnvidia queue (noteuse your project name with parameter -A
in the qsub command) and execute the binary file
$ qsub -I -q qnvidia -A OPEN-0-0
$ module load cuda
@@ -35,37 +36,37 @@ Expected output of the deviceQuery example executed on a node with Tesla
K20m is
CUDA Device Query (Runtime API) version (CUDART static linking)
Detected 1 CUDA Capable device(s)
- Device 0 "Tesla K20m"
+ Device 0"Tesla K20m"
CUDA Driver Version / Runtime Version 5.0 / 5.0
- CUDA Capability Major/Minor version number 3.5
- Total amount of global memory 4800 MBytes (5032706048 bytes)
- (13) Multiprocessors x (192) CUDA Cores/MP 2496 CUDA Cores
- GPU Clock rate 706 MHz (0.71 GHz)
- Memory Clock rate 2600 MhzÂ
- Memory Bus Width 320-bit
- L2 Cache Size 1310720 bytes
+ CUDA Capability Major/Minor version number3.5
+ Total amount of global memory4800 MBytes (5032706048 bytes)
+ (13) Multiprocessors x (192) CUDA Cores/MP2496 CUDA Cores
+ GPU Clock rate706 MHz (0.71 GHz)
+ Memory Clock rate2600 MhzÂ
+ Memory Bus Width320-bit
+ L2 Cache Size1310720 bytes
Max Texture Dimension Size (x,y,z) 1D=(65536), 2D=(65536,65536), 3D=(4096,4096,4096)
Max Layered Texture Size (dim) x layers 1D=(16384) x 2048, 2D=(16384,16384) x 2048
- Total amount of constant memory 65536 bytesÂ
- Total amount of shared memory per block 49152 bytes
- Total number of registers available per block 65536
- Warp size 32
- Maximum number of threads per multiprocessor 2048
- Maximum number of threads per block 1024Â
- Maximum sizes of each dimension of a block 1024 x 1024 x 64
- Maximum sizes of each dimension of a grid 2147483647 x 65535 x 65535
- Maximum memory pitch 2147483647 bytes
- Texture alignment 512 bytes
- Concurrent copy and kernel execution Yes with 2 copy engine(s)
- Run time limit on kernels No
- Integrated GPU sharing Host Memory No
- Support host page-locked memory mapping Yes
- Alignment requirement for Surfaces YesÂ
- Device has ECC support EnabledÂ
- Device supports Unified Addressing (UVA) Yes
- Device PCI Bus ID / PCI location ID 2 / 0
- Compute ModeÂ
- Â
+ Total amount of constant memory65536 bytesÂ
+ Total amount of shared memory per block49152 bytes
+ Total number of registers available per block65536
+ Warp size32
+ Maximum number of threads per multiprocessor2048
+ Maximum number of threads per block1024Â
+ Maximum sizes of each dimension of a block1024 x 1024 x 64
+ Maximum sizes of each dimension of a grid2147483647 x 65535 x 65535
+ Maximum memory pitch2147483647 bytes
+ Texture alignment512 bytes
+ Concurrent copy and kernel executionYes with 2 copy engine(s)
+ Run time limit on kernelsNo
+ Integrated GPU sharing Host MemoryNo
+ Support host page-locked memory mappingYes
+ Alignment requirement for SurfacesYesÂ
+ Device has ECC supportEnabledÂ
+ Device supports Unified Addressing (UVA)Yes
+ Device PCI Bus ID / PCI location ID2 / 0
+ Compute Mode:Â
+ < Default (multiple host threads can use ::cudaSetDevice() with device simultaneously) >Â
deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 5.0, CUDA Runtime Version = 5.0, NumDevs = 1, Device0 = Tesla K20mÂ
### Code example
In this section we provide a basic CUDA based vector addition code
@@ -73,8 +74,8 @@ example. You can directly copy and paste the code to test it.Â
$ vim test.cu
#define N (2048*2048)
#define THREADS_PER_BLOCK 512
- #include
- #include
+ #include <stdio.h>
+ #include <stdlib.h>
// GPU kernel function to add two vectors
__global__ void add_gpu( int *a, int *b, int *c, int n){
 int index = threadIdx.x + blockIdx.x * blockDim.x;
@@ -124,7 +125,7 @@ example. You can directly copy and paste the code to test it.Â
 cudaMemcpy( dev_a, a, size, cudaMemcpyHostToDevice );
 cudaMemcpy( dev_b, b, size, cudaMemcpyHostToDevice );
 // launch add_gpu() kernel with blocks and threads
- Â add_gpu>>( dev_a, dev_b, dev_c, N );
+ Â add_gpu<<< N/THREADS_PER_BLOCK, THREADS_PER_BLOCK >>>( dev_a, dev_b, dev_c, N );
 // copy device result back to host copy of c
 cudaMemcpy( c, dev_c, size, cudaMemcpyDeviceToHost );
 //Check the results with CPU implementation
@@ -153,19 +154,19 @@ The NVIDIA CUDA Basic Linear Algebra Subroutines (cuBLAS) library is a
GPU-accelerated version of the complete standard BLAS library with 152
standard BLAS routines. Basic description of the library together with
basic performance comparison with MKL can be found
-[here](https//developer.nvidia.com/cublas "Nvidia cuBLAS").
-**CuBLAS example SAXPY**
+[here](https://developer.nvidia.com/cublas "Nvidia cuBLAS").
+**CuBLAS exampleSAXPY**
SAXPY function multiplies the vector x by the scalar alpha and adds it
to the vector y overwriting the latest vector with the result. The
description of the cuBLAS function can be found in [NVIDIA CUDA
-documentation](http//docs.nvidia.com/cuda/cublas/index.html#cublas-lt-t-gt-axpy "Nvidia CUDA documentation ").
+documentation](http://docs.nvidia.com/cuda/cublas/index.html#cublas-lt-t-gt-axpy "Nvidia CUDA documentation ").
Code can be pasted in the file and compiled without any modification.
/* Includes, system */
- #include
- #include
+ #include <stdio.h>
+ #include <stdlib.h>
/* Includes, cuda */
- #include
- #include
+ #include <cuda_runtime.h>
+ #include <cublas_v2.h>
/* Vector size */
#define NÂ (32)
/* Host implementation of a simple version of saxpi */
@@ -218,84 +219,21 @@ Code can be pasted in the file and compiled without any modification.
   /* Shutdown */
   cublasDestroy(handle);
}
-Â Please note cuBLAS has its own function for data transfers between CPU
-and GPU memory
+Â Please notecuBLAS has its own function for data transfers between CPU
+and GPU memory:
 -
-[cublasSetVector](http//docs.nvidia.com/cuda/cublas/index.html#cublassetvector)
+[cublasSetVector](http://docs.nvidia.com/cuda/cublas/index.html#cublassetvector)
- transfers data from CPU to GPU memory
 -
-[cublasGetVector](http//docs.nvidia.com/cuda/cublas/index.html#cublasgetvector)
+[cublasGetVector](http://docs.nvidia.com/cuda/cublas/index.html#cublasgetvector)
- transfers data from GPU to CPU memory
 To compile the code using NVCC compiler a "-lcublas" compiler flag has
-to be specified
+to be specified:
$ module load cuda
$ nvcc -lcublas test_cublas.cu -o test_cublas_nvcc
-To compile the same code with GCC
+To compile the same code with GCC:
$ module load cuda
$ gcc -std=c99 test_cublas.c -o test_cublas_icc -lcublas -lcudart
-To compile the same code with Intel compiler
+To compile the same code with Intel compiler:
$ module load cuda intel
$ icc -std=c99 test_cublas.c -o test_cublas_icc -lcublas -lcudart
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage-1.html)
-
- - [Network](../network.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
- - [Chemistry and Materials
- science](chemistry.html "Tools for computational chemistry.")
-
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- studio](intel-suite.html "The Intel Parallel Studio XE")
-
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-
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- Libraries](numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](numerical-languages.html "Interpreted languages for numerical computations")
-
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diff --git a/anselm-cluster-documentation/software/omics-master-1.html b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1.html
old mode 100755
new mode 100644
similarity index 61%
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<title>Diagnostic component (TEAM) — IT4I Docs</title>
- <link rel="canonical" href="diagnostic-component-team.html" />
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- <a accesskey="6" href="diagnostic-component-team.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
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<span id="breadcrumbs-1" dir="ltr">
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<span id="breadcrumbs-3" dir="ltr">
- <a href="../omics-master-1.html">OMICS Master</a>
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<div>
<h3 class=" ">Access</h3>
<p>TEAM is available at the following address :Â <a class="external-link" href="http://omics.it4i.cz/team/" target="_self" title="">http://omics.it4i.cz/team/</a></p>
-<p class="exclamation">The address is accessible only via <a target="_self" title="" class="internal-link" href="../../accessing-the-cluster/vpn-access.html">VPN. </a></p>
+<p class="exclamation">The address is accessible only via <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access">VPN. </a></p>
<h3 class=" ">Diagnostic component (TEAM)</h3>
<p class="6Tekstletter">VCF files are scanned by this diagnostic tool for known diagnostic disease-associated variants. When no diagnostic mutation is found, the file can be sent to the disease-causing gene discovery tool to see wheter new disease associated variants can be found.</p>
<p class="6Tekstletter">TEAM <span>(27)</span> is an intuitive and easy-to-use web tool that fills the gap between the predicted mutations and the final diagnostic in targeted enrichment sequencing analysis. The tool searches for known diagnostic mutations, corresponding to a disease panel, among the predicted patient’s variants. Diagnostic variants for the disease are taken from four databases of disease-related variants (HGMD-public, HUMSAVAR , ClinVar and COSMIC) If no primary diagnostic variant is found, then a list of secondary findings that can help to establish a diagnostic is produced. TEAM also provides with an interface for the definition of and customization of panels, by means of which, genes and mutations can be added or discarded to adjust panel definitions. </p>
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+<p class="6Tekstletter"><img alt="Interface of the application. Panels for defining targeted regions of interest can be set up by just drag and drop known disease genes or disease definitions from the lists. Thus, virtual panels can be interactively improved as the knowledge of the disease increases." class="image-inline" title="fig5.png" src="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig5.png" /></p>
</div>
<p>Â </p>
<p align="center" class="6Tekstletter"><b><i>Figure 5. </i></b><i>Interface of the application. Panels for defining targeted regions of interest can be set up by just drag and drop known disease genes or disease definitions from the lists. Thus, virtual panels can be interactively improved as the knowledge of the disease increases.</i></p>
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<span>COMSOL</span>
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<span>MPI</span>
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<span>Numerical Libraries</span>
</a>
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<span>Numerical languages</span>
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<span>Virtualization</span>
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- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
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- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
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- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
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- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
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<span>Java</span>
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<span>OMICS Master</span>
</a>
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+ <a class="state-published contenttype-document" title="The human NGS data processing solution
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<span>Overview</span>
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<span>Diagnostic component (TEAM)</span>
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- <a title="" class="state-published contenttype-document" href="priorization-component-bierapp.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp">
<span>Priorization component (BiERApp)</span>
</a>
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- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
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</a>
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+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
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+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
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<span>Remote visualization service</span>
</a>
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<span>PRACE User Support</span>
</a>
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<span>Links</span>
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<span>Changelog</span>
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<span>PBSPro Documentation</span>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md
new file mode 100644
index 0000000000000000000000000000000000000000..c58203dfe8ab675cb388815d043503d7033b3f8d
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md
@@ -0,0 +1,37 @@
+Diagnostic component (TEAM)
+===========================
+
+### Access
+TEAM is available at the following address
+:Â <http://omics.it4i.cz/team/>
+The address is accessible only via
+[VPN. ](https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access)
+### Diagnostic component (TEAM) {#diagnostic-component-team}
+VCF files are scanned by this diagnostic tool for known diagnostic
+disease-associated variants. When no diagnostic mutation is found, the
+file can be sent to the disease-causing gene discovery tool to see
+wheter new disease associated variants can be found.
+TEAMÂ <span>(27)</span>Â is an intuitive and easy-to-use web tool that
+fills the gap between the predicted mutations and the final diagnostic
+in targeted enrichment sequencing analysis. The tool searches for known
+diagnostic mutations, corresponding to a disease panel, among the
+predicted patient’s variants. Diagnostic variants for the disease are
+taken from four databases of disease-related variants (HGMD-public,
+HUMSAVAR , ClinVar and COSMIC) If no primary diagnostic variant is
+found, then a list of secondary findings that can help to establish a
+diagnostic is produced. TEAM also provides with an interface for the
+definition of and customization of panels, by means of which, genes and
+mutations can be added or discarded to adjust panel definitions.Â
+
+Â
+***Figure 5. ****Interface of the application. Panels for defining
+targeted regions of interest can be set up by just drag and drop known
+disease genes or disease definitions from the lists. Thus, virtual
+panels can be interactively improved as the knowledge of the disease
+increases.*
+*
+*
diff --git a/anselm-cluster-documentation/software/omics-master-1/images.html b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images.html
old mode 100755
new mode 100644
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rename to docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images.html
index 8089398ddbf253a4bd4f0be916a2906ec7c010c3..9990d347b09ada6bd3f1557a42f14f59596444b6
--- a/anselm-cluster-documentation/software/omics-master-1/images.html
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/" /><!--[if lt IE 7]></base><![endif]-->
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<title>images — IT4I Docs</title>
- <link rel="canonical" href="images.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
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<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="images.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="images.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<div id="portal-advanced-search" class="hiddenStructure">
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</div>
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- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
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/
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<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
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/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../omics-master-1.html">OMICS Master</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">OMICS Master</a>
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/
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig1.png/view" class="contenttype-image state-missing-value url">Fig 1</a>
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<dt class="portletHeader hiddenStructure">
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<span class="portletTopRight"></span>
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<span>Get Started with IT4Innovations</span>
</a>
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<span>Software</span>
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<span>GPI-2</span>
</a>
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<span>Remote visualization service</span>
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<span>PRACE User Support</span>
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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<title>Fig 1 — IT4I Docs</title>
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<a href="http://study.it4i.cz/">HPC Study</a>
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<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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<h2 class=" ">Introduction</h2>
<p>The scope of this OMICS MASTER solution is restricted to human genomics research (disease causing gene discovery in whole human genome or exome) or diagnosis (panel sequencing), although it could be extended in the future to other usages.</p>
<p>The pipeline inputs the raw data produced by the sequencing machines and undergoes a processing procedure that consists on a quality control, the mapping and variant calling steps that result in a file containing the set of variants in the sample. From this point, the prioritization component or the diagnostic component can be launched. </p>
-<p><img title="Fig 1" class="image-inline" alt="OMICS MASTER solution overview. Data is produced in the external labs and comes to IT4I (represented by the blue dashed line). The data pre-processor converts raw data into a list of variants and annotations for each sequenced patient. These lists files together with primary and secondary (alignment) data files are stored in IT4I sequence DB and uploaded to the discovery (candidate priorization) or diagnostic component where they can be analysed directly by the user that produced them, depending of the experimental design carried out." src="images/fig1.png" /></p>
+<p><img alt="OMICS MASTER solution overview. Data is produced in the external labs and comes to IT4I (represented by the blue dashed line). The data pre-processor converts raw data into a list of variants and annotations for each sequenced patient. These lists files together with primary and secondary (alignment) data files are stored in IT4I sequence DB and uploaded to the discovery (candidate priorization) or diagnostic component where they can be analysed directly by the user that produced them, depending of the experimental design carried out." class="image-inline" title="Fig 1" src="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig1.png" /></p>
<p align="center" style="text-align: left; "><b><i>Figure 1.</i></b><i> OMICS MASTER solution overview. D</i><i>ata is produced in the external labs and comes to IT4I (represented by the blue dashed line). The data pre-processor converts raw data into a list of variants and annotations for each sequenced patient. These lists files together with primary and secondary (alignment) data files are stored in IT4I sequence DB and uploaded to the discovery (candidate prioritization) or diagnostic component where they can be analyzed directly by the user that produced them, depending of the experimental design carried out</i>.<span style="text-align: left; ">Â </span></p>
<p>Typical genomics pipelines are composed by several components that need to be launched manually. The advantage of OMICS MASTER pipeline is that all these components are invoked sequentially in an automated way.</p>
<p>OMICS MASTER pipeline inputs a FASTQ file and outputs an enriched VCF file. This pipeline is able to queue all the jobs to PBS by only launching a process taking all the necessary input files and creates the intermediate and final folders</p>
@@ -273,7 +270,7 @@
<p class="6Tekstletter">These steps are carried out over the original FASTQ file with optimized scripts and includes the following steps: sequence cleansing, estimation of base quality scores, elimination of duplicates and statistics.</p>
<p class="6Tekstletter"><b>Input: </b>FASTQ file.</p>
<p class="6Tekstletter"><b>Output: </b>FASTQ file plus an HTML file containing statistics on the data. </p>
-<p class="exclamation"><strong>FASTQ format <br /></strong><span>It represents the nucleotide sequence and its corresponding quality scores.<br /><br /></span><strong><img title="fig2.png" class="image-inline" alt="FASTQ file." src="images/fig2.png" /><br /><b><i>Figure 2.</i></b></strong><i> FASTQ file.</i><strong><br /></strong></p>
+<p class="exclamation"><strong>FASTQ format <br /></strong><span>It represents the nucleotide sequence and its corresponding quality scores.<br /><br /></span><strong><img alt="FASTQ file." class="image-inline" title="fig2.png" src="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig2.png" /><br /><b><i>Figure 2.</i></b></strong><i> FASTQ file.</i><strong><br /></strong></p>
<h4>Mapping</h4>
<p class="6Tekstletter"><b>Component: </b>Hpg-aligner.<b></b></p>
<p class="6Tekstletter">Sequence reads are mapped over the human reference genome. SOLiD reads are not covered by this solution; they should be mapped with specific software (among the few available options, SHRiMP seems to be the best one). For the rest of NGS machine outputs we use HPG Aligner. HPG-Aligner is an innovative solution, based on a combination of mapping with BWT and local alignment with Smith-Waterman (SW), that drastically increases mapping accuracy (97% versus 62-70% by current mappers, in the most common scenarios). This proposal provides a simple and fast solution that maps almost all the reads, even those containing a high number of mismatches or indels.</p>
@@ -418,7 +415,7 @@
</tbody>
</table>
</div>
-<p class=" "><span><br /><br /></span><b><i>Table 1.</i></b><i> Mandatory fields in the SAM format.<br /><span><br />The standard CIGAR description of pairwise alignment defines three operations: â€M’ for match/mismatch, â€I’ for insertion compared with the reference and â€D’ for deletion. The extended CIGAR proposed in SAM added four more operations: â€N’ for skipped bases on the reference, â€S’ for soft clipping, â€H’ for hard clipping and â€P’ for padding. These support splicing, clipping, multi-part and padded alignments. Figure 3 shows examples of CIGAR strings for different types of alignments. <br /><br /><img title="fig3.png" class="image-inline" alt="SAM format file. The â€@SQ’ line in the header section gives the order of reference sequences. Notably, r001 is the name of a read pair. According to FLAG 163 (=1+2+32+128), the read mapped to position 7 is the second read in the pair (128) and regarded as properly paired (1 + 2); its mate is mapped to 37 on the reverse strand (32). Read r002 has three soft-clipped (unaligned) bases. The coordinate shown in SAM is the position of the first aligned base. The CIGAR string for this alignment contains a P (padding) operation which correctly aligns the inserted sequences. Padding operations can be absent when an aligner does not support multiple sequence alignment. The last six bases of read r003 map to position 9, and the first five to position 29 on the reverse strand. The hard clipping operation H indicates that the clipped sequence is not present in the sequence field. The NM tag gives the number of mismatches. Read r004 is aligned across an intron, indicated by the N operation." src="images/fig3.png" /><br /><b><i><br />Figure 3.</i></b><i> SAM format file. The â€@SQ’ line in the header section gives the order of reference sequences. Notably, r001 is the name of a read pair. According to FLAG 163 (=1+2+32+128), the read mapped to position 7 is the second read in the pair (128) and regarded as properly paired (1 + 2); its mate is mapped to 37 on the reverse strand (32). Read r002 has three soft-clipped (unaligned) bases. The coordinate shown in SAM is the position of the first aligned base. The CIGAR string for this alignment contains a P (padding) operation which correctly aligns the inserted sequences. Padding operations can be absent when an aligner does not support multiple sequence alignment. The last six bases of read r003 map to position 9, and the first five to position 29 on the reverse strand. The hard clipping operation H indicates that the clipped sequence is not present in the sequence field. The NM tag gives the number of mismatches. Read r004 is aligned across an intron, indicated by the N operation.</i></span></i></p>
+<p class=" "><span><br /><br /></span><b><i>Table 1.</i></b><i> Mandatory fields in the SAM format.<br /><span><br />The standard CIGAR description of pairwise alignment defines three operations: â€M’ for match/mismatch, â€I’ for insertion compared with the reference and â€D’ for deletion. The extended CIGAR proposed in SAM added four more operations: â€N’ for skipped bases on the reference, â€S’ for soft clipping, â€H’ for hard clipping and â€P’ for padding. These support splicing, clipping, multi-part and padded alignments. Figure 3 shows examples of CIGAR strings for different types of alignments. <br /><br /><img alt="SAM format file. The â€@SQ’ line in the header section gives the order of reference sequences. Notably, r001 is the name of a read pair. According to FLAG 163 (=1+2+32+128), the read mapped to position 7 is the second read in the pair (128) and regarded as properly paired (1 + 2); its mate is mapped to 37 on the reverse strand (32). Read r002 has three soft-clipped (unaligned) bases. The coordinate shown in SAM is the position of the first aligned base. The CIGAR string for this alignment contains a P (padding) operation which correctly aligns the inserted sequences. Padding operations can be absent when an aligner does not support multiple sequence alignment. The last six bases of read r003 map to position 9, and the first five to position 29 on the reverse strand. The hard clipping operation H indicates that the clipped sequence is not present in the sequence field. The NM tag gives the number of mismatches. Read r004 is aligned across an intron, indicated by the N operation." class="image-inline" title="fig3.png" src="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig3.png" /><br /><b><i><br />Figure 3.</i></b><i> SAM format file. The â€@SQ’ line in the header section gives the order of reference sequences. Notably, r001 is the name of a read pair. According to FLAG 163 (=1+2+32+128), the read mapped to position 7 is the second read in the pair (128) and regarded as properly paired (1 + 2); its mate is mapped to 37 on the reverse strand (32). Read r002 has three soft-clipped (unaligned) bases. The coordinate shown in SAM is the position of the first aligned base. The CIGAR string for this alignment contains a P (padding) operation which correctly aligns the inserted sequences. Padding operations can be absent when an aligner does not support multiple sequence alignment. The last six bases of read r003 map to position 9, and the first five to position 29 on the reverse strand. The hard clipping operation H indicates that the clipped sequence is not present in the sequence field. The NM tag gives the number of mismatches. Read r004 is aligned across an intron, indicated by the N operation.</i></span></i></p>
<p class=" "><strong>Binary Alignment/Map (BAM)</strong><br /><br /><span>BAM is the binary representation of SAM and keeps exactly the same information as SAM. BAM uses lossless compression to reduce the size of the data by about 75% and provides an indexing system that allows reads that overlap a region of the genome to be retrieved and rapidly traversed. </span></p>
<h4>Quality control, preprocessing and statistics for BAM</h4>
<p class="6Tekstletter"><b>Component: </b>Hpg-Fastq & FastQC. Some features:</p>
@@ -437,7 +434,7 @@
<p>Identification of single nucleotide variants and indels on the alignments is performed using the Genome Analysis Toolkit (GATK). GATK <sup>(2)</sup> is a software package developed at the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance.</p>
<p><b>Input:</b> BAM</p>
<p><b>Output:</b> VCF</p>
-<p class=" "><strong>Variant Call Format (VCF)</strong><br /><br /><span>VCF </span><sup>(3)</sup><span> is a standardized format for storing the most prevalent types of sequence variation, including SNPs, indels and larger structural variants, together with rich annotations. The format was developed with the primary intention to represent human genetic variation, but its use is not restricted </span><span>to diploid genomes and can be used in different contexts as well. Its flexibility and user extensibility allows representation of a wide variety of genomic variation with respect to a single reference sequence.<br /><br /></span>A VCF file consists of a header section and a data section. The header contains an arbitrary number of metainformation lines, each starting with characters â€##’, and a TAB delimited field definition line, starting with a single â€#’ character. The meta-information header lines provide a standardized description of tags and annotations used in the data section. The use of meta-information allows the information stored within a VCF file to be tailored to the dataset in question. It can be also used to provide information about the means of file creation, date of creation, version of the reference sequence, software used and any other information relevant to the history of the file. The field definition line names eight mandatory columns, corresponding to data columns representing the chromosome (CHROM), a 1-based position of the start of the variant (POS), unique identifiers of the variant (ID), the reference allele (REF), a comma separated list of alternate non-reference alleles (ALT), a phred-scaled quality score (QUAL), site filtering information (FILTER) and a semicolon separated list of additional, user extensible annotation (INFO). In addition, if samples are present in the file, the mandatory header columns are followed by a FORMAT column and an arbitrary number of sample IDs that define the samples included in the VCF file. The FORMAT column is used to define the information contained within each subsequent genotype column, which consists of a colon separated list of fields. For example, the FORMAT field GT:GQ:DP in the fourth data entry of Figure 1a indicates that the subsequent entries contain information regarding the genotype, genotype quality and read depth for each sample. All data lines are TAB delimited and the number of fields in each data line must match the number of fields in the header line. It is strongly recommended that all annotation tags used are declared in the VCF header section.<br /><br /><img title="" class="image-inline" alt="a) Example of valid VCF. The header lines ##fileformat and #CHROM are mandatory, the rest is optional but strongly recommended. Each line of the body describes variants present in the sampled population at one genomic position or region. All alternate alleles are listed in the ALT column and referenced from the genotype fields as 1-based indexes to this list; the reference haplotype is designated as 0. For multiploid data, the separator indicates whether the data are phased (|) or unphased (/). Thus, the two alleles C and G at the positions 2 and 5 in this figure occur on the same chromosome in SAMPLE1. The first data line shows an example of a deletion (present in SAMPLE1) and a replacement of two bases by another base (SAMPLE2); the second line shows a SNP and an insertion; the third a SNP; the fourth a large structural variant described by the annotation in the INFO column, the coordinate is that of the base before the variant. (b–f ) Alignments and VCF representations of different sequence variants: SNP, insertion, deletion, replacement, and a large deletion. The REF columns shows the reference bases replaced by the haplotype in the ALT column. The coordinate refers to the first reference base. (g) Users are advised to use simplest representation possible and lowest coordinate in cases where the position is ambiguous." src="images/fig4.png" /><br /><b><br />Figure 4.</b><span> (a) Example of valid VCF. The header lines ##fileformat and #CHROM are mandatory, the rest is optional but strongly recommended. Each line of the body describes variants present in the sampled population at one genomic position or region. All alternate alleles are listed in the ALT column and referenced from the genotype fields as 1-based indexes to this list; the reference haplotype is designated as 0. For multiploid data, the separator indicates whether the data are phased (|) or unphased (/). Thus, the two alleles C and G at the positions 2 and 5 in this figure occur on the same chromosome in SAMPLE1. The first data line shows an example of a deletion (present in SAMPLE1) and a replacement of two bases by another base (SAMPLE2); the second line shows a SNP and an insertion; the third a SNP; the fourth a large structural variant described by the annotation in the INFO column, the coordinate is that of the base before the variant. (b–f ) Alignments and VCF representations of different sequence variants: SNP, insertion, deletion, replacement, and a large deletion. The REF columns shows the reference bases replaced by the haplotype in the ALT column. The coordinate refers to the first reference base. (g) Users are advised to use simplest representation possible and lowest coordinate in cases where the position is ambiguous.</span></p>
+<p class=" "><strong>Variant Call Format (VCF)</strong><br /><br /><span>VCF </span><sup>(3)</sup><span> is a standardized format for storing the most prevalent types of sequence variation, including SNPs, indels and larger structural variants, together with rich annotations. The format was developed with the primary intention to represent human genetic variation, but its use is not restricted </span><span>to diploid genomes and can be used in different contexts as well. Its flexibility and user extensibility allows representation of a wide variety of genomic variation with respect to a single reference sequence.<br /><br /></span>A VCF file consists of a header section and a data section. The header contains an arbitrary number of metainformation lines, each starting with characters â€##’, and a TAB delimited field definition line, starting with a single â€#’ character. The meta-information header lines provide a standardized description of tags and annotations used in the data section. The use of meta-information allows the information stored within a VCF file to be tailored to the dataset in question. It can be also used to provide information about the means of file creation, date of creation, version of the reference sequence, software used and any other information relevant to the history of the file. The field definition line names eight mandatory columns, corresponding to data columns representing the chromosome (CHROM), a 1-based position of the start of the variant (POS), unique identifiers of the variant (ID), the reference allele (REF), a comma separated list of alternate non-reference alleles (ALT), a phred-scaled quality score (QUAL), site filtering information (FILTER) and a semicolon separated list of additional, user extensible annotation (INFO). In addition, if samples are present in the file, the mandatory header columns are followed by a FORMAT column and an arbitrary number of sample IDs that define the samples included in the VCF file. The FORMAT column is used to define the information contained within each subsequent genotype column, which consists of a colon separated list of fields. For example, the FORMAT field GT:GQ:DP in the fourth data entry of Figure 1a indicates that the subsequent entries contain information regarding the genotype, genotype quality and read depth for each sample. All data lines are TAB delimited and the number of fields in each data line must match the number of fields in the header line. It is strongly recommended that all annotation tags used are declared in the VCF header section.<br /><br /><img alt="a) Example of valid VCF. The header lines ##fileformat and #CHROM are mandatory, the rest is optional but strongly recommended. Each line of the body describes variants present in the sampled population at one genomic position or region. All alternate alleles are listed in the ALT column and referenced from the genotype fields as 1-based indexes to this list; the reference haplotype is designated as 0. For multiploid data, the separator indicates whether the data are phased (|) or unphased (/). Thus, the two alleles C and G at the positions 2 and 5 in this figure occur on the same chromosome in SAMPLE1. The first data line shows an example of a deletion (present in SAMPLE1) and a replacement of two bases by another base (SAMPLE2); the second line shows a SNP and an insertion; the third a SNP; the fourth a large structural variant described by the annotation in the INFO column, the coordinate is that of the base before the variant. (b–f ) Alignments and VCF representations of different sequence variants: SNP, insertion, deletion, replacement, and a large deletion. The REF columns shows the reference bases replaced by the haplotype in the ALT column. The coordinate refers to the first reference base. (g) Users are advised to use simplest representation possible and lowest coordinate in cases where the position is ambiguous." class="image-inline" title="" src="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig4.png" /><br /><b><br />Figure 4.</b><span> (a) Example of valid VCF. The header lines ##fileformat and #CHROM are mandatory, the rest is optional but strongly recommended. Each line of the body describes variants present in the sampled population at one genomic position or region. All alternate alleles are listed in the ALT column and referenced from the genotype fields as 1-based indexes to this list; the reference haplotype is designated as 0. For multiploid data, the separator indicates whether the data are phased (|) or unphased (/). Thus, the two alleles C and G at the positions 2 and 5 in this figure occur on the same chromosome in SAMPLE1. The first data line shows an example of a deletion (present in SAMPLE1) and a replacement of two bases by another base (SAMPLE2); the second line shows a SNP and an insertion; the third a SNP; the fourth a large structural variant described by the annotation in the INFO column, the coordinate is that of the base before the variant. (b–f ) Alignments and VCF representations of different sequence variants: SNP, insertion, deletion, replacement, and a large deletion. The REF columns shows the reference bases replaced by the haplotype in the ALT column. The coordinate refers to the first reference base. (g) Users are advised to use simplest representation possible and lowest coordinate in cases where the position is ambiguous.</span></p>
<h3 class=" "><span>Annotating</span></h3>
<p><b>Component:</b> HPG-Variant</p>
<p>The functional consequences of every variant found are then annotated using the HPG-Variant software, which extracts from CellBase<b>, </b>the Knowledge database, all the information relevant on the predicted pathologic effect of the variants.</p>
@@ -457,8 +454,8 @@
<p><b>Systems biology</b></p>
<p>We also import systems biology information like interactome information from IntAct <sup>(24)</sup>. Reactome <sup>(25)</sup><span> stores pathway and interaction information in BioPAX </span><sup>(26)</sup><span> format. BioPAX data exchange format </span><span>enables the integration of diverse pathway resources. We successfully solved the problem of storing data released in BioPAX format into a SQL relational schema, which allowed us importing Reactome in CellBase.</span></p>
<div>
-<h3 class=" "><a target="_self" title="" class="internal-link" href="diagnostic-component-team.html">Diagnostic component (TEAM)</a></h3>
-<h3 class=" "><a target="_self" title="" class="internal-link" href="priorization-component-bierapp.html"> Priorization component (BiERApp)</a></h3>
+<h3 class=" "><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team">Diagnostic component (TEAM)</a></h3>
+<h3 class=" "><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp"> Priorization component (BiERApp)</a></h3>
</div>
<h2 class=" ">Usage</h2>
<p>First of all, we should load <span class="monospace">ngsPipeline</span> module:</p>
@@ -477,7 +474,7 @@
<p>Â Â Â Â <i>-s, --start & -e, --end. </i>Â Initial and final stage. If we want to launch the pipeline in a specific stage we must use -s. If we want to end the pipeline in a specific stage we must use -e.</p>
<p>Â Â Â Â Â <i>--log</i>. Using log argument NGSpipeline will prompt all the logs to this file.</p>
<p><span>    </span><i>--project</i><span>. Project ID of your supercomputer allocation. </span></p>
-<p><span>Â Â Â Â <i>--queue</i>. <a target="_self" title="" class="internal-link" href="../../resource-allocation-and-job-execution/introduction.html">Queue</a> to run the jobs in.</span></p>
+<p><span>Â Â Â Â <i>--queue</i>. <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction">Queue</a> to run the jobs in.</span></p>
<p>Â <span>Input, output and ped arguments are mandatory. If the output folder does not exist, the pipeline will create it.</span></p>
<h2 class=" "><span>Examples</span></h2>
<p>This is an example usage of NGSpipeline:</p>
@@ -485,11 +482,11 @@
<pre class=" ">/apps/bio/omics/1.0/sample_data<br />└── data<br /> ├── file.ped<br /> ├── sample1<br /> │  ├── sample1_1.fq<br /> │  └── sample1_2.fq<br /> └── sample2<br /> ├── sample2_1.fq<br /> └── sample2_2.fq</pre>
<p>The ped file (<span class="monospace">file.ped</span>) contains the following info:<span>Â </span></p>
<pre class=" ">#family_ID sample_ID parental_ID maternal_ID sex phenotype <br />FAM sample_A 0 0 1 1 <br />FAM sample_B 0 0 2 2 </pre>
-<p>Now, lets load the NGSPipeline module and copy the sample data to a <a target="_self" title="" class="internal-link" href="../../storage-1/storage.html">scratch directory</a> :</p>
+<p>Now, lets load the NGSPipeline module and copy the sample data to a <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage">scratch directory</a> :</p>
<pre class=" ">$ module load ngsPipeline<br />$ mkdir -p /scratch/$USER/omics/results<br />$ cp -r /apps/bio/omics/1.0/sample_data /scratch/$USER/omics/</pre>
<p class=" ">Now, we can launch the pipeline (replace OPEN-0-0 with your Project ID) :</p>
<pre class=" ">$ ngsPipeline -i /scratch/$USER/omics/sample_data/data -o /scratch/$USER/omics/results -p /scratch/$USER/omics/sample_data/data/file.ped --project OPEN-0-0 --queue qprod</pre>
-<p>This command submits the processing <a target="_self" title="" class="internal-link" href="../../resource-allocation-and-job-execution/job-submission-and-execution.html">jobs to the queue</a>. </p>
+<p>This command submits the processing <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">jobs to the queue</a>. </p>
<p>If we want to re-launch the pipeline from stage 4 until stage 20 we should use the next command:</p>
<pre class=" ">$ ngsPipeline -i /scratch/$USER/omics/sample_data/data -o /scratch/$USER/omics/results -p /scratch/$USER/omics/sample_data/data/file.ped -s 4 -e 20 --project OPEN-0-0 --queue qprod </pre>
<h2 class=" "><span>Details on the pipeline</span></h2>
@@ -539,17 +536,17 @@
<li><span>stage-28: hpg-variant</span></li>
</ul>
<h2 class=" "><span>Interpretation</span></h2>
-<p>The output folder contains all the subfolders with the intermediate data. This folder contains the final VCF with all the variants. This file can be uploaded into <a target="_self" title="" class="internal-link" href="diagnostic-component-team.html">TEAM</a> by using the VCF file button. It is important to note here that the entire management of the VCF file is local: no patient’s sequence data is sent over the Internet thus avoiding any problem of data privacy or confidentiality.</p>
-<p><span><img title="fig7.png" class="image-inline" alt="TEAM upload panel. Once the file has been uploaded, a panel must be chosen from the Panel list. Then, pressing the Run button the diagnostic process starts." src="images/fig7.png" /></span></p>
+<p>The output folder contains all the subfolders with the intermediate data. This folder contains the final VCF with all the variants. This file can be uploaded into <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team">TEAM</a> by using the VCF file button. It is important to note here that the entire management of the VCF file is local: no patient’s sequence data is sent over the Internet thus avoiding any problem of data privacy or confidentiality.</p>
+<p><span><img alt="TEAM upload panel. Once the file has been uploaded, a panel must be chosen from the Panel list. Then, pressing the Run button the diagnostic process starts." class="image-inline" title="fig7.png" src="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig7.png" /></span></p>
<p align="center" style="text-align: left; "><b><i>Figure 7</i></b>. <i>TEAM upload panel.</i> <i>Once the file has been uploaded, a panel must be chosen from the Panel<b> </b>list. Then, pressing the Run button the diagnostic process starts.</i></p>
<p>Once the file has been uploaded, a panel must be chosen from the Panel list. Then, pressing the Run button the diagnostic process starts. TEAM searches first for known diagnostic mutation(s) taken from four databases: HGMD-public <sup>(20)</sup>, <a class="external-link" href="http://www.uniprot.org/docs/humsavar" target="_self" title="">HUMSAVAR</a>, ClinVar <sup>(29)</sup> and COSMIC <sup>(23)</sup>.</p>
-<p><img title="fig7x.png" class="image-inline" alt="The panel manager. The elements used to define a panel are (A) disease terms, (B) diagnostic mutations and (C) genes. Arrows represent actions that can be taken in the panel manager. Panels can be defined by using the known mutations and genes of a particular disease. This can be done by dragging them to the Primary Diagnostic box (action D). This action, in addition to defining the diseases in the Primary Diagnostic box, automatically adds the corresponding genes to the Genes box. The panels can be customized by adding new genes (action F) or removing undesired genes (action G). New disease mutations can be added independently or associated to an already existing disease term (action E). Disease terms can be removed by simply dragging themback (action H)." src="images/fig7x.png" /></p>
+<p><img alt="The panel manager. The elements used to define a panel are (A) disease terms, (B) diagnostic mutations and (C) genes. Arrows represent actions that can be taken in the panel manager. Panels can be defined by using the known mutations and genes of a particular disease. This can be done by dragging them to the Primary Diagnostic box (action D). This action, in addition to defining the diseases in the Primary Diagnostic box, automatically adds the corresponding genes to the Genes box. The panels can be customized by adding new genes (action F) or removing undesired genes (action G). New disease mutations can be added independently or associated to an already existing disease term (action E). Disease terms can be removed by simply dragging themback (action H)." class="image-inline" title="fig7x.png" src="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig7x.png" /></p>
<p align="center" style="text-align: left; "><b><i>Figure 7.</i></b><i> The panel manager. The elements used to define a panel are (<b>A</b>) disease terms, (<b>B</b>) diagnostic mutations and (<b>C</b>) genes. Arrows represent actions that can be taken in the panel manager. Panels can be defined by using the known mutations and genes of a particular disease. This can be done by dragging them to the <b>Primary Diagnostic </b>box (action <b>D</b>). This action, in addition to defining the diseases in the <b>Primary Diagnostic </b>box, automatically adds the corresponding genes to the <b>Genes </b>box. The panels can be customized by adding new genes (action <b>F</b>) or removing undesired genes (action <b>G</b>). New disease mutations can be added independently or associated to an already existing disease term (action <b>E</b>). Disease terms can be removed by simply dragging them </i><i>back (action <b>H</b>).</i></p>
<p>For variant discovering/filtering we should upload the VCF file into BierApp by using the following form:</p>
-<p align="center" style="text-align: left; "><i><img title="fig8.png" class="image-inline" alt="BierApp VCF upload panel. It is recommended to choose a name for the job as well as a description. " src="images/fig8.png" /></i></p>
+<p align="center" style="text-align: left; "><i><img alt="BierApp VCF upload panel. It is recommended to choose a name for the job as well as a description. " class="image-inline" title="fig8.png" src="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig8.png" /></i></p>
<p align="center" style="text-align: left; "><i> <b><i>Figure 8.</i></b><i> BierApp VCF upload panel. It is recommended to choose a name for the job as well as a description.</i></i></p>
<p>Each prioritization (â€job’) has three associated screens that facilitate the filtering steps. The first one, the â€Summary’ tab, displays a statistic of the data set analyzed, containing the samples analyzed, the number and types of variants found and its distribution according to consequence types. The second screen, in the â€Variants and effect’ tab, is the actual filtering tool, and the third one, the â€Genome view’ tab, offers a representation of the selected variants within the genomic context provided by an embedded version of <span>the Genome Maps Tool </span><sup>(30)</sup><span>.</span></p>
-<p align="center" style="text-align: left; "><i><i><img title="fig9.png" class="image-inline" alt="This picture shows all the information associated to the variants. If a variant has an associated phenotype we could see it in the last column. In this case, the variant 7:132481242 C>T is associated to the phenotype: large intestine tumor." src="images/fig9.png" /></i></i></p>
+<p align="center" style="text-align: left; "><i><i><img alt="This picture shows all the information associated to the variants. If a variant has an associated phenotype we could see it in the last column. In this case, the variant 7:132481242 C>T is associated to the phenotype: large intestine tumor." class="image-inline" title="fig9.png" src="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig9.png" /></i></i></p>
<p align="center" style="text-align: left; "><i><i> <b><i>Figure 9.</i></b><i> This picture shows all the information associated to the variants. If a variant has an associated phenotype we could see it in the last column. In this case, the variant 7:132481242 C>T is associated to the phenotype: large intestine tumor.</i></i></i></p>
<p align="center" style="text-align: left; "><i><br /></i></p>
<p><span><br /></span></p>
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<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
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+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
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<span>What's New</span>
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<span>Get Started with IT4Innovations</span>
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<span>Salomon Cluster Documentation</span>
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<span>Anselm Cluster Documentation</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
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-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -875,7 +872,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -891,7 +888,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -907,7 +904,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
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- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
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- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -955,7 +952,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
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- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -987,7 +984,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -1019,7 +1016,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -1035,7 +1032,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -1051,7 +1048,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
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- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
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- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../omics-master-1.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
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- <a title="The human NGS data processing solution
-" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="overview.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="The human NGS data processing solution
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview">
<span>Overview</span>
</a>
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- <a title="" class="state-published contenttype-document" href="diagnostic-component-team.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team">
<span>Diagnostic component (TEAM)</span>
</a>
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- <a title="" class="state-published contenttype-document" href="priorization-component-bierapp.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp">
<span>Priorization component (BiERApp)</span>
</a>
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- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -1189,7 +1186,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -1205,7 +1202,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -1221,7 +1218,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
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+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
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- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1408,7 +1405,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:40 GMT -->
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diff --git a/anselm-cluster-documentation/software/omics-master-1/overview.md b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md
similarity index 62%
rename from anselm-cluster-documentation/software/omics-master-1/overview.md
rename to docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md
index dc41153a147aff0d41b4ff8081e610a6001cc5b0..926745ff46a7d8354021fa192b0aa33a7cd0b5ed 100644
--- a/anselm-cluster-documentation/software/omics-master-1/overview.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md
@@ -1,8 +1,7 @@
Overview
========
The human NGS data processing solution
-
-
+
Introduction
------------
The scope of this OMICS MASTER solution is restricted to human genomics
@@ -22,7 +21,7 @@ secondary (alignment) data files are stored in IT4I sequence DB and
uploaded to the discovery (candidate priorization) or diagnostic
component where they can be analysed directly by the user that produced
them, depending of the experimental design carried
-out.](images/fig1.png "Fig 1")
+out.](https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig1.png "Fig 1")
***Figure 1.*** *OMICS MASTER solution overview. Data is produced in the
external labs and comes to IT4I (represented by the blue dashed line).
The data pre-processor converts raw data into a list of variants and
@@ -31,7 +30,7 @@ primary and secondary (alignment) data files are stored in IT4I sequence
DB and uploaded to the discovery (candidate prioritization) or
diagnostic component where they can be analyzed directly by the user
that produced them, depending of the experimental design carried
-out*.Â
+out*.<span style="text-alignleft; ">Â </span>
Typical genomics pipelines are composed by several components that need
to be launched manually. The advantage of OMICS MASTER pipeline is that
all these components are invoked sequentially in an automated way.
@@ -39,7 +38,7 @@ OMICS MASTER pipeline inputs a FASTQ file and outputs an enriched VCF
file. This pipeline is able to queue all the jobs to PBS by only
launching a process taking all the necessary input files and creates the
intermediate and final folders
-Let’s see each of the OMICS MASTER solution components
+Let’s see each of the OMICS MASTER solution components:
Components
----------
### Processing
@@ -48,7 +47,7 @@ controls, alignment, realignment, variant calling and variant
annotation. It turns raw data from the sequencing machine into files
containing lists of variants (VCF) that once annotated, can be used by
the following components (discovery and diagnosis).
-We distinguish three types of sequencing instruments bench sequencers
+We distinguish three types of sequencing instrumentsbench sequencers
(MySeq, IonTorrent, and Roche Junior, although this last one is about
being discontinued), which produce relatively Genomes in the clinic
low throughput (tens of million reads), and high end sequencers, which
@@ -61,22 +60,22 @@ identical. Anyway, SOLiD is a technology which is also about being
discontinued by the manufacturer so, this type of data will be scarce in
the future.
#### Quality control, preprocessing and statistics for FASTQ
-**Component** Hpg-Fastq & FastQC.
+**Component:**<span> Hpg-Fastq & FastQC.</span>
These steps are carried out over the original FASTQ file with optimized
-scripts and includes the following steps sequence cleansing, estimation
+scripts and includes the following stepssequence cleansing, estimation
of base quality scores, elimination of duplicates and statistics.
-**Input** FASTQ file.
-**Output** FASTQ file plus an HTML file containing statistics on the
+**Input:** FASTQ file.
+**Output:** FASTQ file plus an HTML file containing statistics on the
data.Â
**FASTQ formatÂ
-**It represents the nucleotide sequence and its corresponding
+**<span>It represents the nucleotide sequence and its corresponding
quality scores.
-
-**
+</span>**
***Figure 2.******Â FASTQ file.***
**
#### Mapping
-**Component** Hpg-aligner.****
+**Component:** Hpg-aligner.****
Sequence reads are mapped over the human reference genome. SOLiD reads
are not covered by this solution; they should be mapped with specific
software (among the few available options, SHRiMP seems to be the best
@@ -87,73 +86,101 @@ increases mapping accuracy (97% versus 62-70% by current mappers, in the
most common scenarios). This proposal provides a simple and fast
solution that maps almost all the reads, even those containing a high
number of mismatches or indels.
-**Input** FASTQ file.
-**Output** Aligned file in BAM format.****
+**Input:** FASTQ file.
+**Output:** Aligned file in BAM format.****
**Sequence Alignment/Map (SAM)**
-
-It is a human readable tab-delimited format in which each read and
+<span>It is a human readable tab-delimited format in which each read and
its alignment is represented on a single line. The format can represent
unmapped reads, reads that are mapped to unique locations, and reads
that are mapped to multiple locations.
-
-The SAM format ^(1)^ consists of one header
+</span><span>The SAM format </span>^(1)^<span> consists of one header
section and one alignment section. The lines in the header section start
with character â€@’, and lines in the alignment section do not. All lines
are TAB delimited.
-
-In SAM, each alignment line has 11 mandatory fields and a variable
+<span>In SAM, each alignment line has 11 mandatory fields and a variable
number of optional fields. The mandatory fields are briefly described in
Table 1. They must be present but their value can be a
-â€*’ or a zero (depending on the field) if the
-corresponding information is unavailable. Â
-No.
-Name
-Description
-1
-QNAME
-Query NAME of the read or the read pair
-2
-FLAG
-Bitwise FLAG (pairing,strand,mate strand,etc.)
-3
-RNAMEÂ
-Reference sequence NAME
-4
-POSÂ
-1-Based  leftmost POSition of clipped alignment
-5
-MAPQÂ
-MAPping Quality (Phred-scaled)
-6
-CIGARÂ
-Extended CIGAR string (operationsMIDNSHP)
-7
-MRNMÂ
-Mate REference NaMe ('=^' if same RNAME)
-8
-MPOSÂ
-1-Based leftmost Mate POSition
-9
-ISIZEÂ
-Inferred Insert SIZEÂ
-10
-SEQÂ
-Query SEQuence on the same strand as the reference
-11
-QUALÂ
-Query QUALity (ASCII-33=Phred base quality)
-
-
-***Table 1.*** *Mandatory fields in the SAM format.
-
+</span></span>â€*’<span><span> or a zero (depending on the field) if the
+corresponding information is unavailable.</span>Â Â </span>
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<tbody>
+<tr class="odd">
+<td align="left"><p><strong>No.</strong></p></td>
+<td align="left"><p><strong>Name</strong></p></td>
+<td align="left"><p><strong>Description</strong></p></td>
+</tr>
+<tr class="even">
+<td align="left"><p>1</p></td>
+<td align="left"><p>QNAME</p></td>
+<td align="left"><p>Query NAME of the read or the read pair</p></td>
+</tr>
+<tr class="odd">
+<td align="left"><p>2</p></td>
+<td align="left"><p>FLAG</p></td>
+<td align="left"><p>Bitwise FLAG (pairing,strand,mate strand,etc.)</p></td>
+</tr>
+<tr class="even">
+<td align="left"><p>3</p></td>
+<td align="left"><p>RNAMEÂ </p></td>
+<td align="left"><p>Reference sequence NAME</p></td>
+</tr>
+<tr class="odd">
+<td align="left"><p>4</p></td>
+<td align="left"><p>POSÂ </p></td>
+<td align="left"><p>1-Based  leftmost POSition of clipped alignment</p></td>
+</tr>
+<tr class="even">
+<td align="left"><p>5</p></td>
+<td align="left"><p>MAPQÂ </p></td>
+<td align="left"><p>MAPping Quality (Phred-scaled)</p></td>
+</tr>
+<tr class="odd">
+<td align="left"><p>6</p></td>
+<td align="left"><p>CIGARÂ </p></td>
+<td align="left"><p>Extended CIGAR string (operations:MIDNSHP)</p></td>
+</tr>
+<tr class="even">
+<td align="left"><p>7</p></td>
+<td align="left"><p>MRNMÂ </p></td>
+<td align="left"><p>Mate REference NaMe ('=^' if same RNAME)</p></td>
+</tr>
+<tr class="odd">
+<td align="left"><p>8</p></td>
+<td align="left"><p>MPOSÂ </p></td>
+<td align="left"><p>1-Based leftmost Mate POSition</p></td>
+</tr>
+<tr class="even">
+<td align="left"><p>9</p></td>
+<td align="left"><p>ISIZEÂ </p></td>
+<td align="left"><p>Inferred Insert SIZEÂ </p></td>
+</tr>
+<tr class="odd">
+<td align="left"><p>10</p></td>
+<td align="left"><p>SEQÂ </p></td>
+<td align="left"><p>Query SEQuence on the same strand as the reference</p></td>
+</tr>
+<tr class="even">
+<td align="left"><p>11</p></td>
+<td align="left"><p>QUALÂ </p></td>
+<td align="left"><p>Query QUALity (ASCII-33=Phred base quality)</p></td>
+</tr>
+</tbody>
+</table>
+<span>
+</span>***Table 1.*** *Mandatory fields in the SAM format.
+<span>
The standard CIGAR description of pairwise alignment defines three
-operations â€M’ for match/mismatch, â€I’ for insertion compared with the
+operationsâ€M’ for match/mismatch, â€I’ for insertion compared with the
reference and â€D’ for deletion. The extended CIGAR proposed in SAM added
-four more operations â€N’ for skipped bases on the reference, â€S’ for
+four more operationsâ€N’ for skipped bases on the reference, â€S’ for
soft clipping, â€H’ for hard clipping and â€P’ for padding. These support
splicing, clipping, multi-part and padded alignments. Figure 3 shows
examples of CIGAR strings for different types of alignments.Â
-
+operation.](https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig3.png "fig3.png")
***
Figure 3.*** *SAM format file. The â€@SQ’ line in the header section
gives the order of reference sequences. Notably, r001 is the name of a
@@ -184,44 +211,41 @@ r003 map to position 9, and the first five to position 29 on the reverse
strand. The hard clipping operation H indicates that the clipped
sequence is not present in the sequence field. The NM tag gives the
number of mismatches. Read r004 is aligned across an intron, indicated
-by the N operation.**
+by the N operation.*</span>*
**Binary Alignment/Map (BAM)**
-
-BAM is the binary representation of SAM and keeps exactly the same
+<span>BAM is the binary representation of SAM and keeps exactly the same
information as SAM. BAM uses lossless compression to reduce the size of
the data by about 75% and provides an indexing system that allows reads
that overlap a region of the genome to be retrieved and rapidly
-traversed.Â
+traversed. </span>
#### Quality control, preprocessing and statistics for BAM
-**Component** Hpg-Fastq & FastQC. Some features
-- Quality control % reads with N errors, % reads with multiple
+**Component:** Hpg-Fastq & FastQC. Some features:
+- Quality control% reads with N errors, % reads with multiple
mappings, strand bias, paired-end insert, ...
-- Filtering by number of errors, number of hits, …
- - Comparator stats, intersection, ...
-**Input** BAM file.
-**Output** BAM file plus an HTML file containing statistics.Â
+- Filteringby number of errors, number of hits, …
+ - Comparatorstats, intersection, ...
+**Input:** BAM file.
+**Output:** BAM file plus an HTML file containing statistics.Â
#### Variant Calling
-**Component** GATK.
+**Component:** GATK.
Identification of single nucleotide variants and indels on the
alignments is performed using the Genome Analysis Toolkit (GATK). GATK
^(2)^ is a software package developed at the Broad Institute to analyze
high-throughput sequencing data. The toolkit offers a wide variety of
tools, with a primary focus on variant discovery and genotyping as well
as strong emphasis on data quality assurance.
-**Input** BAM
-**Output** VCF
+**Input:** BAM
+**Output:** VCF
**Variant Call Format (VCF)**
-
-VCF ^(3)^ is a standardized format for storing the
+<span>VCF </span>^(3)^<span> is a standardized format for storing the
most prevalent types of sequence variation, including SNPs, indels and
larger structural variants, together with rich annotations. The format
was developed with the primary intention to represent human genetic
-variation, but its use is not restricted to diploid genomes
+variation, but its use is not restricted </span><span>to diploid genomes
and can be used in different contexts as well. Its flexibility and user
extensibility allows representation of a wide variety of genomic
variation with respect to a single reference sequence.
-
-A VCF file consists of a header section and a data section. The
+</span>A VCF file consists of a header section and a data section. The
header contains an arbitrary number of metainformation lines, each
starting with characters â€##’, and a TAB delimited field definition
line, starting with a single â€#’ character. The meta-information header
@@ -243,13 +267,12 @@ FORMAT column and an arbitrary number of sample IDs that define the
samples included in the VCF file. The FORMAT column is used to defineÂ
the information contained within each subsequent genotype column, which
consists of a colon separated list of fields. For example, the FORMAT
-field GTGQDP in the fourth data entry of Figure 1a indicates that the
+field GT:GQ:DP in the fourth data entry of Figure 1a indicates that the
subsequent entries contain information regarding the genotype, genotype
quality and read depth for each sample. All data lines are TAB
delimited and the number of fields in each data line must match the
number of fields in the header line. It is strongly recommended that all
annotation tags used are declared in the VCF header section.
-
+where the position is
+ambiguous.](https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig4.png)
**
-Figure 4.** (a) Example of valid VCF. The header lines
+Figure 4.**<span> (a) Example of valid VCF. The header lines
##fileformat and #CHROM are mandatory, the rest is optional but
strongly recommended. Each line of the body describes variants present
in the sampled population at one genomic position or region. All
@@ -285,14 +309,14 @@ SAMPLE1) and a replacement of two bases by another base (SAMPLE2); the
second line shows a SNP and an insertion; the third a SNP; the fourth a
large structural variant described by the annotation in the INFO column,
the coordinate is that of the base before the variant. (b–f ) Alignments
-and VCF representations of different sequence variants SNP, insertion,
+and VCF representations of different sequence variantsSNP, insertion,
deletion, replacement, and a large deletion. The REF columns shows the
reference bases replaced by the haplotype in the ALT column. The
coordinate refers to the first reference base. (g) Users are advised to
use simplest representation possible and lowest coordinate in cases
-where the position is ambiguous.
-### Annotating
-**Component** HPG-Variant
+where the position is ambiguous.</span>
+### <span>Annotating</span>
+**Component:** HPG-Variant
The functional consequences of every variant found are then annotated
using the HPG-Variant software, which extracts from CellBase**,** the
Knowledge database, all the information relevant on the predicted
@@ -310,26 +334,26 @@ sites affected by the variation. This information allows extending the
conventional reports beyond the coding regions and expands the knowledge
on the contribution of non-coding or synonymous variants to the
phenotype studied.
-**Input** VCF
-**Output** The output of this step is the Variant Calling Format (VCF)
+**Input:** VCF
+**Output:** The output of this step is the Variant Calling Format (VCF)
file, which contains changes with respect to the reference genome with
the corresponding QC and functional annotations.
#### CellBase
CellBase^(5)^Â is a relational database integrates biological information
-from different sources and includes
-**Core features**
+from different sources and includes:
+**Core features:**
We took genome sequences, genes, transcripts, exons, cytobands or cross
-references (xrefs) identifiers (IDs)Â from Ensembl
-^(6)^. Protein information including sequences, xrefs or
+references (xrefs) identifiers (IDs)Â <span>from Ensembl
+</span>^(6)^<span>. Protein information including sequences, xrefs or
protein features (natural variants, mutagenesis sites,
post-translational modifications, etc.) were imported from UniProt
-^(7)^.
-**Regulatory**
+</span>^(7)^<span>.</span>
+**Regulatory:**
CellBase imports miRNA from miRBase ^(8)^; curated and non-curated miRNA
-targets from miRecords ^(9)^, miRTarBase ^(10)^,
-TargetScan^(11)^ and microRNA.org ^(12)^ and
+targets from miRecords ^(9)^, <span>miRTarBase </span>^(10)^<span>,
+TargetScan</span>^(11)^<span> and microRNA.org </span>^(12)^<span> and
CpG islands and conserved regions from the UCSC database
-^(13)^.Â
+</span>^(13)^<span>.</span><span>Â </span>
**Functional annotation**
OBO Foundry ^(14)^ develops many biomedical ontologies that are
implemented in OBO format. We designed a SQL schema to store these OBO
@@ -340,38 +364,38 @@ were also imported.
CellBase includes SNPs from dbSNP ^(16)^; SNP population frequencies
from HapMap ^(17)^, 1000 genomes project ^(18)^ and Ensembl ^(6)^;
phenotypically annotated SNPs were imported from NHRI GWAS Catalog
-^(19)^,^Â ^HGMD ^(20)^, Open Access GWAS Database
-^(21)^, UniProt ^(7)^ and OMIM
-^(22)^; mutations from COSMICÂ ^(23)^ and
+^(19)^,^Â ^<span>HGMD </span>^(20)^<span>, Open Access GWAS Database
+</span>^(21)^<span>, UniProt </span>^(7)^<span> and OMIM
+</span>^(22)^<span>; mutations from COSMICÂ </span>^(23)^<span> and
structural variations from Ensembl
-^(6)^.Â
+</span>^(6)^<span>.</span><span>Â </span>
**Systems biology**
We also import systems biology information like interactome information
-from IntAct ^(24)^. Reactome ^(25)^ stores pathway and interaction
-information in BioPAX ^(26)^ format. BioPAX data exchange
-format enables the integration of diverse pathway
+from IntAct ^(24)^. Reactome ^(25)^<span> stores pathway and interaction
+information in BioPAX </span>^(26)^<span> format. BioPAX data exchange
+format </span><span>enables the integration of diverse pathway
resources. We successfully solved the problem of storing data released
in BioPAX format into a SQL relational schema, which allowed us
-importing Reactome in CellBase.
-### [Diagnostic component (TEAM)](diagnostic-component-team.html)
-### [Priorization component (BiERApp)](priorization-component-bierapp.html)
+importing Reactome in CellBase.</span>
+### [Diagnostic component (TEAM)](https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team)
+### [Priorization component (BiERApp)](https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp)
Usage
-----
-First of all, we should load ngsPipeline
-module
+First of all, we should load <span class="monospace">ngsPipeline</span>
+module:
$ module load ngsPipeline
-This command will load python/2.7.5
-module and all the required modules (
-class="monospace">hpg-aligner,
-class="monospace">gatk, etc)
- If we launch ngsPipeline with â€-h’, we will get the usage
-helpÂ
+This command will load <span class="monospace">python/2.7.5</span>
+module and all the required modules (<span
+class="monospace">hpg-aligner</span>, <span
+class="monospace">gatk</span>, etc)
+<span> If we launch ngsPipeline with â€-h’, we will get the usage
+help:Â </span>
$ ngsPipeline -h
- Usage ngsPipeline.py [-h] -i INPUT -o OUTPUT -p PED --project PROJECT --queue
+ UsagengsPipeline.py [-h] -i INPUT -o OUTPUT -p PED --project PROJECT --queue
           QUEUE [--stages-path STAGES_PATH] [--email EMAIL]
[--prefix PREFIX] [-s START] [-e END] --log
Python pipeline
- optional arguments
+ optional arguments:
 -h, --help       show this help message and exit
 -i INPUT, --input INPUT
 -o OUTPUT, --output OUTPUT
@@ -388,7 +412,7 @@ helpÂ
 -e END, --end END   Final stage
 --log         Log to file
Â
-Let us see a brief description of the arguments
+Let us see a brief description of the arguments:
     *-h --help*. Show the help.
     *-i, --input.* The input data directory. This directory must to
have a special structure. We have to create one folder per sample (with
@@ -411,18 +435,18 @@ launch the pipeline in a specific stage we must use -s. If we want to
end the pipeline in a specific stage we must use -e.
     *--log*. Using log argument NGSpipeline will prompt all the logs
to this file.
-Â Â Â Â *--project*. Project ID of your supercomputer
-allocation.Â
-Â Â Â Â *--queue*.
-[Queue](../../resource-allocation-and-job-execution/introduction.html)
-to run the jobs in.
-Â Input, output and ped arguments are mandatory. If the output
-folder does not exist, the pipeline will create it.
-Examples
+<span>Â Â Â Â </span>*--project*<span>. Project ID of your supercomputer
+allocation. </span>
+<span>Â Â Â Â *--queue*.
+[Queue](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction)
+to run the jobs in.</span>
+Â <span>Input, output and ped arguments are mandatory. If the output
+folder does not exist, the pipeline will create it.</span>
+<span>Examples</span>
---------------------
-This is an example usage of NGSpipeline
-We have a folder with the following structure in
-class="monospace">/apps/bio/omics/1.0/sample_data/Â
+This is an example usage of NGSpipeline:
+We have a folder with the following structure in <span><span
+class="monospace">/apps/bio/omics/1.0/sample_data/</span>Â </span><span>:</span>
/apps/bio/omics/1.0/sample_data
└── data
├── file.ped
@@ -432,119 +456,123 @@ class="monospace">/apps/bio/omics/1.0/sample_data/Â
└── sample2
├── sample2_1.fq
└── sample2_2.fq
-The ped file (file.ped) contains the
-following infoÂ
+The ped file (<span class="monospace">file.ped</span>) contains the
+following info:<span>Â </span>
#family_ID sample_ID parental_ID maternal_ID sex phenotype
FAM sample_A 0 0 1 1
FAM sample_B 0 0 2 2
Now, lets load the NGSPipeline module and copy the sample data to a
-[scratch directory](../../storage-1/storage.html)
+[scratch
+directory](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage)
+:
$ module load ngsPipeline
$ mkdir -p /scratch/$USER/omics/results
$ cp -r /apps/bio/omics/1.0/sample_data /scratch/$USER/omics/
Now, we can launch the pipeline (replace OPEN-0-0 with your Project ID)
-
+:
$ ngsPipeline -i /scratch/$USER/omics/sample_data/data -o /scratch/$USER/omics/results -p /scratch/$USER/omics/sample_data/data/file.ped --project OPEN-0-0 --queue qprod
This command submits the processing [jobs to the
-queue](../../resource-allocation-and-job-execution/job-submission-and-execution.html).Â
+queue](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution).Â
If we want to re-launch the pipeline from stage 4 until stage 20 we
-should use the next command
+should use the next command:
$ ngsPipeline -i /scratch/$USER/omics/sample_data/data -o /scratch/$USER/omics/results -p /scratch/$USER/omics/sample_data/data/file.ped -s 4 -e 20 --project OPEN-0-0 --queue qprod
-Details on the pipeline
-------------------------------------
-The pipeline calls the following tools
-- [fastqc](http//www.bioinformatics.babraham.ac.uk/projects/fastqc/),
- a quality control tool for high throughput
- sequence data.
-- [gatk](https//www.broadinstitute.org/gatk/), The
+<span>Details on the pipeline</span>
+-------------
+<span>The pipeline calls the following tools:</span>
+- <span>[fastqc](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/),
+ a<span>Â quality control tool for high throughput
+ sequence data.</span></span>
+- <span>[gatk](https://www.broadinstitute.org/gatk/), <span>The
Genome Analysis Toolkit or GATK is a software package developed at
the Broad Institute to analyze high-throughput sequencing data. The
toolkit offers a wide variety of tools, with a primary focus on
variant discovery and genotyping as well as strong emphasis on data
quality assurance. Its robust architecture, powerful processing
engine and high-performance computing features make it capable of
- taking on projects of any size.
-- [hpg-aligner](http//wiki.opencb.org/projects/hpg/doku.php?id=alignerdownloads), HPG
+ taking on projects of any size.</span></span>
+- <span>[hpg-aligner](http://wiki.opencb.org/projects/hpg/doku.php?id=aligner:downloads), <span>HPG
Aligner has been designed to align short and long reads with high
sensitivity, therefore any number of mismatches or indels
are allowed. HPG Aligner implements and combines two well known
- algorithms *Burrows-Wheeler Transform* (BWT) to
+ algorithms:Â </span>*Burrows-Wheeler Transform*<span>Â (BWT) to
speed-up mapping high-quality reads,
- and *Smith-Waterman* (SW) to increase sensitivity when
- reads cannot be mapped using BWT.
-- [hpg-fastq](http//docs.bioinfo.cipf.es/projects/fastqhpc/wiki),  a
+ and </span>*Smith-Waterman*<span> (SW) to increase sensitivity when
+ reads cannot be mapped using BWT.</span></span>
+- <span><span><span>[hpg-fastq](http://docs.bioinfo.cipf.es/projects/fastqhpc/wiki), <span> a
quality control tool for high throughput
- sequence data.
-- [hpg-variant](http//wiki.opencb.org/projects/hpg/doku.php?id=variantdownloads), The
+ sequence data.</span></span></span></span>
+- <span><span><span><span>[hpg-variant](http://wiki.opencb.org/projects/hpg/doku.php?id=variant:downloads), <span>The
HPG Variant suite is an ambitious project aimed to provide a
complete suite of tools to work with genomic variation data, from
VCF tools to variant profiling or genomic statistics. It is being
implemented using High Performance Computing technologies to provide
- the best performance possible.
-- [picard](http//picard.sourceforge.net/), Picard
+ the best performance possible.</span></span></span></span></span>
+- <span><span><span><span>[picard](http://picard.sourceforge.net/), <span>Picard
comprises Java-based command-line utilities that manipulate SAM
files, and a Java API (HTSJDK) for creating new programs that read
and write SAM files. Both SAM text format and SAM binary (BAM)
- format are supported.
-- [samtools](http//samtools.sourceforge.net/samtools-c.shtml), SAM
+ format are supported.</span></span></span></span></span>
+- <span><span><span><span>[samtools](http://samtools.sourceforge.net/samtools-c.shtml), <span>SAM
Tools provide various utilities for manipulating alignments in the
SAM format, including sorting, merging, indexing and generating
alignments in a
- per-position format.
-- [snpEff](http//snpeff.sourceforge.net/), Genetic
+ per-position format.</span></span></span></span></span>
+- <span><span><span><span><span>[snpEff](http://snpeff.sourceforge.net/), <span>Genetic
variant annotation and effect
- prediction toolbox.
-This listing show which tools are used in each step of the pipeline
-- stage-00 fastqc
-- stage-01 hpg_fastq
-- stage-02 fastqc
-- stage-03 hpg_aligner and samtools
-- stage-04 samtools
-- stage-05 samtools
-- stage-06 fastqc
-- stage-07 picard
-- stage-08 fastqc
-- stage-09 picard
-- stage-10 gatk
-- stage-11 gatk
-- stage-12 gatk
-- stage-13 gatk
-- stage-14 gatk
-- stage-15 gatk
-- stage-16 samtools
-- stage-17 samtools
-- stage-18 fastqc
-- stage-19 gatk
-- stage-20 gatk
-- stage-21 gatk
-- stage-22 gatk
-- stage-23 gatk
-- stage-24 hpg-variant
-- stage-25 hpg-variant
-- stage-26 snpEff
-- stage-27 snpEff
-- stage-28 hpg-variant
-Interpretation
----------------------------
+ prediction toolbox.</span></span></span></span></span></span>
+This listing show which tools are used in each step of the pipeline :
+<!-- -->
+- <span>stage-00fastqc</span>
+- <span>stage-01hpg_fastq</span>
+- <span>stage-02fastqc</span>
+- <span>stage-03hpg_aligner and samtools</span>
+- <span>stage-04samtools</span>
+- <span>stage-05samtools</span>
+- <span>stage-06fastqc</span>
+- <span>stage-07picard</span>
+- <span>stage-08fastqc</span>
+- <span>stage-09picard</span>
+- <span>stage-10gatk</span>
+- <span>stage-11gatk</span>
+- <span>stage-12gatk</span>
+- <span>stage-13gatk</span>
+- <span>stage-14gatk</span>
+- <span>stage-15gatk</span>
+- <span>stage-16samtools</span>
+- <span>stage-17samtools</span>
+- <span>stage-18fastqc</span>
+- <span>stage-19gatk</span>
+- <span>stage-20gatk</span>
+- <span>stage-21gatk</span>
+- <span>stage-22gatk</span>
+- <span>stage-23gatk</span>
+- <span>stage-24hpg-variant</span>
+- <span>stage-25hpg-variant</span>
+- <span>stage-26snpEff</span>
+- <span>stage-27snpEff</span>
+- <span>stage-28hpg-variant</span>
+<span>Interpretation</span>
+----
The output folder contains all the subfolders with the intermediate
data. This folder contains the final VCF with all the variants. This
file can be uploaded into
-[TEAM](diagnostic-component-team.html) by using the VCF
-file button. It is important to note here that the entire management of
-the VCF file is local no patient’s sequence data is sent over the
-Internet thus avoiding any problem of data privacy or confidentiality.
-
+by using the VCF file button. It is important to note here that the
+entire management of the VCF file is localno patient’s sequence data
+is sent over the Internet thus avoiding any problem of data privacy or
+confidentiality.
+<span>
+starts.](https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig7.png "fig7.png")</span>
***Figure 7***. *TEAM upload panel.* *Once the file has been uploaded, a
panel must be chosen from the Panel **** list. Then, pressing the Run
button the diagnostic process starts.*
Once the file has been uploaded, a panel must be chosen from the Panel
list. Then, pressing the Run button the diagnostic process starts. TEAM
searches first for known diagnostic mutation(s) taken from four
-databases HGMD-public ^(20)^,
-[HUMSAVAR](http//www.uniprot.org/docs/humsavar),
+databasesHGMD-public ^(20)^,
+[HUMSAVAR](http://www.uniprot.org/docs/humsavar),
ClinVar ^(29)^ and COSMIC ^(23)^.
+H).](https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig7x.png "fig7x.png")
***Figure 7.*** *The panel manager. The elements used to define a panel
are (**A**) disease terms, (**B**) diagnostic mutations and (**C**)
genes. Arrows represent actions that can be taken in the panel manager.
@@ -571,10 +599,10 @@ by adding new genes (action **F**) or removing undesired genes (action
to an already existing disease term (action **E**). Disease terms can be
removed by simply dragging them back (action **H**).*
For variant discovering/filtering we should upload the VCF file into
-BierApp by using the following form
+BierApp by using the following form:
**
+](https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig8.png "fig8.png")*
****Figure 8.*** *BierApp VCF upload panel. It is recommended to choose
a name for the job as well as a description.**
Each prioritization (â€job’) has three associated screens that facilitate
@@ -584,226 +612,154 @@ number and types of variants found and its distribution according to
consequence types. The second screen, in the â€Variants and effect’ tab,
is the actual filtering tool, and the third one, the â€Genome view’ tab,
offers a representation of the selected variants within the genomic
-context provided by an embedded version of the Genome Maps Tool
-^(30)^.
+context provided by an embedded version of <span>the Genome Maps Tool
+</span>^(30)^<span>.</span>
****
+column. In this case, the variant 7:132481242 C>T is associated to
+the phenotypelarge intestine
+tumor.](https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig9.png "fig9.png")**
*****Figure 9.*** *This picture shows all the information associated to
the variants. If a variant has an associated phenotype we could see it
-in the last column. In this case, the variant 7132481242 C>T is
-associated to the phenotype large intestine tumor.***
+in the last column. In this case, the variant 7:132481242 C>T is
+associated to the phenotypelarge intestine tumor.***
*
*
-
-References
------------------------
-1. Heng Li, Bob Handsaker, Alec Wysoker, Tim
+<span>
+</span>
+<span>References</span>
+1. <span class="discreet">Heng Li, Bob Handsaker, Alec Wysoker, Tim
Fennell, Jue Ruan, Nils Homer, Gabor Marth5, Goncalo Abecasis6,
- Richard Durbin and 1000 Genome Project Data Processing Subgroup The
+ Richard Durbin and 1000 Genome Project Data Processing SubgroupThe
Sequence Alignment/Map format and SAMtools. Bioinformatics 2009,
- 25 2078-2079.
-2. McKenna A, Hanna M, Banks E, Sivachenko
+ 252078-2079.</span>
+2. <span class="discreet"><span>McKenna A, Hanna M, Banks E, Sivachenko
A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S,
- Daly M, DePristo MA The Genome Analysis Toolkit a MapReduce
+ Daly M, DePristo MAThe Genome Analysis Toolkita MapReduce
framework for analyzing next-generation DNA sequencing data.
- *Genome Res* 2010, 201297-1303.
-3. Petr Danecek, Adam Auton, Goncalo Abecasis,
+ </span>*Genome Res* <span>2010, 20:1297-1303.</span></span>
+3. <span class="discreet">Petr Danecek, Adam Auton, Goncalo Abecasis,
Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert E.
Handsaker, Gerton Lunter, Gabor T. Marth, Stephen T. Sherry, Gilean
McVean, Richard Durbin, and 1000 Genomes Project Analysis Group. The
variant call format and VCFtools. Bioinformatics 2011,
- 27 2156-2158.
-4. Medina I, De Maria A, Bleda M, Salavert F,
- Alonso R, Gonzalez CY, Dopazo J VARIANT Command Line, Web service
+ 272156-2158.</span>
+4. <span class="discreet">Medina I, De Maria A, Bleda M, Salavert F,
+ Alonso R, Gonzalez CY, Dopazo JVARIANTCommand Line, Web service
and Web interface for fast and accurate functional characterization
of variants found by Next-Generation Sequencing. Nucleic Acids Res
- 2012, 40W54-58.
-5. Bleda M, Tarraga J, de Maria A, Salavert F,
- Garcia-Alonso L, Celma M, Martin A, Dopazo J, Medina I CellBase, a
+ 2012, 40:W54-58.</span>
+5. <span class="discreet">Bleda M, Tarraga J, de Maria A, Salavert F,
+ Garcia-Alonso L, Celma M, Martin A, Dopazo J, Medina ICellBase, a
comprehensive collection of RESTful web services for retrieving
relevant biological information from heterogeneous sources. Nucleic
- Acids Res 2012, 40W609-614.
-6. Flicek,P., Amode,M.R., Barrell,D., Beal,K.,
+ Acids Res 2012, 40:W609-614.</span>
+6. <span class="discreet">Flicek,P., Amode,M.R., Barrell,D., Beal,K.,
Brent,S., Carvalho-Silva,D., Clapham,P., Coates,G.,
Fairley,S., Fitzgerald,S. et al. (2012) Ensembl 2012. Nucleic Acids
- Res., 40, D84–D90.
-7. UniProt Consortium. (2012) Reorganizing the
+ Res., 40, D84–D90.</span>
+7. <span class="discreet">UniProt Consortium. (2012) Reorganizing the
protein space at the Universal Protein Resource (UniProt). Nucleic
- Acids Res., 40, D71–D75.
-8. Kozomara,A. and Griffiths-Jones,S. (2011)
- miRBase integrating microRNA annotation and deep-sequencing data.
- Nucleic Acids Res., 39, D152–D157.
-9. Xiao,F., Zuo,Z., Cai,G., Kang,S., Gao,X.
- and Li,T. (2009) miRecords an integrated resource for
+ Acids Res., 40, D71–D75.</span>
+8. <span class="discreet">Kozomara,A. and Griffiths-Jones,S. (2011)
+ miRBaseintegrating microRNA annotation and deep-sequencing data.
+ Nucleic Acids Res., 39, D152–D157.</span>
+9. <span class="discreet">Xiao,F., Zuo,Z., Cai,G., Kang,S., Gao,X.
+ and Li,T. (2009) miRecordsan integrated resource for
microRNA-target interactions. Nucleic Acids Res.,
- 37, D105–D110.
-10. Hsu,S.D., Lin,F.M., Wu,W.Y., Liang,C.,
+ 37, D105–D110.</span>
+10. <span class="discreet">Hsu,S.D., Lin,F.M., Wu,W.Y., Liang,C.,
Huang,W.C., Chan,W.L., Tsai,W.T., Chen,G.Z., Lee,C.J., Chiu,C.M.
- et al. (2011) miRTarBase a database curates experimentally
+ et al. (2011) miRTarBasea database curates experimentally
validated microRNA-target interactions. Nucleic Acids Res.,
- 39, D163–D169.
-11. Friedman,R.C., Farh,K.K., Burge,C.B.
+ 39, D163–D169.</span>
+11. <span class="discreet">Friedman,R.C., Farh,K.K., Burge,C.B.
and Bartel,D.P. (2009) Most mammalian mRNAs are conserved targets
- of microRNAs. Genome Res., 19, 92–105.
-12. Betel,D., Wilson,M., Gabow,A., Marks,D.S.
- and Sander,C. (2008) The microRNA.org resource targets
- and expression. Nucleic Acids Res., 36, D149–D153.
-13. Dreszer,T.R., Karolchik,D., Zweig,A.S.,
+ of microRNAs. Genome Res., 19, 92–105.</span>
+12. <span class="discreet">Betel,D., Wilson,M., Gabow,A., Marks,D.S.
+ and Sander,C. (2008) The microRNA.org resourcetargets
+ and expression. Nucleic Acids Res., 36, D149–D153.</span>
+13. <span class="discreet">Dreszer,T.R., Karolchik,D., Zweig,A.S.,
Hinrichs,A.S., Raney,B.J., Kuhn,R.M., Meyer,L.R., Wong,M.,
Sloan,C.A., Rosenbloom,K.R. et al. (2012) The UCSC genome browser
- database extensions and updates 2011. Nucleic Acids Res.,
- 40, D918–D923.
-14. Smith,B., Ashburner,M., Rosse,C., Bard,J.,
+ databaseextensions and updates 2011. Nucleic Acids Res.,
+ 40, D918–D923.</span>
+14. <span class="discreet">Smith,B., Ashburner,M., Rosse,C., Bard,J.,
Bug,W., Ceusters,W., Goldberg,L.J., Eilbeck,K.,
- Ireland,A., Mungall,C.J. et al. (2007) The OBO Foundry coordinated
+ Ireland,A., Mungall,C.J. et al. (2007) The OBO Foundrycoordinated
evolution of ontologies to support biomedical data integration. Nat.
- Biotechnol., 25, 1251–1255.
-15. Hunter,S., Jones,P., Mitchell,A.,
+ Biotechnol., 25, 1251–1255.</span>
+15. <span class="discreet">Hunter,S., Jones,P., Mitchell,A.,
Apweiler,R., Attwood,T.K.,Bateman,A., Bernard,T., Binns,D.,
- Bork,P., Burge,S. et al. (2012) InterPro in 2011 new developments
+ Bork,P., Burge,S. et al. (2012) InterPro in 2011new developments
in the family and domain prediction database. Nucleic Acids Res.,
- 40, D306–D312.
-16. Sherry,S.T., Ward,M.H., Kholodov,M.,
- Baker,J., Phan,L., Smigielski,E.M. and Sirotkin,K. (2001) dbSNP the
+ 40, D306–D312.</span>
+16. <span class="discreet">Sherry,S.T., Ward,M.H., Kholodov,M.,
+ Baker,J., Phan,L., Smigielski,E.M. and Sirotkin,K. (2001) dbSNPthe
NCBI database of genetic variation. Nucleic Acids Res.,
- 29, 308–311.
-17. Altshuler,D.M., Gibbs,R.A., Peltonen,L.,
+ 29, 308–311.</span>
+17. <span class="discreet">Altshuler,D.M., Gibbs,R.A., Peltonen,L.,
Dermitzakis,E., Schaffner,S.F., Yu,F., Bonnen,P.E., de Bakker,P.I.,
Deloukas,P., Gabriel,S.B. et al. (2010) Integrating common and rare
genetic variation in diverse human populations. Nature,
- 467, 52–58.
-18. 1000 Genomes Project Consortium. (2010) A map
+ 467, 52–58.</span>
+18. <span class="discreet">1000 Genomes Project Consortium. (2010) A map
of human genome variation from population-scale sequencing. Nature,
- 467, 1061–1073.
-19. Hindorff,L.A., Sethupathy,P., Junkins,H.A.,
+ 467, 1061–1073.</span>
+19. <span class="discreet">Hindorff,L.A., Sethupathy,P., Junkins,H.A.,
Ramos,E.M., Mehta,J.P., Collins,F.S. and Manolio,T.A. (2009)
Potential etiologic and functional implications of genome-wide
association loci for human diseases and traits. Proc. Natl Acad.
- Sci. USA, 106, 9362–9367.
-20. Stenson,P.D., Ball,E.V., Mort,M.,
+ Sci. USA, 106, 9362–9367.</span>
+20. <span class="discreet">Stenson,P.D., Ball,E.V., Mort,M.,
Phillips,A.D., Shiel,J.A., Thomas,N.S., Abeysinghe,S., Krawczak,M.
- and Cooper,D.N. (2003) Human gene mutation database (HGMD)
- 2003 update. Hum. Mutat., 21, 577–581.
-21. Johnson,A.D. and O’Donnell,C.J. (2009) An
+ and Cooper,D.N. (2003) Human gene mutation database (HGMD):
+ 2003 update. Hum. Mutat., 21, 577–581.</span>
+21. <span class="discreet">Johnson,A.D. and O’Donnell,C.J. (2009) An
open access database of genome-wide association results. BMC Med.
- Genet, 10, 6.
-22. McKusick,V. (1998) A Catalog of Human Genes
+ Genet, 10, 6.</span>
+22. <span class="discreet">McKusick,V. (1998) A Catalog of Human Genes
and Genetic Disorders, 12th edn. John Hopkins University
- Press,Baltimore, MD.
-23. Forbes,S.A., Bindal,N., Bamford,S., Cole,C.,
+ Press,Baltimore, MD.</span>
+23. <span class="discreet">Forbes,S.A., Bindal,N., Bamford,S., Cole,C.,
Kok,C.Y., Beare,D., Jia,M., Shepherd,R., Leung,K., Menzies,A. et al.
- (2011) COSMIC mining complete cancer genomes in the catalogue of
+ (2011) COSMICmining complete cancer genomes in the catalogue of
somatic mutations in cancer. Nucleic Acids Res.,
- 39, D945–D950.
-24. Kerrien,S., Aranda,B., Breuza,L., Bridge,A.,
+ 39, D945–D950.</span>
+24. <span class="discreet">Kerrien,S., Aranda,B., Breuza,L., Bridge,A.,
Broackes-Carter,F., Chen,C., Duesbury,M., Dumousseau,M.,
Feuermann,M., Hinz,U. et al. (2012) The Intact molecular interaction
- database in 2012. Nucleic Acids Res., 40, D841–D846.
-25. Croft,D., O’Kelly,G., Wu,G., Haw,R.,
+ database in 2012. Nucleic Acids Res., 40, D841–D846.</span>
+25. <span class="discreet">Croft,D., O’Kelly,G., Wu,G., Haw,R.,
Gillespie,M., Matthews,L., Caudy,M., Garapati,P.,
- Gopinath,G., Jassal,B. et al. (2011) Reactome a database of
+ Gopinath,G., Jassal,B. et al. (2011) Reactomea database of
reactions, pathways and biological processes. Nucleic Acids Res.,
- 39, D691–D697.
-26. Demir,E., Cary,M.P., Paley,S., Fukuda,K.,
+ 39, D691–D697.</span>
+26. <span class="discreet">Demir,E., Cary,M.P., Paley,S., Fukuda,K.,
Lemer,C., Vastrik,I.,Wu,G., D’Eustachio,P., Schaefer,C., Luciano,J.
et al. (2010) The BioPAX community standard for pathway
- data sharing. Nature Biotechnol., 28, 935–942.
-27. Alemán Z, GarcĂa-GarcĂa F, Medina I, Dopazo J
- (2014) A web tool for the design and management of panels of genes
+ data sharing. Nature Biotechnol., 28, 935–942.</span>
+27. <span class="discreet">Alemán Z, GarcĂa-GarcĂa F, Medina I, Dopazo J
+ (2014)A web tool for the design and management of panels of genes
for targeted enrichment and massive sequencing for
- clinical applications. Nucleic Acids Res 42 W83-7.
-28. [Alemán
- A](http//www.ncbi.nlm.nih.gov/pubmed?term=Alem%C3%A1n%20A%5BAuthor%5D&cauthor=true&cauthor_uid=24803668), [Garcia-Garcia
- F](http//www.ncbi.nlm.nih.gov/pubmed?term=Garcia-Garcia%20F%5BAuthor%5D&cauthor=true&cauthor_uid=24803668), [Salavert
- F](http//www.ncbi.nlm.nih.gov/pubmed?term=Salavert%20F%5BAuthor%5D&cauthor=true&cauthor_uid=24803668), [Medina
- I](http//www.ncbi.nlm.nih.gov/pubmed?term=Medina%20I%5BAuthor%5D&cauthor=true&cauthor_uid=24803668), [Dopazo
- J](http//www.ncbi.nlm.nih.gov/pubmed?term=Dopazo%20J%5BAuthor%5D&cauthor=true&cauthor_uid=24803668) (2014).
+ clinical applications. Nucleic Acids Res 42W83-7.</span>
+28. <span class="discreet">[Alemán
+ A](http://www.ncbi.nlm.nih.gov/pubmed?term=Alem%C3%A1n%20A%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)<span>, </span>[Garcia-Garcia
+ F](http://www.ncbi.nlm.nih.gov/pubmed?term=Garcia-Garcia%20F%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)<span>, </span>[Salavert
+ F](http://www.ncbi.nlm.nih.gov/pubmed?term=Salavert%20F%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)<span>, </span>[Medina
+ I](http://www.ncbi.nlm.nih.gov/pubmed?term=Medina%20I%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)<span>, </span>[Dopazo
+ J](http://www.ncbi.nlm.nih.gov/pubmed?term=Dopazo%20J%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)<span> (2014).
A web-based interactive framework to assist in the prioritization of
disease candidate genes in whole-exome sequencing studies.
- [Nucleic
- Acids Res.](http//www.ncbi.nlm.nih.gov/pubmed/?term=BiERapp "Nucleic acids research.")42 W88-93.
-29. Landrum,M.J., Lee,J.M., Riley,G.R., Jang,W.,
- Rubinstein,W.S., Church,D.M. and Maglott,D.R. (2014) ClinVar public
+ </span>[Nucleic
+ Acids Res.](http://www.ncbi.nlm.nih.gov/pubmed/?term=BiERapp "Nucleic acids research.")<span>42 :W88-93.</span></span>
+29. <span class="discreet">Landrum,M.J., Lee,J.M., Riley,G.R., Jang,W.,
+ Rubinstein,W.S., Church,D.M. and Maglott,D.R. (2014) ClinVarpublic
archive of relationships among sequence variation and
- human phenotype. Nucleic Acids Res., 42, D980–D985.
-30. Medina I, Salavert F, Sanchez R, de Maria A,
- Alonso R, Escobar P, Bleda M, Dopazo J Genome Maps, a new
- generation genome browser. Nucleic Acids Res 2013, 41W41-46.
+ human phenotype. Nucleic Acids Res., 42, D980–D985.</span>
+30. <span class="discreet">Medina I, Salavert F, Sanchez R, de Maria A,
+ Alonso R, Escobar P, Bleda M, Dopazo JGenome Maps, a new
+ generation genome browser. Nucleic Acids Res 2013, 41:W41-46.</span>
Â
-
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- - [MPI](../mpi-1.html "Message Passing Interface libraries on ANSELM")
-
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-
- - [Numerical
- languages](../numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](../virtualization.html)
-
- - [Compilers](../compilers.html "Available compilers, including GNU, INTEL and UPC compilers")
-
- - [Intel Xeon
- Phi](../intel-xeon-phi.html "A guide to Intel Xeon Phi usage")
-
- - [ISV
- Licenses](../isv_licenses.html "A guide to managing Independent Software Vendor licences")
-
- - [Java](../java.html "Java on ANSELM")
+<span>
+</span>
diff --git a/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.html b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.html
old mode 100755
new mode 100644
similarity index 63%
rename from anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.html
index ed304e513b91d9c9ee3416c8b0b41c01881cae1d..782eec49d3a30a2e8b44aa831eddb04dcca26658
--- a/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.html
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<title>Priorization component (BiERApp) — IT4I Docs</title>
- <link rel="canonical" href="priorization-component-bierapp.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
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<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="priorization-component-bierapp.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="priorization-component-bierapp.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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<div id="portal-advanced-search" class="hiddenStructure">
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+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
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@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
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@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
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<span id="breadcrumbs-3" dir="ltr">
- <a href="../omics-master-1.html">OMICS Master</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">OMICS Master</a>
<span class="breadcrumbSeparator">
/
@@ -249,12 +246,12 @@
<div>
<h3 class=" ">Access</h3>
<p>BiERApp is available at the following address :Â <a class="external-link" href="http://omics.it4i.cz/bierapp/" target="_self" title="">http://omics.it4i.cz/bierapp/</a></p>
-<p class="exclamation">The address is accessible only via <a target="_self" title="" class="internal-link" href="../../accessing-the-cluster/vpn-access.html">VPN. </a></p>
+<p class="exclamation">The address is accessible only via <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access">VPN. </a></p>
<h3 class=" "><span>BiERApp</span></h3>
<h3 class=" "><span>This tool is aimed to discover new disease genes or variants by studying affected families or cases and controls. It carries out a filtering process to sequentially remove:Â (i) variants which are not no compatible with the disease because are not expected to have impact on the protein function; (ii) variants that exist at frequencies incompatible with the disease; (iii) variants that do not segregate with the disease. The result is a reduced set of disease gene candidates that should be further validated experimentally.</span></h3>
</div>
<p class="6Tekstletter">BiERapp <span>(28)</span> efficiently helps in the identification of causative variants in family and sporadic genetic diseases. The program reads lists of predicted variants (nucleotide substitutions and indels) in affected individuals or tumor samples and controls. In family studies, different modes of inheritance can easily be defined to filter out variants that do not segregate with the disease along the family. Moreover, BiERapp integrates additional information such as allelic frequencies in the general population and the most popular damaging scores to further narrow down the number of putative variants in successive filtering steps. BiERapp provides an interactive and user-friendly interface that implements the filtering strategy used in the context of a large-scale genomic project carried out by the Spanish Network for Research, in Rare Diseases (CIBERER) and the Medical Genome Project. in which more than 800 exomes have been analyzed.</p>
-<p class="6Tekstletter"><img title="fig6.png" class="image-inline" alt="Web interface to the prioritization tool. This figure shows the interface of the web tool for candidate gene prioritization with the filters available. The tool includes a genomic viewer (Genome Maps 30) that enables the representation of the variants in the corresponding genomic coordinates." src="images/fig6.png" /></p>
+<p class="6Tekstletter"><img alt="Web interface to the prioritization tool. This figure shows the interface of the web tool for candidate gene prioritization with the filters available. The tool includes a genomic viewer (Genome Maps 30) that enables the representation of the variants in the corresponding genomic coordinates." class="image-inline" title="fig6.png" src="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig6.png" /></p>
<p align="center" class="Default"><b><i>Figure 6</i></b>. <i>Web interface to the prioritization tool.</i> <i>This figure</i> <i>shows the interface of the web tool for candidate gene prioritization with the filters available. The tool includes a genomic viewer (Genome Maps <span>30</span>) that enables the representation of the variants in the corresponding genomic coordinates.</i></p>
</div>
@@ -331,7 +328,7 @@
<dt class="portletHeader hiddenStructure">
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- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -443,7 +440,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
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<span>Network</span>
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-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
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<span>Software</span>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
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- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
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- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
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- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
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- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
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- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
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- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
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- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
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- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -718,7 +715,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="../isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -734,7 +731,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
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- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="../nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
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+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
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- <a title="The human NGS data processing solution
-" class="state-published contenttype-document" href="overview.html">
+ <a class="state-published contenttype-document" title="The human NGS data processing solution
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview">
<span>Overview</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team">
<span>Diagnostic component (TEAM)</span>
</a>
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- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="priorization-component-bierapp.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp">
<span>Priorization component (BiERApp)</span>
</a>
@@ -840,7 +837,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="../openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -856,7 +853,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -872,7 +869,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="../paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -888,7 +885,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="../gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
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<span>Remote visualization service</span>
</a>
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<span>PRACE User Support</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
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+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
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- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.md b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.md
new file mode 100644
index 0000000000000000000000000000000000000000..0666e3909b77c460e4e6b801ba8733ab03c1be3d
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.md
@@ -0,0 +1,34 @@
+Priorization component (BiERApp)
+================================
+### Access
+BiERApp is available at the following address
+:Â <http://omics.it4i.cz/bierapp/>
+The address is accessible only
+via [VPN. ](https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access)
+### <span>BiERApp</span>
+### <span>This tool is aimed to discover new disease genes or variants by studying affected families or cases and controls. It carries out a filtering process to sequentially remove:Â (i) variants which are not no compatible with the disease because are not expected to have impact on the protein function; (ii) variants that exist at frequencies incompatible with the disease; (iii) variants that do not segregate with the disease. The result is a reduced set of disease gene candidates that should be further validated experimentally.</span>
+BiERapp <span>(28)</span> efficiently helps in the identification of
+causative variants in family and sporadic genetic diseases. The program
+reads lists of predicted variants (nucleotide substitutions and indels)
+in affected individuals or tumor samples and controls. In family
+studies, different modes of inheritance can easily be defined to filter
+out variants that do not segregate with the disease along the family.
+Moreover, BiERapp integrates additional information such as allelic
+frequencies in the general population and the most popular damaging
+scores to further narrow down the number of putative variants in
+successive filtering steps. BiERapp provides an interactive and
+user-friendly interface that implements the filtering strategy used in
+the context of a large-scale genomic project carried out by the Spanish
+Network for Research, in Rare Diseases (CIBERER) and the Medical Genome
+Project. in which more than 800 exomes have been analyzed.
+
+***Figure 6***. *Web interface to the prioritization tool.* *This
+figure*Â *shows the interface of the web tool for candidate gene
+prioritization with the filters available. The tool includes a genomic
+viewer (Genome Maps <span>30</span>) that enables the representation of
+the variants in the corresponding genomic coordinates.*
diff --git a/anselm-cluster-documentation/software/openfoam.html b/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.html
old mode 100755
new mode 100644
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rename to docs.it4i.cz/anselm-cluster-documentation/software/openfoam.html
index 08e63b96344d45e0f834a4a87baf54caa74da883..bd472cb3ddfd72371a82256b8b39c06e8f20df26
--- a/anselm-cluster-documentation/software/openfoam.html
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam" /><!--[if lt IE 7]></base><![endif]-->
<meta content="A free, open source CFD software package" name="description" />
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- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>OpenFOAM — IT4I Docs</title>
- <link rel="canonical" href="openfoam.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="openfoam.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="openfoam.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
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- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
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</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -265,7 +262,7 @@
</div>
<p class=" ">In /opt/modules/modulefiles/engineering you can see installed engineering softwares:</p>
<pre class=" "><br />------------------------------------ /opt/modules/modulefiles/engineering -------------------------------------------------------------<br />ansys/14.5.x              matlab/R2013a-COM                               openfoam/2.2.1-icc-impi4.1.1.036-DP<br />comsol/43b-COM            matlab/R2013a-EDU                               openfoam/2.2.1-icc-openmpi1.6.5-DP<br />comsol/43b-EDU            openfoam/2.2.1-gcc481-openmpi1.6.5-DP           paraview/4.0.1-gcc481-bullxmpi1.2.4.1-osmesa10.0<br />lsdyna/7.x.x              openfoam/2.2.1-gcc481-openmpi1.6.5-SP<br /><br /></pre>
-<p>For information how to use modules please <a target="_self" title="Environment and Modules " class="external-link" href="../environment-and-modules.html">look here</a>.</p>
+<p>For information how to use modules please <a title="Environment and Modules " class="external-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">look here</a>.</p>
<h2 class=" "><b>Getting Started</b></h2>
<p>To create OpenFOAM environment on ANSELM give the commands:</p>
<pre class=" ">$ module load openfoam/2.2.1-icc-openmpi1.6.5-DP<br /><br />$ source $FOAM_BASHRC</pre>
@@ -300,7 +297,7 @@
<div><span> </span>
<pre class=" "><span>$ qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=16,walltime=03:00:00 test.sh</span></pre>
<span> </span></div>
-<p class=" "><span> </span>For information about job submission please <a target="_self" title="Job submission" class="external-link" href="../resource-allocation-and-job-execution/job-submission-and-execution.html">look here</a>.</p>
+<p class=" "><span> </span>For information about job submission please <a title="Job submission" class="external-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">look here</a>.</p>
<h2 class=" "><b><span>Running applications in parallel</span></b></h2>
<div class="visualClear"><span>Run the second case for example external incompressible turbulent flow - case - motorBike.</span></div>
<div class="visualClear"><span>First we must run serial application bockMesh and decomposePar for preparation of parallel computation.</span></div>
@@ -436,7 +433,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -468,7 +465,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -484,7 +481,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -500,7 +497,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -516,7 +513,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -532,7 +529,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -548,7 +545,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -564,7 +561,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -580,7 +577,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
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- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
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- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -663,7 +660,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -679,7 +676,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -695,7 +692,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -711,7 +708,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -727,7 +724,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -743,7 +740,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -759,7 +756,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -775,7 +772,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -791,7 +788,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
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+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -823,7 +820,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -839,7 +836,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
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+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -887,7 +884,7 @@
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+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -903,7 +900,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -919,7 +916,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -935,7 +932,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -960,7 +957,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -976,7 +973,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1001,7 +998,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
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+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1033,7 +1030,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.md b/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.md
new file mode 100644
index 0000000000000000000000000000000000000000..64dd985ceb86a9863c14c4d0ca002912af8bfba1
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.md
@@ -0,0 +1,173 @@
+OpenFOAM
+========
+A free, open source CFD software package
+
+**Introduction**
+----------------
+OpenFOAM is a free, open source CFD software package developed
+by [**OpenCFD Ltd**](http://www.openfoam.com/about) at [**ESI
+Group**](http://www.esi-group.com/) and distributed by the [**OpenFOAM
+Foundation **](http://www.openfoam.org/). It has a large user base
+across most areas of engineering and science, from both commercial and
+academic organisations.Â
+Homepage<http://www.openfoam.com/>
+### **Installed version**
+Currently, several version compiled by GCC/ICC compilers in
+single/double precision with several version of openmpi are available on
+Anselm.
+For example syntax of available OpenFOAM module is:
+<span>< openfoam/2.2.1-icc-openmpi1.6.5-DP ></span>
+this means openfoam version <span>2.2.1</span> compiled by
+<span>ICC</span> compiler with <span>openmpi1.6.5</span> in<span> double
+precision</span>.
+Naming convection of the installed versions is following:
+<span>Â Â
+openfoam/<</span><span>VERSION</span><span>>-<</span><span>COMPILER</span><span>>-<</span><span>openmpiVERSION</span><span>>-<</span><span>PRECISION</span><span>></span>
+- <span><</span><span>VERSION</span><span>> - version of
+ openfoam</span>
+- <span><<span>COMPILER</span>> - version of used
+ compiler</span>
+- <span><<span>openmpiVERSION</span>> - version of used
+ openmpi/impi</span>
+- <span><<span>PRECISION</span>> - DP/</span><span>SP –
+ double/single precision</span>
+### **Available OpenFOAM modules**
+To check available modules use
+ $ module avail
+In /opt/modules/modulefiles/engineering you can see installed
+engineering softwares:
+ ------------- /opt/modules/modulefiles/engineering ---------------
+ ansys/14.5.x              matlab/R2013a-COM                               openfoam/2.2.1-icc-impi4.1.1.036-DP
+ comsol/43b-COMÂ Â Â Â Â Â Â Â Â Â Â Â matlab/R2013a-EDUÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â openfoam/2.2.1-icc-openmpi1.6.5-DP
+ comsol/43b-EDUÂ Â Â Â Â Â Â Â Â Â Â Â openfoam/2.2.1-gcc481-openmpi1.6.5-DPÂ Â Â Â Â Â Â Â Â Â Â paraview/4.0.1-gcc481-bullxmpi1.2.4.1-osmesa10.0
+ lsdyna/7.x.x              openfoam/2.2.1-gcc481-openmpi1.6.5-SP
+For information how to use modules please [look
+here](https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules "Environment and Modules ").
+**Getting Started**
+-------------------
+To create OpenFOAM environment on ANSELM give the commands:
+ $ module load openfoam/2.2.1-icc-openmpi1.6.5-DP
+ $ source $FOAM_BASHRC
+Pleas load correct module with your requirements “compiler - GCC/ICC,
+precision - DP/SP”.
+Create a project directory within the $HOME/OpenFOAM directory
+named <span><USER></span>-<OFversion> and create a directory
+named run within it, e.g. by typing:
+ $ mkdir -p $FOAM_RUN
+Project directory is now available by typing:
+ $ cd /home/<USER>/OpenFOAM/<USER>-<OFversion>/run
+<OFversion> - for example <2.2.1>
+or
+ $ cd $FOAM_RUN
+Copy the tutorial examples directory in the OpenFOAM distribution to
+the run directory:
+ $ cp -r $FOAM_TUTORIALS $FOAM_RUN
+Now you can run the first case for example incompressible laminar flow
+in a cavity.
+**Running Serial Applications**
+--------
+<span>Create a Bash script </span><span>test.sh</span>Â
+<span></span>
+<span> </span>
+ #!/bin/bash
+ module load openfoam/2.2.1-icc-openmpi1.6.5-DP
+ source $FOAM_BASHRC
+ # source to run functions
+ . $WM_PROJECT_DIR/bin/tools/RunFunctions
+ cd $FOAM_RUN/tutorials/incompressible/icoFoam/cavity
+ runApplication blockMesh
+ runApplication icoFoam
+<span> </span>
+<span> </span>
+<span>Job submission</span>
+<span> </span>
+ $ qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=16,walltime=03:00:00 test.sh
+<span> </span>
+<span> </span>For information about job submission please [look
+here](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution "Job submission").
+**<span>Running applications in parallel</span>**
+---
+<span>Run the second case for example external incompressible turbulent
+flow - case - motorBike.</span>
+<span>First we must run serial application bockMesh and decomposePar for
+preparation of parallel computation.</span>
+<span>
+</span>
+<span>Create a Bash scrip test.sh:</span>
+<span> </span>
+ #!/bin/bash
+ module load openfoam/2.2.1-icc-openmpi1.6.5-DP
+ source $FOAM_BASHRC
+ # source to run functions
+ . $WM_PROJECT_DIR/bin/tools/RunFunctions
+ cd $FOAM_RUN/tutorials/incompressible/simpleFoam/motorBike
+ runApplication blockMesh
+ runApplication decomposePar
+<span>
+</span>
+<span> </span>
+<span>Job submission</span>
+<span> </span>
+ $ qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=16,walltime=03:00:00 test.sh
+<span> </span>
+<span><span>This job create simple block mesh and domain decomposition.
+Check your decomposition, and submit parallel computation:</span></span>
+<span><span>Create a PBS script<span>
+testParallel.pbs</span>:</span></span>
+<span> </span>
+ #!/bin/bash
+ #PBS -N motorBike
+ #PBS -l select=2:ncpus=16
+ #PBS -l walltime=01:00:00
+ #PBS -q qprod
+ #PBS -A OPEN-0-0
+ module load openfoam/2.2.1-icc-openmpi1.6.5-DP
+ source $FOAM_BASHRC
+ cd $FOAM_RUN/tutorials/incompressible/simpleFoam/motorBike
+ nproc = 32
+ mpirun -hostfile ${PBS_NODEFILE} -np $nproc snappyHexMesh -overwrite -parallel | tee snappyHexMesh.log
+ mpirun -hostfile ${PBS_NODEFILE} -np $nproc potentialFoam -noFunctionObject-writep -parallel | tee potentialFoam.log
+ mpirun -hostfile ${PBS_NODEFILE} -np $nproc simpleFoam -parallel | tee simpleFoam.log
+<span> </span>
+<span>nproc – number of subdomains</span>
+<span>Job submission</span>
+<span> </span>
+ $ qsub testParallel.pbs
+<span> </span>
+**<span>Compile your own solver</span>**
+-----------------
+<span>Initialize OpenFOAM environment before compiling your solver
+</span>
+<span> </span>
+ $ module load openfoam/2.2.1-icc-openmpi1.6.5-DP
+ $ source $FOAM_BASHRC
+ $ cd $FOAM_RUN/
+<span>Create directory applications/solvers in user directory</span>
+<span> </span>
+ $ mkdir -p applications/solvers
+ $ cd applications/solvers
+<span> </span>
+<span>Copy icoFoam solver’s source files</span>
+<span> </span>
+ $ cp -r $FOAM_SOLVERS/incompressible/icoFoam/ My_icoFoam
+ $ cd My_icoFoam
+<span>Rename icoFoam.C to My_icoFOAM.C</span>
+<span> </span>
+ $ mv icoFoam.C My_icoFoam.C
+<span> </span>
+<span>Edit <span>*files*</span> file in *Make* directory:</span>
+<span> </span>
+ icoFoam.C
+ EXE = $(FOAM_APPBIN)/icoFoam
+<span>and change to:</span>
+ My_icoFoam.C
+ EXE = $(FOAM_USER_APPBIN)/My_icoFoam
+<span></span>
+<span>In directory My_icoFoam give the compilation command:</span>
+<span> </span>
+ $ wmake
+---
+Â
+**Â Have a fun with OpenFOAM :)**
+Â <span id="__caret"><span id="__caret"></span></span>
+Â
diff --git a/anselm-cluster-documentation/software/operating-system.html b/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.html
old mode 100755
new mode 100644
similarity index 62%
rename from anselm-cluster-documentation/software/operating-system.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/operating-system.html
index c60f9265293602d30cc342ee138b34b3842015ad..a39f8154183428265f531b205d6de3c0c6e7df9c
--- a/anselm-cluster-documentation/software/operating-system.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.html
@@ -10,45 +10,42 @@
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<title>Operating System — IT4I Docs</title>
- <link rel="canonical" href="operating-system.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system" />
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<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="operating-system.html#content">PĹ™ejĂt na obsah</a> |
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<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
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<span id="breadcrumbs-1" dir="ltr">
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
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<span id="breadcrumbs-2" dir="ltr">
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<dt class="portletHeader hiddenStructure">
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<span>Get Started with IT4Innovations</span>
</a>
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<span>Salomon Cluster Documentation</span>
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<span>Anselm Cluster Documentation</span>
</a>
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</a>
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<span>Accessing the Cluster</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
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<span>Compute Nodes</span>
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<span>Storage</span>
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<span>Network</span>
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<span>Software</span>
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</a>
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<span>COMSOL</span>
</a>
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<span>Debuggers and profilers</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
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</a>
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<span>MPI</span>
</a>
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<span>Numerical languages</span>
</a>
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<span>Virtualization</span>
</a>
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- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
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- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
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- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -722,7 +719,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
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+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
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+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
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- <a title="The operating system, deployed on ANSELM" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="operating-system.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
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+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
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+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -843,7 +840,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -859,7 +856,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -884,7 +881,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -900,7 +897,7 @@
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+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</div>
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.md b/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.md
new file mode 100644
index 0000000000000000000000000000000000000000..02a808b1ba8b4f39005e9b431e5208a50e513088
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.md
@@ -0,0 +1,8 @@
+Operating System
+================
+The operating system, deployed on ANSELM
+
+The operating system on Anselm is Linux - bullx Linux Server release
+6.3.
+bullx Linux is based on Red Hat Enterprise Linux. bullx Linux is a Linux
+distribution provided by Bull and dedicated to HPC applications.
diff --git a/anselm-cluster-documentation/software/paraview.html b/docs.it4i.cz/anselm-cluster-documentation/software/paraview.html
old mode 100755
new mode 100644
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rename from anselm-cluster-documentation/software/paraview.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/paraview.html
index f244a8258bddc1e07b917b182fa69c159eb0fb69..62b89b56f1e27e406d6505d13f7564a0c4f3be52
--- a/anselm-cluster-documentation/software/paraview.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/paraview.html
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview" /><!--[if lt IE 7]></base><![endif]-->
<meta content="An open-source, multi-platform data analysis and visualization application " name="description" />
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- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
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<title>ParaView — IT4I Docs</title>
- <link rel="canonical" href="paraview.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="paraview.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="paraview.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
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- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../software.html">Software</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -253,7 +250,7 @@
<h3 class=" ">Launching server</h3>
<p>To launch the server, you must first allocate compute nodes, for example :<span>Â </span></p>
<pre class=" ">$ qsub -I -q qprod -A OPEN-0-0 -l select=2</pre>
-<p>to launch an interactive session on 2 nodes. Refer to <a target="_self" title="" class="internal-link" href="../resource-allocation-and-job-execution/introduction.html">Resource Allocation and Job Execution</a> for details.</p>
+<p>to launch an interactive session on 2 nodes. Refer to <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction">Resource Allocation and Job Execution</a> for details.</p>
<p>After the interactive session is opened, load the ParaView module :</p>
<pre class=" ">$ module add paraview</pre>
<p>Now launch the parallel server, with number of nodes times 16 processes :</p>
@@ -262,7 +259,7 @@
<h3 class=" ">Client connection</h3>
<p>Because a direct connection is not allowed to compute nodes on Anselm, you must establish a SSH tunnel to connect to the server. Choose a port number on your PC to be forwarded to ParaView server, for example 12345. If your PC is running Linux, use this command to estabilish a SSH tunnel :</p>
<pre class=" ">ssh -TN -L 12345:cn77:11111 username@anselm.it4i.cz</pre>
-<p>replace <span class="monospace">username</span> with your login and cn77 with the name of compute node your ParaView server is running on (see previous step). If you use PuTTY on Windows, load Anselm connection configuration, t<span>hen go to Connection-></span><span class="highlightedSearchTerm">SSH</span><span>->Tunnels to set up the port forwarding. Click Remote radio button. Insert 12345 to Source port textbox. Insert cn77:11111. Click Add button, then Open. </span><a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html">Read more about port forwarding.</a></p>
+<p>replace <span class="monospace">username</span> with your login and cn77 with the name of compute node your ParaView server is running on (see previous step). If you use PuTTY on Windows, load Anselm connection configuration, t<span>hen go to Connection-></span><span class="highlightedSearchTerm">SSH</span><span>->Tunnels to set up the port forwarding. Click Remote radio button. Insert 12345 to Source port textbox. Insert cn77:11111. Click Add button, then Open. </span><a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">Read more about port forwarding.</a></p>
<p>Now launch ParaView client installed on your desktop PC. Select File->Connect..., click Add Server. Fill in the following :</p>
<p>Name : Anselm tunnel</p>
<p>Server Type : Client/Server</p>
@@ -350,7 +347,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -366,7 +363,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -382,7 +379,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -398,7 +395,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -414,7 +411,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -430,7 +427,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -446,7 +443,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -462,7 +459,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -478,7 +475,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -494,7 +491,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -510,7 +507,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -526,7 +523,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -542,10 +539,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -561,7 +558,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -577,7 +574,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -593,7 +590,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -609,7 +606,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -625,7 +622,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -641,7 +638,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -657,7 +654,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -673,7 +670,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -689,7 +686,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="virtualization.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -705,7 +702,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -721,7 +718,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -737,7 +734,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -753,7 +750,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -769,7 +766,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -785,7 +782,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -801,7 +798,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -817,7 +814,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -833,7 +830,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="paraview.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -849,7 +846,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -874,7 +871,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -890,7 +887,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -915,7 +912,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -931,7 +928,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -947,7 +944,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1036,7 +1033,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/paraview.md b/docs.it4i.cz/anselm-cluster-documentation/software/paraview.md
new file mode 100644
index 0000000000000000000000000000000000000000..52fae86d68e3144b3f13a03e66c7bad528343097
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/paraview.md
@@ -0,0 +1,85 @@
+ParaView
+========
+An open-source, multi-platform data analysis and visualization
+application
+
+Introduction
+------------
+**ParaView**Â is an open-source, multi-platform data analysis and
+visualization application. ParaView users can quickly build
+visualizations to analyze their data using qualitative and quantitative
+techniques. The data exploration can be done interactively in 3D or
+programmatically using ParaView's batch processing capabilities.
+ParaView was developed to analyze extremely large datasets using
+distributed memory computing resources. It can be run on supercomputers
+to analyze datasets of exascale size as well as on laptops for smaller
+data.
+Homepage :Â <http://www.paraview.org/>
+Installed version
+-----------------
+Currently, version 4.0.1 compiled with GCC 4.8.1 against Bull MPI
+library and OSMesa 10.0 is installed on Anselm.
+Usage
+-----
+On Anselm, ParaView is to be used in client-server mode. A parallel
+ParaView server is launched on compute nodes by the user, and client is
+launched on your desktop PC to control and view the visualization.
+Download ParaView client application for your OS here
+:Â <http://paraview.org/paraview/resources/software.php>. Important :
+**your version must match the version number installed on Anselm** !
+(currently v4.0.1)
+### Launching server
+To launch the server, you must first allocate compute nodes, for example
+:<span>Â </span>
+ $ qsub -I -q qprod -A OPEN-0-0 -l select=2
+to launch an interactive session on 2 nodes. Refer to [Resource
+Allocation and Job
+Execution](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction)
+for details.
+After the interactive session is opened, load the ParaView module :
+ $ module add paraview
+Now launch the parallel server, with number of nodes times 16 processes
+:
+ $ mpirun -np 32 pvserver --use-offscreen-rendering
+ Waiting for client...
+ Connection URLcs://cn77:11111
+ Accepting connection(s)cn77:11111
+Â Note the that the server is listening on compute node cn77 in this
+case, we shall use this information later.
+### Client connection
+Because a direct connection is not allowed to compute nodes on Anselm,
+you must establish a SSH tunnel to connect to the server. Choose a port
+number on your PC to be forwarded to ParaView server, for example 12345.
+If your PC is running Linux, use this command to estabilish a SSH tunnel
+:
+ ssh -TN -L 12345:cn77:11111 username@anselm.it4i.cz
+replace <span class="monospace">username</span>Â with your login and cn77
+with the name of compute node your ParaView server is running on (see
+previous step). If you use PuTTY on Windows, load Anselm connection
+configuration, t<span>hen go to Connection-></span><span
+class="highlightedSearchTerm">SSH</span><span>->Tunnels to set up the
+port forwarding. Click Remote radio button. Insert 12345 to Source port
+textbox. Insert cn77:11111. Click Add button, then Open. </span>[Read
+more about port
+forwarding.](resolveuid/11e53ad0d2fd4c5187537f4baeedff33)
+Now launch ParaView client installed on your desktop PC. Select
+File->Connect..., click Add Server. Fill in the following :
+Name Anselm tunnel
+Server Type Client/Server
+Host localhost
+Port 12345
+Click Configure, Save, the configuration is now saved for later use. Now
+click Connect to connect to the ParaView server. In your terminal where
+you have interactive session with ParaView server launched, you should
+see :
+ Client connected.
+You can now use Parallel ParaView.
+### Close server
+Remember to close the interactive session after you finish working with
+ParaView server, as it will remain launched even after your client is
+disconnected and will continue to consume resources.
+GPU support
+-----------
+Currently, GPU acceleration is not supported in the server and ParaView
+will not take advantage of accelerated nodes on Anselm. Support for GPU
+acceleration might be added in the future.
diff --git a/anselm-cluster-documentation/software/virtualization.html b/docs.it4i.cz/anselm-cluster-documentation/software/virtualization.html
old mode 100755
new mode 100644
similarity index 76%
rename from anselm-cluster-documentation/software/virtualization.html
rename to docs.it4i.cz/anselm-cluster-documentation/software/virtualization.html
index 5aa8059a5746b7977dc904e1d26344dfd3382126..3e3889d1d4dc7493262f27ccaf45ec081c7133ed
--- a/anselm-cluster-documentation/software/virtualization.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/virtualization.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization" /><!--[if lt IE 7]></base><![endif]-->
<meta content="Running virtual machines on compute nodes" name="description" />
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<title>Virtualization — IT4I Docs</title>
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- <a accesskey="2" href="virtualization.html#content">PĹ™ejĂt na obsah</a> |
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- <a accesskey="6" href="virtualization.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization#portal-globalnav">PĹ™ejĂt na navigaci</a>
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@@ -153,7 +150,7 @@
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<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
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@@ -163,7 +160,7 @@
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<span id="breadcrumbs-2" dir="ltr">
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+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software">Software</a>
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@@ -251,7 +248,7 @@
<li>Application requires privileged access to operating system</li>
<li>... and combinations of above cases</li>
</ul>
-<p style="text-align: justify; ">Â We offer solution for these cases - <strong>virtualization</strong>. Anselm's environment gives the possibility to run virtual machines on compute nodes. Users can create their own images of operating system with specific software stack and run instances of these images as virtual machines on compute nodes. Run of virtual machines is provided by standard mechanism of <a target="_self" title="" class="internal-link" href="../resource-allocation-and-job-execution/introduction.html">Resource Allocation and Job Execution</a>.</p>
+<p style="text-align: justify; ">Â We offer solution for these cases - <strong>virtualization</strong>. Anselm's environment gives the possibility to run virtual machines on compute nodes. Users can create their own images of operating system with specific software stack and run instances of these images as virtual machines on compute nodes. Run of virtual machines is provided by standard mechanism of <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction">Resource Allocation and Job Execution</a>.</p>
<p>Solution is based on QEMU-KVM software stack and provides hardware-assisted x86 virtualization.</p>
<h2 class=" ">Limitations</h2>
<p style="text-align: justify; ">Anselm's infrastructure was not designed for virtualization. Anselm's environment is not intended primary for virtualization, compute nodes, storages and all infrastructure of Anselm is intended and optimized for running HPC jobs, this implies suboptimal configuration of virtualization and limitations.</p>
@@ -267,7 +264,7 @@
<h2 class=" "><a name="howto"></a>Â HOWTO</h2>
<h3 class=" "><a name="virtual-machine-job-workflow"></a>Virtual Machine Job Workflow</h3>
<p>We propose this job workflow:</p>
-<p>Â <img title="Virtualization Job Workflow" class="image-inline" alt="Virtualization Job Workflow" src="virtualization/virtualization-job-workflow.png" /></p>
+<p>Â <img alt="Virtualization Job Workflow" class="image-inline" title="Virtualization Job Workflow" src="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization-job-workflow" /></p>
<p>Our recommended solution is that job script creates distinct shared job directory, which makes a central point for data exchange between Anselm's environment, compute node (host) (e.g HOME, SCRATCH, local scratch and other local or cluster filesystems) and virtual machine (guest). Job script links or copies input data and instructions what to do (run script) for virtual machine to job directory and virtual machine process input data according instructions in job directory and store output back to job directory. We recommend, that virtual machine is running in so called <a class="anchor-link" href="#snapshot-mode" target="_self" title="">snapshot mode</a>, image is immutable - image does not change, so one image can be used for many concurrent jobs.</p>
<h3 class=" ">Procedure</h3>
<ol>
@@ -322,7 +319,7 @@
<pre class=" ">z:<br />cd \win\appl<br />call application.bat z:\data z:\output</pre>
<p class=" ">Run script runs application from shared job directory (mapped as drive z:), process input data (z:\data) from job directory and store output to job directory (z:\output).</p>
<h3 class=" ">Run jobs</h3>
-<p>Run jobs as usual, see <a target="_self" title="" class="internal-link" href="../resource-allocation-and-job-execution/introduction.html">Resource Allocation and Job Execution</a>. Use only full node allocation for virtualization jobs.</p>
+<p>Run jobs as usual, see <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction">Resource Allocation and Job Execution</a>. Use only full node allocation for virtualization jobs.</p>
<h3 class=" ">Running Virtual Machines</h3>
<p>Virtualization is enabled only on compute nodes, virtualization does not work on login nodes.</p>
<p>Load QEMU environment module:</p>
@@ -331,12 +328,12 @@
<pre class=" ">$ man qemu</pre>
<p class=" ">Run virtual machine (simple)</p>
<pre class=" ">$ qemu-system-x86_64 -hda linux.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -vnc :0<br /><br />$ qemu-system-x86_64 -hda win.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -vnc :0</pre>
-<p class=" ">You can access virtual machine by VNC viewer (option -vnc) connecting to IP address of compute node. For VNC you must use <a target="_self" title="" class="internal-link" href="../accessing-the-cluster/vpn-access.html">VPN network</a>.</p>
+<p class=" ">You can access virtual machine by VNC viewer (option -vnc) connecting to IP address of compute node. For VNC you must use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access">VPN network</a>.</p>
<p class=" ">Install virtual machine from iso file</p>
<pre class=" ">$ qemu-system-x86_64 -hda linux.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -cdrom linux-install.iso -boot d -vnc :0<br /><br />$ qemu-system-x86_64 -hda win.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -cdrom win-install.iso -boot d -vnc :0</pre>
<p class=" ">Run virtual machine using optimized devices, user network backend with sharing and port forwarding, in snapshot mode</p>
<pre class=" ">$ qemu-system-x86_64 -drive file=linux.img,media=disk,if=virtio -enable-kvm -cpu host -smp 16 -m 32768 -vga std -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp::2222-:22 -vnc :0 -snapshot<br /><br />$ qemu-system-x86_64 -drive file=win.img,media=disk,if=virtio -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp::3389-:3389 -vnc :0 -snapshot</pre>
-<p class=" ">Thanks to port forwarding you can access virtual machine via SSH (Linux) or RDP (Windows) connecting to IP address of compute node (and port 2222 for SSH). You must use <a target="_self" title="" class="internal-link" href="../accessing-the-cluster/vpn-access.html">VPN network</a>.</p>
+<p class=" ">Thanks to port forwarding you can access virtual machine via SSH (Linux) or RDP (Windows) connecting to IP address of compute node (and port 2222 for SSH). You must use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access">VPN network</a>.</p>
<p class="callout">Keep in mind, that if you use virtio devices, you must have virtio drivers installed on your virtual machine.</p>
<h3 class=" ">Networking and data sharing</h3>
<p class=" ">For networking virtual machine we suggest to use (default) user network backend (sometimes called slirp). This network backend NATs virtual machines and provides useful services for virtual machines as DHCP, DNS, SMB sharing, port forwarding.</p>
@@ -467,7 +464,7 @@
<dt class="portletHeader hiddenStructure">
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- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
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@@ -483,7 +480,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -499,7 +496,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -515,7 +512,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -531,7 +528,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -547,7 +544,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -563,7 +560,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -579,7 +576,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -595,7 +592,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -611,7 +608,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -627,7 +624,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -643,7 +640,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -659,10 +656,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -678,7 +675,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
<span>ANSYS</span>
</a>
@@ -694,7 +691,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
<span>COMSOL</span>
</a>
@@ -710,7 +707,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -726,7 +723,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
<span>Chemistry and Materials science</span>
</a>
@@ -742,7 +739,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -758,7 +755,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
<span>MPI</span>
</a>
@@ -774,7 +771,7 @@
- <a title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-libraries.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
<span>Numerical Libraries</span>
</a>
@@ -790,7 +787,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -806,7 +803,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="virtualization.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
<span>Virtualization</span>
</a>
@@ -822,7 +819,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
<span>Compilers</span>
</a>
@@ -838,7 +835,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -854,7 +851,7 @@
- <a title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document" href="isv_licenses.html">
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
<span>ISV Licenses</span>
</a>
@@ -870,7 +867,7 @@
- <a title="Java on ANSELM" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
<span>Java</span>
</a>
@@ -886,7 +883,7 @@
- <a title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document" href="nvidia-cuda.html">
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
<span>nVidia CUDA</span>
</a>
@@ -902,7 +899,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="omics-master-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
<span>OMICS Master</span>
</a>
@@ -918,7 +915,7 @@
- <a title="A free, open source CFD software package" class="state-published contenttype-document" href="openfoam.html">
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
<span>OpenFOAM</span>
</a>
@@ -934,7 +931,7 @@
- <a title="The operating system, deployed on ANSELM" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
<span>Operating System</span>
</a>
@@ -950,7 +947,7 @@
- <a title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document" href="paraview.html">
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
<span>ParaView</span>
</a>
@@ -966,7 +963,7 @@
- <a title="A library that implements the GASPI specification" class="state-published contenttype-document" href="gpi2.html">
+ <a class="state-published contenttype-document" title="A library that implements the GASPI specification" href="https://docs.it4i.cz/anselm-cluster-documentation/software/gpi2">
<span>GPI-2</span>
</a>
@@ -991,7 +988,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -1007,7 +1004,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -1032,7 +1029,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1048,7 +1045,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1064,7 +1061,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1103,14 +1100,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1132,12 +1129,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1153,7 +1150,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/software/virtualization by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:51 GMT -->
</html>
diff --git a/anselm-cluster-documentation/software/virtualization.md b/docs.it4i.cz/anselm-cluster-documentation/software/virtualization.md
similarity index 74%
rename from anselm-cluster-documentation/software/virtualization.md
rename to docs.it4i.cz/anselm-cluster-documentation/software/virtualization.md
index 572d27fd65d2438bf5be891bafd913afeeeb5768..88fa64f1d31f9802f03d328b24d140e65f8d7bbe 100644
--- a/anselm-cluster-documentation/software/virtualization.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/virtualization.md
@@ -1,6 +1,7 @@
+Virtualization
+==============
Running virtual machines on compute nodes
-
-
+
Introduction
------------
There are situations when Anselm's environment is not suitable for user
@@ -19,7 +20,7 @@ nodes. Users can create their own images of operating system with
specific software stack and run instances of these images as virtual
machines on compute nodes. Run of virtual machines is provided by
standard mechanism of [Resource Allocation and Job
-Execution](../resource-allocation-and-job-execution/introduction.html).
+Execution](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction).
Solution is based on QEMU-KVM software stack and provides
hardware-assisted x86 virtualization.
Limitations
@@ -35,8 +36,8 @@ in I/O performance (storage, network). Anselm's virtualization is not
suitable for I/O (disk, network) intensive workloads.
Virtualization has also some drawbacks, it is not so easy to setup
efficient solution.
-Solution described in chapter [HOWTO](#howto)
-class="anchor-link"> is suitable for single node tasks, does not
+Solution described in chapter [HOWTO](#howto)<span
+class="anchor-link"> is suitable for </span>single node tasks, does not
introduce virtual machine clustering.
Please consider virtualization as last resort solution for your needs.
Please consult use of virtualization with IT4Innovation's support.
@@ -47,9 +48,9 @@ with less effort and better performance than when using virtualization.
Licensing
---------
IT4Innovations does not provide any licenses for operating systems and
-software of virtual machines. Users are (
-class="hps">in accordance with [Acceptable use policy
-document](http//www.it4i.cz/acceptable-use-policy.pdf))
+software of virtual machines. Users are (<span id="result_box"><span
+class="hps">in accordance with</span></span> [Acceptable use policy
+document](http://www.it4i.cz/acceptable-use-policy.pdf))
fully responsible for licensing all software running in virtual machines
on Anselm. Be aware of complex conditions of licensing software in
virtual environments.
@@ -58,9 +59,9 @@ running in their virtual machines.
[]()Â HOWTO
----------
### []()Virtual Machine Job Workflow
-We propose this job workflow
+We propose this job workflow:
 
+Workflow](https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization-job-workflow "Virtualization Job Workflow")
Our recommended solution is that job script creates distinct shared job
directory, which makes a central point for data exchange between
Anselm's environment, compute node (host) (e.g HOME, SCRATCH, local
@@ -80,7 +81,7 @@ many concurrent jobs.
5. Run jobs
### Prepare image of your virtual machine
You can either use your existing image or create new image from scratch.
-QEMU currently supports these image types or formats
+QEMU currently supports these image types or formats:
- rawÂ
- cloopÂ
- cowÂ
@@ -91,27 +92,27 @@ QEMU currently supports these image types or formats
- vdi - VirtualBox 1.1 compatible image format, for exchanging images
with VirtualBox.
You can convert your existing image using qemu-img convert command.
-Supported formats of this command are blkdebug blkverify bochs cloop
+Supported formats of this command areblkdebug blkverify bochs cloop
cow dmg file ftp ftps host_cdrom host_device host_floppy http https
nbd parallels qcow qcow2 qed raw sheepdog tftp vdi vhdx vmdk vpc vvfat.
We recommend using advanced QEMU native image format qcow2.
[More about QEMU
-Images](http//en.wikibooks.org/wiki/QEMU/Images)
+Images](http://en.wikibooks.org/wiki/QEMU/Images)
### Optimize image of your virtual machine
Use virtio devices (for disk/drive and network adapter) and install
virtio drivers (paravirtualized drivers) into virtual machine. There is
significant performance gain when using virtio drivers. For more
information see [Virtio
-Linux](http//www.linux-kvm.org/page/Virtio) and [Virtio
-Windows](http//www.linux-kvm.org/page/WindowsGuestDrivers/Download_Drivers).
-Disable all
-class="hps trans-target-highlight">unnecessary services
+Linux](http://www.linux-kvm.org/page/Virtio) and [Virtio
+Windows](http://www.linux-kvm.org/page/WindowsGuestDrivers/Download_Drivers).
+Disable all <span id="result_box" class="short_text"><span
+class="hps trans-target-highlight">unnecessary</span></span> services
and tasks. Restrict all unnecessary operating system operations.
-Remove all
+Remove all <span id="result_box" class="short_text"><span
class="hps trans-target-highlight">unnecessary software and
-files.
-
-class="hps trans-target-highlight">Remove all paging
+files.</span></span>
+<span id="result_box" class="short_text"><span
+class="hps trans-target-highlight"></span></span>Remove all paging
space, swap files, partitions, etc.
Shrink your image. (It is recommended to zero all free space and
reconvert image using qemu-img.)
@@ -129,17 +130,17 @@ shutdowns/quits OS
For Windows operating systems we suggest using Local Group Policy
Startup script, for Linux operating systems rc.local, runlevel init
script or similar service.
-Example startup script for Windows virtual machine
+Example startup script for Windows virtual machine:
@echo off
- set LOG=cstartup.log
- set MAPDRIVE=z
+ set LOG=c:startup.log
+ set MAPDRIVE=z:
set SCRIPT=%MAPDRIVE%run.bat
set TIMEOUT=300
echo %DATE% %TIME% Running startup script>%LOG%
rem Mount share
echo %DATE% %TIME% Mounting shared drive>>%LOG%
- net use z 10.0.2.4qemu >>%LOG% 2>&1
- dir z >>%LOG% 2>&1
+ net use z10.0.2.4qemu >>%LOG% 2>&1
+ dir z>>%LOG% 2>&1
echo. >>%LOG%
if exist %MAPDRIVE% (
 echo %DATE% %TIME% The drive "%MAPDRIVE%" exists>>%LOG%
@@ -158,15 +159,15 @@ Example startup script for Windows virtual machine
timeout /T %TIMEOUT%
echo %DATE% %TIME% Shut down>>%LOG%
shutdown /s /t 0
-Example startup script maps shared job script as drive z and looks for
+Example startup script maps shared job script as drive zand looks for
run script called run.bat. If run script is found it is run else wait
for 5 minutes, then shutdown virtual machine.
### Create job script for executing virtual machine
-Create job script according recommended id="result_box"
-class="short_text">
-class="hps trans-target-highlight">[Virtual Machine Job
+Create job script according recommended <span id="result_box"
+class="short_text"><span
+class="hps trans-target-highlight"></span></span>[Virtual Machine Job
Workflow](#virtual-machine-job-workflow).
-Example job for Windows virtual machine
+Example job for Windows virtual machine:
#/bin/sh
JOB_DIR=/scratch/$USER/win/${PBS_JOBID}
#Virtual machine settings
@@ -190,47 +191,47 @@ Example job for Windows virtual machine
 -localtime
 -usb -usbdevice tablet
 -device virtio-net-pci,netdev=net0
- Â -netdev user,id=net0,smb=${JOB_DIR},hostfwd=tcp3389-3389
+ Â -netdev user,id=net0,smb=${JOB_DIR},hostfwd=tcp::3389-:3389
 -drive file=${VM_IMAGE},media=disk,if=virtio
 -snapshot
 -nographic
Job script links application data (win), input data (data) and run
script (run.bat) into job directory and runs virtual machine.
-Example run script (run.bat) for Windows virtual machine
- z
+Example run script (run.bat) for Windows virtual machine:
+ z:
cd winappl
- call application.bat zdata zoutput
+ call application.bat z:data z:output
Run script runs application from shared job directory (mapped as drive
-z), process input data (zdata) from job directory and store output
-to job directory (zoutput).
+z:), process input data (z:data) from job directory and store output
+to job directory (z:output).
### Run jobs
Run jobs as usual, see [Resource Allocation and Job
-Execution](../resource-allocation-and-job-execution/introduction.html).
+Execution](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction).
Use only full node allocation for virtualization jobs.
### Running Virtual Machines
Virtualization is enabled only on compute nodes, virtualization does not
work on login nodes.
-Load QEMU environment module
+Load QEMU environment module:
$ module add qemu
Get help
$ man qemu
Run virtual machine (simple)
- $ qemu-system-x86_64 -hda linux.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -vnc 0
- $ qemu-system-x86_64 -hda win.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -vnc 0
+ $ qemu-system-x86_64 -hda linux.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -vnc :0
+ $ qemu-system-x86_64 -hda win.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -vnc :0
You can access virtual machine by VNC viewer (option -vnc) connecting to
IP address of compute node. For VNC you must use [VPN
-network](../accessing-the-cluster/vpn-access.html).
+network](https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access).
Install virtual machine from iso file
- $ qemu-system-x86_64 -hda linux.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -cdrom linux-install.iso -boot d -vnc 0
- $ qemu-system-x86_64 -hda win.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -cdrom win-install.iso -boot d -vnc 0
+ $ qemu-system-x86_64 -hda linux.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -cdrom linux-install.iso -boot d -vnc :0
+ $ qemu-system-x86_64 -hda win.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -cdrom win-install.iso -boot d -vnc :0
Run virtual machine using optimized devices, user network backend with
sharing and port forwarding, in snapshot mode
- $ qemu-system-x86_64 -drive file=linux.img,media=disk,if=virtio -enable-kvm -cpu host -smp 16 -m 32768 -vga std -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp2222-22 -vnc 0 -snapshot
- $ qemu-system-x86_64 -drive file=win.img,media=disk,if=virtio -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp3389-3389 -vnc 0 -snapshot
+ $ qemu-system-x86_64 -drive file=linux.img,media=disk,if=virtio -enable-kvm -cpu host -smp 16 -m 32768 -vga std -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp::2222-:22 -vnc :0 -snapshot
+ $ qemu-system-x86_64 -drive file=win.img,media=disk,if=virtio -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp::3389-:3389 -vnc :0 -snapshot
Thanks to port forwarding you can access virtual machine via SSH (Linux)
or RDP (Windows) connecting to IP address of compute node (and port 2222
for SSH). You must use [VPN
-network](../accessing-the-cluster/vpn-access.html).
+network](https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access).
Keep in mind, that if you use virtio devices, you must have virtio
drivers installed on your virtual machine.
### Networking and data sharing
@@ -245,12 +246,11 @@ have access to Anselm's network via NAT on compute node (host).
Simple network setup
$ qemu-system-x86_64 ... -net nic -net user
(It is default when no -net options are given.)
-
Simple network setup with sharing and port forwarding (obsolete but
simpler syntax, lower performance)
- $ qemu-system-x86_64 ... -net nic -net user,smb=/scratch/$USER/tmp,hostfwd=tcp3389-3389
+ $ qemu-system-x86_64 ... -net nic -net user,smb=/scratch/$USER/tmp,hostfwd=tcp::3389-:3389
Optimized network setup with sharing and port forwarding
- $ qemu-system-x86_64 ... -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp2222-22
+ $ qemu-system-x86_64 ... -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp::2222-:22
### Advanced networking
**Internet access**
Sometime your virtual machine needs access to internet (install
@@ -282,7 +282,7 @@ machine (guest) we suggest using Linux kernel TAP device.
Cluster Anselm provides TAP device tap0 for your job. TAP interconnect
does not provide any services (like NAT, DHCP, DNS, SMB, etc.) just raw
networking, so you should provide your services if you need them.
-Run qemu with TAP network backend
+Run qemu with TAP network backend:
$ qemu-system-x86_64 ... -device virtio-net-pci,netdev=net1
-netdev tap,id=net1,ifname=tap0,script=no,downscript=no
Interface tap0 has IP address 192.168.1.1 and network mask 255.255.255.0
@@ -290,14 +290,14 @@ Interface tap0 has IP address 192.168.1.1 and network mask 255.255.255.0
192.168.1.2-192.168.1.254. For your convenience some ports on tap0
interface are redirected to higher numbered ports, so you as
non-privileged user can provide services on these ports.
-Redirected ports
+Redirected ports:
- DNS udp/53->udp/3053, tcp/53->tcp3053
- DHCP udp/67->udp3067
- SMB tcp/139->tcp3139, tcp/445->tcp3445).
You can configure IP address of virtual machine statically or
dynamically. For dynamic addressing provide your DHCP server on port
3067 of tap0 interface, you can also provide your DNS server on port
-3053 of tap0 interface for example
+3053 of tap0 interface for example:
$ dnsmasq --interface tap0 --bind-interfaces -p 3053 --dhcp-alternate-port=3067,68 --dhcp-range=192.168.1.15,192.168.1.32 --dhcp-leasefile=/tmp/dhcp.leasefile
You can also provide your SMB services (on ports 3139, 3445) to obtain
high performance data sharing.
@@ -344,68 +344,5 @@ variable to local scratch directory for placement temporary files.
$ export TMPDIR=/lscratch/${PBS_JOBID}
$ qemu-system-x86_64 ... -snapshot
### Windows guests
-For Windows guests we recommend these options, life will be easier
+For Windows guests we recommend these options, life will be easier:
$ qemu-system-x86_64 ... -localtime -usb -usbdevice tablet
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
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- - [What's New](../../whats-new.html)
-
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- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
-
- - [Hardware
- Overview](../hardware-overview.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
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-
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- Execution](../resource-allocation-and-job-execution.html)
-
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- Nodes](../compute-nodes.html)
-
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-
- - [Network](../network.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
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- science](chemistry.html "Tools for computational chemistry.")
-
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- studio](intel-suite.html "The Intel Parallel Studio XE")
-
- - [MPI](mpi-1.html "Message Passing Interface libraries on ANSELM")
-
- - [Numerical
- Libraries](numerical-libraries.html "Libraries for numerical computations")
-
- - [Numerical
- languages](numerical-languages.html "Interpreted languages for numerical computations")
-
- - [Virtualization](virtualization.html)
-
diff --git a/anselm-cluster-documentation/software/virtualization/virtualization-job-workflow.png b/docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization-job-workflow
old mode 100755
new mode 100644
similarity index 100%
rename from anselm-cluster-documentation/software/virtualization/virtualization-job-workflow.png
rename to docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization-job-workflow
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization.html b/docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization.html
new file mode 100644
index 0000000000000000000000000000000000000000..f302b418ca5a363e09b22516cbf0a62b6a989db7
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization.html
@@ -0,0 +1,1154 @@
+
+<!DOCTYPE html>
+
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+
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+ Running virtual machines on compute nodes
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+ <h2 class=" ">Introduction</h2>
+<p>There are situations when Anselm's environment is not suitable for user needs.</p>
+<ul>
+<li>Application requires different operating system (e.g Windows), application is not available for Linux</li>
+<li>Application requires different versions of base system libraries and tools</li>
+<li>Application requires specific setup (installation, configuration) of complex software stack</li>
+<li>Application requires privileged access to operating system</li>
+<li>... and combinations of above cases</li>
+</ul>
+<p style="text-align: justify; ">Â We offer solution for these cases - <strong>virtualization</strong>. Anselm's environment gives the possibility to run virtual machines on compute nodes. Users can create their own images of operating system with specific software stack and run instances of these images as virtual machines on compute nodes. Run of virtual machines is provided by standard mechanism of <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction">Resource Allocation and Job Execution</a>.</p>
+<p>Solution is based on QEMU-KVM software stack and provides hardware-assisted x86 virtualization.</p>
+<h2 class=" ">Limitations</h2>
+<p style="text-align: justify; ">Anselm's infrastructure was not designed for virtualization. Anselm's environment is not intended primary for virtualization, compute nodes, storages and all infrastructure of Anselm is intended and optimized for running HPC jobs, this implies suboptimal configuration of virtualization and limitations.</p>
+<p style="text-align: justify; ">Anselm's virtualization does not provide performance and all features of native environment. There is significant performance hit (degradation) in I/O performance (storage, network). Anselm's virtualization is not suitable for I/O (disk, network) intensive workloads.</p>
+<p>Virtualization has also some drawbacks, it is not so easy to setup efficient solution.</p>
+<p>Solution described in chapter <a class="anchor-link" href="#howto" target="_self" title="">HOWTO</a><span class="anchor-link"> is suitable for </span>single node tasks, does not introduce virtual machine clustering.</p>
+<p class="exclamation">Please consider virtualization as last resort solution for your needs.</p>
+<p class="exclamation">Please consult use of virtualization with IT4Innovation's support.</p>
+<p class="exclamation">For running Windows application (when source code and Linux native application are not available) consider use of Wine, Windows compatibility layer. Many Windows applications can be run using Wine with less effort and better performance than when using virtualization.</p>
+<h2 class=" ">Licensing</h2>
+<p style="text-align: justify; ">IT4Innovations does not provide any licenses for operating systems and software of virtual machines. Users are (<span id="result_box"><span class="hps">in accordance with</span></span> <a class="external-link" href="http://www.it4i.cz/acceptable-use-policy.pdf" target="_self" title="">Acceptable use policy document</a>) fully responsible for licensing all software running in virtual machines on Anselm. Be aware of complex conditions of licensing software in virtual environments.</p>
+<p class="exclamation" style="text-align: justify; ">Users are responsible for licensing OS e.g. MS Windows and all software running in their virtual machines.</p>
+<h2 class=" "><a name="howto"></a>Â HOWTO</h2>
+<h3 class=" "><a name="virtual-machine-job-workflow"></a>Virtual Machine Job Workflow</h3>
+<p>We propose this job workflow:</p>
+<p>Â <img alt="Virtualization Job Workflow" class="image-inline" title="Virtualization Job Workflow" src="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization-job-workflow" /></p>
+<p>Our recommended solution is that job script creates distinct shared job directory, which makes a central point for data exchange between Anselm's environment, compute node (host) (e.g HOME, SCRATCH, local scratch and other local or cluster filesystems) and virtual machine (guest). Job script links or copies input data and instructions what to do (run script) for virtual machine to job directory and virtual machine process input data according instructions in job directory and store output back to job directory. We recommend, that virtual machine is running in so called <a class="anchor-link" href="#snapshot-mode" target="_self" title="">snapshot mode</a>, image is immutable - image does not change, so one image can be used for many concurrent jobs.</p>
+<h3 class=" ">Procedure</h3>
+<ol>
+<li>Prepare image of your virtual machine</li>
+<li>Optimize image of your virtual machine for Anselm's virtualization</li>
+<li>Modify your image for running jobs</li>
+<li>Create job script for executing virtual machine</li>
+<li>Run jobs</li>
+</ol>
+<h3 class=" ">Prepare image of your virtual machine</h3>
+<p>You can either use your existing image or create new image from scratch.</p>
+<p>QEMU currently supports these image types or formats:</p>
+<ul>
+<li>raw </li>
+<li>cloop </li>
+<li>cow </li>
+<li>qcow </li>
+<li>qcow2Â </li>
+<li class="extiw" title="w:VMware">vmdk - VMware 3 & 4, or 6 image format, for exchanging images with that product</li>
+<li>vdi - VirtualBox 1.1 compatible image format, for exchanging images with VirtualBox.</li>
+</ul>
+<p class=" ">You can convert your existing image using qemu-img convert command. Supported formats of this command are: blkdebug blkverify bochs cloop cow dmg file ftp ftps host_cdrom host_device host_floppy http https nbd parallels qcow qcow2 qed raw sheepdog tftp vdi vhdx vmdk vpc vvfat.</p>
+<p class=" ">We recommend using advanced QEMU native image format qcow2.</p>
+<p class=" "><a class="external-link" href="http://en.wikibooks.org/wiki/QEMU/Images" target="_blank" title="">More about QEMU Images</a></p>
+<h3 class=" ">Optimize image of your virtual machine</h3>
+<p>Use virtio devices (for disk/drive and network adapter) and install virtio drivers (paravirtualized drivers) into virtual machine. There is significant performance gain when using virtio drivers. For more information see <a class="external-link" href="http://www.linux-kvm.org/page/Virtio" target="_blank" title="">Virtio Linux</a> and <a class="external-link" href="http://www.linux-kvm.org/page/WindowsGuestDrivers/Download_Drivers" target="_blank" title="">Virtio Windows</a>.</p>
+<p>Disable all <span class="short_text" id="result_box"><span class="hps trans-target-highlight">unnecessary</span></span> services and tasks. Restrict all unnecessary operating system operations.</p>
+<p>Remove all <span class="short_text" id="result_box"><span class="hps trans-target-highlight">unnecessary software and files.</span></span></p>
+<p><span class="short_text" id="result_box"><span class="hps trans-target-highlight"></span></span>Remove all paging space, swap files, partitions, etc.</p>
+<p>Shrink your image. (It is recommended to zero all free space and reconvert image using qemu-img.)</p>
+<h3 class=" ">Modify your image for running jobs</h3>
+<p>Your image should run some kind of operating system startup script. Startup script should run application and when application exits run shutdown or quit virtual machine.</p>
+<p>We recommend, that startup script</p>
+<ul>
+<li>maps Job Directory from host (from compute node)</li>
+<li>runs script (we call it "run script") from Job Directory and waits for application's exit</li>
+<ul>
+<li>for management purposes if run script does not exist wait for some time period (few minutes)</li>
+</ul>
+<li>shutdowns/quits OS</li>
+</ul>
+<p>For Windows operating systems we suggest using Local Group Policy Startup script, for Linux operating systems rc.local, runlevel init script or similar service.</p>
+<p>Example startup script for Windows virtual machine:</p>
+<pre class=" ">@echo off<br />set LOG=c:\startup.log<br />set MAPDRIVE=z:<br />set SCRIPT=%MAPDRIVE%\run.bat<br />set TIMEOUT=300<br /><br />echo %DATE% %TIME% Running startup script>%LOG%<br /><br />rem Mount share<br />echo %DATE% %TIME% Mounting shared drive>>%LOG%<br />net use z: \\10.0.2.4\qemu >>%LOG% 2>&1<br />dir z:\ >>%LOG% 2>&1<br />echo. >>%LOG%<br /><br /><br />if exist %MAPDRIVE%\ (<br />Â echo %DATE% %TIME% The drive "%MAPDRIVE%" exists>>%LOG%<br /><br />Â if exist %SCRIPT% (<br />Â Â Â echo %DATE% %TIME% The script file "%SCRIPT%"exists>>%LOG%<br />Â Â Â echo %DATE% %TIME% Running script %SCRIPT%>>%LOG%<br />Â Â Â set TIMEOUT=0<br />Â Â Â call %SCRIPT%<br />Â ) else (<br />Â Â Â echo %DATE% %TIME% The script file "%SCRIPT%"does not exist>>%LOG%<br />Â )<br /><br />) else (<br />Â echo %DATE% %TIME% The drive "%MAPDRIVE%" does not exist>>%LOG%<br />)<br />echo. >>%LOG%<br /><br />timeout /T %TIMEOUT%<br /><br />echo %DATE% %TIME% Shut down>>%LOG%<br />shutdown /s /t 0</pre>
+<p class=" ">Example startup script maps shared job script as drive z: and looks for run script called run.bat. If run script is found it is run else wait for 5 minutes, then shutdown virtual machine.</p>
+<h3 class=" ">Create job script for executing virtual machine</h3>
+<p>Create job script according recommended <span class="short_text" id="result_box"><span class="hps trans-target-highlight"></span></span><a class="anchor-link" href="#virtual-machine-job-workflow" target="_self" title="">Virtual Machine Job Workflow</a>.</p>
+<p>Example job for Windows virtual machine:</p>
+<pre class=" ">#/bin/sh<br /><br />JOB_DIR=/scratch/$USER/win/${PBS_JOBID}<br /><br />#Virtual machine settings<br />VM_IMAGE=~/work/img/win.img<br />VM_MEMORY=49152<br />VM_SMP=16<br /><br /># Prepare job dir<br />mkdir -p ${JOB_DIR} && cd ${JOB_DIR} || exit 1<br />ln -s ~/work/win .<br />ln -s /scratch/$USER/data .<br />ln -s ~/work/win/script/run/run-appl.bat run.bat<br /><br /># Run virtual machine<br />export TMPDIR=/lscratch/${PBS_JOBID}<br />module add qemu<br />qemu-system-x86_64 \<br />Â -enable-kvm \<br />Â -cpu host \<br />Â -smp ${VM_SMP} \<br />Â -m ${VM_MEMORY} \<br />Â -vga std \<br />Â -localtime \<br />Â -usb -usbdevice tablet \<br />Â -device virtio-net-pci,netdev=net0 \<br />Â -netdev user,id=net0,smb=${JOB_DIR},hostfwd=tcp::3389-:3389 \<br />Â -drive file=${VM_IMAGE},media=disk,if=virtio \<br />Â -snapshot \<br />Â -nographic<br /><br /></pre>
+<p class=" ">Job script links application data (win), input data (data) and run script (run.bat) into job directory and runs virtual machine.</p>
+<p class=" ">Example run script (run.bat) for Windows virtual machine:</p>
+<pre class=" ">z:<br />cd \win\appl<br />call application.bat z:\data z:\output</pre>
+<p class=" ">Run script runs application from shared job directory (mapped as drive z:), process input data (z:\data) from job directory and store output to job directory (z:\output).</p>
+<h3 class=" ">Run jobs</h3>
+<p>Run jobs as usual, see <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction">Resource Allocation and Job Execution</a>. Use only full node allocation for virtualization jobs.</p>
+<h3 class=" ">Running Virtual Machines</h3>
+<p>Virtualization is enabled only on compute nodes, virtualization does not work on login nodes.</p>
+<p>Load QEMU environment module:</p>
+<pre class=" ">$ module add qemu</pre>
+<p class=" ">Get help</p>
+<pre class=" ">$ man qemu</pre>
+<p class=" ">Run virtual machine (simple)</p>
+<pre class=" ">$ qemu-system-x86_64 -hda linux.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -vnc :0<br /><br />$ qemu-system-x86_64 -hda win.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -vnc :0</pre>
+<p class=" ">You can access virtual machine by VNC viewer (option -vnc) connecting to IP address of compute node. For VNC you must use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access">VPN network</a>.</p>
+<p class=" ">Install virtual machine from iso file</p>
+<pre class=" ">$ qemu-system-x86_64 -hda linux.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -cdrom linux-install.iso -boot d -vnc :0<br /><br />$ qemu-system-x86_64 -hda win.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -cdrom win-install.iso -boot d -vnc :0</pre>
+<p class=" ">Run virtual machine using optimized devices, user network backend with sharing and port forwarding, in snapshot mode</p>
+<pre class=" ">$ qemu-system-x86_64 -drive file=linux.img,media=disk,if=virtio -enable-kvm -cpu host -smp 16 -m 32768 -vga std -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp::2222-:22 -vnc :0 -snapshot<br /><br />$ qemu-system-x86_64 -drive file=win.img,media=disk,if=virtio -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp::3389-:3389 -vnc :0 -snapshot</pre>
+<p class=" ">Thanks to port forwarding you can access virtual machine via SSH (Linux) or RDP (Windows) connecting to IP address of compute node (and port 2222 for SSH). You must use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access">VPN network</a>.</p>
+<p class="callout">Keep in mind, that if you use virtio devices, you must have virtio drivers installed on your virtual machine.</p>
+<h3 class=" ">Networking and data sharing</h3>
+<p class=" ">For networking virtual machine we suggest to use (default) user network backend (sometimes called slirp). This network backend NATs virtual machines and provides useful services for virtual machines as DHCP, DNS, SMB sharing, port forwarding.</p>
+<p class=" ">In default configuration IP network 10.0.2.0/24 is used, host has IP address 10.0.2.2, DNS server 10.0.2.3, SMB server 10.0.2.4 and virtual machines obtain address from range 10.0.2.15-10.0.2.31. Virtual machines have access to Anselm's network via NAT on compute node (host).</p>
+<p class=" ">Simple network setup</p>
+<pre class=" ">$ qemu-system-x86_64 ... -net nic -net user</pre>
+<p class=" ">(It is default when no -net options are given.)<br /><br />Simple network setup with sharing and port forwarding (obsolete but simpler syntax, lower performance)</p>
+<pre class=" ">$ qemu-system-x86_64 ... -net nic -net user,smb=/scratch/$USER/tmp,hostfwd=tcp::3389-:3389</pre>
+<p class=" ">Optimized network setup with sharing and port forwarding</p>
+<pre class=" ">$ qemu-system-x86_64 ... -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp::2222-:22</pre>
+<h3 class=" ">Advanced networking</h3>
+<p><strong>Internet access</strong></p>
+<p class=" ">Sometime your virtual machine needs access to internet (install software, updates, software activation, etc). We suggest solution using Virtual Distributed Ethernet (VDE) enabled QEMU with SLIRP running on login node tunnelled to compute node. Be aware, this setup has very low performance, the worst performance of all described solutions.</p>
+<p class=" ">Load VDE enabled QEMU environment module (unload standard QEMU module first if necessary).</p>
+<pre class=" ">$ module add qemu/2.1.2-vde2</pre>
+<p class=" ">Create virtual network switch.</p>
+<pre class=" ">$ vde_switch -sock /tmp/sw0 -mgmt /tmp/sw0.mgmt -daemon</pre>
+<p class=" ">Run SLIRP daemon over SSH tunnel on login node and connect it to virtual network switch.</p>
+<pre class=" ">$ dpipe vde_plug /tmp/sw0 = ssh login1 $VDE2_DIR/bin/slirpvde -s - --dhcp &</pre>
+<p class=" ">Run qemu using vde network backend, connect to created virtual switch.</p>
+<p class=" ">Basic setup (obsolete syntax)</p>
+<pre class=" ">$ qemu-system-x86_64 ... -net nic -net vde,sock=/tmp/sw0</pre>
+<p class=" ">Setup using virtio device (obsolete syntax)</p>
+<pre class=" ">$ qemu-system-x86_64 ... -net nic,model=virtio -net vde,sock=/tmp/sw0<strong></strong></pre>
+<p class=" ">Optimized setup</p>
+<pre class=" ">$ qemu-system-x86_64 ... -device virtio-net-pci,netdev=net0 -netdev vde,id=net0,sock=/tmp/sw0</pre>
+<p class=" "><strong><br /></strong></p>
+<p class=" "><strong>TAP interconnect</strong></p>
+<p class=" ">Both user and vde network backend have low performance. For fast interconnect (10Gbps and more) of compute node (host) and virtual machine (guest) we suggest using Linux kernel TAP device.</p>
+<p class=" ">Cluster Anselm provides TAP device tap0 for your job. TAP interconnect does not provide any services (like NAT, DHCP, DNS, SMB, etc.) just raw networking, so you should provide your services if you need them.</p>
+<p class=" ">Run qemu with TAP network backend:</p>
+<pre class=" ">$ qemu-system-x86_64 ... -device virtio-net-pci,netdev=net1 \<br /> -netdev tap,id=net1,ifname=tap0,script=no,downscript=no</pre>
+<p class=" ">Interface tap0 has IP address 192.168.1.1 and network mask 255.255.255.0 (/24). In virtual machine use IP address from range 192.168.1.2-192.168.1.254. For your convenience some ports on tap0 interface are redirected to higher numbered ports, so you as non-privileged user can provide services on these ports.</p>
+<p class=" ">Redirected ports:</p>
+<ul>
+<li>DNS udp/53->udp/3053, tcp/53->tcp3053</li>
+<li>DHCP udp/67->udp3067</li>
+<li>SMB tcp/139->tcp3139, tcp/445->tcp3445).</li>
+</ul>
+<p class=" ">You can configure IP address of virtual machine statically or dynamically. For dynamic addressing provide your DHCP server on port 3067 of tap0 interface, you can also provide your DNS server on port 3053 of tap0 interface for example:</p>
+<pre class=" ">$ dnsmasq --interface tap0 --bind-interfaces -p 3053 --dhcp-alternate-port=3067,68 --dhcp-range=192.168.1.15,192.168.1.32 --dhcp-leasefile=/tmp/dhcp.leasefile</pre>
+<p class=" ">You can also provide your SMB services (on ports 3139, 3445) to obtain high performance data sharing.</p>
+<p class=" ">Example smb.conf (not optimized)</p>
+<pre class=" ">[global]<br />socket address=192.168.1.1<br />smb ports = 3445 3139<br /><br />private dir=/tmp/qemu-smb<br />pid directory=/tmp/qemu-smb<br />lock directory=/tmp/qemu-smb<br />state directory=/tmp/qemu-smb<br />ncalrpc dir=/tmp/qemu-smb/ncalrpc<br />log file=/tmp/qemu-smb/log.smbd<br />smb passwd file=/tmp/qemu-smb/smbpasswd<br />security = user<br />map to guest = Bad User<br />unix extensions = no<br />load printers = no<br />printing = bsd<br />printcap name = /dev/null<br />disable spoolss = yes<br />log level = 1<br />guest account = USER<br />[qemu]<br />path=/scratch/USER/tmp<br />read only=no<br />guest ok=yes<br />writable=yes<br />follow symlinks=yes<br />wide links=yes<br />force user=USER</pre>
+<p class=" ">(Replace USER with your login name.)</p>
+<p class=" ">Run SMB services</p>
+<pre class=" ">smbd -s /tmp/qemu-smb/smb.conf</pre>
+<p class=" ">Â </p>
+<p class=" ">Virtual machine can of course have more than one network interface controller, virtual machine can use more than one network backend. So, you can combine for example use network backend and TAP interconnect.</p>
+<h3 class=" "><a name="snapshot-mode"></a>Snapshot mode</h3>
+<p>In snapshot mode image is not written, changes are written to temporary file (and discarded after virtual machine exits).<strong> It is strongly recommended mode for running your jobs.</strong> Set TMPDIR environment variable to local scratch directory for placement temporary files.</p>
+<pre class=" ">$ export TMPDIR=/lscratch/${PBS_JOBID}<br />$ qemu-system-x86_64 ... -snapshot</pre>
+<h3 class=" ">Windows guests</h3>
+<p>For Windows guests we recommend these options, life will be easier:</p>
+<pre class=" ">$ qemu-system-x86_64 ... -localtime -usb -usbdevice tablet</pre>
+
+ </div>
+
+
+ <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
+
+ <div id="plone-discussions">
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization.md b/docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization.md
new file mode 100644
index 0000000000000000000000000000000000000000..88fa64f1d31f9802f03d328b24d140e65f8d7bbe
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization.md
@@ -0,0 +1,348 @@
+Virtualization
+==============
+Running virtual machines on compute nodes
+
+Introduction
+------------
+There are situations when Anselm's environment is not suitable for user
+needs.
+- Application requires different operating system (e.g Windows),
+ application is not available for Linux
+- Application requires different versions of base system libraries and
+ tools
+- Application requires specific setup (installation, configuration) of
+ complex software stack
+- Application requires privileged access to operating system
+- ... and combinations of above cases
+Â We offer solution for these cases - **virtualization**. Anselm's
+environment gives the possibility to run virtual machines on compute
+nodes. Users can create their own images of operating system with
+specific software stack and run instances of these images as virtual
+machines on compute nodes. Run of virtual machines is provided by
+standard mechanism of [Resource Allocation and Job
+Execution](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction).
+Solution is based on QEMU-KVM software stack and provides
+hardware-assisted x86 virtualization.
+Limitations
+-----------
+Anselm's infrastructure was not designed for virtualization. Anselm's
+environment is not intended primary for virtualization, compute nodes,
+storages and all infrastructure of Anselm is intended and optimized for
+running HPC jobs, this implies suboptimal configuration of
+virtualization and limitations.
+Anselm's virtualization does not provide performance and all features of
+native environment. There is significant performance hit (degradation)
+in I/O performance (storage, network). Anselm's virtualization is not
+suitable for I/O (disk, network) intensive workloads.
+Virtualization has also some drawbacks, it is not so easy to setup
+efficient solution.
+Solution described in chapter [HOWTO](#howto)<span
+class="anchor-link"> is suitable for </span>single node tasks, does not
+introduce virtual machine clustering.
+Please consider virtualization as last resort solution for your needs.
+Please consult use of virtualization with IT4Innovation's support.
+For running Windows application (when source code and Linux native
+application are not available) consider use of Wine, Windows
+compatibility layer. Many Windows applications can be run using Wine
+with less effort and better performance than when using virtualization.
+Licensing
+---------
+IT4Innovations does not provide any licenses for operating systems and
+software of virtual machines. Users are (<span id="result_box"><span
+class="hps">in accordance with</span></span> [Acceptable use policy
+document](http://www.it4i.cz/acceptable-use-policy.pdf))
+fully responsible for licensing all software running in virtual machines
+on Anselm. Be aware of complex conditions of licensing software in
+virtual environments.
+Users are responsible for licensing OS e.g. MS Windows and all software
+running in their virtual machines.
+[]()Â HOWTO
+----------
+### []()Virtual Machine Job Workflow
+We propose this job workflow:
+Â 
+Our recommended solution is that job script creates distinct shared job
+directory, which makes a central point for data exchange between
+Anselm's environment, compute node (host) (e.g HOME, SCRATCH, local
+scratch and other local or cluster filesystems) and virtual machine
+(guest). Job script links or copies input data and instructions what to
+do (run script) for virtual machine to job directory and virtual machine
+process input data according instructions in job directory and store
+output back to job directory. We recommend, that virtual machine is
+running in so called [snapshot mode](#snapshot-mode),
+image is immutable - image does not change, so one image can be used for
+many concurrent jobs.
+### Procedure
+1. Prepare image of your virtual machine
+2. Optimize image of your virtual machine for Anselm's virtualization
+3. Modify your image for running jobs
+4. Create job script for executing virtual machine
+5. Run jobs
+### Prepare image of your virtual machine
+You can either use your existing image or create new image from scratch.
+QEMU currently supports these image types or formats:
+- rawÂ
+- cloopÂ
+- cowÂ
+- qcowÂ
+- qcow2Â
+- vmdk - VMware 3 & 4, or 6 image format, for exchanging images with
+ that product
+- vdi - VirtualBox 1.1 compatible image format, for exchanging images
+ with VirtualBox.
+You can convert your existing image using qemu-img convert command.
+Supported formats of this command areblkdebug blkverify bochs cloop
+cow dmg file ftp ftps host_cdrom host_device host_floppy http https
+nbd parallels qcow qcow2 qed raw sheepdog tftp vdi vhdx vmdk vpc vvfat.
+We recommend using advanced QEMU native image format qcow2.
+[More about QEMU
+Images](http://en.wikibooks.org/wiki/QEMU/Images)
+### Optimize image of your virtual machine
+Use virtio devices (for disk/drive and network adapter) and install
+virtio drivers (paravirtualized drivers) into virtual machine. There is
+significant performance gain when using virtio drivers. For more
+information see [Virtio
+Linux](http://www.linux-kvm.org/page/Virtio) and [Virtio
+Windows](http://www.linux-kvm.org/page/WindowsGuestDrivers/Download_Drivers).
+Disable all <span id="result_box" class="short_text"><span
+class="hps trans-target-highlight">unnecessary</span></span> services
+and tasks. Restrict all unnecessary operating system operations.
+Remove all <span id="result_box" class="short_text"><span
+class="hps trans-target-highlight">unnecessary software and
+files.</span></span>
+<span id="result_box" class="short_text"><span
+class="hps trans-target-highlight"></span></span>Remove all paging
+space, swap files, partitions, etc.
+Shrink your image. (It is recommended to zero all free space and
+reconvert image using qemu-img.)
+### Modify your image for running jobs
+Your image should run some kind of operating system startup script.
+Startup script should run application and when application exits run
+shutdown or quit virtual machine.
+We recommend, that startup script
+maps Job Directory from host (from compute node)
+runs script (we call it "run script") from Job Directory and waits for
+application's exit
+- for management purposes if run script does not exist wait for some
+ time period (few minutes)
+shutdowns/quits OS
+For Windows operating systems we suggest using Local Group Policy
+Startup script, for Linux operating systems rc.local, runlevel init
+script or similar service.
+Example startup script for Windows virtual machine:
+ @echo off
+ set LOG=c:startup.log
+ set MAPDRIVE=z:
+ set SCRIPT=%MAPDRIVE%run.bat
+ set TIMEOUT=300
+ echo %DATE% %TIME% Running startup script>%LOG%
+ rem Mount share
+ echo %DATE% %TIME% Mounting shared drive>>%LOG%
+ net use z10.0.2.4qemu >>%LOG% 2>&1
+ dir z>>%LOG% 2>&1
+ echo. >>%LOG%
+ if exist %MAPDRIVE% (
+ Â echo %DATE% %TIME% The drive "%MAPDRIVE%" exists>>%LOG%
+ Â if exist %SCRIPT% (
+ Â Â Â echo %DATE% %TIME% The script file "%SCRIPT%"exists>>%LOG%
+ Â Â Â echo %DATE% %TIME% Running script %SCRIPT%>>%LOG%
+ Â Â Â set TIMEOUT=0
+ Â Â Â call %SCRIPT%
+ Â ) else (
+ Â Â Â echo %DATE% %TIME% The script file "%SCRIPT%"does not exist>>%LOG%
+ Â )
+ ) else (
+ Â echo %DATE% %TIME% The drive "%MAPDRIVE%" does not exist>>%LOG%
+ )
+ echo. >>%LOG%
+ timeout /T %TIMEOUT%
+ echo %DATE% %TIME% Shut down>>%LOG%
+ shutdown /s /t 0
+Example startup script maps shared job script as drive zand looks for
+run script called run.bat. If run script is found it is run else wait
+for 5 minutes, then shutdown virtual machine.
+### Create job script for executing virtual machine
+Create job script according recommended <span id="result_box"
+class="short_text"><span
+class="hps trans-target-highlight"></span></span>[Virtual Machine Job
+Workflow](#virtual-machine-job-workflow).
+Example job for Windows virtual machine:
+ #/bin/sh
+ JOB_DIR=/scratch/$USER/win/${PBS_JOBID}
+ #Virtual machine settings
+ VM_IMAGE=~/work/img/win.img
+ VM_MEMORY=49152
+ VM_SMP=16
+ # Prepare job dir
+ mkdir -p ${JOB_DIR} && cd ${JOB_DIR} || exit 1
+ ln -s ~/work/win .
+ ln -s /scratch/$USER/data .
+ ln -s ~/work/win/script/run/run-appl.bat run.bat
+ # Run virtual machine
+ export TMPDIR=/lscratch/${PBS_JOBID}
+ module add qemu
+ qemu-system-x86_64
+ Â -enable-kvm
+ Â -cpu host
+ Â -smp ${VM_SMP}
+ Â -m ${VM_MEMORY}
+ Â -vga std
+ Â -localtime
+ Â -usb -usbdevice tablet
+ Â -device virtio-net-pci,netdev=net0
+ Â -netdev user,id=net0,smb=${JOB_DIR},hostfwd=tcp::3389-:3389
+ Â -drive file=${VM_IMAGE},media=disk,if=virtio
+ Â -snapshot
+ Â -nographic
+Job script links application data (win), input data (data) and run
+script (run.bat) into job directory and runs virtual machine.
+Example run script (run.bat) for Windows virtual machine:
+ z:
+ cd winappl
+ call application.bat z:data z:output
+Run script runs application from shared job directory (mapped as drive
+z:), process input data (z:data) from job directory and store output
+to job directory (z:output).
+### Run jobs
+Run jobs as usual, see [Resource Allocation and Job
+Execution](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction).
+Use only full node allocation for virtualization jobs.
+### Running Virtual Machines
+Virtualization is enabled only on compute nodes, virtualization does not
+work on login nodes.
+Load QEMU environment module:
+ $ module add qemu
+Get help
+ $ man qemu
+Run virtual machine (simple)
+ $ qemu-system-x86_64 -hda linux.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -vnc :0
+ $ qemu-system-x86_64 -hda win.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -vnc :0
+You can access virtual machine by VNC viewer (option -vnc) connecting to
+IP address of compute node. For VNC you must use [VPN
+network](https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access).
+Install virtual machine from iso file
+ $ qemu-system-x86_64 -hda linux.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -cdrom linux-install.iso -boot d -vnc :0
+ $ qemu-system-x86_64 -hda win.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -cdrom win-install.iso -boot d -vnc :0
+Run virtual machine using optimized devices, user network backend with
+sharing and port forwarding, in snapshot mode
+ $ qemu-system-x86_64 -drive file=linux.img,media=disk,if=virtio -enable-kvm -cpu host -smp 16 -m 32768 -vga std -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp::2222-:22 -vnc :0 -snapshot
+ $ qemu-system-x86_64 -drive file=win.img,media=disk,if=virtio -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp::3389-:3389 -vnc :0 -snapshot
+Thanks to port forwarding you can access virtual machine via SSH (Linux)
+or RDP (Windows) connecting to IP address of compute node (and port 2222
+for SSH). You must use [VPN
+network](https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access).
+Keep in mind, that if you use virtio devices, you must have virtio
+drivers installed on your virtual machine.
+### Networking and data sharing
+For networking virtual machine we suggest to use (default) user network
+backend (sometimes called slirp). This network backend NATs virtual
+machines and provides useful services for virtual machines as DHCP, DNS,
+SMB sharing, port forwarding.
+In default configuration IP network 10.0.2.0/24 is used, host has IP
+address 10.0.2.2, DNS server 10.0.2.3, SMB server 10.0.2.4 and virtual
+machines obtain address from range 10.0.2.15-10.0.2.31. Virtual machines
+have access to Anselm's network via NAT on compute node (host).
+Simple network setup
+ $ qemu-system-x86_64 ... -net nic -net user
+(It is default when no -net options are given.)
+Simple network setup with sharing and port forwarding (obsolete but
+simpler syntax, lower performance)
+ $ qemu-system-x86_64 ... -net nic -net user,smb=/scratch/$USER/tmp,hostfwd=tcp::3389-:3389
+Optimized network setup with sharing and port forwarding
+ $ qemu-system-x86_64 ... -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp::2222-:22
+### Advanced networking
+**Internet access**
+Sometime your virtual machine needs access to internet (install
+software, updates, software activation, etc). We suggest solution using
+Virtual Distributed Ethernet (VDE) enabled QEMU with SLIRP running on
+login node tunnelled to compute node. Be aware, this setup has very low
+performance, the worst performance of all described solutions.
+Load VDE enabled QEMU environment module (unload standard QEMU module
+first if necessary).
+ $ module add qemu/2.1.2-vde2
+Create virtual network switch.
+ $ vde_switch -sock /tmp/sw0 -mgmt /tmp/sw0.mgmt -daemon
+Run SLIRP daemon over SSH tunnel on login node and connect it to virtual
+network switch.
+ $ dpipe vde_plug /tmp/sw0 = ssh login1 $VDE2_DIR/bin/slirpvde -s - --dhcp &
+Run qemu using vde network backend, connect to created virtual switch.
+Basic setup (obsolete syntax)
+ $ qemu-system-x86_64 ... -net nic -net vde,sock=/tmp/sw0
+Setup using virtio device (obsolete syntax)
+ $ qemu-system-x86_64 ... -net nic,model=virtio -net vde,sock=/tmp/sw0
+Optimized setup
+ $ qemu-system-x86_64 ... -device virtio-net-pci,netdev=net0 -netdev vde,id=net0,sock=/tmp/sw0
+**
+**
+**TAP interconnect**
+Both user and vde network backend have low performance. For fast
+interconnect (10Gbps and more) of compute node (host) and virtual
+machine (guest) we suggest using Linux kernel TAP device.
+Cluster Anselm provides TAP device tap0 for your job. TAP interconnect
+does not provide any services (like NAT, DHCP, DNS, SMB, etc.) just raw
+networking, so you should provide your services if you need them.
+Run qemu with TAP network backend:
+ $ qemu-system-x86_64 ... -device virtio-net-pci,netdev=net1
+ -netdev tap,id=net1,ifname=tap0,script=no,downscript=no
+Interface tap0 has IP address 192.168.1.1 and network mask 255.255.255.0
+(/24). In virtual machine use IP address from range
+192.168.1.2-192.168.1.254. For your convenience some ports on tap0
+interface are redirected to higher numbered ports, so you as
+non-privileged user can provide services on these ports.
+Redirected ports:
+- DNS udp/53->udp/3053, tcp/53->tcp3053
+- DHCP udp/67->udp3067
+- SMB tcp/139->tcp3139, tcp/445->tcp3445).
+You can configure IP address of virtual machine statically or
+dynamically. For dynamic addressing provide your DHCP server on port
+3067 of tap0 interface, you can also provide your DNS server on port
+3053 of tap0 interface for example:
+ $ dnsmasq --interface tap0 --bind-interfaces -p 3053 --dhcp-alternate-port=3067,68 --dhcp-range=192.168.1.15,192.168.1.32 --dhcp-leasefile=/tmp/dhcp.leasefile
+You can also provide your SMB services (on ports 3139, 3445) to obtain
+high performance data sharing.
+Example smb.conf (not optimized)
+ [global]
+ socket address=192.168.1.1
+ smb ports = 3445 3139
+ private dir=/tmp/qemu-smb
+ pid directory=/tmp/qemu-smb
+ lock directory=/tmp/qemu-smb
+ state directory=/tmp/qemu-smb
+ ncalrpc dir=/tmp/qemu-smb/ncalrpc
+ log file=/tmp/qemu-smb/log.smbd
+ smb passwd file=/tmp/qemu-smb/smbpasswd
+ security = user
+ map to guest = Bad User
+ unix extensions = no
+ load printers = no
+ printing = bsd
+ printcap name = /dev/null
+ disable spoolss = yes
+ log level = 1
+ guest account = USER
+ [qemu]
+ path=/scratch/USER/tmp
+ read only=no
+ guest ok=yes
+ writable=yes
+ follow symlinks=yes
+ wide links=yes
+ force user=USER
+(Replace USER with your login name.)
+Run SMB services
+ smbd -s /tmp/qemu-smb/smb.conf
+Â
+Virtual machine can of course have more than one network interface
+controller, virtual machine can use more than one network backend. So,
+you can combine for example use network backend and TAP interconnect.
+### []()Snapshot mode
+In snapshot mode image is not written, changes are written to temporary
+file (and discarded after virtual machine exits). **It is strongly
+recommended mode for running your jobs.** Set TMPDIR environment
+variable to local scratch directory for placement temporary files.
+ $ export TMPDIR=/lscratch/${PBS_JOBID}
+ $ qemu-system-x86_64 ... -snapshot
+### Windows guests
+For Windows guests we recommend these options, life will be easier:
+ $ qemu-system-x86_64 ... -localtime -usb -usbdevice tablet
diff --git a/anselm-cluster-documentation/storage-1.html b/docs.it4i.cz/anselm-cluster-documentation/storage-1.html
old mode 100755
new mode 100644
similarity index 84%
rename from anselm-cluster-documentation/storage-1.html
rename to docs.it4i.cz/anselm-cluster-documentation/storage-1.html
index 027e8ea36f55b0dffb8979525602bc231ddb61aa..93d09b8d1273e14582807e4d4c4c5cc62a9dab06
--- a/anselm-cluster-documentation/storage-1.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/storage-1.html
@@ -10,45 +10,42 @@
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<title>Storage — IT4I Docs</title>
- <link rel="canonical" href="storage-1.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1" />
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@@ -87,9 +84,9 @@
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<div id="portal-header">
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@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
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@@ -153,7 +150,7 @@
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<span id="breadcrumbs-1" dir="ltr">
- <a href="../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
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@@ -232,11 +229,11 @@
<div id="parent-fieldname-text-1d1e813ad5694098ada90d35a6148610" class="">
<p>There are two main shared file systems on Anselm cluster, the <a class="anchor-link" href="#home" target="_self" title="">HOME</a> and <a class="anchor-link" href="#scratch" target="_self" title="">SCRATCH</a>. All login and compute nodes may access same data on shared filesystems. Compute nodes are also equipped with local (non-shared) scratch, ramdisk and tmp filesystems.</p>
<h2 class=" ">Archiving</h2>
-<p>Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use <a target="_self" title="" class="internal-link" href="storage-1/cesnet-data-storage.html">CESNET storage service</a>, which is available via SSHFS.</p>
+<p>Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage">CESNET storage service</a>, which is available via SSHFS.</p>
<h2 class=" ">Shared Filesystems</h2>
<p class=" ">Anselm computer provides two main shared filesystems, the <a class="anchor-link" href="#home" target="_self" title="">HOME filesystem</a> and the <a class="anchor-link" href="#scratch" target="_self" title="">SCRATCH filesystem</a>. Both HOME and SCRATCH filesystems are realized as a parallel Lustre filesystem. Both shared file systems are accessible via the Infiniband network. Extended ACLs are provided on both Lustre filesystems for the purpose of sharing data with other users using fine-grained control.</p>
<h3 class=" ">Understanding the Lustre Filesystems</h3>
-<p>(source <a class="external-link" href="http://www.nas.nasa.gov/" target="_self" title="">http://www.nas.nasa.gov</a>)</p>
+<p>(source <a class="external-link" href="http://www.nas.nasa.gov" target="_self" title="">http://www.nas.nasa.gov</a>)</p>
<p>A user file on the Lustre filesystem can be divided into multiple chunks (stripes) and stored across a subset of the object storage targets (OSTs) (disks). The stripes are distributed among the OSTs in a round-robin fashion to ensure load balancing.</p>
<p>When a client (a <span class="glossaryItem">compute <span class="glossaryItem">node</span></span> from your job) needs to create or access a file, the client queries the metadata server (<span class="glossaryItem">MDS</span>) and the metadata target (<span class="glossaryItem">MDT</span>) for the layout and location of the <a href="http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping">file's stripes</a>. Once the file is opened and the client obtains the striping information, the <span class="glossaryItem">MDS</span> is no longer involved in the file I/O process. The client interacts directly with the object storage servers (OSSes) and OSTs to perform I/O operations such as locking, disk allocation, storage, and retrieval.</p>
<p>If multiple clients try to read and write the same part of a file at the same time, the Lustre distributed lock manager enforces coherency so that all clients see consistent results.</p>
@@ -305,7 +302,7 @@
<p>The HOME filesystem is mounted in directory /home. Users home directories /home/username reside on this filesystem. Accessible capacity is 320TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 250GB per user. <span>If 250GB should prove as insufficient for particular user, please contact</span>Â <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">support</a>, the quota may be lifted upon request.</p>
<p class="callout">The HOME filesystem is intended for preparation, evaluation, processing and storage of data generated by active Projects.</p>
<p>The HOME filesystem should not be used to archive data of past Projects or other unrelated data.</p>
-<p>The files on HOME filesystem will not be deleted until end of the <a target="_self" title="" class="internal-link" href="../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html">users lifecycle</a>.</p>
+<p>The files on HOME filesystem will not be deleted until end of the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials">users lifecycle</a>.</p>
<p class=" ">The filesystem is backed up, such that it can be restored in case of catasthropic failure resulting in significant data loss. This backup however is not intended to restore old versions of user data or to restore (accidentaly) deleted files. </p>
<p class=" ">The HOME filesystem is realized as Lustre parallel filesystem and is available on all login and computational nodes. <br />Default stripe size is 1MB, stripe count is 1. There are 22 OSTs dedicated for the HOME filesystem.</p>
<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
@@ -613,7 +610,7 @@
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@@ -629,7 +626,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -645,7 +642,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -661,7 +658,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -677,7 +674,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -693,7 +690,7 @@
- <a title="" class="state-published contenttype-document" href="hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -709,7 +706,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -725,7 +722,7 @@
- <a title="" class="state-published contenttype-document" href="environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -741,7 +738,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -757,7 +754,7 @@
- <a title="" class="state-published contenttype-document" href="compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -773,7 +770,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="storage-1.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -789,7 +786,7 @@
- <a title="" class="state-published contenttype-document" href="storage-1/cesnet-data-storage.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage">
<span>CESNET Data Storage</span>
</a>
@@ -814,7 +811,7 @@
- <a title="" class="state-published contenttype-document" href="network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -830,10 +827,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -849,7 +846,7 @@
- <a title="" class="state-published contenttype-document" href="remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -865,7 +862,7 @@
- <a title="" class="state-published contenttype-document" href="prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -890,7 +887,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -906,7 +903,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -922,7 +919,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -961,14 +958,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -990,12 +987,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1011,7 +1008,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/storage-1 by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:50 GMT -->
</html>
diff --git a/anselm-cluster-documentation/accessing-the-cluster/storage-1.md b/docs.it4i.cz/anselm-cluster-documentation/storage-1.md
similarity index 77%
rename from anselm-cluster-documentation/accessing-the-cluster/storage-1.md
rename to docs.it4i.cz/anselm-cluster-documentation/storage-1.md
index 9f03a712ab884945ec37373faad7c0923474e598..8fca8932e4dd28e96ea3b96c0c2383987a62c404 100644
--- a/anselm-cluster-documentation/accessing-the-cluster/storage-1.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/storage-1.md
@@ -1,3 +1,6 @@
+Storage
+=======
+
There are two main shared file systems on Anselm cluster, the
[HOME](#home) and [SCRATCH](#scratch). All
login and compute nodes may access same data on shared filesystems.
@@ -8,8 +11,8 @@ Archiving
Please don't use shared filesystems as a backup for large amount of data
or long-term archiving mean. The academic staff and students of research
institutions in the Czech Republic can use [CESNET storage
-service](../storage-1/cesnet-data-storage.html), which
-is available via SSHFS.
+service](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage),
+which is available via SSHFS.
Shared Filesystems
------------------
Anselm computer provides two main shared filesystems, the [HOME
@@ -20,21 +23,20 @@ are accessible via the Infiniband network. Extended ACLs are provided on
both Lustre filesystems for the purpose of sharing data with other users
using fine-grained control.
### Understanding the Lustre Filesystems
-(source
-[http//www.nas.nasa.gov](http//www.nas.nasa.gov/))
+(source <http://www.nas.nasa.gov>)
A user file on the Lustre filesystem can be divided into multiple chunks
(stripes) and stored across a subset of the object storage targets
(OSTs) (disks). The stripes are distributed among the OSTs in a
round-robin fashion to ensure load balancing.
-When a client (a compute
-class="glossaryItem">node from your job) needs to create
-or access a file, the client queries the metadata server (
-class="glossaryItem">MDS) and the metadata target (
-class="glossaryItem">MDT) for the layout and location of the
+When a client (a <span class="glossaryItem">compute <span
+class="glossaryItem">node</span></span> from your job) needs to create
+or access a file, the client queries the metadata server (<span
+class="glossaryItem">MDS</span>) and the metadata target (<span
+class="glossaryItem">MDT</span>) for the layout and location of the
[file's
-stripes](http//www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping).
+stripes](http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping).
Once the file is opened and the client obtains the striping information,
-the MDS is no longer involved in the
+the <span class="glossaryItem">MDS</span> is no longer involved in the
file I/O process. The client interacts directly with the object storage
servers (OSSes) and OSTs to perform I/O operations such as locking, disk
allocation, storage, and retrieval.
@@ -43,16 +45,16 @@ same time, the Lustre distributed lock manager enforces coherency so
that all clients see consistent results.
There is default stripe configuration for Anselm Lustre filesystems.
However, users can set the following stripe parameters for their own
-directories or files to get optimum I/O performance
-1. stripe_size the size of the chunk in bytes; specify with k, m, or
+directories or files to get optimum I/O performance:
+1. stripe_sizethe size of the chunk in bytes; specify with k, m, or
g to use units of KB, MB, or GB, respectively; the size must be an
even multiple of 65,536 bytes; default is 1MB for all Anselm Lustre
filesystems
2. stripe_count the number of OSTs to stripe across; default is 1 for
Anselm Lustre filesystems one can specify -1 to use all OSTs in
the filesystem.
-3. stripe_offset The index of the
- class="glossaryItem">OST where the first stripe is to be
+3. stripe_offset The index of the <span
+ class="glossaryItem">OST</span> where the first stripe is to be
placed; default is -1 which results in random selection; using a
non-default value is NOT recommended.
Â
@@ -66,15 +68,15 @@ access patterns.Â
$ lfs getstripe dir|filename
$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir|filename
```
-Example
+Example:
``` {.prettyprint .lang-sh}
$ lfs getstripe /scratch/username/
/scratch/username/
-stripe_count 1 stripe_size 1048576 stripe_offset -1
+stripe_count 1 stripe_size 1048576 stripe_offset -1
$ lfs setstripe -c -1 /scratch/username/
$ lfs getstripe /scratch/username/
/scratch/username/
-stripe_count 10 stripe_size 1048576 stripe_offset -1
+stripe_count 10 stripe_size 1048576 stripe_offset -1
```
In this example, we view current stripe setting of the
/scratch/username/ directory. The stripe count is changed to all OSTs,
@@ -109,30 +111,31 @@ part of a file. However, it can be counterproductive in some cases if it
does not match your I/O pattern. The choice of stripe size has no effect
on a single-stripe file.
Read more on
+<http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html>
### Lustre on Anselm
The architecture of Lustre on Anselm is composed of two metadata
servers (MDS) and four data/object storage servers (OSS). Two object
storage servers are used for file system HOME and another two object
storage servers are used for file system SCRATCH.
-Configuration of the storages
-- HOME Lustre object storage
-
+<span class="emphasis">Configuration of the storages</span>
+- <span class="emphasis">HOME Lustre object storage</span>
+ <div class="itemizedlist">
- One disk array NetApp E5400
- 22 OSTs
- 227 2TB NL-SAS 7.2krpm disks
- 22 groups of 10 disks in RAID6 (8+2)
- 7 hot-spare disks
-- SCRATCH Lustre object storage
-
+- <span class="emphasis">SCRATCH Lustre object storage</span>
+ <div class="itemizedlist">
- Two disk arrays NetApp E5400
- 10 OSTs
- 106 2TB NL-SAS 7.2krpm disks
- 10 groups of 10 disks in RAID6 (8+2)
- 6 hot-spare disks
-- Lustre metadata storage
-
+- <span class="emphasis">Lustre metadata storage</span>
+ <div class="itemizedlist">
- One disk array NetApp E2600
- 12 300GB SAS 15krpm disks
- 2 groups of 5 disks in RAID5
@@ -142,16 +145,16 @@ Configuration of the storages
The HOME filesystem is mounted in directory /home. Users home
directories /home/username reside on this filesystem. Accessible
capacity is 320TB, shared among all users. Individual users are
-restricted by filesystem usage quotas, set to 250GB per user. If
+restricted by filesystem usage quotas, set to 250GB per user. <span>If
250GB should prove as insufficient for particular user, please
-contact [support](https//support.it4i.cz/rt),
+contact</span>Â [support](https://support.it4i.cz/rt),
the quota may be lifted upon request.
The HOME filesystem is intended for preparation, evaluation, processing
and storage of data generated by active Projects.
The HOME filesystem should not be used to archive data of past Projects
or other unrelated data.
The files on HOME filesystem will not be deleted until end of the [users
-lifecycle](../../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html).
+lifecycle](https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials).
The filesystem is backed up, such that it can be restored in case ofÂ
catasthropic failure resulting in significant data loss. This backup
however is not intended to restore old versions of user data or to
@@ -183,19 +186,17 @@ freely create subdirectories and files on the filesystem. Accessible
capacity is 146TB, shared among all users. Individual users are
restricted by filesystem usage quotas, set to 100TB per user. The
purpose of this quota is to prevent runaway programs from filling the
-entire filesystem and deny service to other users. If 100TB should
+entire filesystem and deny service to other users. <span>If 100TB should
prove as insufficient for particular user, please contact
-[support](https//support.it4i.cz/rt), the quota may be
-lifted upon request.Â
+[support](https://support.it4i.cz/rt), the quota may be
+lifted upon request. </span>
The Scratch filesystem is intended for temporary scratch data generated
during the calculation as well as for high performance access to input
and output files. All I/O intensive jobs must use the SCRATCH filesystem
as their working directory.
-
Users are advised to save the necessary data from the SCRATCH filesystem
to HOME filesystem after the calculations and clean up the scratch
files.
-
Files on the SCRATCH filesystem that are **not accessed for more than 90
days** will be automatically **deleted**.
The SCRATCH filesystem is realized as Lustre parallel filesystem and is
@@ -219,31 +220,31 @@ Default stripe count
1
Number of OSTs
10
-### Disk usage and quota commands
-User quotas on the file systems can be checked and reviewed using
-following command
+### <span>Disk usage and quota commands</span>
+<span>User quotas on the file systems can be checked and reviewed using
+following command:</span>
``` {.prettyprint .lang-sh}
$ lfs quota dir
```
-Example for Lustre HOME directory
+Example for Lustre HOME directory:
``` {.prettyprint .lang-sh}
$ lfs quota /home
-Disk quotas for user user001 (uid 1234)
+Disk quotas for user user001 (uid 1234):
Filesystem kbytes quota limit grace files quota limit grace
/home 300096 0 250000000 - 2102 0 500000 -
-Disk quotas for group user001 (gid 1234)
+Disk quotas for group user001 (gid 1234):
Filesystem kbytes quota limit grace files quota limit grace
/home 300096 0 0 - 2102 0 0 -
```
In this example, we view current quota size limit of 250GB and 300MB
currently used by user001.
-Example for Lustre SCRATCH directory
+Example for Lustre SCRATCH directory:
``` {.prettyprint .lang-sh}
$ lfs quota /scratch
-Disk quotas for user user001 (uid 1234)
+Disk quotas for user user001 (uid 1234):
Filesystem kbytes quota limit grace files quota limit grace
 /scratch    8    0 100000000000    -    3    0    0    -
-Disk quotas for group user001 (gid 1234)
+Disk quotas for group user001 (gid 1234):
Filesystem kbytes quota limit grace files quota limit grace
/scratch    8    0    0    -    3    0    0    -
```
@@ -255,7 +256,7 @@ can use following command to find out.
``` {.prettyprint .lang-sh}
$ du -hs dir
```
-Example for your HOME directory
+Example for your HOME directory:
``` {.prettyprint .lang-sh}
$ cd /home
$ du -hs * .[a-zA-z0-9]* | grep -E "[0-9]*G|[0-9]*M" | sort -hr
@@ -269,9 +270,8 @@ This will list all directories which are having MegaBytes or GigaBytes
of consumed space in your actual (in this example HOME) directory. List
is sorted in descending order from largest to smallest
files/directories.
-
-To have a better understanding of previous commands, you can read
-manpages.
+<span>To have a better understanding of previous commands, you can read
+manpages.</span>
``` {.prettyprint .lang-sh}
$ man lfs
```
@@ -291,33 +291,33 @@ manner. Below, we create a directory and allow a specific user access.
[vop999@login1.anselm ~]$ umask 027
[vop999@login1.anselm ~]$ mkdir test
[vop999@login1.anselm ~]$ ls -ld test
-drwxr-x--- 2 vop999 vop999 4096 Nov 5 1417 test
+drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.anselm ~]$ getfacl test
-# file test
-# owner vop999
-# group vop999
-userrwx
-groupr-x
-other---
-[vop999@login1.anselm ~]$ setfacl -m userjohnsmrwx test
+# filetest
+# ownervop999
+# groupvop999
+user::rwx
+group::r-x
+other::---
+[vop999@login1.anselm ~]$ setfacl -m user:johnsm:rwx test
[vop999@login1.anselm ~]$ ls -ld test
-drwxrwx---+ 2 vop999 vop999 4096 Nov 5 1417 test
+drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.anselm ~]$ getfacl test
-# file test
-# owner vop999
-# group vop999
-userrwx
-userjohnsmrwx
-groupr-x
-maskrwx
-other---
+# filetest
+# ownervop999
+# groupvop999
+user::rwx
+user:johnsm:rwx
+group::r-x
+mask::rwx
+other::---
```
Default ACL mechanism can be used to replace setuid/setgid permissions
on directories. Setting a default ACL on a directory (-d flag to
setfacl) will cause the ACL permissions to be inherited by any newly
created file or subdirectory within the directory. Refer to this page
-for more information on Linux ACL
-[http//www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html ](http//www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html)
+for more information on Linux ACL:
+[http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html ](http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html)
Local Filesystems
-----------------
### Local Scratch
@@ -368,9 +368,9 @@ immediately after the calculation end. Users should take care to save
the output data from within the jobscript.
RAM disk
Mountpoint
-/ramdisk
+<span class="monospace">/ramdisk</span>
Accesspoint
-/ramdisk/$PBS_JOBID
+<span class="monospace">/ramdisk/$PBS_JOBID</span>
Capacity
60GB at compute nodes without accelerator
90GB at compute nodes with accelerator
@@ -388,27 +388,10 @@ files in /tmp directory are automatically purged.
**
----------
Mountpoint Usage Protocol Net Capacity Throughput Limitations Access Services
- ------------------------------------------ --------------------------- ---------- ---------------- ------------ ------------- ------------------------- -----------------------------
- /home home directory Lustre 320 TiB 2 GB/s Quota 250GB Compute and login nodes backed up
- /scratch cluster shared jobs' data Lustre 146 TiB 6 GB/s Quota 100TB Compute and login nodes files older 90 days removed
- /lscratch node local jobs' data local 330 GB 100 MB/s none Compute nodes purged after job ends
- /ramdisk node local jobs' data local 60, 90, 500 GB 5-50 GB/s none Compute nodes purged after job ends
- /tmp local temporary files local 100 MB/s none Compute and login nodes auto purged
+ ------------------- ---- ---------- ---------------- ------------ ------------- -- ------
+ <span class="monospace">/home</span> home directory Lustre 320 TiB 2 GB/s Quota 250GB Compute and login nodes backed up
+ <span class="monospace">/scratch</span> cluster shared jobs' data Lustre 146 TiB 6 GB/s Quota 100TB Compute and login nodes files older 90 days removed
+ <span class="monospace">/lscratch</span> node local jobs' data local 330 GB 100 MB/s none Compute nodes purged after job ends
+ <span class="monospace">/ramdisk</span> node local jobs' data local 60, 90, 500 GB 5-50 GB/s none Compute nodes purged after job ends
+ <span class="monospace">/tmp</span> local temporary files local 100 MB/s none Compute and login nodes auto purged
Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
diff --git a/anselm-cluster-documentation/storage-1/cesnet-data-storage.html b/docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.html
old mode 100755
new mode 100644
similarity index 75%
rename from anselm-cluster-documentation/storage-1/cesnet-data-storage.html
rename to docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.html
index 1929c44fc06b01e0fd627cf7b02cc75489e71840..5d126c47d138db4a8d4adea8e17e476a30032913
--- a/anselm-cluster-documentation/storage-1/cesnet-data-storage.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:39 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>CESNET Data Storage — IT4I Docs</title>
- <link rel="canonical" href="cesnet-data-storage.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="cesnet-data-storage.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="cesnet-data-storage.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../storage-1.html">Storage</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">Storage</a>
<span class="breadcrumbSeparator">
/
@@ -350,7 +347,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -366,7 +363,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -382,7 +379,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -398,7 +395,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -414,7 +411,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -430,7 +427,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -446,7 +443,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -462,7 +459,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -478,7 +475,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -494,7 +491,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -510,7 +507,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -526,7 +523,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="cesnet-data-storage.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage">
<span>CESNET Data Storage</span>
</a>
@@ -551,7 +548,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -567,10 +564,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -586,7 +583,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -602,7 +599,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -627,7 +624,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -643,7 +640,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -659,7 +656,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -698,14 +695,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -727,12 +724,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -748,7 +745,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/salomon/storage/cesnet-data-storage.md b/docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.md
similarity index 69%
rename from salomon/storage/cesnet-data-storage.md
rename to docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.md
index bdd3eb33d30ac2665dab619aeec300c145a06d1d..51eb708c8ba89f571f846712728ebbb61fbf8ad8 100644
--- a/salomon/storage/cesnet-data-storage.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.md
@@ -1,4 +1,6 @@
-
+CESNET Data Storage
+===================
+
Introduction
------------
Do not use shared filesystems at IT4Innovations as a backup for large
@@ -6,40 +8,38 @@ amount of data or long-term archiving purposes.
The IT4Innovations does not provide storage capacity for data archiving.
Academic staff and students of research institutions in the Czech
Republic can use [CESNET Storage
-service](https//du.cesnet.cz/).
+service](https://du.cesnet.cz/).
The CESNET Storage service can be used for research purposes, mainly by
academic staff and students of research institutions in the Czech
Republic.
-
User of data storage CESNET (DU) association can become organizations or
an individual person who is either in the current employment
relationship (employees) or the current study relationship (students) to
a legal entity (organization) that meets the “Principles for access to
CESNET Large infrastructure (Access Policy)”.
-
User may only use data storage CESNET for data transfer and storage
which are associated with activities in science, research, development,
the spread of education, culture and prosperity. In detail see
“Acceptable Use Policy CESNET Large Infrastructure (Acceptable Use
Policy, AUP)”.
The service is documented at
-. For special requirements
+<https://du.cesnet.cz/wiki/doku.php/en/start>. For special requirements
please contact directly CESNET Storage Department via e-mail
-[du-support(at)cesnet.cz](mailtodu-support@cesnet.cz){.email-link}.
+[du-support(at)cesnet.cz](mailto:du-support@cesnet.cz){.email-link}.
The procedure to obtain the CESNET access is quick and trouble-free.
(source
-[https//du.cesnet.cz/](https//du.cesnet.cz/wiki/doku.php/en/start "CESNET Data Storage"))
+[https://du.cesnet.cz/](https://du.cesnet.cz/wiki/doku.php/en/start "CESNET Data Storage"))
CESNET storage access
---------------------
### Understanding Cesnet storage
It is very important to understand the Cesnet storage before uploading
data. Please read
- first.
+<https://du.cesnet.cz/en/navody/home-migrace-plzen/start> first.
Once registered for CESNET Storage, you may [access the
-storage](https//du.cesnet.cz/en/navody/faq/start) in
+storage](https://du.cesnet.cz/en/navody/faq/start) in
number of ways. We recommend the SSHFS and RSYNC methods.
### SSHFS Access
-SSHFS The storage will be mounted like a local hard drive
+SSHFSThe storage will be mounted like a local hard drive
The SSHFSÂ provides a very convenient way to access the CESNET Storage.
The storage will be mounted onto a local directory, exposing the vast
CESNET Storage as if it was a local removable harddrive. Files can be
@@ -48,12 +48,12 @@ First, create the mountpoint
$ mkdir cesnet
Mount the storage. Note that you can choose among the ssh.du1.cesnet.cz
(Plzen), ssh.du2.cesnet.cz (Jihlava), ssh.du3.cesnet.cz (Brno)
-Mount tier1_home **(only 5120M !)**
- $ sshfs username@ssh.du1.cesnet.cz. cesnet/
+Mount tier1_home **(only 5120M !)**:
+ $ sshfs username@ssh.du1.cesnet.cz:. cesnet/
For easy future access from Anselm, install your public key
$ cp .ssh/id_rsa.pub cesnet/.ssh/authorized_keys
-Mount tier1_cache_tape for the Storage VO
- $ sshfs username@ssh.du1.cesnet.cz/cache_tape/VO_storage/home/username cesnet/
+Mount tier1_cache_tape for the Storage VO:
+ $ sshfs username@ssh.du1.cesnet.cz:/cache_tape/VO_storage/home/username cesnet/
View the archive, copy the files and directories in and out
$ ls cesnet/
$ cp -a mydir cesnet/.
@@ -69,7 +69,6 @@ data sent over the network by sending only the differences between the
source files and the existing files in the destination. Rsync is widely
used for backups and mirroring and as an improved copy command for
everyday use.
-
Rsync finds files that need to be transferred using a "quick check"
algorithm (by default) that looks for files that have changed in size or
in last-modified time. Any changes in the other preserved attributes
@@ -77,29 +76,13 @@ in last-modified time. Any changes in the other preserved attributes
the quick check indicates that the file's data does not need to be
updated.
More about Rsync at
+<https://du.cesnet.cz/en/navody/rsync/start#pro_bezne_uzivatele>
Transfer large files to/from Cesnet storage, assuming membership in the
Storage VO
- $ rsync --progress datafile username@ssh.du1.cesnet.czVO_storage-cache_tape/.
- $ rsync --progress username@ssh.du1.cesnet.czVO_storage-cache_tape/datafile .
+ $ rsync --progress datafile username@ssh.du1.cesnet.cz:VO_storage-cache_tape/.
+ $ rsync --progress username@ssh.du1.cesnet.cz:VO_storage-cache_tape/datafile .
Transfer large directories to/from Cesnet storage, assuming membership
in the Storage VO
- $ rsync --progress -av datafolder username@ssh.du1.cesnet.czVO_storage-cache_tape/.
- $ rsync --progress -av username@ssh.du1.cesnet.czVO_storage-cache_tape/datafolder .
+ $ rsync --progress -av datafolder username@ssh.du1.cesnet.cz:VO_storage-cache_tape/.
+ $ rsync --progress -av username@ssh.du1.cesnet.cz:VO_storage-cache_tape/datafolder .
Transfer rates of about 28MB/s can be expected.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
diff --git a/anselm-cluster-documentation/storage-1/storage.html b/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.html
old mode 100755
new mode 100644
similarity index 84%
rename from anselm-cluster-documentation/storage-1/storage.html
rename to docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.html
index b39f4d4612da3d1c1dab701bb3a636a1030a281a..9fb62b38e37eb74e99b4e25893c2c71efd3d4815
--- a/anselm-cluster-documentation/storage-1/storage.html
+++ b/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.html
@@ -10,45 +10,42 @@
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<title>Storage — IT4I Docs</title>
- <link rel="canonical" href="../storage-1.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1" />
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+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
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@@ -64,7 +61,7 @@
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="storage.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="storage.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
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@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../anselm-cluster-documentation.html">Anselm Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -232,11 +229,11 @@
<div id="parent-fieldname-text-1d1e813ad5694098ada90d35a6148610" class="">
<p>There are two main shared file systems on Anselm cluster, the <a class="anchor-link" href="#home" target="_self" title="">HOME</a> and <a class="anchor-link" href="#scratch" target="_self" title="">SCRATCH</a>. All login and compute nodes may access same data on shared filesystems. Compute nodes are also equipped with local (non-shared) scratch, ramdisk and tmp filesystems.</p>
<h2 class=" ">Archiving</h2>
-<p>Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use <a target="_self" title="" class="internal-link" href="cesnet-data-storage.html">CESNET storage service</a>, which is available via SSHFS.</p>
+<p>Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage">CESNET storage service</a>, which is available via SSHFS.</p>
<h2 class=" ">Shared Filesystems</h2>
<p class=" ">Anselm computer provides two main shared filesystems, the <a class="anchor-link" href="#home" target="_self" title="">HOME filesystem</a> and the <a class="anchor-link" href="#scratch" target="_self" title="">SCRATCH filesystem</a>. Both HOME and SCRATCH filesystems are realized as a parallel Lustre filesystem. Both shared file systems are accessible via the Infiniband network. Extended ACLs are provided on both Lustre filesystems for the purpose of sharing data with other users using fine-grained control.</p>
<h3 class=" ">Understanding the Lustre Filesystems</h3>
-<p>(source <a class="external-link" href="http://www.nas.nasa.gov/" target="_self" title="">http://www.nas.nasa.gov</a>)</p>
+<p>(source <a class="external-link" href="http://www.nas.nasa.gov" target="_self" title="">http://www.nas.nasa.gov</a>)</p>
<p>A user file on the Lustre filesystem can be divided into multiple chunks (stripes) and stored across a subset of the object storage targets (OSTs) (disks). The stripes are distributed among the OSTs in a round-robin fashion to ensure load balancing.</p>
<p>When a client (a <span class="glossaryItem">compute <span class="glossaryItem">node</span></span> from your job) needs to create or access a file, the client queries the metadata server (<span class="glossaryItem">MDS</span>) and the metadata target (<span class="glossaryItem">MDT</span>) for the layout and location of the <a href="http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping">file's stripes</a>. Once the file is opened and the client obtains the striping information, the <span class="glossaryItem">MDS</span> is no longer involved in the file I/O process. The client interacts directly with the object storage servers (OSSes) and OSTs to perform I/O operations such as locking, disk allocation, storage, and retrieval.</p>
<p>If multiple clients try to read and write the same part of a file at the same time, the Lustre distributed lock manager enforces coherency so that all clients see consistent results.</p>
@@ -305,7 +302,7 @@
<p>The HOME filesystem is mounted in directory /home. Users home directories /home/username reside on this filesystem. Accessible capacity is 320TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 250GB per user. <span>If 250GB should prove as insufficient for particular user, please contact</span>Â <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">support</a>, the quota may be lifted upon request.</p>
<p class="callout">The HOME filesystem is intended for preparation, evaluation, processing and storage of data generated by active Projects.</p>
<p>The HOME filesystem should not be used to archive data of past Projects or other unrelated data.</p>
-<p>The files on HOME filesystem will not be deleted until end of the <a target="_self" title="" class="internal-link" href="../../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html">users lifecycle</a>.</p>
+<p>The files on HOME filesystem will not be deleted until end of the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials">users lifecycle</a>.</p>
<p class=" ">The filesystem is backed up, such that it can be restored in case of catasthropic failure resulting in significant data loss. This backup however is not intended to restore old versions of user data or to restore (accidentaly) deleted files. </p>
<p class=" ">The HOME filesystem is realized as Lustre parallel filesystem and is available on all login and computational nodes. <br />Default stripe size is 1MB, stripe count is 1. There are 22 OSTs dedicated for the HOME filesystem.</p>
<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
@@ -613,7 +610,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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@@ -629,7 +626,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -645,7 +642,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -661,7 +658,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -677,7 +674,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -693,7 +690,7 @@
- <a title="" class="state-published contenttype-document" href="../hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -709,7 +706,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -725,7 +722,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -741,7 +738,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -757,7 +754,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -773,7 +770,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="../storage-1.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -789,7 +786,7 @@
- <a title="" class="state-published contenttype-document" href="cesnet-data-storage.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage">
<span>CESNET Data Storage</span>
</a>
@@ -814,7 +811,7 @@
- <a title="" class="state-published contenttype-document" href="../network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -830,10 +827,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -849,7 +846,7 @@
- <a title="" class="state-published contenttype-document" href="../remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -865,7 +862,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -890,7 +887,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -906,7 +903,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -922,7 +919,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -961,14 +958,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -990,12 +987,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1011,7 +1008,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/anselm-cluster-documentation/storage-1/storage by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:03 GMT -->
</html>
diff --git a/anselm-cluster-documentation/storage-1/storage.md b/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.md
similarity index 77%
rename from anselm-cluster-documentation/storage-1/storage.md
rename to docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.md
index 95c85a5583e29a2939ffa012a9de9bfbf9c24e26..8fca8932e4dd28e96ea3b96c0c2383987a62c404 100644
--- a/anselm-cluster-documentation/storage-1/storage.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.md
@@ -1,3 +1,6 @@
+Storage
+=======
+
There are two main shared file systems on Anselm cluster, the
[HOME](#home) and [SCRATCH](#scratch). All
login and compute nodes may access same data on shared filesystems.
@@ -8,8 +11,8 @@ Archiving
Please don't use shared filesystems as a backup for large amount of data
or long-term archiving mean. The academic staff and students of research
institutions in the Czech Republic can use [CESNET storage
-service](cesnet-data-storage.html), which is available
-via SSHFS.
+service](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage),
+which is available via SSHFS.
Shared Filesystems
------------------
Anselm computer provides two main shared filesystems, the [HOME
@@ -20,21 +23,20 @@ are accessible via the Infiniband network. Extended ACLs are provided on
both Lustre filesystems for the purpose of sharing data with other users
using fine-grained control.
### Understanding the Lustre Filesystems
-(source
-[http//www.nas.nasa.gov](http//www.nas.nasa.gov/))
+(source <http://www.nas.nasa.gov>)
A user file on the Lustre filesystem can be divided into multiple chunks
(stripes) and stored across a subset of the object storage targets
(OSTs) (disks). The stripes are distributed among the OSTs in a
round-robin fashion to ensure load balancing.
-When a client (a compute
-class="glossaryItem">node from your job) needs to create
-or access a file, the client queries the metadata server (
-class="glossaryItem">MDS) and the metadata target (
-class="glossaryItem">MDT) for the layout and location of the
+When a client (a <span class="glossaryItem">compute <span
+class="glossaryItem">node</span></span> from your job) needs to create
+or access a file, the client queries the metadata server (<span
+class="glossaryItem">MDS</span>) and the metadata target (<span
+class="glossaryItem">MDT</span>) for the layout and location of the
[file's
-stripes](http//www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping).
+stripes](http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping).
Once the file is opened and the client obtains the striping information,
-the MDS is no longer involved in the
+the <span class="glossaryItem">MDS</span> is no longer involved in the
file I/O process. The client interacts directly with the object storage
servers (OSSes) and OSTs to perform I/O operations such as locking, disk
allocation, storage, and retrieval.
@@ -43,16 +45,16 @@ same time, the Lustre distributed lock manager enforces coherency so
that all clients see consistent results.
There is default stripe configuration for Anselm Lustre filesystems.
However, users can set the following stripe parameters for their own
-directories or files to get optimum I/O performance
-1. stripe_size the size of the chunk in bytes; specify with k, m, or
+directories or files to get optimum I/O performance:
+1. stripe_sizethe size of the chunk in bytes; specify with k, m, or
g to use units of KB, MB, or GB, respectively; the size must be an
even multiple of 65,536 bytes; default is 1MB for all Anselm Lustre
filesystems
2. stripe_count the number of OSTs to stripe across; default is 1 for
Anselm Lustre filesystems one can specify -1 to use all OSTs in
the filesystem.
-3. stripe_offset The index of the
- class="glossaryItem">OST where the first stripe is to be
+3. stripe_offset The index of the <span
+ class="glossaryItem">OST</span> where the first stripe is to be
placed; default is -1 which results in random selection; using a
non-default value is NOT recommended.
Â
@@ -66,15 +68,15 @@ access patterns.Â
$ lfs getstripe dir|filename
$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir|filename
```
-Example
+Example:
``` {.prettyprint .lang-sh}
$ lfs getstripe /scratch/username/
/scratch/username/
-stripe_count 1 stripe_size 1048576 stripe_offset -1
+stripe_count 1 stripe_size 1048576 stripe_offset -1
$ lfs setstripe -c -1 /scratch/username/
$ lfs getstripe /scratch/username/
/scratch/username/
-stripe_count 10 stripe_size 1048576 stripe_offset -1
+stripe_count 10 stripe_size 1048576 stripe_offset -1
```
In this example, we view current stripe setting of the
/scratch/username/ directory. The stripe count is changed to all OSTs,
@@ -109,30 +111,31 @@ part of a file. However, it can be counterproductive in some cases if it
does not match your I/O pattern. The choice of stripe size has no effect
on a single-stripe file.
Read more on
+<http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html>
### Lustre on Anselm
The architecture of Lustre on Anselm is composed of two metadata
servers (MDS) and four data/object storage servers (OSS). Two object
storage servers are used for file system HOME and another two object
storage servers are used for file system SCRATCH.
-Configuration of the storages
-- HOME Lustre object storage
-
+<span class="emphasis">Configuration of the storages</span>
+- <span class="emphasis">HOME Lustre object storage</span>
+ <div class="itemizedlist">
- One disk array NetApp E5400
- 22 OSTs
- 227 2TB NL-SAS 7.2krpm disks
- 22 groups of 10 disks in RAID6 (8+2)
- 7 hot-spare disks
-- SCRATCH Lustre object storage
-
+- <span class="emphasis">SCRATCH Lustre object storage</span>
+ <div class="itemizedlist">
- Two disk arrays NetApp E5400
- 10 OSTs
- 106 2TB NL-SAS 7.2krpm disks
- 10 groups of 10 disks in RAID6 (8+2)
- 6 hot-spare disks
-- Lustre metadata storage
-
+- <span class="emphasis">Lustre metadata storage</span>
+ <div class="itemizedlist">
- One disk array NetApp E2600
- 12 300GB SAS 15krpm disks
- 2 groups of 5 disks in RAID5
@@ -142,16 +145,16 @@ Configuration of the storages
The HOME filesystem is mounted in directory /home. Users home
directories /home/username reside on this filesystem. Accessible
capacity is 320TB, shared among all users. Individual users are
-restricted by filesystem usage quotas, set to 250GB per user. If
+restricted by filesystem usage quotas, set to 250GB per user. <span>If
250GB should prove as insufficient for particular user, please
-contact [support](https//support.it4i.cz/rt),
+contact</span>Â [support](https://support.it4i.cz/rt),
the quota may be lifted upon request.
The HOME filesystem is intended for preparation, evaluation, processing
and storage of data generated by active Projects.
The HOME filesystem should not be used to archive data of past Projects
or other unrelated data.
The files on HOME filesystem will not be deleted until end of the [users
-lifecycle](../../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html).
+lifecycle](https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials).
The filesystem is backed up, such that it can be restored in case ofÂ
catasthropic failure resulting in significant data loss. This backup
however is not intended to restore old versions of user data or to
@@ -183,19 +186,17 @@ freely create subdirectories and files on the filesystem. Accessible
capacity is 146TB, shared among all users. Individual users are
restricted by filesystem usage quotas, set to 100TB per user. The
purpose of this quota is to prevent runaway programs from filling the
-entire filesystem and deny service to other users. If 100TB should
+entire filesystem and deny service to other users. <span>If 100TB should
prove as insufficient for particular user, please contact
-[support](https//support.it4i.cz/rt), the quota may be
-lifted upon request.Â
+[support](https://support.it4i.cz/rt), the quota may be
+lifted upon request. </span>
The Scratch filesystem is intended for temporary scratch data generated
during the calculation as well as for high performance access to input
and output files. All I/O intensive jobs must use the SCRATCH filesystem
as their working directory.
-
Users are advised to save the necessary data from the SCRATCH filesystem
to HOME filesystem after the calculations and clean up the scratch
files.
-
Files on the SCRATCH filesystem that are **not accessed for more than 90
days** will be automatically **deleted**.
The SCRATCH filesystem is realized as Lustre parallel filesystem and is
@@ -219,31 +220,31 @@ Default stripe count
1
Number of OSTs
10
-### Disk usage and quota commands
-User quotas on the file systems can be checked and reviewed using
-following command
+### <span>Disk usage and quota commands</span>
+<span>User quotas on the file systems can be checked and reviewed using
+following command:</span>
``` {.prettyprint .lang-sh}
$ lfs quota dir
```
-Example for Lustre HOME directory
+Example for Lustre HOME directory:
``` {.prettyprint .lang-sh}
$ lfs quota /home
-Disk quotas for user user001 (uid 1234)
+Disk quotas for user user001 (uid 1234):
Filesystem kbytes quota limit grace files quota limit grace
/home 300096 0 250000000 - 2102 0 500000 -
-Disk quotas for group user001 (gid 1234)
+Disk quotas for group user001 (gid 1234):
Filesystem kbytes quota limit grace files quota limit grace
/home 300096 0 0 - 2102 0 0 -
```
In this example, we view current quota size limit of 250GB and 300MB
currently used by user001.
-Example for Lustre SCRATCH directory
+Example for Lustre SCRATCH directory:
``` {.prettyprint .lang-sh}
$ lfs quota /scratch
-Disk quotas for user user001 (uid 1234)
+Disk quotas for user user001 (uid 1234):
Filesystem kbytes quota limit grace files quota limit grace
 /scratch    8    0 100000000000    -    3    0    0    -
-Disk quotas for group user001 (gid 1234)
+Disk quotas for group user001 (gid 1234):
Filesystem kbytes quota limit grace files quota limit grace
/scratch    8    0    0    -    3    0    0    -
```
@@ -255,7 +256,7 @@ can use following command to find out.
``` {.prettyprint .lang-sh}
$ du -hs dir
```
-Example for your HOME directory
+Example for your HOME directory:
``` {.prettyprint .lang-sh}
$ cd /home
$ du -hs * .[a-zA-z0-9]* | grep -E "[0-9]*G|[0-9]*M" | sort -hr
@@ -269,9 +270,8 @@ This will list all directories which are having MegaBytes or GigaBytes
of consumed space in your actual (in this example HOME) directory. List
is sorted in descending order from largest to smallest
files/directories.
-
-To have a better understanding of previous commands, you can read
-manpages.
+<span>To have a better understanding of previous commands, you can read
+manpages.</span>
``` {.prettyprint .lang-sh}
$ man lfs
```
@@ -291,33 +291,33 @@ manner. Below, we create a directory and allow a specific user access.
[vop999@login1.anselm ~]$ umask 027
[vop999@login1.anselm ~]$ mkdir test
[vop999@login1.anselm ~]$ ls -ld test
-drwxr-x--- 2 vop999 vop999 4096 Nov 5 1417 test
+drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.anselm ~]$ getfacl test
-# file test
-# owner vop999
-# group vop999
-userrwx
-groupr-x
-other---
-[vop999@login1.anselm ~]$ setfacl -m userjohnsmrwx test
+# filetest
+# ownervop999
+# groupvop999
+user::rwx
+group::r-x
+other::---
+[vop999@login1.anselm ~]$ setfacl -m user:johnsm:rwx test
[vop999@login1.anselm ~]$ ls -ld test
-drwxrwx---+ 2 vop999 vop999 4096 Nov 5 1417 test
+drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.anselm ~]$ getfacl test
-# file test
-# owner vop999
-# group vop999
-userrwx
-userjohnsmrwx
-groupr-x
-maskrwx
-other---
+# filetest
+# ownervop999
+# groupvop999
+user::rwx
+user:johnsm:rwx
+group::r-x
+mask::rwx
+other::---
```
Default ACL mechanism can be used to replace setuid/setgid permissions
on directories. Setting a default ACL on a directory (-d flag to
setfacl) will cause the ACL permissions to be inherited by any newly
created file or subdirectory within the directory. Refer to this page
-for more information on Linux ACL
-[http//www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html ](http//www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html)
+for more information on Linux ACL:
+[http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html ](http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html)
Local Filesystems
-----------------
### Local Scratch
@@ -368,9 +368,9 @@ immediately after the calculation end. Users should take care to save
the output data from within the jobscript.
RAM disk
Mountpoint
-/ramdisk
+<span class="monospace">/ramdisk</span>
Accesspoint
-/ramdisk/$PBS_JOBID
+<span class="monospace">/ramdisk/$PBS_JOBID</span>
Capacity
60GB at compute nodes without accelerator
90GB at compute nodes with accelerator
@@ -388,27 +388,10 @@ files in /tmp directory are automatically purged.
**
----------
Mountpoint Usage Protocol Net Capacity Throughput Limitations Access Services
- ------------------------------------------ --------------------------- ---------- ---------------- ------------ ------------- ------------------------- -----------------------------
- /home home directory Lustre 320 TiB 2 GB/s Quota 250GB Compute and login nodes backed up
- /scratch cluster shared jobs' data Lustre 146 TiB 6 GB/s Quota 100TB Compute and login nodes files older 90 days removed
- /lscratch node local jobs' data local 330 GB 100 MB/s none Compute nodes purged after job ends
- /ramdisk node local jobs' data local 60, 90, 500 GB 5-50 GB/s none Compute nodes purged after job ends
- /tmp local temporary files local 100 MB/s none Compute and login nodes auto purged
+ ------------------- ---- ---------- ---------------- ------------ ------------- -- ------
+ <span class="monospace">/home</span> home directory Lustre 320 TiB 2 GB/s Quota 250GB Compute and login nodes backed up
+ <span class="monospace">/scratch</span> cluster shared jobs' data Lustre 146 TiB 6 GB/s Quota 100TB Compute and login nodes files older 90 days removed
+ <span class="monospace">/lscratch</span> node local jobs' data local 330 GB 100 MB/s none Compute nodes purged after job ends
+ <span class="monospace">/ramdisk</span> node local jobs' data local 60, 90, 500 GB 5-50 GB/s none Compute nodes purged after job ends
+ <span class="monospace">/tmp</span> local temporary files local 100 MB/s none Compute and login nodes auto purged
Â
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+ <p>There are two main shared file systems on Anselm cluster, the <a class="anchor-link" href="#home" target="_self" title="">HOME</a> and <a class="anchor-link" href="#scratch" target="_self" title="">SCRATCH</a>. All login and compute nodes may access same data on shared filesystems. Compute nodes are also equipped with local (non-shared) scratch, ramdisk and tmp filesystems.</p>
+<h2 class=" ">Archiving</h2>
+<p>Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage">CESNET storage service</a>, which is available via SSHFS.</p>
+<h2 class=" ">Shared Filesystems</h2>
+<p class=" ">Anselm computer provides two main shared filesystems, the <a class="anchor-link" href="#home" target="_self" title="">HOME filesystem</a> and the <a class="anchor-link" href="#scratch" target="_self" title="">SCRATCH filesystem</a>. Both HOME and SCRATCH filesystems are realized as a parallel Lustre filesystem. Both shared file systems are accessible via the Infiniband network. Extended ACLs are provided on both Lustre filesystems for the purpose of sharing data with other users using fine-grained control.</p>
+<h3 class=" ">Understanding the Lustre Filesystems</h3>
+<p>(source <a class="external-link" href="http://www.nas.nasa.gov" target="_self" title="">http://www.nas.nasa.gov</a>)</p>
+<p>A user file on the Lustre filesystem can be divided into multiple chunks (stripes) and stored across a subset of the object storage targets (OSTs) (disks). The stripes are distributed among the OSTs in a round-robin fashion to ensure load balancing.</p>
+<p>When a client (a <span class="glossaryItem">compute <span class="glossaryItem">node</span></span> from your job) needs to create or access a file, the client queries the metadata server (<span class="glossaryItem">MDS</span>) and the metadata target (<span class="glossaryItem">MDT</span>) for the layout and location of the <a href="http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping">file's stripes</a>. Once the file is opened and the client obtains the striping information, the <span class="glossaryItem">MDS</span> is no longer involved in the file I/O process. The client interacts directly with the object storage servers (OSSes) and OSTs to perform I/O operations such as locking, disk allocation, storage, and retrieval.</p>
+<p>If multiple clients try to read and write the same part of a file at the same time, the Lustre distributed lock manager enforces coherency so that all clients see consistent results.</p>
+<p>There is default stripe configuration for Anselm Lustre filesystems. However, users can set the following stripe parameters for their own directories or files to get optimum I/O performance:</p>
+<ol><ol>
+<li>stripe_size: the size of the chunk in bytes; specify with k, m, or g to use units of KB, MB, or GB, respectively; the size must be an even multiple of 65,536 bytes; default is 1MB for all Anselm Lustre filesystems</li>
+<li>stripe_count the number of OSTs to stripe across; default is 1 for Anselm Lustre filesystems one can specify -1 to use all OSTs in the filesystem.</li>
+<li>stripe_offset The index of the <span class="glossaryItem">OST</span> where the first stripe is to be placed; default is -1 which results in random selection; using a non-default value is NOT recommended.</li>
+</ol></ol>
+<p class=" ">Â </p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<p class=" ">Use the lfs getstripe for getting the stripe parameters. Use the lfs setstripe command for setting the stripe parameters to get optimal I/O performance The correct stripe setting depends on your needs and file access patterns. </p>
+<pre class="prettyprint lang-sh"><code>$ lfs getstripe dir|filename <br />$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir|filename </code></pre>
+<p>Example:</p>
+<pre class="prettyprint lang-sh">$ lfs getstripe /scratch/username/<br />/scratch/username/<br />stripe_count: 1 stripe_size: 1048576 stripe_offset: -1<br /><br />$ lfs setstripe -c -1 /scratch/username/<br />$ lfs getstripe /scratch/username/<br />/scratch/username/<br />stripe_count: 10 stripe_size: 1048576 stripe_offset: -1</pre>
+<p>In this example, we view current stripe setting of the /scratch/username/ directory. The stripe count is changed to all OSTs, and verified. All files written to this directory will be striped over 10 OSTs</p>
+<p>Use lfs check OSTs to see the number and status of active OSTs for each filesystem on Anselm. Learn more by reading the man page</p>
+<pre class="prettyprint lang-sh">$ lfs check osts<br />$ man lfs</pre>
+<h3 class=" ">Hints on Lustre Stripping</h3>
+<p class="callout">Increase the stripe_count for parallel I/O to the same file.</p>
+<p>When multiple processes are writing blocks of data to the same file in parallel, the I/O performance for large files will improve when the stripe_count is set to a larger value. The stripe count sets the number of OSTs the file will be written to. By default, the stripe count is set to 1. While this default setting provides for efficient access of metadata (for example to support the ls -l command), large files should use stripe counts of greater than 1. This will increase the aggregate I/O bandwidth by using multiple OSTs in parallel instead of just one. A rule of thumb is to use a stripe count approximately equal to the number of gigabytes in the file.</p>
+<p>Another good practice is to make the stripe count be an integral factor of the number of processes performing the write in parallel, so that you achieve load balance among the OSTs. For example, set the stripe count to 16 instead of 15 when you have 64 processes performing the writes.</p>
+<p class="callout">Using a large stripe size can improve performance when accessing very large files</p>
+<p>Large stripe size allows each client to have exclusive access to its own part of a file. However, it can be counterproductive in some cases if it does not match your I/O pattern. The choice of stripe size has no effect on a single-stripe file.</p>
+<p>Read more on <a class="external-link" href="http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html" target="_self" title="">http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html</a></p>
+<h3 class=" ">Lustre on Anselm</h3>
+<p>The architecture of Lustre on Anselm is composed of two metadata servers (MDS) and four data/object storage servers (OSS). Two object storage servers are used for file system HOME and another two object storage servers are used for file system SCRATCH.</p>
+<p class=" "><span class="emphasis">Configuration of the storages</span></p>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem"><span class="emphasis">HOME Lustre object storage</span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">One disk array NetApp E5400</li>
+<li class="listitem">22 OSTs</li>
+<li class="listitem">227 2TB NL-SAS 7.2krpm disks</li>
+<li class="listitem">22 groups of 10 disks in RAID6 (8+2)</li>
+<li class="listitem">7 hot-spare disks</li>
+</ul>
+</div>
+</li>
+<li class="listitem"><span class="emphasis">SCRATCH Lustre object storage</span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">Two disk arrays NetApp E5400</li>
+<li class="listitem">10 OSTs</li>
+<li class="listitem">106 2TB NL-SAS 7.2krpm disks</li>
+<li class="listitem">10 groups of 10 disks in RAID6 (8+2)</li>
+<li class="listitem">6 hot-spare disks</li>
+</ul>
+</div>
+</li>
+<li class="listitem"><span class="emphasis">Lustre metadata storage</span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">One disk array NetApp E2600</li>
+<li class="listitem">12 300GB SAS 15krpm disks</li>
+<li class="listitem">2 groups of 5 disks in RAID5</li>
+<li class="listitem">2 hot-spare disks</li>
+</ul>
+</div>
+</li>
+</ul>
+</div>
+<h3 class=" "><a name="home"></a><a name="home"></a>HOME</h3>
+<p>The HOME filesystem is mounted in directory /home. Users home directories /home/username reside on this filesystem. Accessible capacity is 320TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 250GB per user. <span>If 250GB should prove as insufficient for particular user, please contact</span>Â <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">support</a>, the quota may be lifted upon request.</p>
+<p class="callout">The HOME filesystem is intended for preparation, evaluation, processing and storage of data generated by active Projects.</p>
+<p>The HOME filesystem should not be used to archive data of past Projects or other unrelated data.</p>
+<p>The files on HOME filesystem will not be deleted until end of the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials">users lifecycle</a>.</p>
+<p class=" ">The filesystem is backed up, such that it can be restored in case of catasthropic failure resulting in significant data loss. This backup however is not intended to restore old versions of user data or to restore (accidentaly) deleted files. </p>
+<p class=" ">The HOME filesystem is realized as Lustre parallel filesystem and is available on all login and computational nodes. <br />Default stripe size is 1MB, stripe count is 1. There are 22 OSTs dedicated for the HOME filesystem.</p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">HOME filesystem</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td>/home</td>
+</tr>
+<tr class="odd">
+<td>Capacity</td>
+<td>320TB</td>
+</tr>
+<tr class="even">
+<td>Throughput</td>
+<td>2GB/s</td>
+</tr>
+<tr class="odd">
+<td>User quota</td>
+<td>250GB</td>
+</tr>
+<tr class="even">
+<td>Default stripe size</td>
+<td>1MB</td>
+</tr>
+<tr class="odd">
+<td>Default stripe count</td>
+<td>1</td>
+</tr>
+<tr class="even">
+<td>Number of OSTs</td>
+<td>22</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" "><a name="scratch"></a><a name="scratch"></a>SCRATCH</h3>
+<p>The SCRATCH filesystem is mounted in directory /scratch. Users may freely create subdirectories and files on the filesystem. Accessible capacity is 146TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 100TB per user. The purpose of this quota is to prevent runaway programs from filling the entire filesystem and deny service to other users. <span>If 100TB should prove as insufficient for particular user, please contact <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">support</a>, the quota may be lifted upon request. </span></p>
+<p class="callout">The Scratch filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs must use the SCRATCH filesystem as their working directory.<br /><br />Users are advised to save the necessary data from the SCRATCH filesystem to HOME filesystem after the calculations and clean up the scratch files.<br /><br />Files on the SCRATCH filesystem that are <strong>not accessed for more than 90 days</strong> will be automatically <strong>deleted</strong>.</p>
+<p>The SCRATCH filesystem is realized as Lustre parallel filesystem and is available from all login and computational nodes. <br />Default stripe size is 1MB, stripe count is 1. There are 10 OSTs dedicated for the SCRATCH filesystem.</p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">SCRATCH filesystem</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td>/scratch</td>
+</tr>
+<tr class="odd">
+<td>Capacity</td>
+<td>146TB</td>
+</tr>
+<tr class="even">
+<td>Throughput</td>
+<td>6GB/s</td>
+</tr>
+<tr class="odd">
+<td>User quota</td>
+<td>100TB</td>
+</tr>
+<tr class="even">
+<td>Default stripe size</td>
+<td>1MB</td>
+</tr>
+<tr class="odd">
+<td>Default stripe count</td>
+<td>1</td>
+</tr>
+<tr class="even">
+<td>Number of OSTs</td>
+<td>10</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" "><span>Disk usage and quota commands</span></h3>
+<p><span>User quotas on the file systems can be checked and reviewed using following command:</span></p>
+<pre class="prettyprint lang-sh">$ lfs quota dir</pre>
+<p>Example for Lustre HOME directory:</p>
+<pre class="prettyprint lang-sh">$ lfs quota /home<br />Disk quotas for user user001 (uid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br /> /home 300096 0 250000000 - 2102 0 500000 -<br />Disk quotas for group user001 (gid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br /> /home 300096 0 0 - 2102 0 0 -</pre>
+<p>In this example, we view current quota size limit of 250GB and 300MB currently used by user001.</p>
+<p>Example for Lustre SCRATCH directory:</p>
+<pre class="prettyprint lang-sh">$ lfs quota /scratch<br />Disk quotas for user user001 (uid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br />  /scratch    8    0 100000000000    -    3    0    0    -<br />Disk quotas for gro<span>up user001 (gid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br /> /scratch    8    0    0    -    3    0    0    -<br /></span></pre>
+<p>In this example, we view current quota size limit of 100TB and 8KB currently used by user001.</p>
+<p>Â </p>
+<p>To have a better understanding of where the space is exactly used, you can use following command to find out.</p>
+<pre class="prettyprint lang-sh">$ du -hs dir</pre>
+<p>Example for your HOME directory:</p>
+<pre class="prettyprint lang-sh">$ cd /home<br />$ du -hs * .[a-zA-z0-9]* | grep -E "[0-9]*G|[0-9]*M" | sort -hr<br />258M cuda-samples<br />15M .cache<br />13M .mozilla<br />5,5M .eclipse<br />2,7M .idb_13.0_linux_intel64_app</pre>
+<p>This will list all directories which are having MegaBytes or GigaBytes of consumed space in your actual (in this example HOME) directory. List is sorted in descending order from largest to smallest files/directories.</p>
+<p><br /> <span>To have a better understanding of previous commands, you can read manpages.</span></p>
+<pre class="prettyprint lang-sh">$ man lfs</pre>
+<pre class="prettyprint lang-sh">$ man du </pre>
+<h3 class=" ">Extended ACLs</h3>
+<p class=" ">Extended ACLs provide another security mechanism beside the standard POSIX ACLs which are defined by three entries (for owner/group/others). Extended ACLs have more than the three basic entries. In addition, they also contain a mask entry and may contain any number of named user and named group entries.</p>
+<p class=" ">ACLs on a Lustre file system work exactly like ACLs on any Linux file system. They are manipulated with the standard tools in the standard manner. Below, we create a directory and allow a specific user access.</p>
+<pre class="prettyprint lang-sh">[vop999@login1.anselm ~]$ umask 027<br />[vop999@login1.anselm ~]$ mkdir test<br />[vop999@login1.anselm ~]$ ls -ld test<br />drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test<br />[vop999@login1.anselm ~]$ getfacl test<br /># file: test<br /># owner: vop999<br /># group: vop999<br />user::rwx<br />group::r-x<br />other::---<br /><br />[vop999@login1.anselm ~]$ setfacl -m user:johnsm:rwx test<br />[vop999@login1.anselm ~]$ ls -ld test<br />drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test<br />[vop999@login1.anselm ~]$ getfacl test<br /># file: test<br /># owner: vop999<br /># group: vop999<br />user::rwx<br />user:johnsm:rwx<br />group::r-x<br />mask::rwx<br />other::---</pre>
+<p class=" ">Default ACL mechanism can be used to replace setuid/setgid permissions on directories. Setting a default ACL on a directory (-d flag to setfacl) will cause the ACL permissions to be inherited by any newly created file or subdirectory within the directory. Refer to this page for more information on Linux ACL:</p>
+<p class=" "><a class="external-link" href="http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html" target="_self" title="">http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html </a></p>
+<h2 class=" ">Local Filesystems</h2>
+<h3 class=" ">Local Scratch</h3>
+<p>Every computational node is equipped with 330GB local scratch disk.</p>
+<p class="callout">Use local scratch in case you need to access large amount of small files during your calculation.</p>
+<p><a name="LocalScratch"></a>The local scratch disk is mounted as /lscratch and is accessible to user at /lscratch/$PBS_JOBID directory.</p>
+<p class=" ">The local scratch filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs that access large number of small files within the calculation must use the local scratch filesystem as their working directory. This is required for performance reasons, as frequent access to number of small files may overload the metadata servers (MDS) of the Lustre filesystem.</p>
+<p class="callout">The local scratch directory /lscratch/$PBS_JOBID will be deleted immediately after the calculation end. Users should take care to save the output data from within the jobscript.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">local SCRATCH filesystem</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td>/lscratch</td>
+</tr>
+<tr class="odd">
+<td>Accesspoint</td>
+<td>/lscratch/$PBS_JOBID</td>
+</tr>
+<tr class="even">
+<td>Capacity</td>
+<td>330GB</td>
+</tr>
+<tr class="odd">
+<td>Throughput</td>
+<td>100MB/s</td>
+</tr>
+<tr class="even">
+<td>User quota</td>
+<td>none</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" ">RAM disk</h3>
+<p>Every computational node is equipped with filesystem realized in memory, so called RAM disk.</p>
+<p class="callout">Use RAM disk in case you need really fast access to your data of limited size during your calculation.<br />Be very careful, use of RAM disk filesystem is at the expense of operational memory.</p>
+<p><a name="LocalScratch"></a>The local RAM disk is mounted as /ramdisk and is accessible to user at /ramdisk/$PBS_JOBID directory.</p>
+<p class=" ">The local RAM disk filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. Size of RAM disk filesystem is limited. Be very careful, use of RAM disk filesystem is at the expense of operational memory. It is not recommended to allocate large amount of memory and use large amount of data in RAM disk filesystem at the same time.</p>
+<p class="callout">The local RAM disk directory /ramdisk/$PBS_JOBID will be deleted immediately after the calculation end. Users should take care to save the output data from within the jobscript.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">RAM disk</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td><span class="monospace">/ramdisk</span></td>
+</tr>
+<tr class="odd">
+<td>Accesspoint</td>
+<td><span class="monospace">/ramdisk/$PBS_JOBID</span></td>
+</tr>
+<tr class="even">
+<td>Capacity</td>
+<td>
+<p>60GB at compute nodes without accelerator</p>
+<p>90GB at compute nodes with accelerator</p>
+<p>500GB at fat nodes</p>
+</td>
+</tr>
+<tr class="odd">
+<td>Throughput</td>
+<td>
+<p>over 1.5 GB/s write, over 5 GB/s read, single thread<br />over 10 GB/s write, over 50 GB/s read, 16 threads</p>
+</td>
+</tr>
+<tr class="even">
+<td>User quota</td>
+<td>none</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" ">tmp</h3>
+<p>Each node is equipped with local /tmp directory of few GB capacity. The /tmp directory should be used to work with small temporary files. Old files in /tmp directory are automatically purged.</p>
+<div class="table">
+<h2 class=" "><strong>Summary<br /></strong></h2>
+<div class="table-contents">
+<table class="listing" summary="Best usage of the file systems"><colgroup><col><col><col><col><col><col><col><col></colgroup>
+<thead>
+<tr><th align="center" style="text-align: center; ">Mountpoint</th><th align="center" style="text-align: center; ">Usage</th><th align="center" style="text-align: center; ">Protocol</th><th align="center" style="text-align: center; ">Net Capacity</th><th align="center" style="text-align: center; ">Throughput</th><th align="center" style="text-align: center; ">Limitations</th><th align="center" style="text-align: center; ">Access</th><th align="center" style="text-align: center; ">Services</th></tr>
+</thead>
+<tbody>
+<tr class="even">
+<td><span class="monospace">/home</span></td>
+<td align="center">home directory</td>
+<td align="center">Lustre</td>
+<td align="center">320 TiB</td>
+<td align="center">2 GB/s</td>
+<td align="center">Quota 250GB</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">backed up</td>
+</tr>
+<tr class="odd">
+<td><span class="monospace">/scratch</span></td>
+<td align="center">cluster shared jobs' data</td>
+<td align="center">Lustre</td>
+<td align="center">146 TiB</td>
+<td align="center">6 GB/s</td>
+<td align="center">Quota 100TB</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">files older 90 days removed</td>
+</tr>
+<tr class="even">
+<td><span class="monospace">/lscratch</span></td>
+<td align="center">node local jobs' data</td>
+<td align="center">local</td>
+<td align="center">330 GB</td>
+<td align="center">100 MB/s</td>
+<td align="center">none</td>
+<td align="center">Compute nodes</td>
+<td align="center">purged after job ends</td>
+</tr>
+<tr class="odd">
+<td><span class="monospace">/ramdisk</span></td>
+<td align="center">node local jobs' data</td>
+<td align="center">local</td>
+<td align="center">60, 90, 500 GB</td>
+<td align="center">5-50 GB/s</td>
+<td align="center">none</td>
+<td align="center">Compute nodes</td>
+<td align="center">purged after job ends</td>
+</tr>
+<tr class="even">
+<td><span class="monospace">/tmp</span></td>
+<td align="center">local temporary files</td>
+<td align="center">local</td>
+<td align="center"></td>
+<td align="center">100 MB/s</td>
+<td align="center">none</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">auto purged</td>
+</tr>
+</tbody>
+</table>
+</div>
+</div>
+<p>Â </p>
+
+ </div>
+
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
+
+ <span>Network</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-software">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
+
+
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
+
+ <span>Software</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-remote-visualization">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
+
+ <span>Remote visualization service</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-prace">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
+
+ <span>PRACE User Support</span>
+ </a>
+
+
+
+
+</li>
+
+
+
+
+ </ul>
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-links">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
+
+ <span>Links</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-changelog">
+
+
+
+
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
+
+ <span>Changelog</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-pbspro-documentation">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
+
+ <span>PBSPro Documentation</span>
+ </a>
+
+
+
+
+</li>
+
+
+
+
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/storage.md b/docs.it4i.cz/anselm-cluster-documentation/storage.md
new file mode 100644
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@@ -0,0 +1,397 @@
+Storage
+=======
+
+There are two main shared file systems on Anselm cluster, the
+[HOME](#home) and [SCRATCH](#scratch). All
+login and compute nodes may access same data on shared filesystems.
+Compute nodes are also equipped with local (non-shared) scratch, ramdisk
+and tmp filesystems.
+Archiving
+---------
+Please don't use shared filesystems as a backup for large amount of data
+or long-term archiving mean. The academic staff and students of research
+institutions in the Czech Republic can use [CESNET storage
+service](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage),
+which is available via SSHFS.
+Shared Filesystems
+------------------
+Anselm computer provides two main shared filesystems, the [HOME
+filesystem](#home) and the [SCRATCH
+filesystem](#scratch). Both HOME and SCRATCH filesystems
+are realized as a parallel Lustre filesystem. Both shared file systems
+are accessible via the Infiniband network. Extended ACLs are provided on
+both Lustre filesystems for the purpose of sharing data with other users
+using fine-grained control.
+### Understanding the Lustre Filesystems
+(source <http://www.nas.nasa.gov>)
+A user file on the Lustre filesystem can be divided into multiple chunks
+(stripes) and stored across a subset of the object storage targets
+(OSTs) (disks). The stripes are distributed among the OSTs in a
+round-robin fashion to ensure load balancing.
+When a client (a <span class="glossaryItem">compute <span
+class="glossaryItem">node</span></span> from your job) needs to create
+or access a file, the client queries the metadata server (<span
+class="glossaryItem">MDS</span>) and the metadata target (<span
+class="glossaryItem">MDT</span>) for the layout and location of the
+[file's
+stripes](http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping).
+Once the file is opened and the client obtains the striping information,
+the <span class="glossaryItem">MDS</span> is no longer involved in the
+file I/O process. The client interacts directly with the object storage
+servers (OSSes) and OSTs to perform I/O operations such as locking, disk
+allocation, storage, and retrieval.
+If multiple clients try to read and write the same part of a file at the
+same time, the Lustre distributed lock manager enforces coherency so
+that all clients see consistent results.
+There is default stripe configuration for Anselm Lustre filesystems.
+However, users can set the following stripe parameters for their own
+directories or files to get optimum I/O performance:
+1. stripe_sizethe size of the chunk in bytes; specify with k, m, or
+ g to use units of KB, MB, or GB, respectively; the size must be an
+ even multiple of 65,536 bytes; default is 1MB for all Anselm Lustre
+ filesystems
+2. stripe_count the number of OSTs to stripe across; default is 1 for
+ Anselm Lustre filesystems one can specify -1 to use all OSTs in
+ the filesystem.
+3. stripe_offset The index of the <span
+ class="glossaryItem">OST</span> where the first stripe is to be
+ placed; default is -1 which results in random selection; using a
+ non-default value is NOT recommended.
+Â
+Setting stripe size and stripe count correctly for your needs may
+significantly impact the I/O performance you experience.
+Use the lfs getstripe for getting the stripe parameters. Use the lfs
+setstripe command for setting the stripe parameters to get optimal I/O
+performance The correct stripe setting depends on your needs and file
+access patterns.Â
+``` {.prettyprint .lang-sh}
+$ lfs getstripe dir|filename
+$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir|filename
+```
+Example:
+``` {.prettyprint .lang-sh}
+$ lfs getstripe /scratch/username/
+/scratch/username/
+stripe_count 1 stripe_size 1048576 stripe_offset -1
+$ lfs setstripe -c -1 /scratch/username/
+$ lfs getstripe /scratch/username/
+/scratch/username/
+stripe_count 10 stripe_size 1048576 stripe_offset -1
+```
+In this example, we view current stripe setting of the
+/scratch/username/ directory. The stripe count is changed to all OSTs,
+and verified. All files written to this directory will be striped over
+10 OSTs
+Use lfs check OSTs to see the number and status of active OSTs for each
+filesystem on Anselm. Learn more by reading the man page
+``` {.prettyprint .lang-sh}
+$ lfs check osts
+$ man lfs
+```
+### Hints on Lustre Stripping
+Increase the stripe_count for parallel I/O to the same file.
+When multiple processes are writing blocks of data to the same file in
+parallel, the I/O performance for large files will improve when the
+stripe_count is set to a larger value. The stripe count sets the number
+of OSTs the file will be written to. By default, the stripe count is set
+to 1. While this default setting provides for efficient access of
+metadata (for example to support the ls -l command), large files should
+use stripe counts of greater than 1. This will increase the aggregate
+I/O bandwidth by using multiple OSTs in parallel instead of just one. A
+rule of thumb is to use a stripe count approximately equal to the number
+of gigabytes in the file.
+Another good practice is to make the stripe count be an integral factor
+of the number of processes performing the write in parallel, so that you
+achieve load balance among the OSTs. For example, set the stripe count
+to 16 instead of 15 when you have 64 processes performing the writes.
+Using a large stripe size can improve performance when accessing very
+large files
+Large stripe size allows each client to have exclusive access to its own
+part of a file. However, it can be counterproductive in some cases if it
+does not match your I/O pattern. The choice of stripe size has no effect
+on a single-stripe file.
+Read more on
+<http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html>
+### Lustre on Anselm
+The architecture of Lustre on Anselm is composed of two metadata
+servers (MDS) and four data/object storage servers (OSS). Two object
+storage servers are used for file system HOME and another two object
+storage servers are used for file system SCRATCH.
+<span class="emphasis">Configuration of the storages</span>
+- <span class="emphasis">HOME Lustre object storage</span>
+ <div class="itemizedlist">
+ - One disk array NetApp E5400
+ - 22 OSTs
+ - 227 2TB NL-SAS 7.2krpm disks
+ - 22 groups of 10 disks in RAID6 (8+2)
+ - 7 hot-spare disks
+
+- <span class="emphasis">SCRATCH Lustre object storage</span>
+ <div class="itemizedlist">
+ - Two disk arrays NetApp E5400
+ - 10 OSTs
+ - 106 2TB NL-SAS 7.2krpm disks
+ - 10 groups of 10 disks in RAID6 (8+2)
+ - 6 hot-spare disks
+
+- <span class="emphasis">Lustre metadata storage</span>
+ <div class="itemizedlist">
+ - One disk array NetApp E2600
+ - 12 300GB SAS 15krpm disks
+ - 2 groups of 5 disks in RAID5
+ - 2 hot-spare disks
+
+### []()[]()HOME
+The HOME filesystem is mounted in directory /home. Users home
+directories /home/username reside on this filesystem. Accessible
+capacity is 320TB, shared among all users. Individual users are
+restricted by filesystem usage quotas, set to 250GB per user. <span>If
+250GB should prove as insufficient for particular user, please
+contact</span>Â [support](https://support.it4i.cz/rt),
+the quota may be lifted upon request.
+The HOME filesystem is intended for preparation, evaluation, processing
+and storage of data generated by active Projects.
+The HOME filesystem should not be used to archive data of past Projects
+or other unrelated data.
+The files on HOME filesystem will not be deleted until end of the [users
+lifecycle](https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials).
+The filesystem is backed up, such that it can be restored in case ofÂ
+catasthropic failure resulting in significant data loss. This backup
+however is not intended to restore old versions of user data or to
+restore (accidentaly) deleted files.Â
+The HOME filesystem is realized as Lustre parallel filesystem and is
+available on all login and computational nodes.
+Default stripe size is 1MB, stripe count is 1. There are 22 OSTs
+dedicated for the HOME filesystem.
+Setting stripe size and stripe count correctly for your needs may
+significantly impact the I/O performance you experience.
+HOME filesystem
+Mountpoint
+/home
+Capacity
+320TB
+Throughput
+2GB/s
+User quota
+250GB
+Default stripe size
+1MB
+Default stripe count
+1
+Number of OSTs
+22
+### []()[]()SCRATCH
+The SCRATCH filesystem is mounted in directory /scratch. Users may
+freely create subdirectories and files on the filesystem. Accessible
+capacity is 146TB, shared among all users. Individual users are
+restricted by filesystem usage quotas, set to 100TB per user. The
+purpose of this quota is to prevent runaway programs from filling the
+entire filesystem and deny service to other users. <span>If 100TB should
+prove as insufficient for particular user, please contact
+[support](https://support.it4i.cz/rt), the quota may be
+lifted upon request. </span>
+The Scratch filesystem is intended for temporary scratch data generated
+during the calculation as well as for high performance access to input
+and output files. All I/O intensive jobs must use the SCRATCH filesystem
+as their working directory.
+Users are advised to save the necessary data from the SCRATCH filesystem
+to HOME filesystem after the calculations and clean up the scratch
+files.
+Files on the SCRATCH filesystem that are **not accessed for more than 90
+days** will be automatically **deleted**.
+The SCRATCH filesystem is realized as Lustre parallel filesystem and is
+available from all login and computational nodes.
+Default stripe size is 1MB, stripe count is 1. There are 10 OSTs
+dedicated for the SCRATCH filesystem.
+Setting stripe size and stripe count correctly for your needs may
+significantly impact the I/O performance you experience.
+SCRATCH filesystem
+Mountpoint
+/scratch
+Capacity
+146TB
+Throughput
+6GB/s
+User quota
+100TB
+Default stripe size
+1MB
+Default stripe count
+1
+Number of OSTs
+10
+### <span>Disk usage and quota commands</span>
+<span>User quotas on the file systems can be checked and reviewed using
+following command:</span>
+``` {.prettyprint .lang-sh}
+$ lfs quota dir
+```
+Example for Lustre HOME directory:
+``` {.prettyprint .lang-sh}
+$ lfs quota /home
+Disk quotas for user user001 (uid 1234):
+ Filesystem kbytes quota limit grace files quota limit grace
+ /home 300096 0 250000000 - 2102 0 500000 -
+Disk quotas for group user001 (gid 1234):
+ Filesystem kbytes quota limit grace files quota limit grace
+ /home 300096 0 0 - 2102 0 0 -
+```
+In this example, we view current quota size limit of 250GB and 300MB
+currently used by user001.
+Example for Lustre SCRATCH directory:
+``` {.prettyprint .lang-sh}
+$ lfs quota /scratch
+Disk quotas for user user001 (uid 1234):
+ Filesystem kbytes quota limit grace files quota limit grace
+  /scratch    8    0 100000000000    -    3    0    0    -
+Disk quotas for group user001 (gid 1234):
+ Filesystem kbytes quota limit grace files quota limit grace
+ /scratch    8    0    0    -    3    0    0    -
+```
+In this example, we view current quota size limit of 100TB and 8KB
+currently used by user001.
+Â
+To have a better understanding of where the space is exactly used, you
+can use following command to find out.
+``` {.prettyprint .lang-sh}
+$ du -hs dir
+```
+Example for your HOME directory:
+``` {.prettyprint .lang-sh}
+$ cd /home
+$ du -hs * .[a-zA-z0-9]* | grep -E "[0-9]*G|[0-9]*M" | sort -hr
+258M cuda-samples
+15M .cache
+13M .mozilla
+5,5M .eclipse
+2,7M .idb_13.0_linux_intel64_app
+```
+This will list all directories which are having MegaBytes or GigaBytes
+of consumed space in your actual (in this example HOME) directory. List
+is sorted in descending order from largest to smallest
+files/directories.
+<span>To have a better understanding of previous commands, you can read
+manpages.</span>
+``` {.prettyprint .lang-sh}
+$ man lfs
+```
+``` {.prettyprint .lang-sh}
+$ man du
+```
+### Extended ACLs
+Extended ACLs provide another security mechanism beside the standard
+POSIX ACLs which are defined by three entries (for
+owner/group/others). Extended ACLs have more than the three basic
+entries. In addition, they also contain a mask entry and may contain any
+number of named user and named group entries.
+ACLs on a Lustre file system work exactly like ACLs on any Linux file
+system. They are manipulated with the standard tools in the standard
+manner. Below, we create a directory and allow a specific user access.
+``` {.prettyprint .lang-sh}
+[vop999@login1.anselm ~]$ umask 027
+[vop999@login1.anselm ~]$ mkdir test
+[vop999@login1.anselm ~]$ ls -ld test
+drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test
+[vop999@login1.anselm ~]$ getfacl test
+# filetest
+# ownervop999
+# groupvop999
+user::rwx
+group::r-x
+other::---
+[vop999@login1.anselm ~]$ setfacl -m user:johnsm:rwx test
+[vop999@login1.anselm ~]$ ls -ld test
+drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test
+[vop999@login1.anselm ~]$ getfacl test
+# filetest
+# ownervop999
+# groupvop999
+user::rwx
+user:johnsm:rwx
+group::r-x
+mask::rwx
+other::---
+```
+Default ACL mechanism can be used to replace setuid/setgid permissions
+on directories. Setting a default ACL on a directory (-d flag to
+setfacl) will cause the ACL permissions to be inherited by any newly
+created file or subdirectory within the directory. Refer to this page
+for more information on Linux ACL:
+[http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html ](http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html)
+Local Filesystems
+-----------------
+### Local Scratch
+Every computational node is equipped with 330GB local scratch disk.
+Use local scratch in case you need to access large amount of small files
+during your calculation.
+[]()The local scratch disk is mounted as /lscratch and is accessible to
+user at /lscratch/$PBS_JOBID directory.
+The local scratch filesystem is intended for temporary scratch data
+generated during the calculation as well as for high performance access
+to input and output files. All I/O intensive jobs that access large
+number of small files within the calculation must use the local scratch
+filesystem as their working directory. This is required for performance
+reasons, as frequent access to number of small files may overload the
+metadata servers (MDS) of the Lustre filesystem.
+The local scratch directory /lscratch/$PBS_JOBID will be deleted
+immediately after the calculation end. Users should take care to save
+the output data from within the jobscript.
+local SCRATCH filesystem
+Mountpoint
+/lscratch
+Accesspoint
+/lscratch/$PBS_JOBID
+Capacity
+330GB
+Throughput
+100MB/s
+User quota
+none
+### RAM disk
+Every computational node is equipped with filesystem realized in memory,
+so called RAM disk.
+Use RAM disk in case you need really fast access to your data of limited
+size during your calculation.
+Be very careful, use of RAM disk filesystem is at the expense of
+operational memory.
+[]()The local RAM disk is mounted as /ramdisk and is accessible to user
+at /ramdisk/$PBS_JOBID directory.
+The local RAM disk filesystem is intended for temporary scratch data
+generated during the calculation as well as for high performance access
+to input and output files. Size of RAM disk filesystem is limited. Be
+very careful, use of RAM disk filesystem is at the expense of
+operational memory. It is not recommended to allocate large amount of
+memory and use large amount of data in RAM disk filesystem at the same
+time.
+The local RAM disk directory /ramdisk/$PBS_JOBID will be deleted
+immediately after the calculation end. Users should take care to save
+the output data from within the jobscript.
+RAM disk
+Mountpoint
+<span class="monospace">/ramdisk</span>
+Accesspoint
+<span class="monospace">/ramdisk/$PBS_JOBID</span>
+Capacity
+60GB at compute nodes without accelerator
+90GB at compute nodes with accelerator
+500GB at fat nodes
+Throughput
+over 1.5 GB/s write, over 5 GB/s read, single thread
+over 10 GB/s write, over 50 GB/s read, 16 threads
+User quota
+none
+### tmp
+Each node is equipped with local /tmp directory of few GB capacity. The
+/tmp directory should be used to work with small temporary files. Old
+files in /tmp directory are automatically purged.
+**Summary
+**
+----------
+ Mountpoint Usage Protocol Net Capacity Throughput Limitations Access Services
+ ------------------- ---- ---------- ---------------- ------------ ------------- -- ------
+ <span class="monospace">/home</span> home directory Lustre 320 TiB 2 GB/s Quota 250GB Compute and login nodes backed up
+ <span class="monospace">/scratch</span> cluster shared jobs' data Lustre 146 TiB 6 GB/s Quota 100TB Compute and login nodes files older 90 days removed
+ <span class="monospace">/lscratch</span> node local jobs' data local 330 GB 100 MB/s none Compute nodes purged after job ends
+ <span class="monospace">/ramdisk</span> node local jobs' data local 60, 90, 500 GB 5-50 GB/s none Compute nodes purged after job ends
+ <span class="monospace">/tmp</span> local temporary files local 100 MB/s none Compute and login nodes auto purged
+Â
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index abc64e3bd17f7abf66c02c74febef591bb8eee15..d079059f40df94517cbb2c1a0db7d5a4adebe955
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<title>Introduction — IT4I Docs</title>
- <link rel="canonical" href="../anselm-cluster-documentation.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/anselm-cluster-documentation" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="introduction.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/anselm-cluster-documentation#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="introduction.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/anselm-cluster-documentation#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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</div>
</div>
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- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -220,11 +217,11 @@
<div id="parent-fieldname-text-519a21511a404ed6acc09c81711a65aa" class="">
- <p>Welcome to Anselm supercomputer cluster. The Anselm cluster consists of 209 compute nodes, totaling 3344 compute cores with 15TB RAM and giving over 94 Tflop/s theoretical peak performance. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 16 cores, at least 64GB RAM, and 500GB harddrive. Nodes are interconnected by fully non-blocking fat-tree Infiniband network and equipped with Intel Sandy Bridge processors. A few nodes are also equipped with NVIDIA Kepler GPU or Intel Xeon Phi MIC accelerators. Read more in <a target="_self" title="" class="internal-link" href="hardware-overview.html">Hardware Overview</a>.</p>
-<p>The cluster runs bullx Linux <a class="external-link" href="http://www.bull.com/bullx-logiciels/systeme-exploitation.html" target="_self" title=""><span class="WYSIWYG_LINK"></span></a><a target="_self" title="" class="internal-link" href="software/operating-system.html">operating system</a>, which is compatible with the <span class="WYSIWYG_LINK">RedHat</span> <a class="external-link" href="http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg" target="_self" title=""><span class="WYSIWYG_LINK">Linux family.</span></a> We have installed a wide range of <a target="_self" title="" class="internal-link" href="software.html">software</a> packages targeted at different scientific domains. These packages are accessible via the <a target="_self" title="" class="internal-link" href="environment-and-modules.html">modules environment</a>.</p>
+ <p>Welcome to Anselm supercomputer cluster. The Anselm cluster consists of 209 compute nodes, totaling 3344 compute cores with 15TB RAM and giving over 94 Tflop/s theoretical peak performance. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 16 cores, at least 64GB RAM, and 500GB harddrive. Nodes are interconnected by fully non-blocking fat-tree Infiniband network and equipped with Intel Sandy Bridge processors. A few nodes are also equipped with NVIDIA Kepler GPU or Intel Xeon Phi MIC accelerators. Read more in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">Hardware Overview</a>.</p>
+<p>The cluster runs bullx Linux <a class="external-link" href="http://www.bull.com/bullx-logiciels/systeme-exploitation.html" target="_self" title=""><span class="WYSIWYG_LINK"></span></a><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">operating system</a>, which is compatible with the <span class="WYSIWYG_LINK">RedHat</span> <a class="external-link" href="http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg" target="_self" title=""><span class="WYSIWYG_LINK">Linux family.</span></a> We have installed a wide range of <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software">software</a> packages targeted at different scientific domains. These packages are accessible via the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">modules environment</a>.</p>
<p>User data shared file-system (HOME, 320TB) and job data shared file-system (SCRATCH, 146TB) are available to users.</p>
-<p>The PBS Professional workload manager provides <a target="_self" title="" class="internal-link" href="resource-allocation-and-job-execution.html">computing resources allocations and job execution</a>.</p>
-<p>Read more on how to <a target="_self" title="" class="internal-link" href="../get-started-with-it4innovations/applying-for-resources.html">apply for resources</a>, <a target="_self" title="" class="internal-link" href="../get-started-with-it4innovations/obtaining-login-credentials.html">obtain login credentials,</a> and <a target="_self" title="" class="internal-link" href="accessing-the-cluster/shell-and-data-access.html">access the cluster</a>.</p>
+<p>The PBS Professional workload manager provides <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">computing resources allocations and job execution</a>.</p>
+<p>Read more on how to <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources">apply for resources</a>, <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">obtain login credentials,</a> and <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">access the cluster</a>.</p>
</div>
@@ -300,7 +297,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -332,7 +329,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -348,7 +345,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -364,7 +361,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -380,7 +377,7 @@
- <a title="" class="state-published contenttype-document" href="hardware-overview.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
<span>Hardware Overview</span>
</a>
@@ -396,7 +393,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -412,7 +409,7 @@
- <a title="" class="state-published contenttype-document" href="environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -428,7 +425,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -444,7 +441,7 @@
- <a title="" class="state-published contenttype-document" href="compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -460,7 +457,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="storage-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
<span>Storage</span>
</a>
@@ -476,7 +473,7 @@
- <a title="" class="state-published contenttype-document" href="network.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
<span>Network</span>
</a>
@@ -492,10 +489,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
<span>Software</span>
</a>
@@ -511,7 +508,7 @@
- <a title="" class="state-published contenttype-document" href="remote-visualization.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/remote-visualization">
<span>Remote visualization service</span>
</a>
@@ -527,7 +524,7 @@
- <a title="" class="state-published contenttype-document" href="prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/prace">
<span>PRACE User Support</span>
</a>
@@ -552,7 +549,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -568,7 +565,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -584,7 +581,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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(function() {
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+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -652,12 +649,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -673,7 +670,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/docs.it4i.cz/anselm.md b/docs.it4i.cz/anselm.md
new file mode 100644
index 0000000000000000000000000000000000000000..7d1bde3e9229026bb5cd0d102710e86979641d53
--- /dev/null
+++ b/docs.it4i.cz/anselm.md
@@ -0,0 +1,34 @@
+Introduction
+============
+
+Welcome to Anselm supercomputer cluster. The Anselm cluster consists of
+209 compute nodes, totaling 3344 compute cores with 15TB RAM and giving
+over 94 Tflop/s theoretical peak performance. Each node is a <span
+class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 16
+cores, at least 64GB RAM, and 500GB harddrive. Nodes are interconnected
+by fully non-blocking fat-tree Infiniband network and equipped with
+Intel Sandy Bridge processors. A few nodes are also equipped with NVIDIA
+Kepler GPU or Intel Xeon Phi MIC accelerators. Read more in [Hardware
+Overview](https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview).
+The cluster runs bullx Linux [<span
+class="WYSIWYG_LINK"></span>](http://www.bull.com/bullx-logiciels/systeme-exploitation.html)[operating
+system](https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system),
+which is compatible with the <span class="WYSIWYG_LINK">RedHat</span>
+[<span class="WYSIWYG_LINK">Linux
+family.</span>](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
+We have installed a wide range of
+[software](https://docs.it4i.cz/anselm-cluster-documentation/software)
+packages targeted at different scientific domains. These packages are
+accessible via the [modules
+environment](https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules).
+User data shared file-system (HOME, 320TB) and job data shared
+file-system (SCRATCH, 146TB) are available to users.
+The PBS Professional workload manager provides [computing resources
+allocations and job
+execution](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution).
+Read more on how to [apply for
+resources](https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources),
+[obtain login
+credentials,](https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials)
+and [access the
+cluster](https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster).
diff --git a/application.png b/docs.it4i.cz/application.png
old mode 100755
new mode 100644
similarity index 100%
rename from application.png
rename to docs.it4i.cz/application.png
diff --git a/atom.xml b/docs.it4i.cz/atom.xml
old mode 100755
new mode 100644
similarity index 96%
rename from atom.xml
rename to docs.it4i.cz/atom.xml
index 12fdb9546e2c43ef48ad5d2a76557e461e4fecc8..a50e95e894d44a3d1c5519c35d55849cd14188fa
--- a/atom.xml
+++ b/docs.it4i.cz/atom.xml
@@ -65,8 +65,8 @@
<div id="parent-fieldname-text-50ee0f8999e14a08822bd423d24de7ef" class="">
- <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
-<h2 class=" "><img title="Vampir screenshot" class="image-inline" alt="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
+ <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
+<h2 class=" "><img alt="Vampir screenshot" class="image-inline" title="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
<h2 class=" ">Installed versions</h2>
<p>Version 8.5.0 is currently installed as module <span class="monospace">Vampir/8.5.0</span> :</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir &</pre>
@@ -127,8 +127,8 @@
<div id="parent-fieldname-text-f6e25102d1244fb4ab355175867747b5" class="">
- <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
-<h2 class=" "><img title="Vampir screenshot" class="image-inline" alt="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
+ <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
+<h2 class=" "><img alt="Vampir screenshot" class="image-inline" title="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
<h2 class=" ">Installed versions</h2>
<p>Version 8.5.0 is currently installed as module <span class="monospace">Vampir/8.5.0</span> :</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir &</pre>
@@ -309,8 +309,8 @@
<pre class="prettyprint lang-sh"><span style="text-align: left; float: none; ">[usename@login1.anselm ~]$ gnome-session &<br />[1] 23691<br />[<span style="text-align: left; float: none; ">usename</span>@login1.anselm ~]$ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused<br />PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused<br /><br />** (gnome-session:23691): WARNING **: Cannot open display:<br /></span></pre>
<p><span style="text-align: left; float: none; ">Â </span></p>
<ol>
-<li><span style="text-align: left; float: none; ">Locate and modify <span style="text-align: left; float: none; ">Cygwin shortcut that uses<span class="Apple-converted-space">Â </span></span><a href="http://x.cygwin.com/docs/man1/startxwin.1.html" rel="nofollow" style="text-align: left; ">startxwin</a><br />locate<br />C:\cygwin64\bin\XWin.exe<br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">change it to</span></span></span><br />C:\<i class="moz-txt-slash">cygwin64\bin\XWin.exe -listen tcp</i><br /><br /><img title="XWin-listen-tcp.png" class="image-inline" alt="XWin-listen-tcp.png" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/XWinlistentcp.png" /><br /></span><br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span></span></li>
-<li><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">Check Putty settings:<br /><span style="text-align: left; float: none; ">Enable X11 forwarding</span><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span><span class="Apple-converted-space"><br /></span></span><br /><a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding"><img title="" class="image-inline" alt="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwinX11forwarding.png/@@images/0f5b58e3-253c-4f87-a3b2-16f75cbf090f.png" /></a><br /></span></span></li>
+<li><span style="text-align: left; float: none; ">Locate and modify <span style="text-align: left; float: none; ">Cygwin shortcut that uses<span class="Apple-converted-space">Â </span></span><a href="http://x.cygwin.com/docs/man1/startxwin.1.html" rel="nofollow" style="text-align: left; ">startxwin</a><br />locate<br />C:\cygwin64\bin\XWin.exe<br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">change it to</span></span></span><br />C:\<i class="moz-txt-slash">cygwin64\bin\XWin.exe -listen tcp</i><br /><br /><img alt="XWin-listen-tcp.png" class="image-inline" title="XWin-listen-tcp.png" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/XWinlistentcp.png" /><br /></span><br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span></span></li>
+<li><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">Check Putty settings:<br /><span style="text-align: left; float: none; ">Enable X11 forwarding</span><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span><span class="Apple-converted-space"><br /></span></span><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding"><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwinX11forwarding.png/@@images/0f5b58e3-253c-4f87-a3b2-16f75cbf090f.png" /></a><br /></span></span></li>
</ol>
<p>Â </p>
@@ -395,7 +395,7 @@
<div id="parent-fieldname-text" class="plain">
- <p>We have implemented a new way to run parallel MATLAB jobs. Unlike the previously documented method, it does not submit a separate new job to run the workers, all is done within a single job. Read about it here:Â <a target="_self" title="" class="external-link" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6">https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6</a></p>
+ <p>We have implemented a new way to run parallel MATLAB jobs. Unlike the previously documented method, it does not submit a separate new job to run the workers, all is done within a single job. Read about it here:Â <a title="" class="external-link" target="_self" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6">https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6</a></p>
</div>
@@ -706,13 +706,13 @@
<pre class="prettyprint lang-sh">$ module load phono3py/0.9.14-ictce-7.3.5-Python-2.7.9</pre>
<h2>Example of calculating thermal conductivity of Si using VASP code.</h2>
<h3>Calculating force constants</h3>
-<p>One needs to calculate second order and third order force constants using the diamond structure of silicon stored in <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/poscar-si">POSCAR</a>Â (the same form as in VASP) using single displacement calculations within supercell.</p>
+<p>One needs to calculate second order and third order force constants using the diamond structure of silicon stored in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/poscar-si">POSCAR</a>Â (the same form as in VASP) using single displacement calculations within supercell.</p>
<pre class="prettyprint lang-sh">$ cat POSCAR<br />Â Si<br />Â Â 1.0<br />Â Â Â Â 5.4335600309153529Â Â Â 0.0000000000000000Â Â Â 0.0000000000000000<br />Â Â Â Â 0.0000000000000000Â Â Â 5.4335600309153529Â Â Â 0.0000000000000000<br />Â Â Â Â 0.0000000000000000Â Â Â 0.0000000000000000Â Â Â 5.4335600309153529<br />Â Si<br />Â Â 8<br />Direct<br />Â Â 0.8750000000000000Â 0.8750000000000000Â 0.8750000000000000<br />Â Â 0.8750000000000000Â 0.3750000000000000Â 0.3750000000000000<br />Â Â 0.3750000000000000Â 0.8750000000000000Â 0.3750000000000000<br />Â Â 0.3750000000000000Â 0.3750000000000000Â 0.8750000000000000<br />Â Â 0.1250000000000000Â 0.1250000000000000Â 0.1250000000000000<br />Â Â 0.1250000000000000Â 0.6250000000000000Â 0.6250000000000000<br />Â Â 0.6250000000000000Â 0.1250000000000000Â 0.6250000000000000<br />Â Â 0.6250000000000000Â 0.6250000000000000Â 0.1250000000000000<br /><br /></pre>
<h3>Generating displacement using 2x2x2 supercell for both second and third order force constants</h3>
<pre class="prettyprint lang-sh">$ <span class="n">phono3py</span> <span class="o">-</span><span class="n">d</span> <span class="o">--</span><span class="n">dim</span><span class="o">=</span><span class="s2">"2 2 2"</span> <span class="o">-</span><span class="n">c</span> <span class="n">POSCAR</span><span class="o"></span><span class="n"></span></pre>
<p class=" "><span class="n">111 displacements is created stored in <span class="n">disp_fc3.yaml</span>, and the structure input files with this displacements are POSCAR-00XXX, where the XXX=111.<br /></span></p>
<pre class="prettyprint lang-sh"><span class="n">disp_fc3.yaml POSCAR-00008 POSCAR-00017 POSCAR-00026 POSCAR-00035 POSCAR-00044 POSCAR-00053 POSCAR-00062 POSCAR-00071 POSCAR-00080 POSCAR-00089 POSCAR-00098 POSCAR-00107<br />POSCAR        POSCAR-00009 POSCAR-00018 POSCAR-00027 POSCAR-00036 POSCAR-00045 POSCAR-00054 POSCAR-00063 POSCAR-00072 POSCAR-00081 POSCAR-00090 POSCAR-00099 POSCAR-00108<br />POSCAR-00001  POSCAR-00010 POSCAR-00019 POSCAR-00028 POSCAR-00037 POSCAR-00046 POSCAR-00055 POSCAR-00064 POSCAR-00073 POSCAR-00082 POSCAR-00091 POSCAR-00100 POSCAR-00109<br />POSCAR-00002  POSCAR-00011 POSCAR-00020 POSCAR-00029 POSCAR-00038 POSCAR-00047 POSCAR-00056 POSCAR-00065 POSCAR-00074 POSCAR-00083 POSCAR-00092 POSCAR-00101 POSCAR-00110<br />POSCAR-00003  POSCAR-00012 POSCAR-00021 POSCAR-00030 POSCAR-00039 POSCAR-00048 POSCAR-00057 POSCAR-00066 POSCAR-00075 POSCAR-00084 POSCAR-00093 POSCAR-00102 POSCAR-00111<br />POSCAR-00004  POSCAR-00013 POSCAR-00022 POSCAR-00031 POSCAR-00040 POSCAR-00049 POSCAR-00058 POSCAR-00067 POSCAR-00076 POSCAR-00085 POSCAR-00094 POSCAR-00103<br />POSCAR-00005  POSCAR-00014 POSCAR-00023 POSCAR-00032 POSCAR-00041 POSCAR-00050 POSCAR-00059 POSCAR-00068 POSCAR-00077 POSCAR-00086 POSCAR-00095 POSCAR-00104<br />POSCAR-00006  POSCAR-00015 POSCAR-00024 POSCAR-00033 POSCAR-00042 POSCAR-00051 POSCAR-00060 POSCAR-00069 POSCAR-00078 POSCAR-00087 POSCAR-00096 POSCAR-00105<br />POSCAR-00007  POSCAR-00016 POSCAR-00025 POSCAR-00034 POSCAR-00043 POSCAR-00052 POSCAR-00061 POSCAR-00070 POSCAR-00079 POSCAR-00088 POSCAR-00097 POSCAR-00106</span></pre>
-<p class=" "><span class="n"> For each displacement the forces needs to be calculated, i.e. in form of the output file of VASP (vasprun.xml). For a single VASP calculations one needs <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/KPOINTS">KPOINTS</a>, <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/POTCAR">POTCAR</a>, <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/INCAR">INCAR</a> in your case directory (where you have POSCARS) and those 111 displacements calculations can be generated by <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/prepare.sh">prepare.sh</a> script. Then each of the single 111 calculations is submitted <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/run.sh">run.sh</a> by <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/submit.sh">submit.sh</a>.</span></p>
+<p class=" "><span class="n"> For each displacement the forces needs to be calculated, i.e. in form of the output file of VASP (vasprun.xml). For a single VASP calculations one needs <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/KPOINTS">KPOINTS</a>, <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/POTCAR">POTCAR</a>, <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/INCAR">INCAR</a> in your case directory (where you have POSCARS) and those 111 displacements calculations can be generated by <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/prepare.sh">prepare.sh</a> script. Then each of the single 111 calculations is submitted <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/run.sh">run.sh</a> by <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/submit.sh">submit.sh</a>.</span></p>
<pre class="prettyprint lang-sh"><span class="n">$./prepare.sh<br />$ls<br />disp-00001Â disp-00009Â disp-00017Â disp-00025Â disp-00033Â disp-00041Â disp-00049Â disp-00057Â disp-00065Â disp-00073Â disp-00081Â disp-00089Â disp-00097Â disp-00105Â Â Â Â INCAR<br />disp-00002Â disp-00010Â disp-00018Â disp-00026Â disp-00034Â disp-00042Â disp-00050Â disp-00058Â disp-00066Â disp-00074Â disp-00082Â disp-00090Â disp-00098Â disp-00106Â Â Â Â KPOINTS<br />disp-00003Â disp-00011Â disp-00019Â disp-00027Â disp-00035Â disp-00043Â disp-00051Â disp-00059Â disp-00067Â disp-00075Â disp-00083Â disp-00091Â disp-00099Â disp-00107Â Â Â Â POSCAR<br />disp-00004Â disp-00012Â disp-00020Â disp-00028Â disp-00036Â disp-00044Â disp-00052Â disp-00060Â disp-00068Â disp-00076Â disp-00084Â disp-00092Â disp-00100Â disp-00108Â Â Â Â POTCAR<br />disp-00005Â disp-00013Â disp-00021Â disp-00029Â disp-00037Â disp-00045Â disp-00053Â disp-00061Â disp-00069Â disp-00077Â disp-00085Â disp-00093Â disp-00101Â disp-00109Â Â Â Â prepare.sh<br />disp-00006Â disp-00014Â disp-00022Â disp-00030Â disp-00038Â disp-00046Â disp-00054Â disp-00062Â disp-00070Â disp-00078Â disp-00086Â disp-00094Â disp-00102Â disp-00110Â Â Â Â run.sh<br />disp-00007Â disp-00015Â disp-00023Â disp-00031Â disp-00039Â disp-00047Â disp-00055Â disp-00063Â disp-00071Â disp-00079Â disp-00087Â disp-00095Â disp-00103Â disp-00111Â Â Â Â submit.sh<br />disp-00008Â disp-00016Â disp-00024Â disp-00032Â disp-00040Â disp-00048Â disp-00056Â disp-00064Â disp-00072Â disp-00080Â disp-00088Â disp-00096Â disp-00104Â disp_fc3.yaml<br /></span></pre>
<p class=" "><span class="n">Taylor your run.sh script to fit into your project and other needs and submit all 111 calculations using submit.sh script</span></p>
<pre class="prettyprint lang-sh"><span class="n">$ ./submit.sh</span></pre>
@@ -729,7 +729,7 @@
<pre class="prettyprint lang-sh">$ grep grid_point ir_grid_points.yaml<br />num_reduced_ir_grid_points: 35<br />ir_grid_points:Â # [address, weight]<br />- grid_point: 0<br />- grid_point: 1<br />- grid_point: 2<br />- grid_point: 3<br />- grid_point: 4<br />- grid_point: 10<br />- grid_point: 11<br />- grid_point: 12<br />- grid_point: 13<br />- grid_point: 20<br />- grid_point: 21<br />- grid_point: 22<br />- grid_point: 30<br />- grid_point: 31<br />- grid_point: 40<br />- grid_point: 91<br />- grid_point: 92<br />- grid_point: 93<br />- grid_point: 94<br />- grid_point: 101<br />- grid_point: 102<br />- grid_point: 103<br />- grid_point: 111<br />- grid_point: 112<br />- grid_point: 121<br />- grid_point: 182<br />- grid_point: 183<br />- grid_point: 184<br />- grid_point: 192<br />- grid_point: 193<br />- grid_point: 202<br />- grid_point: 273<br />- grid_point: 274<br />- grid_point: 283<br />- grid_point: 364</pre>
<p>one finds which grid points needed to be calculated, for instance using following</p>
<pre class="prettyprint lang-sh"><span class="n">$ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCARÂ --sigma 0.1 --br --write-gamma --gp="0 1 2</span></pre>
-<p><span class="n">one calculates grid points 0, 1, 2. To automize one can use for instance scripts to submit 5 points in series, see <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/gofree-cond1.sh">gofree-cond1.sh </a></span></p>
+<p><span class="n">one calculates grid points 0, 1, 2. To automize one can use for instance scripts to submit 5 points in series, see <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/gofree-cond1.sh">gofree-cond1.sh </a></span></p>
<pre class="prettyprint lang-sh"><span class="n">$ qsub gofree-cond1.sh</span></pre>
<p><span class="n">Finally the thermal conductivity result is produced by grouping single conductivity per grid calculations using </span></p>
<pre class="prettyprint lang-sh"><span class="n">$ <span class="n">phono3py</span> <span class="o">--</span><span class="n">fc3</span> <span class="o">--</span><span class="n">fc2</span> <span class="o">--</span><span class="n">dim</span><span class="o">=</span><span class="s2">"2 2 2"</span> <span class="o">--</span><span class="n">mesh</span><span class="o">=</span><span class="s2">"</span>9 9 9" <span class="o">--</span><span class="n">br</span> <span class="o">--</span><span class="n">read_gamma</span></span></pre>
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diff --git a/changelog.html b/docs.it4i.cz/changelog.html
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rename from changelog.html
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Changelog — IT4I Docs</title>
- <link rel="canonical" href="changelog.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/changelog" />
- <link rel="shortcut icon" type="image/x-icon" href="favicon.ico" />
- <link rel="apple-touch-icon" href="touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -63,14 +60,14 @@
- <link rel="alternate" href="changelog/RSS" title="Changelog - RSS 1.0" type="application/rss+xml" />
+ <link rel="alternate" href="https://docs.it4i.cz/changelog/RSS" title="Changelog - RSS 1.0" type="application/rss+xml" />
- <link rel="alternate" href="changelog/rss.xml" title="Changelog - RSS 2.0" type="application/rss+xml" />
+ <link rel="alternate" href="https://docs.it4i.cz/changelog/rss.xml" title="Changelog - RSS 2.0" type="application/rss+xml" />
- <link rel="alternate" href="changelog/atom.xml" title="Changelog - Atom" type="application/rss+xml" />
+ <link rel="alternate" href="https://docs.it4i.cz/changelog/atom.xml" title="Changelog - Atom" type="application/rss+xml" />
- <link rel="search" href="%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -93,9 +90,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="changelog.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/changelog#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="changelog.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/changelog#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -131,13 +128,13 @@
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
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- <img src="logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -151,7 +148,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -241,14 +238,14 @@
<td class="listing-body-ModificationDate">
- Středa 13.07.2016 20:04
+ ÄŚtvrtek 14.07.2016 20:49
</td>
<td class="listing-body-Title">
- <a href="whats-new/downtimes_history.html" title="History of Downtimes">History of Downtimes</a>
+ <a href="https://docs.it4i.cz/whats-new/downtimes_history" title="History of Downtimes">History of Downtimes</a>
</td>
@@ -265,14 +262,14 @@
<td class="listing-body-ModificationDate">
- Středa 13.07.2016 16:11
+ ÄŚtvrtek 14.07.2016 02:00
</td>
<td class="listing-body-Title">
- <a href="anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.html" title="Matlab">Matlab</a>
+ <a href="https://docs.it4i.cz/salomon/list_of_modules" title="List of Available Modules">List of Available Modules</a>
</td>
@@ -289,14 +286,14 @@
<td class="listing-body-ModificationDate">
- Středa 13.07.2016 16:10
+ Středa 13.07.2016 16:11
</td>
<td class="listing-body-Title">
- <a href="salomon/software/numerical-languages/matlab.html" title="Matlab">Matlab</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab" title="Matlab">Matlab</a>
</td>
@@ -313,14 +310,14 @@
<td class="listing-body-ModificationDate">
- Středa 13.07.2016 15:41
+ Středa 13.07.2016 16:10
</td>
<td class="listing-body-Title">
- <a href="anselm-cluster-documentation/software/numerical-languages/matlab.html" title="Matlab 2013-2014">Matlab 2013-2014</a>
+ <a href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab" title="Matlab">Matlab</a>
</td>
@@ -337,14 +334,14 @@
<td class="listing-body-ModificationDate">
- Středa 13.07.2016 15:38
+ Středa 13.07.2016 15:41
</td>
<td class="listing-body-Title">
- <a href="whats-new/news-feed/matlab-2015b.html" title="MATLAB 2015b">MATLAB 2015b</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab" title="Matlab 2013-2014">Matlab 2013-2014</a>
</td>
@@ -361,14 +358,14 @@
<td class="listing-body-ModificationDate">
- Středa 13.07.2016 15:35
+ Středa 13.07.2016 15:38
</td>
<td class="listing-body-Title">
- <a href="anselm-cluster-documentation/software/numerical-languages/introduction.html" title="Numerical languages">Numerical languages</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/matlab-2015b" title="MATLAB 2015b">MATLAB 2015b</a>
</td>
@@ -385,14 +382,14 @@
<td class="listing-body-ModificationDate">
- Středa 13.07.2016 02:00
+ Středa 13.07.2016 15:35
</td>
<td class="listing-body-Title">
- <a href="salomon/list_of_modules.html" title="List of Available Modules">List of Available Modules</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction" title="Numerical languages">Numerical languages</a>
</td>
@@ -416,7 +413,7 @@
<td class="listing-body-Title">
- <a href="whats-new/news-feed/vampir-installed.html" title="Vampir installed">Vampir installed</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/vampir-installed" title="Vampir installed">Vampir installed</a>
</td>
@@ -440,7 +437,7 @@
<td class="listing-body-Title">
- <a href="anselm-cluster-documentation/software/debuggers/summary.html" title="Debuggers and profilers summary">Debuggers and profilers summary</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary" title="Debuggers and profilers summary">Debuggers and profilers summary</a>
</td>
@@ -464,7 +461,7 @@
<td class="listing-body-Title">
- <a href="salomon/software/debuggers/vampir.html" title="Vampir">Vampir</a>
+ <a href="https://docs.it4i.cz/salomon/software/debuggers/vampir" title="Vampir">Vampir</a>
</td>
@@ -488,7 +485,7 @@
<td class="listing-body-Title">
- <a href="salomon/software/debuggers/summary.html" title="Debuggers and profilers summary">Debuggers and profilers summary</a>
+ <a href="https://docs.it4i.cz/salomon/software/debuggers/summary" title="Debuggers and profilers summary">Debuggers and profilers summary</a>
</td>
@@ -512,7 +509,7 @@
<td class="listing-body-Title">
- <a href="anselm-cluster-documentation/software/debuggers/vampir.html" title="Vampir">Vampir</a>
+ <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir" title="Vampir">Vampir</a>
</td>
@@ -536,7 +533,7 @@
<td class="listing-body-Title">
- <a href="salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/view.html" title="Vampir screenshot">Vampir screenshot</a>
+ <a href="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/view" title="Vampir screenshot">Vampir screenshot</a>
</td>
@@ -560,7 +557,7 @@
<td class="listing-body-Title">
- <a href="whats-new/news-feed/allinea-tools-updated-to-6-0.html" title="Allinea Tools updated to 6.0.6">Allinea Tools updated to 6.0.6</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/allinea-tools-updated-to-6-0.6" title="Allinea Tools updated to 6.0.6">Allinea Tools updated to 6.0.6</a>
</td>
@@ -584,7 +581,7 @@
<td class="listing-body-Title">
- <a href="whats-new/news-feed/intel-vtune-amplifier-support-for-xeon-phi-on-salomon.html" title="Intel VTune Amplifier support for Xeon Phi on Salomon">Intel VTune Amplifier support for Xeon Phi on Salomon</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/intel-vtune-amplifier-support-for-xeon-phi-on-salomon" title="Intel VTune Amplifier support for Xeon Phi on Salomon">Intel VTune Amplifier support for Xeon Phi on Salomon</a>
</td>
@@ -608,31 +605,7 @@
<td class="listing-body-Title">
- <a href="salomon/software/debuggers/intel-vtune-amplifier.html" title="Intel VTune Amplifier XE">Intel VTune Amplifier XE</a>
- </td>
-
-
-
-
-
- </tr>
-
-
- <tr class="odd">
-
-
-
-
-
- <td class="listing-body-ModificationDate">
- Středa 29.06.2016 14:03
- </td>
-
-
-
-
- <td class="listing-body-Title">
- <a href="anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.html" title="Intel VTune Amplifier">Intel VTune Amplifier</a>
+ <a href="https://docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier" title="Intel VTune Amplifier XE">Intel VTune Amplifier XE</a>
</td>
@@ -699,7 +672,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -715,7 +688,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -731,7 +704,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -747,7 +720,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -763,7 +736,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -779,7 +752,7 @@
- <a title="" class="state-published contenttype-document" href="links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -795,7 +768,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-collection" href="changelog.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -811,7 +784,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -850,14 +823,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
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+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -879,12 +852,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -900,8 +873,6 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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diff --git a/whats-new/news-feed/salomon-pbs-changes.md b/docs.it4i.cz/changelog.md
similarity index 100%
rename from whats-new/news-feed/salomon-pbs-changes.md
rename to docs.it4i.cz/changelog.md
diff --git a/changelog/RSS b/docs.it4i.cz/changelog/RSS
old mode 100755
new mode 100644
similarity index 92%
rename from changelog/RSS
rename to docs.it4i.cz/changelog/RSS
index 03c7fac348eaee360b6c28b3194475b13afe984b..88517bbeb9b94544321feb8ae1cc75bbec1ff845
--- a/changelog/RSS
+++ b/docs.it4i.cz/changelog/RSS
@@ -15,6 +15,9 @@
<rdf:li rdf:resource="https://docs.it4i.cz/whats-new/downtimes_history"/>
+ <rdf:li rdf:resource="https://docs.it4i.cz/salomon/list_of_modules"/>
+
+
<rdf:li rdf:resource="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab"/>
@@ -30,9 +33,6 @@
<rdf:li rdf:resource="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction"/>
- <rdf:li rdf:resource="https://docs.it4i.cz/salomon/list_of_modules"/>
-
-
<rdf:li rdf:resource="https://docs.it4i.cz/whats-new/news-feed/vampir-installed"/>
@@ -59,9 +59,6 @@
<rdf:li rdf:resource="https://docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier"/>
-
- <rdf:li rdf:resource="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier"/>
-
</rdf:Seq>
</items>
@@ -72,7 +69,16 @@
<title>History of Downtimes</title>
<link>https://docs.it4i.cz/whats-new/downtimes_history</link>
<description>Full history of important announcements related to IT4I infrastructure, planned downtimes, outages etc.</description>
- <dc:date>2016-07-13T18:04:07Z</dc:date>
+ <dc:date>2016-07-14T18:49:24Z</dc:date>
+ <dc:type>Document</dc:type>
+ </item>
+
+
+ <item rdf:about="https://docs.it4i.cz/salomon/list_of_modules">
+ <title>List of Available Modules</title>
+ <link>https://docs.it4i.cz/salomon/list_of_modules</link>
+ <description>List of Available Modules on Salomon Cluster</description>
+ <dc:date>2016-07-14T00:00:02Z</dc:date>
<dc:type>Document</dc:type>
</item>
@@ -122,15 +128,6 @@
</item>
- <item rdf:about="https://docs.it4i.cz/salomon/list_of_modules">
- <title>List of Available Modules</title>
- <link>https://docs.it4i.cz/salomon/list_of_modules</link>
- <description>List of Available Modules on Salomon Cluster</description>
- <dc:date>2016-07-13T00:00:02Z</dc:date>
- <dc:type>Document</dc:type>
- </item>
-
-
<item rdf:about="https://docs.it4i.cz/whats-new/news-feed/vampir-installed">
<title>Vampir installed</title>
<link>https://docs.it4i.cz/whats-new/news-feed/vampir-installed</link>
@@ -212,14 +209,5 @@
</item>
- <item rdf:about="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier">
- <title>Intel VTune Amplifier</title>
- <link>https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier</link>
- <description></description>
- <dc:date>2016-06-29T12:03:01Z</dc:date>
- <dc:type>Document</dc:type>
- </item>
-
-
</rdf:RDF>
\ No newline at end of file
diff --git a/changelog/atom.xml b/docs.it4i.cz/changelog/atom.xml
old mode 100755
new mode 100644
similarity index 97%
rename from changelog/atom.xml
rename to docs.it4i.cz/changelog/atom.xml
index 347a3acf57c2c5220104a03e221db75116a1ff93..c5b4d10faa06d59f404193a9594f6d16c60d9a22
--- a/changelog/atom.xml
+++ b/docs.it4i.cz/changelog/atom.xml
@@ -18,14 +18,14 @@
<title>History of Downtimes</title>
<link rel="alternate" type="text/html" href="https://docs.it4i.cz/whats-new/downtimes_history"/>
- <id>urn:syndication:4dd38593eea94c1081575284a571f1b7</id>
+ <id>urn:syndication:afd31d559759479bb0cefe1718fb3b12</id>
<summary>Full history of important announcements related to IT4I infrastructure, planned downtimes, outages etc.</summary>
<content type="xhtml" xml:base="https://docs.it4i.cz/changelog" xml:lang="cs" xml:space="preserve">
<div xmlns="http://www.w3.org/1999/xhtml">
- <div id="parent-fieldname-text-4dd38593eea94c1081575284a571f1b7" class="">
+ <div id="parent-fieldname-text-afd31d559759479bb0cefe1718fb3b12" class="">
<br />
<div>
<table class="listing">
@@ -471,9 +471,9 @@
</author>
- <published>2016-07-13T20:04:07+02:00</published>
+ <published>2016-07-14T20:49:24+02:00</published>
- <updated>2016-07-13T20:04:07+02:00</updated>
+ <updated>2016-07-14T20:49:24+02:00</updated>
</entry>
@@ -481,714 +481,83 @@
<entry>
- <title>Matlab</title>
- <link rel="alternate" type="text/html" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab"/>
-
- <id>urn:syndication:73e8cd3babab4da398f316c8d257916d</id>
+ <title>List of Available Modules</title>
+ <link rel="alternate" type="text/html" href="https://docs.it4i.cz/salomon/list_of_modules"/>
+ <id>urn:syndication:12f4645a6b084b17bca6411df10a8022</id>
+ <summary>List of Available Modules on Salomon Cluster</summary>
<content type="xhtml" xml:base="https://docs.it4i.cz/changelog" xml:lang="cs" xml:space="preserve">
<div xmlns="http://www.w3.org/1999/xhtml">
- <div id="parent-fieldname-text-73e8cd3babab4da398f316c8d257916d" class="">
- <h2 class=" ">Introduction</h2>
-<p>Matlab is available in versions R2015a and R2015b. There are always two variants of the release:</p>
-<ul>
-<li>Non commercial or so called EDU variant, which can be used for common research and educational purposes.</li>
-<li>Commercial or so called COM variant, which can used also for commercial activities. The licenses for commercial variant are much more expensive, so usually the commercial variant has only subset of features compared to the EDU available.</li>
-</ul>
-<p>Â </p>
-<p>To load the latest version of Matlab load the module</p>
-<pre class=" ">$ module load MATLAB</pre>
-<p>By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use</p>
-<pre class=" ">$ module avail MATLAB</pre>
-<p>If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.</p>
-<p>If you require the Matlab GUI, please follow the general informations about <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">running graphical applications</a>.</p>
-<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">here</a>) is recommended.</p>
-<p>To run Matlab with GUI, use</p>
-<pre class=" ">$ matlab</pre>
-<p>To run Matlab in text mode, without the Matlab Desktop GUI environment, use</p>
-<pre class=" ">$ matlab -nodesktop -nosplash</pre>
-<p>plots, images, etc... will be still available.</p>
-<h2 class=" "><a name="running-parallel-matlab-using-distributed-computing-toolbox---engine"></a>Running parallel Matlab using Distributed Computing Toolbox / Engine</h2>
-<p class="exclamation">Distributed toolbox is available only for the EDU variant</p>
-<p class=" ">The MPIEXEC mode available in previous versions is no longer available in MATLAB 2015. Also, the programming interface has changed. Refer to <a class="external-link" href="http://www.mathworks.com/help/distcomp/release-notes.html#buanp9e-1" target="_self" title="">Release Notes</a>.</p>
-<p class=" ">Delete previously used file mpiLibConf.m, we have observed crashes when using Intel MPI.</p>
-<p class=" ">To use Distributed Computing, you first need to setup a parallel profile. We have provided the profile for you, you can either import it in MATLAB command line:</p>
-<pre class=" ">>> parallel.importProfile('/apps/all/MATLAB/2015a-EDU/SalomonPBSPro.settings')<br /><br />ans = <br /><br />SalomonPBSPro </pre>
-<p class=" ">Or in the GUI, go to tab HOME -> Parallel -> Manage Cluster Profiles..., click Import and navigate to :</p>
-<p class=" ">/apps/all/MATLAB/2015a-EDU/SalomonPBSPro.settings</p>
-<p class=" ">With the new mode, MATLAB itself launches the workers via PBS, so you can either use interactive mode or a batch mode on one node, but the actual parallel processing will be done in a separate job started by MATLAB itself. Alternatively, you can use "local" mode to run parallel code on just a single node.</p>
-<p class="exclamation">The profile is confusingly named Salomon, but you can use it also on Anselm.</p>
-<h3 class=" ">Parallel Matlab interactive session</h3>
-<p>Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">this page</a>.</p>
-<pre class=" ">$ xhost +<br />$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00 \<br />-l feature__matlab__MATLAB=1 </pre>
-<p>This qsub command example shows how to run Matlab on a single node.</p>
-<p>The second part of the command shows how to request all necessary licenses. In this case 1 Matlab-EDU license and 48 Distributed Computing Engines licenses.</p>
-<p>Once the access to compute nodes is granted by PBS, user can load following modules and start Matlab:Â </p>
-<pre class=" ">r1i0n17$ module load MATLAB/2015b-EDU<br />r1i0n17$ matlab &</pre>
-<h3 class=" "><a name="parallel-matlab-batch-job-in-local-mode"></a>Parallel Matlab batch job in Local mode</h3>
-<p>To run matlab in batch mode, write an matlab script, then write a bash jobscript and execute via the qsub command. By default, matlab will execute one matlab worker instance per allocated core.</p>
-<pre class=" ">#!/bin/bash<br />#PBS -A PROJECT ID<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=16:mpiprocs=16:ompthreads=1<br /><br /># change to shared scratch directory<br />SCR=/scratch/work/user/$USER/$PBS_JOBID<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/matlabcode.m .<br /><br /># load modules<br />module load MATLAB/2015a-EDU<br /><br /># execute the calculation<br />matlab -nodisplay -r matlabcode > output.out<br /><br /># copy output file to home<br />cp output.out $PBS_O_WORKDIR/.</pre>
-<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs and matlab script are in matlabcode.m file, outputs in output.out file. Note the missing .m extension in the matlab -r matlabcodefile call, <strong>the .m must not be included</strong>. Note that the <strong>shared /scratch must be used</strong>. Further, it is <strong>important to include quit</strong> statement at the end of the matlabcode.m script.</p>
-<p>Submit the jobscript using qsub</p>
-<pre class=" ">$ qsub ./jobscript</pre>
-<h3 class=" ">Parallel Matlab Local mode program example</h3>
-<p>The last part of the configuration is done directly in the user Matlab script before Distributed Computing Toolbox is started.</p>
-<pre class=" ">cluster = parcluster('local')</pre>
-<p class=" ">This script creates scheduler object "cluster" of type "local" that starts workers locally. </p>
-<p class="callout">Please note: Every Matlab script that needs to initialize/use matlabpool has to contain these three lines prior to calling parpool(sched, ...) function. </p>
-<p class=" ">The last step is to start matlabpool with "cluster" object and correct number of workers. We have 24 cores per node, so we start 24 workers.</p>
-<pre class=" ">parpool(cluster,16);<br /> <br /> <br />... parallel code ...<br /> <br /> <br />parpool close</pre>
-<p>The complete example showing how to use Distributed Computing Toolbox in local mode is shown here. </p>
-<pre class=" ">cluster = parcluster('local');<br />cluster<br /><br />parpool(cluster,24);<br /><br />n=2000;<br /><br />W = rand(n,n);<br />W = distributed(W);<br />x = (1:n)';<br />x = distributed(x);<br />spmd<br />[~, name] = system('hostname')<br />   <br />   T = W*x; % Calculation performed on labs, in parallel.<br />            % T and W are both codistributed arrays here.<br />end<br />T;<br />whos        % T and W are both distributed arrays here.<br /><br />parpool close<br />quit</pre>
-<p>You can copy and paste the example in a .m file and execute. Note that the parpool size should correspond to <strong>total number of cores</strong> available on allocated nodes.</p>
-<h3 class=" ">Parallel Matlab Batch job using PBS mode (workers spawned in a separate job)</h3>
-<p>This mode uses PBS scheduler to launch the parallel pool. It uses the SalomonPBSPro profile that needs to be imported to Cluster Manager, as mentioned before. This methodod uses MATLAB's PBS Scheduler interface - it spawns the workers in a separate job submitted by MATLAB using qsub.</p>
-<p>This is an example of m-script using PBS mode:</p>
-<pre class=" ">cluster = parcluster('SalomonPBSPro');
-set(cluster, 'SubmitArguments', '-A OPEN-0-0');
-set(cluster, 'ResourceTemplate', '-q qprod -l select=10:ncpus=16');
-set(cluster, 'NumWorkers', 160);
-
-pool = parpool(cluster, 160);
-
-n=2000;
-
-W = rand(n,n);
-W = distributed(W);
-x = (1:n)';
-x = distributed(x);
-spmd
-[~, name] = system('hostname')
-
- T = W*x; % Calculation performed on labs, in parallel.
- % T and W are both codistributed arrays here.
-end
-whos % T and W are both distributed arrays here.
-
-% shut down parallel pool
-delete(pool)
-</pre>
-<p class=" ">Note that we first construct a cluster object using the imported profile, then set some important options, namely : SubmitArguments, where you need to specify accounting id, and ResourceTemplate, where you need to specify number of nodes to run the job. </p>
-<p class=" ">You can start this script using batch mode the same way as in Local mode example.</p>
-<h3 class=" ">Parallel Matlab Batch with direct launch (workers spawned within the existing job)</h3>
-<p>This method is a "hack" invented by us to emulate the mpiexec functionality found in previous MATLAB versions. We leverage the MATLAB Generic Scheduler interface, but instead of submitting the workers to PBS, we launch the workers directly within the running job, thus we avoid the issues with master script and workers running in separate jobs (issues with license not available, waiting for the worker's job to spawn etc.)</p>
-<p>Please note that this method is experimental.</p>
-<p>For this method, you need to use SalomonDirect profile, import it using <a class="anchor-link" href="#running-parallel-matlab-using-distributed-computing-toolbox---engine" target="_self" title="">the same way as SalomonPBSPro</a> </p>
-<p>This is an example of m-script using direct mode:</p>
-<pre class=" "><br />parallel.importProfile('/apps/all/MATLAB/2015a-EDU/SalomonDirect.settings')<br />cluster = parcluster('SalomonDirect');
-set(cluster, 'NumWorkers', 48);
-
-pool = parpool(cluster, 48);
-
-n=2000;
-
-W = rand(n,n);
-W = distributed(W);
-x = (1:n)';
-x = distributed(x);
-spmd
-[~, name] = system('hostname')
-
- T = W*x; % Calculation performed on labs, in parallel.
- % T and W are both codistributed arrays here.
-end
-whos % T and W are both distributed arrays here.
-
-% shut down parallel pool
-delete(pool)</pre>
-<h3 class=" ">Non-interactive Session and Licenses</h3>
-<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">look here</a>.</p>
-<p>In case of non-interactive session please read the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
-<h3 class=" ">Matlab Distributed Computing Engines start up time</h3>
-<p>Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:</p>
-<table class="plain">
-<tbody>
-<tr><th>compute nodes</th><th>number of workers</th><th>start-up time[s]</th></tr>
-<tr>
-<td>16</td>
-<td>384</td>
-<td>831</td>
-</tr>
-<tr>
-<td>8</td>
-<td>192</td>
-<td>807</td>
-</tr>
-<tr>
-<td>4</td>
-<td>96</td>
-<td>483</td>
-</tr>
-<tr>
-<td>2</td>
-<td>48</td>
-<td>16</td>
-</tr>
-</tbody>
-</table>
-<h2>MATLAB on UV2000Â </h2>
-<p>UV2000 machine available in queue "qfat" can be used for MATLAB computations. This is a SMP NUMA machine with large amount of RAM, which can be beneficial for certain types of MATLAB jobs. CPU cores are allocated in chunks of 8 for this machine.</p>
-<p>You can use MATLAB on UV2000 in two parallel modes :</p>
-<h3>Threaded mode</h3>
-<p class=" ">Since this is a SMP machine, you can completely avoid using Parallel Toolbox and use only MATLAB's threading. MATLAB will automatically detect the number of cores you have allocated and will set <span class="monospace">maxNumCompThreads </span>accordingly and certain operations, such as <span class="monospace">fft, \, eig, svd</span>, etc. will be automatically run in threads. The advantage of this mode is that you don't need to modify your existing sequential codes.<span class="monospace"><br /></span></p>
-<h3 class=" ">Local cluster mode</h3>
-<p>You can also use Parallel Toolbox on UV2000. Use l<a class="anchor-link" href="#parallel-matlab-batch-job-in-local-mode" target="_self" title="">ocal cluster mode</a>, "SalomonPBSPro" profile will not work.</p>
-<p>Â </p>
-<p>Â </p>
-
-
- </div>
-
-
- <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
-
- <div id="plone-discussions">
- <hr />
- <b><a id="plone-discussions-href" href="#plone-discussions">Komentáře</a></b>
- </div>
-
- <!-- <div id="contact-form" tal:condition="context/isDiscussable">
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- <tal:contactform tal:content="structure python:getattr(context, 'contact-info')()"></tal:contactform>
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-
- </div>
- </content>
-
- <author>
-
- <name>jansik</name>
-
- </author>
-
- <published>2013-07-24T12:50:00+02:00</published>
-
- <updated>2016-07-13T16:11:19+02:00</updated>
+ <div id="parent-fieldname-text-12f4645a6b084b17bca6411df10a8022" class="">
+ <div>
+ <h2 id="categories">Categories</h2>
- </entry>
-
-
-
- <entry>
- <title>Matlab</title>
- <link rel="alternate" type="text/html" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab"/>
-
- <id>urn:syndication:2efd48d0282d45b7b8fb11393c96d853</id>
-
- <content type="xhtml" xml:base="https://docs.it4i.cz/changelog" xml:lang="cs" xml:space="preserve">
- <div xmlns="http://www.w3.org/1999/xhtml">
-
-
-
- <div id="parent-fieldname-text-2efd48d0282d45b7b8fb11393c96d853" class="">
- <h2 class=" ">Introduction</h2>
-<p>Matlab is available in versions R2015a and R2015b. There are always two variants of the release:</p>
-<ul>
-<li>Non commercial or so called EDU variant, which can be used for common research and educational purposes.</li>
-<li>Commercial or so called COM variant, which can used also for commercial activities. The licenses for commercial variant are much more expensive, so usually the commercial variant has only subset of features compared to the EDU available.</li>
-</ul>
-<p>Â </p>
-<p>To load the latest version of Matlab load the module</p>
-<pre class=" ">$ module load MATLAB</pre>
-<p>By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use</p>
-<pre class=" ">$ module avail MATLAB</pre>
-<p>If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.</p>
-<p>If you require the Matlab GUI, please follow the general informations about <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">running graphical applications</a>.</p>
-<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">here</a>) is recommended.</p>
-<p>To run Matlab with GUI, use</p>
-<pre class=" ">$ matlab</pre>
-<p>To run Matlab in text mode, without the Matlab Desktop GUI environment, use</p>
-<pre class=" ">$ matlab -nodesktop -nosplash</pre>
-<p>plots, images, etc... will be still available.</p>
-<h2 class=" "><a name="running-parallel-matlab-using-distributed-computing-toolbox---engine"></a>Running parallel Matlab using Distributed Computing Toolbox / Engine</h2>
-<p class="exclamation">Distributed toolbox is available only for the EDU variant</p>
-<p class=" ">The MPIEXEC mode available in previous versions is no longer available in MATLAB 2015. Also, the programming interface has changed. Refer to <a class="external-link" href="http://www.mathworks.com/help/distcomp/release-notes.html#buanp9e-1" target="_self" title="">Release Notes</a>.</p>
-<p class=" ">Delete previously used file mpiLibConf.m, we have observed crashes when using Intel MPI.</p>
-<p class=" ">To use Distributed Computing, you first need to setup a parallel profile. We have provided the profile for you, you can either import it in MATLAB command line:</p>
-<pre class=" ">>> parallel.importProfile('/apps/all/MATLAB/2015b-EDU/SalomonPBSPro.settings')<br /><br />ans = <br /><br />SalomonPBSPro </pre>
-<p class=" ">Or in the GUI, go to tab HOME -> Parallel -> Manage Cluster Profiles..., click Import and navigate to :</p>
-<p class=" ">/apps/all/MATLAB/2015b-EDU/SalomonPBSPro.settings</p>
-<p class=" ">With the new mode, MATLAB itself launches the workers via PBS, so you can either use interactive mode or a batch mode on one node, but the actual parallel processing will be done in a separate job started by MATLAB itself. Alternatively, you can use "local" mode to run parallel code on just a single node.</p>
-<h3 class=" ">Parallel Matlab interactive session</h3>
-<p>Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">this page</a>.</p>
-<pre class=" ">$ xhost +<br />$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00 \<br />-l feature__matlab__MATLAB=1 </pre>
-<p>This qsub command example shows how to run Matlab on a single node.</p>
-<p>The second part of the command shows how to request all necessary licenses. In this case 1 Matlab-EDU license and 48 Distributed Computing Engines licenses.</p>
-<p>Once the access to compute nodes is granted by PBS, user can load following modules and start Matlab:Â </p>
-<pre class=" ">r1i0n17$ module load MATLAB/2015a-EDU<br />r1i0n17$ matlab &</pre>
-<h3 class=" "><a name="parallel-matlab-batch-job-in-local-mode"></a>Parallel Matlab batch job in Local mode</h3>
-<p>To run matlab in batch mode, write an matlab script, then write a bash jobscript and execute via the qsub command. By default, matlab will execute one matlab worker instance per allocated core.</p>
-<pre class=" ">#!/bin/bash<br />#PBS -A PROJECT ID<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=24:mpiprocs=24:ompthreads=1<br /><br /># change to shared scratch directory<br />SCR=/scratch/work/user/$USER/$PBS_JOBID<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/matlabcode.m .<br /><br /># load modules<br />module load MATLAB/2015a-EDU<br /><br /># execute the calculation<br />matlab -nodisplay -r matlabcode > output.out<br /><br /># copy output file to home<br />cp output.out $PBS_O_WORKDIR/.</pre>
-<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs and matlab script are in matlabcode.m file, outputs in output.out file. Note the missing .m extension in the matlab -r matlabcodefile call, <strong>the .m must not be included</strong>. Note that the <strong>shared /scratch must be used</strong>. Further, it is <strong>important to include quit</strong> statement at the end of the matlabcode.m script.</p>
-<p>Submit the jobscript using qsub</p>
-<pre class=" ">$ qsub ./jobscript</pre>
-<h3 class=" ">Parallel Matlab Local mode program example</h3>
-<p>The last part of the configuration is done directly in the user Matlab script before Distributed Computing Toolbox is started.</p>
-<pre class=" ">cluster = parcluster('local')</pre>
-<p class=" ">This script creates scheduler object "cluster" of type "local" that starts workers locally. </p>
-<p class="callout">Please note: Every Matlab script that needs to initialize/use matlabpool has to contain these three lines prior to calling parpool(sched, ...) function. </p>
-<p class=" ">The last step is to start matlabpool with "cluster" object and correct number of workers. We have 24 cores per node, so we start 24 workers.</p>
-<pre class=" ">parpool(cluster,24);<br /> <br /> <br />... parallel code ...<br /> <br /> <br />parpool close</pre>
-<p>The complete example showing how to use Distributed Computing Toolbox in local mode is shown here. </p>
-<pre class=" ">cluster = parcluster('local');<br />cluster<br /><br />parpool(cluster,24);<br /><br />n=2000;<br /><br />W = rand(n,n);<br />W = distributed(W);<br />x = (1:n)';<br />x = distributed(x);<br />spmd<br />[~, name] = system('hostname')<br />   <br />   T = W*x; % Calculation performed on labs, in parallel.<br />            % T and W are both codistributed arrays here.<br />end<br />T;<br />whos        % T and W are both distributed arrays here.<br /><br />parpool close<br />quit</pre>
-<p>You can copy and paste the example in a .m file and execute. Note that the parpool size should correspond to <strong>total number of cores</strong> available on allocated nodes.</p>
-<h3 class=" ">Parallel Matlab Batch job using PBS mode (workers spawned in a separate job)</h3>
-<p>This mode uses PBS scheduler to launch the parallel pool. It uses the SalomonPBSPro profile that needs to be imported to Cluster Manager, as mentioned before. This methodod uses MATLAB's PBS Scheduler interface - it spawns the workers in a separate job submitted by MATLAB using qsub.</p>
-<p>This is an example of m-script using PBS mode:</p>
-<pre class=" ">cluster = parcluster('SalomonPBSPro');
-set(cluster, 'SubmitArguments', '-A OPEN-0-0');
-set(cluster, 'ResourceTemplate', '-q qprod -l select=10:ncpus=24');
-set(cluster, 'NumWorkers', 240);
-
-pool = parpool(cluster,240);
-
-n=2000;
-
-W = rand(n,n);
-W = distributed(W);
-x = (1:n)';
-x = distributed(x);
-spmd
-[~, name] = system('hostname')
-
- T = W*x; % Calculation performed on labs, in parallel.
- % T and W are both codistributed arrays here.
-end
-whos % T and W are both distributed arrays here.
-
-% shut down parallel pool
-delete(pool)
-</pre>
-<p class=" ">Note that we first construct a cluster object using the imported profile, then set some important options, namely : SubmitArguments, where you need to specify accounting id, and ResourceTemplate, where you need to specify number of nodes to run the job. </p>
-<p class=" ">You can start this script using batch mode the same way as in Local mode example.</p>
-<h3 class=" ">Parallel Matlab Batch with direct launch (workers spawned within the existing job)</h3>
-<p>This method is a "hack" invented by us to emulate the mpiexec functionality found in previous MATLAB versions. We leverage the MATLAB Generic Scheduler interface, but instead of submitting the workers to PBS, we launch the workers directly within the running job, thus we avoid the issues with master script and workers running in separate jobs (issues with license not available, waiting for the worker's job to spawn etc.)</p>
-<p>Please note that this method is experimental.</p>
-<p>For this method, you need to use SalomonDirect profile, import it using <a class="anchor-link" href="#running-parallel-matlab-using-distributed-computing-toolbox---engine" target="_self" title="">the same way as SalomonPBSPro</a> </p>
-<p>This is an example of m-script using direct mode:</p>
-<pre class=" "><br />parallel.importProfile('/apps/all/MATLAB/2015b-EDU/SalomonDirect.settings')<br />cluster = parcluster('SalomonDirect');
-set(cluster, 'NumWorkers', 48);
-
-pool = parpool(cluster, 48);
-
-n=2000;
-
-W = rand(n,n);
-W = distributed(W);
-x = (1:n)';
-x = distributed(x);
-spmd
-[~, name] = system('hostname')
-
- T = W*x; % Calculation performed on labs, in parallel.
- % T and W are both codistributed arrays here.
-end
-whos % T and W are both distributed arrays here.
-
-% shut down parallel pool
-delete(pool)</pre>
-<h3 class=" ">Non-interactive Session and Licenses</h3>
-<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">look here</a>.</p>
-<p class="exclamation">The licensing feature of PBS is currently disabled.</p>
-<p>In case of non-interactive session please read the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
-<h3 class=" ">Matlab Distributed Computing Engines start up time</h3>
-<p>Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:</p>
-<table class="plain">
-<tbody>
-<tr><th>compute nodes</th><th>number of workers</th><th>start-up time[s]</th></tr>
-<tr>
-<td>16</td>
-<td>384</td>
-<td>831</td>
-</tr>
-<tr>
-<td>8</td>
-<td>192</td>
-<td>807</td>
-</tr>
-<tr>
-<td>4</td>
-<td>96</td>
-<td>483</td>
-</tr>
-<tr>
-<td>2</td>
-<td>48</td>
-<td>16</td>
-</tr>
-</tbody>
-</table>
-<h2>MATLAB on UV2000Â </h2>
-<p>UV2000 machine available in queue "qfat" can be used for MATLAB computations. This is a SMP NUMA machine with large amount of RAM, which can be beneficial for certain types of MATLAB jobs. CPU cores are allocated in chunks of 8 for this machine.</p>
-<p>You can use MATLAB on UV2000 in two parallel modes :</p>
-<h3>Threaded mode</h3>
-<p class=" ">Since this is a SMP machine, you can completely avoid using Parallel Toolbox and use only MATLAB's threading. MATLAB will automatically detect the number of cores you have allocated and will set <span class="monospace">maxNumCompThreads </span>accordingly and certain operations, such as <span class="monospace">fft, \, eig, svd</span>, etc. will be automatically run in threads. The advantage of this mode is that you don't need to modify your existing sequential codes.<span class="monospace"><br /></span></p>
-<h3 class=" ">Local cluster mode</h3>
-<p>You can also use Parallel Toolbox on UV2000. Use l<a class="anchor-link" href="#parallel-matlab-batch-job-in-local-mode" target="_self" title="">ocal cluster mode</a>, "SalomonPBSPro" profile will not work.</p>
-<p>Â </p>
-<p>Â </p>
-
-
- </div>
-
-
- <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
-
- <div id="plone-discussions">
- <hr />
- <b><a id="plone-discussions-href" href="#plone-discussions">Komentáře</a></b>
- </div>
-
- <!-- <div id="contact-form" tal:condition="context/isDiscussable">
- <hr />
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- <tal:contactform tal:content="structure python:getattr(context, 'contact-info')()"></tal:contactform>
- </div> -->
-
-
-
-
- </div>
- </content>
-
- <author>
-
- <name>jansik</name>
-
- </author>
-
- <published>2013-07-24T12:50:00+02:00</published>
-
- <updated>2016-07-13T16:10:41+02:00</updated>
-
-
- </entry>
-
-
-
- <entry>
- <title>Matlab 2013-2014</title>
- <link rel="alternate" type="text/html" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab"/>
-
- <id>urn:syndication:41bf242708954438ac56e1a431788c0e</id>
-
- <content type="xhtml" xml:base="https://docs.it4i.cz/changelog" xml:lang="cs" xml:space="preserve">
- <div xmlns="http://www.w3.org/1999/xhtml">
-
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- <div id="parent-fieldname-text-41bf242708954438ac56e1a431788c0e" class="">
- <h2 class=" ">Introduction</h2>
-<p class="exclamation">This document relates to the old versions R2013 and R2014. For MATLAB 2015, please use <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab">this documentation instead</a>.</p>
-<p>Matlab is available in the latest stable version. There are always two variants of the release:</p>
-<ul>
-<li>Non commercial or so called EDU variant, which can be used for common research and educational purposes.</li>
-<li>Commercial or so called COM variant, which can used also for commercial activities. The licenses for commercial variant are much more expensive, so usually the commercial variant has only subset of features compared to the EDU available.</li>
-</ul>
-<p>Â </p>
-<p>To load the latest version of Matlab load the module</p>
-<pre class=" ">$ module load matlab</pre>
-<p>By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use</p>
-<pre class=" ">$ module avail matlab</pre>
-<p>If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.</p>
-<p>If you require the Matlab GUI, please follow the general informations about <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">running graphical applications</a>.</p>
-<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">here</a>) is recommended.</p>
-<p>To run Matlab with GUI, use</p>
-<pre class=" ">$ matlab</pre>
-<p>To run Matlab in text mode, without the Matlab Desktop GUI environment, use</p>
-<pre class=" ">$ matlab -nodesktop -nosplash</pre>
-<p>plots, images, etc... will be still available.</p>
-<h2 class=" ">Running parallel Matlab using Distributed Computing Toolbox / Engine</h2>
-<p>Recommended parallel mode for running parallel Matlab on Anselm is MPIEXEC mode. In this mode user allocates resources through PBS prior to starting Matlab. Once resources are granted the main Matlab instance is started on the first compute node assigned to job by PBS and workers are started on all remaining nodes. User can use both interactive and non-interactive PBS sessions. This mode guarantees that the data processing is not performed on login nodes, but all processing is on compute nodes.</p>
-<p>Â <img title="Parallel Matlab" class="image-inline" alt="Parallel Matlab" src="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/Matlab.png" /></p>
-<p>For the performance reasons Matlab should use system MPI. On Anselm the supported MPI implementation for Matlab is Intel MPI. To switch to system MPI user has to override default Matlab setting by creating new configuration file in its home directory. The path and file name has to be exactly the same as in the following listing:</p>
-<pre class=" "><strong>$ vim ~/matlab/mpiLibConf.m </strong></pre>
-<pre class=" "><strong>function [lib, extras] = mpiLibConf</strong><br /><strong>%MATLAB MPI Library overloading for Infiniband Networks</strong><br /><br /><strong>mpich = '/opt/intel/impi/4.1.1.036/lib64/';</strong><br /><br /><strong>disp('Using Intel MPI 4.1.1.036 over Infiniband')</strong><br /><br /><strong>lib = strcat(mpich, 'libmpich.so');</strong><br /><strong>mpl = strcat(mpich, 'libmpl.so');</strong><br /><strong>opa = strcat(mpich, 'libopa.so');</strong><br /><br /><strong>extras = {};</strong></pre>
-<p>System MPI library allows Matlab to communicate through 40Gbps Infiniband QDR interconnect instead of slower 1Gb ethernet network.</p>
-<p class="callout">Please note: The path to MPI library in "mpiLibConf.m" has to match with version of loaded Intel MPI module. In this example the version 4.1.1.036 of Iintel MPI is used by Matlab and therefore module impi/4.1.1.036Â has to be loaded prior to starting Matlab.</p>
-<h3 class=" ">Parallel Matlab interactive session</h3>
-<p>Once this file is in place, user can request resources from PBS. Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">this page</a>.</p>
-<pre class=" ">$ xhost +<br />$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=4:ncpus=16:mpiprocs=16 -l walltime=00:30:00 \<br />-l feature__matlab__MATLAB=1 </pre>
-<p>This qsub command example shows how to run Matlab with 32 workers in following configuration: 2 nodes (use all 16 cores per node) and 16 workers = mpirocs per node (-l select=2:ncpus=16:mpiprocs=16). If user requires to run smaller number of workers per node then the "mpiprocs" parameter has to be changed.</p>
-<p>The second part of the command shows how to request all necessary licenses. In this case 1 Matlab-EDU license and 32 Distributed Computing Engines licenses.</p>
-<p>Once the access to compute nodes is granted by PBS, user can load following modules and start Matlab:Â </p>
-<pre class=" ">cn79$ module load matlab/R2013a-EDU<br />cn79$ module load impi/4.1.1.036<br />cn79$ matlab &</pre>
-<h3 class=" ">Parallel Matlab batch job</h3>
-<p>To run matlab in batch mode, write an matlab script, then write a bash jobscript and execute via the qsub command. By default, matlab will execute one matlab worker instance per allocated core.</p>
-<pre class=" ">#!/bin/bash<br />#PBS -A PROJECT ID<br />#PBS -q qprod<br />#PBS -l select=2:ncpus=16:mpiprocs=16:ompthreads=1<br /><br /># change to shared scratch directory<br />SCR=/scratch/$USER/$PBS_JOBID<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/matlabcode.m .<br /><br /># load modules<br />module load matlab/R2013a-EDU<br />module load impi/4.1.1.036<br /><br /># execute the calculation<br />matlab -nodisplay -r matlabcode > output.out<br /><br /># copy output file to home<br />cp output.out $PBS_O_WORKDIR/.</pre>
-<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs and matlab script are in matlabcode.m file, outputs in output.out file. Note the missing .m extension in the matlab -r matlabcodefile call, <strong>the .m must not be included</strong>. Note that the <strong>shared /scratch must be used</strong>. Further, it is <strong>important to include quit</strong> statement at the end of the matlabcode.m script.</p>
-<p>Submit the jobscript using qsub</p>
-<pre class=" ">$ qsub ./jobscript</pre>
-<h3 class=" ">Parallel Matlab program example</h3>
-<p>The last part of the configuration is done directly in the user Matlab script before Distributed Computing Toolbox is started.</p>
-<pre class=" ">sched = findResource('scheduler', 'type', 'mpiexec');<br />set(sched, 'MpiexecFileName', '/apps/intel/impi/4.1.1/bin/mpirun');<br />set(sched, 'EnvironmentSetMethod', 'setenv');</pre>
-<p class=" ">This script creates scheduler object "sched" of type "mpiexec" that starts workers using mpirun tool. To use correct version of mpirun, the second line specifies the path to correct version of system Intel MPI library.</p>
-<p class="callout">Please note: Every Matlab script that needs to initialize/use matlabpool has to contain these three lines prior to calling matlabpool(sched, ...) function. </p>
-<p class=" ">The last step is to start matlabpool with "sched" object and correct number of workers. In this case qsub asked for total number of 32 cores, therefore the number of workers is also set to 32.</p>
-<pre class=" ">matlabpool(sched,32);<br /> <br /> <br />... parallel code ...<br /> <br /> <br />matlabpool close</pre>
-<p>The complete example showing how to use Distributed Computing Toolbox is show here. </p>
-<pre class=" ">sched = findResource('scheduler', 'type', 'mpiexec');<br />set(sched, 'MpiexecFileName', '/apps/intel/impi/4.1.1/bin/mpirun')<br />set(sched, 'EnvironmentSetMethod', 'setenv')<br />set(sched, 'SubmitArguments', '') <br />sched<br /><br />matlabpool(sched,32);<br /><br />n=2000;<br /><br />W = rand(n,n);<br />W = distributed(W);<br />x = (1:n)';<br />x = distributed(x);<br />spmd<br />[~, name] = system('hostname')<br />   <br />   T = W*x; % Calculation performed on labs, in parallel.<br />            % T and W are both codistributed arrays here.<br />end<br />T;<br />whos        % T and W are both distributed arrays here.<br /><br />matlabpool close<br />quit</pre>
-<p>You can copy and paste the example in a .m file and execute. Note that the matlabpool size should correspond to <strong>total number of cores</strong> available on allocated nodes.</p>
-<h3 class=" ">Non-interactive Session and Licenses</h3>
-<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">look here</a>.</p>
-<p>In case of non-interactive session please read the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
-<h3 class=" ">Matlab Distributed Computing Engines start up time</h3>
-<p>Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:</p>
-<table class="plain">
-<tbody>
-<tr><th>compute nodes</th><th>number of workers</th><th>start-up time[s]</th></tr>
-<tr>
-<td>16</td>
-<td>256</td>
-<td>1008</td>
-</tr>
-<tr>
-<td>8</td>
-<td>128</td>
-<td>534</td>
-</tr>
-<tr>
-<td>4</td>
-<td>64</td>
-<td>333</td>
-</tr>
-<tr>
-<td>2</td>
-<td>32</td>
-<td>210</td>
-</tr>
-</tbody>
-</table>
-<p>Â </p>
-<p>Â </p>
-
-
- </div>
-
-
- <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
-
- <div id="plone-discussions">
- <hr />
- <b><a id="plone-discussions-href" href="#plone-discussions">Komentáře</a></b>
- </div>
-
- <!-- <div id="contact-form" tal:condition="context/isDiscussable">
- <hr />
- <b><a id="contact-form-href" href="#contact-form" i18n:translate="">Contact form</a></b>
- <tal:contactform tal:content="structure python:getattr(context, 'contact-info')()"></tal:contactform>
- </div> -->
-
-
-
-
- </div>
- </content>
-
- <author>
-
- <name>jansik</name>
-
- </author>
-
- <published>2013-07-24T12:50:00+02:00</published>
-
- <updated>2016-07-13T15:41:35+02:00</updated>
-
-
- </entry>
-
-
-
- <entry>
- <title>MATLAB 2015b</title>
- <link rel="alternate" type="text/html" href="https://docs.it4i.cz/whats-new/news-feed/matlab-2015b"/>
-
- <id>urn:syndication:9b996ea95ba04f218d1eff951249ac50</id>
-
- <content type="xhtml" xml:base="https://docs.it4i.cz/changelog" xml:lang="cs" xml:space="preserve">
- <div xmlns="http://www.w3.org/1999/xhtml">
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-
-
-
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- <div id="parent-fieldname-text" class="plain">
- <p>MATLAB 2015b has been installed on Anselm and Salomon. Modules are named MATLAB/2015b-COM and MATLAB/2015b-EDU. Release notes:Â http://www.mathworks.com/help/matlab/release-notes.html#R2015b</p>
- </div>
-
-
-
- </div>
- </content>
-
- <author>
-
- <name>sta545</name>
-
- </author>
-
- <published>2016-07-13T15:40:00+02:00</published>
-
- <updated>2016-07-13T15:38:48+02:00</updated>
-
-
- </entry>
-
-
-
- <entry>
- <title>Numerical languages</title>
- <link rel="alternate" type="text/html" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction"/>
-
- <id>urn:syndication:6c3faf66932c4ed6aaf3471f0ab0e081</id>
- <summary>Interpreted languages for numerical computations and analysis</summary>
- <content type="xhtml" xml:base="https://docs.it4i.cz/changelog" xml:lang="cs" xml:space="preserve">
- <div xmlns="http://www.w3.org/1999/xhtml">
-
-
-
- <div id="parent-fieldname-text-6c3faf66932c4ed6aaf3471f0ab0e081" class="">
- <h2 class=" ">Introduction</h2>
-<p>This section contains a collection of high-level interpreted languages, primarily intended for numerical computations.</p>
-<h2 class=" ">Matlab</h2>
-<p>MATLAB<sup>®</sup> is a high-level language and interactive environment for numerical computation, visualization, and programming.</p>
-<pre class=" ">$ module load MATLAB/2015b-EDU<br />$ matlab</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab">Matlab<span class="internal-link"></span> page</a>.</p>
-<h2 class=" ">Octave</h2>
-<p>GNU Octave is a high-level interpreted language, primarily intended for numerical computations. The Octave language is quite similar to Matlab so that most programs are easily portable.</p>
-<pre class=" ">$ module load Octave<br />$ octave</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave">Octave page</a>.</p>
-<h2 class=" ">R</h2>
-<p>The R is an interpreted language and environment for statistical computing and graphics.</p>
-<pre class=" ">$ module load R<br />$ R</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r">R page</a>.</p>
-
- </div>
-
-
- <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
-
- <div id="plone-discussions">
- <hr />
- <b><a id="plone-discussions-href" href="#plone-discussions">Komentáře</a></b>
- </div>
-
- <!-- <div id="contact-form" tal:condition="context/isDiscussable">
- <hr />
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- <tal:contactform tal:content="structure python:getattr(context, 'contact-info')()"></tal:contactform>
- </div> -->
-
-
-
-
- </div>
- </content>
-
- <author>
-
- <name>jansik</name>
-
- </author>
-
- <published>2014-02-25T13:25:00+02:00</published>
-
- <updated>2016-07-13T15:35:37+02:00</updated>
-
-
- </entry>
-
-
-
- <entry>
- <title>List of Available Modules</title>
- <link rel="alternate" type="text/html" href="https://docs.it4i.cz/salomon/list_of_modules"/>
-
- <id>urn:syndication:07f9a79724204a24adc155a93c34b79c</id>
- <summary>List of Available Modules on Salomon Cluster</summary>
- <content type="xhtml" xml:base="https://docs.it4i.cz/changelog" xml:lang="cs" xml:space="preserve">
- <div xmlns="http://www.w3.org/1999/xhtml">
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- <div>
-
- <h2 id="categories">Categories</h2>
-
- <ul>
- <li>
- <a href="#base">base</a><br />
- </li>
- <li>
- <a href="#bio">bio</a><br />
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- <li>
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+ <ul>
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+ <a href="#base">base</a><br />
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+ <a href="#phys">phys</a><br />
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+ </li>
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+ <a href="#toolchain">toolchain</a><br />
+ </li>
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+ <a href="#tools">tools</a><br />
+ </li>
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+ <a href="#vis">vis</a><br />
+ </li>
+ </ul>
<div>
<h2 id="base"><a class="tooltip" title="Go to list of categories..." href="#categories">base</a></h2>
@@ -2590,6 +1959,7 @@ latency hiding, direct access to the protocol, improved threading support, and e
<td>
<ul>
<li style="white-space: nowrap;">1.10-Python-2.7.8</li>
+ <li style="white-space: nowrap;">1.11-Python-2.7.9</li>
<li style="white-space: nowrap;">1.11-foss-2015g-Python-2.7.9</li>
<li style="white-space: nowrap;">1.11-intel-2015b-Python-2.7.9</li>
</ul>
@@ -2871,6 +2241,7 @@ in numerous market categories from gaming and entertainment to scientific and me
<li style="white-space: nowrap;">2.7.11-intel-2015b</li>
<li style="white-space: nowrap;">2.7.8-intel-2015b</li>
<li style="white-space: nowrap;">2.7.8-intel-2016.01</li>
+ <li style="white-space: nowrap;">2.7.9</li>
<li style="white-space: nowrap;">2.7.9-GNU-5.1.0-2.25</li>
<li style="white-space: nowrap;">2.7.9-foss-2015b</li>
<li style="white-space: nowrap;">2.7.9-foss-2015g</li>
@@ -3357,6 +2728,7 @@ latency hiding, direct access to the protocol, improved threading support, and e
<td>
<ul>
<li style="white-space: nowrap;">1.10-Python-2.7.8</li>
+ <li style="white-space: nowrap;">1.11-Python-2.7.9</li>
<li style="white-space: nowrap;">1.11-foss-2015g-Python-2.7.9</li>
<li style="white-space: nowrap;">1.11-intel-2015b-Python-2.7.9</li>
</ul>
@@ -4502,6 +3874,8 @@ is distributed under the GNU General Public License (GPL)</td>
<ul>
<li style="white-space: nowrap;">2015a-COM</li>
<li style="white-space: nowrap;">2015a-EDU</li>
+ <li style="white-space: nowrap;">2015b-COM</li>
+ <li style="white-space: nowrap;">2015b-EDU</li>
</ul>
</td>
</tr>
@@ -4597,6 +3971,7 @@ virtualizer.</td>
<td>Szip compression software, providing lossless compression of scientific data</td>
<td>
<ul>
+ <li style="white-space: nowrap;">2.1</li>
<li style="white-space: nowrap;">2.1-foss-2015b</li>
<li style="white-space: nowrap;">2.1-foss-2015g</li>
<li style="white-space: nowrap;">2.1-ictce-7.3.5</li>
@@ -4805,6 +4180,7 @@ to handle everything from small to very large projects with speed and efficiency
<li style="white-space: nowrap;">2.0.10-GNU-4.9.3-2.25</li>
<li style="white-space: nowrap;">2.0.10-GNU-5.1.0-2.25</li>
<li style="white-space: nowrap;">2.0.10-iccifort-2015.3.187-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">2.0.11</li>
<li style="white-space: nowrap;">2.0.11-GCC-4.9.3-2.25</li>
<li style="white-space: nowrap;">2.0.11-GCC-5.3.0-2.26</li>
<li style="white-space: nowrap;">2.0.9-GCC-4.4.7-system</li>
@@ -4835,6 +4211,7 @@ to handle everything from small to very large projects with speed and efficiency
<td>
<ul>
<li style="white-space: nowrap;">6.18.01-intel-2015b</li>
+ <li style="white-space: nowrap;">6.19.00</li>
</ul>
</td>
</tr>
@@ -5228,6 +4605,7 @@ and documentation</td>
<td>
<ul>
<li style="white-space: nowrap;">1.6.2-Python-2.7.8</li>
+ <li style="white-space: nowrap;">1.6.2-Python-2.7.9</li>
<li style="white-space: nowrap;">1.6.2-foss-2015g-Python-2.7.9</li>
<li style="white-space: nowrap;">1.6.2-intel-2015b-Python-2.7.9</li>
</ul>
@@ -5285,6 +4663,7 @@ useful for allowing clients to interact with the X Display Manager.
<td>
<ul>
<li style="white-space: nowrap;">1.3.2-Python-2.7.8</li>
+ <li style="white-space: nowrap;">1.3.3</li>
<li style="white-space: nowrap;">1.3.3-foss-2015g</li>
<li style="white-space: nowrap;">1.3.3-foss-2015g-Python-2.7.9</li>
<li style="white-space: nowrap;">1.3.3-intel-2015b</li>
@@ -5362,6 +4741,7 @@ useful for allowing clients to interact with the X Display Manager.
<ul>
<li style="white-space: nowrap;">1.1.4-foss-2015g-libX11-1.6.2</li>
<li style="white-space: nowrap;">1.1.4-intel-2015b-libX11-1.6.2</li>
+ <li style="white-space: nowrap;">1.1.4-libX11-1.6.2</li>
<li style="white-space: nowrap;">1.1.5-foss-2015g</li>
</ul>
</td>
@@ -5414,15 +4794,646 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
</table>
</div>
-</div>
+</div>
+
+ </div>
+
+
+ <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
+
+
+
+ <!-- <div id="contact-form" tal:condition="context/isDiscussable">
+ <hr />
+ <b><a id="contact-form-href" href="#contact-form" i18n:translate="">Contact form</a></b>
+ <tal:contactform tal:content="structure python:getattr(context, 'contact-info')()"></tal:contactform>
+ </div> -->
+
+
+
+
+ </div>
+ </content>
+
+ <author>
+
+ <name>admin_write_modules_table</name>
+
+ </author>
+
+ <published>2016-07-14T02:00:02+02:00</published>
+
+ <updated>2016-07-14T02:00:02+02:00</updated>
+
+
+ </entry>
+
+
+
+ <entry>
+ <title>Matlab</title>
+ <link rel="alternate" type="text/html" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab"/>
+
+ <id>urn:syndication:73e8cd3babab4da398f316c8d257916d</id>
+
+ <content type="xhtml" xml:base="https://docs.it4i.cz/changelog" xml:lang="cs" xml:space="preserve">
+ <div xmlns="http://www.w3.org/1999/xhtml">
+
+
+
+ <div id="parent-fieldname-text-73e8cd3babab4da398f316c8d257916d" class="">
+ <h2 class=" ">Introduction</h2>
+<p>Matlab is available in versions R2015a and R2015b. There are always two variants of the release:</p>
+<ul>
+<li>Non commercial or so called EDU variant, which can be used for common research and educational purposes.</li>
+<li>Commercial or so called COM variant, which can used also for commercial activities. The licenses for commercial variant are much more expensive, so usually the commercial variant has only subset of features compared to the EDU available.</li>
+</ul>
+<p>Â </p>
+<p>To load the latest version of Matlab load the module</p>
+<pre class=" ">$ module load MATLAB</pre>
+<p>By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use</p>
+<pre class=" ">$ module avail MATLAB</pre>
+<p>If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.</p>
+<p>If you require the Matlab GUI, please follow the general informations about <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">running graphical applications</a>.</p>
+<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">here</a>) is recommended.</p>
+<p>To run Matlab with GUI, use</p>
+<pre class=" ">$ matlab</pre>
+<p>To run Matlab in text mode, without the Matlab Desktop GUI environment, use</p>
+<pre class=" ">$ matlab -nodesktop -nosplash</pre>
+<p>plots, images, etc... will be still available.</p>
+<h2 class=" "><a name="running-parallel-matlab-using-distributed-computing-toolbox---engine"></a>Running parallel Matlab using Distributed Computing Toolbox / Engine</h2>
+<p class="exclamation">Distributed toolbox is available only for the EDU variant</p>
+<p class=" ">The MPIEXEC mode available in previous versions is no longer available in MATLAB 2015. Also, the programming interface has changed. Refer to <a class="external-link" href="http://www.mathworks.com/help/distcomp/release-notes.html#buanp9e-1" target="_self" title="">Release Notes</a>.</p>
+<p class=" ">Delete previously used file mpiLibConf.m, we have observed crashes when using Intel MPI.</p>
+<p class=" ">To use Distributed Computing, you first need to setup a parallel profile. We have provided the profile for you, you can either import it in MATLAB command line:</p>
+<pre class=" ">>> parallel.importProfile('/apps/all/MATLAB/2015a-EDU/SalomonPBSPro.settings')<br /><br />ans = <br /><br />SalomonPBSPro </pre>
+<p class=" ">Or in the GUI, go to tab HOME -> Parallel -> Manage Cluster Profiles..., click Import and navigate to :</p>
+<p class=" ">/apps/all/MATLAB/2015a-EDU/SalomonPBSPro.settings</p>
+<p class=" ">With the new mode, MATLAB itself launches the workers via PBS, so you can either use interactive mode or a batch mode on one node, but the actual parallel processing will be done in a separate job started by MATLAB itself. Alternatively, you can use "local" mode to run parallel code on just a single node.</p>
+<p class="exclamation">The profile is confusingly named Salomon, but you can use it also on Anselm.</p>
+<h3 class=" ">Parallel Matlab interactive session</h3>
+<p>Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">this page</a>.</p>
+<pre class=" ">$ xhost +<br />$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00 \<br />-l feature__matlab__MATLAB=1 </pre>
+<p>This qsub command example shows how to run Matlab on a single node.</p>
+<p>The second part of the command shows how to request all necessary licenses. In this case 1 Matlab-EDU license and 48 Distributed Computing Engines licenses.</p>
+<p>Once the access to compute nodes is granted by PBS, user can load following modules and start Matlab:Â </p>
+<pre class=" ">r1i0n17$ module load MATLAB/2015b-EDU<br />r1i0n17$ matlab &</pre>
+<h3 class=" "><a name="parallel-matlab-batch-job-in-local-mode"></a>Parallel Matlab batch job in Local mode</h3>
+<p>To run matlab in batch mode, write an matlab script, then write a bash jobscript and execute via the qsub command. By default, matlab will execute one matlab worker instance per allocated core.</p>
+<pre class=" ">#!/bin/bash<br />#PBS -A PROJECT ID<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=16:mpiprocs=16:ompthreads=1<br /><br /># change to shared scratch directory<br />SCR=/scratch/work/user/$USER/$PBS_JOBID<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/matlabcode.m .<br /><br /># load modules<br />module load MATLAB/2015a-EDU<br /><br /># execute the calculation<br />matlab -nodisplay -r matlabcode > output.out<br /><br /># copy output file to home<br />cp output.out $PBS_O_WORKDIR/.</pre>
+<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs and matlab script are in matlabcode.m file, outputs in output.out file. Note the missing .m extension in the matlab -r matlabcodefile call, <strong>the .m must not be included</strong>. Note that the <strong>shared /scratch must be used</strong>. Further, it is <strong>important to include quit</strong> statement at the end of the matlabcode.m script.</p>
+<p>Submit the jobscript using qsub</p>
+<pre class=" ">$ qsub ./jobscript</pre>
+<h3 class=" ">Parallel Matlab Local mode program example</h3>
+<p>The last part of the configuration is done directly in the user Matlab script before Distributed Computing Toolbox is started.</p>
+<pre class=" ">cluster = parcluster('local')</pre>
+<p class=" ">This script creates scheduler object "cluster" of type "local" that starts workers locally. </p>
+<p class="callout">Please note: Every Matlab script that needs to initialize/use matlabpool has to contain these three lines prior to calling parpool(sched, ...) function. </p>
+<p class=" ">The last step is to start matlabpool with "cluster" object and correct number of workers. We have 24 cores per node, so we start 24 workers.</p>
+<pre class=" ">parpool(cluster,16);<br /> <br /> <br />... parallel code ...<br /> <br /> <br />parpool close</pre>
+<p>The complete example showing how to use Distributed Computing Toolbox in local mode is shown here. </p>
+<pre class=" ">cluster = parcluster('local');<br />cluster<br /><br />parpool(cluster,24);<br /><br />n=2000;<br /><br />W = rand(n,n);<br />W = distributed(W);<br />x = (1:n)';<br />x = distributed(x);<br />spmd<br />[~, name] = system('hostname')<br />   <br />   T = W*x; % Calculation performed on labs, in parallel.<br />            % T and W are both codistributed arrays here.<br />end<br />T;<br />whos        % T and W are both distributed arrays here.<br /><br />parpool close<br />quit</pre>
+<p>You can copy and paste the example in a .m file and execute. Note that the parpool size should correspond to <strong>total number of cores</strong> available on allocated nodes.</p>
+<h3 class=" ">Parallel Matlab Batch job using PBS mode (workers spawned in a separate job)</h3>
+<p>This mode uses PBS scheduler to launch the parallel pool. It uses the SalomonPBSPro profile that needs to be imported to Cluster Manager, as mentioned before. This methodod uses MATLAB's PBS Scheduler interface - it spawns the workers in a separate job submitted by MATLAB using qsub.</p>
+<p>This is an example of m-script using PBS mode:</p>
+<pre class=" ">cluster = parcluster('SalomonPBSPro');
+set(cluster, 'SubmitArguments', '-A OPEN-0-0');
+set(cluster, 'ResourceTemplate', '-q qprod -l select=10:ncpus=16');
+set(cluster, 'NumWorkers', 160);
+
+pool = parpool(cluster, 160);
+
+n=2000;
+
+W = rand(n,n);
+W = distributed(W);
+x = (1:n)';
+x = distributed(x);
+spmd
+[~, name] = system('hostname')
+
+ T = W*x; % Calculation performed on labs, in parallel.
+ % T and W are both codistributed arrays here.
+end
+whos % T and W are both distributed arrays here.
+
+% shut down parallel pool
+delete(pool)
+</pre>
+<p class=" ">Note that we first construct a cluster object using the imported profile, then set some important options, namely : SubmitArguments, where you need to specify accounting id, and ResourceTemplate, where you need to specify number of nodes to run the job. </p>
+<p class=" ">You can start this script using batch mode the same way as in Local mode example.</p>
+<h3 class=" ">Parallel Matlab Batch with direct launch (workers spawned within the existing job)</h3>
+<p>This method is a "hack" invented by us to emulate the mpiexec functionality found in previous MATLAB versions. We leverage the MATLAB Generic Scheduler interface, but instead of submitting the workers to PBS, we launch the workers directly within the running job, thus we avoid the issues with master script and workers running in separate jobs (issues with license not available, waiting for the worker's job to spawn etc.)</p>
+<p>Please note that this method is experimental.</p>
+<p>For this method, you need to use SalomonDirect profile, import it using <a class="anchor-link" href="#running-parallel-matlab-using-distributed-computing-toolbox---engine" target="_self" title="">the same way as SalomonPBSPro</a> </p>
+<p>This is an example of m-script using direct mode:</p>
+<pre class=" "><br />parallel.importProfile('/apps/all/MATLAB/2015a-EDU/SalomonDirect.settings')<br />cluster = parcluster('SalomonDirect');
+set(cluster, 'NumWorkers', 48);
+
+pool = parpool(cluster, 48);
+
+n=2000;
+
+W = rand(n,n);
+W = distributed(W);
+x = (1:n)';
+x = distributed(x);
+spmd
+[~, name] = system('hostname')
+
+ T = W*x; % Calculation performed on labs, in parallel.
+ % T and W are both codistributed arrays here.
+end
+whos % T and W are both distributed arrays here.
+
+% shut down parallel pool
+delete(pool)</pre>
+<h3 class=" ">Non-interactive Session and Licenses</h3>
+<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">look here</a>.</p>
+<p>In case of non-interactive session please read the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
+<h3 class=" ">Matlab Distributed Computing Engines start up time</h3>
+<p>Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:</p>
+<table class="plain">
+<tbody>
+<tr><th>compute nodes</th><th>number of workers</th><th>start-up time[s]</th></tr>
+<tr>
+<td>16</td>
+<td>384</td>
+<td>831</td>
+</tr>
+<tr>
+<td>8</td>
+<td>192</td>
+<td>807</td>
+</tr>
+<tr>
+<td>4</td>
+<td>96</td>
+<td>483</td>
+</tr>
+<tr>
+<td>2</td>
+<td>48</td>
+<td>16</td>
+</tr>
+</tbody>
+</table>
+<h2>MATLAB on UV2000Â </h2>
+<p>UV2000 machine available in queue "qfat" can be used for MATLAB computations. This is a SMP NUMA machine with large amount of RAM, which can be beneficial for certain types of MATLAB jobs. CPU cores are allocated in chunks of 8 for this machine.</p>
+<p>You can use MATLAB on UV2000 in two parallel modes :</p>
+<h3>Threaded mode</h3>
+<p class=" ">Since this is a SMP machine, you can completely avoid using Parallel Toolbox and use only MATLAB's threading. MATLAB will automatically detect the number of cores you have allocated and will set <span class="monospace">maxNumCompThreads </span>accordingly and certain operations, such as <span class="monospace">fft, \, eig, svd</span>, etc. will be automatically run in threads. The advantage of this mode is that you don't need to modify your existing sequential codes.<span class="monospace"><br /></span></p>
+<h3 class=" ">Local cluster mode</h3>
+<p>You can also use Parallel Toolbox on UV2000. Use l<a class="anchor-link" href="#parallel-matlab-batch-job-in-local-mode" target="_self" title="">ocal cluster mode</a>, "SalomonPBSPro" profile will not work.</p>
+<p>Â </p>
+<p>Â </p>
+
+
+ </div>
+
+
+ <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
+
+ <div id="plone-discussions">
+ <hr />
+ <b><a id="plone-discussions-href" href="#plone-discussions">Komentáře</a></b>
+ </div>
+
+ <!-- <div id="contact-form" tal:condition="context/isDiscussable">
+ <hr />
+ <b><a id="contact-form-href" href="#contact-form" i18n:translate="">Contact form</a></b>
+ <tal:contactform tal:content="structure python:getattr(context, 'contact-info')()"></tal:contactform>
+ </div> -->
+
+
+
+
+ </div>
+ </content>
+
+ <author>
+
+ <name>jansik</name>
+
+ </author>
+
+ <published>2013-07-24T12:50:00+02:00</published>
+
+ <updated>2016-07-13T16:11:19+02:00</updated>
+
+
+ </entry>
+
+
+
+ <entry>
+ <title>Matlab</title>
+ <link rel="alternate" type="text/html" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab"/>
+
+ <id>urn:syndication:2efd48d0282d45b7b8fb11393c96d853</id>
+
+ <content type="xhtml" xml:base="https://docs.it4i.cz/changelog" xml:lang="cs" xml:space="preserve">
+ <div xmlns="http://www.w3.org/1999/xhtml">
+
+
+
+ <div id="parent-fieldname-text-2efd48d0282d45b7b8fb11393c96d853" class="">
+ <h2 class=" ">Introduction</h2>
+<p>Matlab is available in versions R2015a and R2015b. There are always two variants of the release:</p>
+<ul>
+<li>Non commercial or so called EDU variant, which can be used for common research and educational purposes.</li>
+<li>Commercial or so called COM variant, which can used also for commercial activities. The licenses for commercial variant are much more expensive, so usually the commercial variant has only subset of features compared to the EDU available.</li>
+</ul>
+<p>Â </p>
+<p>To load the latest version of Matlab load the module</p>
+<pre class=" ">$ module load MATLAB</pre>
+<p>By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use</p>
+<pre class=" ">$ module avail MATLAB</pre>
+<p>If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.</p>
+<p>If you require the Matlab GUI, please follow the general informations about <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">running graphical applications</a>.</p>
+<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">here</a>) is recommended.</p>
+<p>To run Matlab with GUI, use</p>
+<pre class=" ">$ matlab</pre>
+<p>To run Matlab in text mode, without the Matlab Desktop GUI environment, use</p>
+<pre class=" ">$ matlab -nodesktop -nosplash</pre>
+<p>plots, images, etc... will be still available.</p>
+<h2 class=" "><a name="running-parallel-matlab-using-distributed-computing-toolbox---engine"></a>Running parallel Matlab using Distributed Computing Toolbox / Engine</h2>
+<p class="exclamation">Distributed toolbox is available only for the EDU variant</p>
+<p class=" ">The MPIEXEC mode available in previous versions is no longer available in MATLAB 2015. Also, the programming interface has changed. Refer to <a class="external-link" href="http://www.mathworks.com/help/distcomp/release-notes.html#buanp9e-1" target="_self" title="">Release Notes</a>.</p>
+<p class=" ">Delete previously used file mpiLibConf.m, we have observed crashes when using Intel MPI.</p>
+<p class=" ">To use Distributed Computing, you first need to setup a parallel profile. We have provided the profile for you, you can either import it in MATLAB command line:</p>
+<pre class=" ">>> parallel.importProfile('/apps/all/MATLAB/2015b-EDU/SalomonPBSPro.settings')<br /><br />ans = <br /><br />SalomonPBSPro </pre>
+<p class=" ">Or in the GUI, go to tab HOME -> Parallel -> Manage Cluster Profiles..., click Import and navigate to :</p>
+<p class=" ">/apps/all/MATLAB/2015b-EDU/SalomonPBSPro.settings</p>
+<p class=" ">With the new mode, MATLAB itself launches the workers via PBS, so you can either use interactive mode or a batch mode on one node, but the actual parallel processing will be done in a separate job started by MATLAB itself. Alternatively, you can use "local" mode to run parallel code on just a single node.</p>
+<h3 class=" ">Parallel Matlab interactive session</h3>
+<p>Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">this page</a>.</p>
+<pre class=" ">$ xhost +<br />$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00 \<br />-l feature__matlab__MATLAB=1 </pre>
+<p>This qsub command example shows how to run Matlab on a single node.</p>
+<p>The second part of the command shows how to request all necessary licenses. In this case 1 Matlab-EDU license and 48 Distributed Computing Engines licenses.</p>
+<p>Once the access to compute nodes is granted by PBS, user can load following modules and start Matlab:Â </p>
+<pre class=" ">r1i0n17$ module load MATLAB/2015a-EDU<br />r1i0n17$ matlab &</pre>
+<h3 class=" "><a name="parallel-matlab-batch-job-in-local-mode"></a>Parallel Matlab batch job in Local mode</h3>
+<p>To run matlab in batch mode, write an matlab script, then write a bash jobscript and execute via the qsub command. By default, matlab will execute one matlab worker instance per allocated core.</p>
+<pre class=" ">#!/bin/bash<br />#PBS -A PROJECT ID<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=24:mpiprocs=24:ompthreads=1<br /><br /># change to shared scratch directory<br />SCR=/scratch/work/user/$USER/$PBS_JOBID<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/matlabcode.m .<br /><br /># load modules<br />module load MATLAB/2015a-EDU<br /><br /># execute the calculation<br />matlab -nodisplay -r matlabcode > output.out<br /><br /># copy output file to home<br />cp output.out $PBS_O_WORKDIR/.</pre>
+<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs and matlab script are in matlabcode.m file, outputs in output.out file. Note the missing .m extension in the matlab -r matlabcodefile call, <strong>the .m must not be included</strong>. Note that the <strong>shared /scratch must be used</strong>. Further, it is <strong>important to include quit</strong> statement at the end of the matlabcode.m script.</p>
+<p>Submit the jobscript using qsub</p>
+<pre class=" ">$ qsub ./jobscript</pre>
+<h3 class=" ">Parallel Matlab Local mode program example</h3>
+<p>The last part of the configuration is done directly in the user Matlab script before Distributed Computing Toolbox is started.</p>
+<pre class=" ">cluster = parcluster('local')</pre>
+<p class=" ">This script creates scheduler object "cluster" of type "local" that starts workers locally. </p>
+<p class="callout">Please note: Every Matlab script that needs to initialize/use matlabpool has to contain these three lines prior to calling parpool(sched, ...) function. </p>
+<p class=" ">The last step is to start matlabpool with "cluster" object and correct number of workers. We have 24 cores per node, so we start 24 workers.</p>
+<pre class=" ">parpool(cluster,24);<br /> <br /> <br />... parallel code ...<br /> <br /> <br />parpool close</pre>
+<p>The complete example showing how to use Distributed Computing Toolbox in local mode is shown here. </p>
+<pre class=" ">cluster = parcluster('local');<br />cluster<br /><br />parpool(cluster,24);<br /><br />n=2000;<br /><br />W = rand(n,n);<br />W = distributed(W);<br />x = (1:n)';<br />x = distributed(x);<br />spmd<br />[~, name] = system('hostname')<br />   <br />   T = W*x; % Calculation performed on labs, in parallel.<br />            % T and W are both codistributed arrays here.<br />end<br />T;<br />whos        % T and W are both distributed arrays here.<br /><br />parpool close<br />quit</pre>
+<p>You can copy and paste the example in a .m file and execute. Note that the parpool size should correspond to <strong>total number of cores</strong> available on allocated nodes.</p>
+<h3 class=" ">Parallel Matlab Batch job using PBS mode (workers spawned in a separate job)</h3>
+<p>This mode uses PBS scheduler to launch the parallel pool. It uses the SalomonPBSPro profile that needs to be imported to Cluster Manager, as mentioned before. This methodod uses MATLAB's PBS Scheduler interface - it spawns the workers in a separate job submitted by MATLAB using qsub.</p>
+<p>This is an example of m-script using PBS mode:</p>
+<pre class=" ">cluster = parcluster('SalomonPBSPro');
+set(cluster, 'SubmitArguments', '-A OPEN-0-0');
+set(cluster, 'ResourceTemplate', '-q qprod -l select=10:ncpus=24');
+set(cluster, 'NumWorkers', 240);
+
+pool = parpool(cluster,240);
+
+n=2000;
+
+W = rand(n,n);
+W = distributed(W);
+x = (1:n)';
+x = distributed(x);
+spmd
+[~, name] = system('hostname')
+
+ T = W*x; % Calculation performed on labs, in parallel.
+ % T and W are both codistributed arrays here.
+end
+whos % T and W are both distributed arrays here.
+
+% shut down parallel pool
+delete(pool)
+</pre>
+<p class=" ">Note that we first construct a cluster object using the imported profile, then set some important options, namely : SubmitArguments, where you need to specify accounting id, and ResourceTemplate, where you need to specify number of nodes to run the job. </p>
+<p class=" ">You can start this script using batch mode the same way as in Local mode example.</p>
+<h3 class=" ">Parallel Matlab Batch with direct launch (workers spawned within the existing job)</h3>
+<p>This method is a "hack" invented by us to emulate the mpiexec functionality found in previous MATLAB versions. We leverage the MATLAB Generic Scheduler interface, but instead of submitting the workers to PBS, we launch the workers directly within the running job, thus we avoid the issues with master script and workers running in separate jobs (issues with license not available, waiting for the worker's job to spawn etc.)</p>
+<p>Please note that this method is experimental.</p>
+<p>For this method, you need to use SalomonDirect profile, import it using <a class="anchor-link" href="#running-parallel-matlab-using-distributed-computing-toolbox---engine" target="_self" title="">the same way as SalomonPBSPro</a> </p>
+<p>This is an example of m-script using direct mode:</p>
+<pre class=" "><br />parallel.importProfile('/apps/all/MATLAB/2015b-EDU/SalomonDirect.settings')<br />cluster = parcluster('SalomonDirect');
+set(cluster, 'NumWorkers', 48);
+
+pool = parpool(cluster, 48);
+
+n=2000;
+
+W = rand(n,n);
+W = distributed(W);
+x = (1:n)';
+x = distributed(x);
+spmd
+[~, name] = system('hostname')
+
+ T = W*x; % Calculation performed on labs, in parallel.
+ % T and W are both codistributed arrays here.
+end
+whos % T and W are both distributed arrays here.
+
+% shut down parallel pool
+delete(pool)</pre>
+<h3 class=" ">Non-interactive Session and Licenses</h3>
+<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">look here</a>.</p>
+<p class="exclamation">The licensing feature of PBS is currently disabled.</p>
+<p>In case of non-interactive session please read the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
+<h3 class=" ">Matlab Distributed Computing Engines start up time</h3>
+<p>Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:</p>
+<table class="plain">
+<tbody>
+<tr><th>compute nodes</th><th>number of workers</th><th>start-up time[s]</th></tr>
+<tr>
+<td>16</td>
+<td>384</td>
+<td>831</td>
+</tr>
+<tr>
+<td>8</td>
+<td>192</td>
+<td>807</td>
+</tr>
+<tr>
+<td>4</td>
+<td>96</td>
+<td>483</td>
+</tr>
+<tr>
+<td>2</td>
+<td>48</td>
+<td>16</td>
+</tr>
+</tbody>
+</table>
+<h2>MATLAB on UV2000Â </h2>
+<p>UV2000 machine available in queue "qfat" can be used for MATLAB computations. This is a SMP NUMA machine with large amount of RAM, which can be beneficial for certain types of MATLAB jobs. CPU cores are allocated in chunks of 8 for this machine.</p>
+<p>You can use MATLAB on UV2000 in two parallel modes :</p>
+<h3>Threaded mode</h3>
+<p class=" ">Since this is a SMP machine, you can completely avoid using Parallel Toolbox and use only MATLAB's threading. MATLAB will automatically detect the number of cores you have allocated and will set <span class="monospace">maxNumCompThreads </span>accordingly and certain operations, such as <span class="monospace">fft, \, eig, svd</span>, etc. will be automatically run in threads. The advantage of this mode is that you don't need to modify your existing sequential codes.<span class="monospace"><br /></span></p>
+<h3 class=" ">Local cluster mode</h3>
+<p>You can also use Parallel Toolbox on UV2000. Use l<a class="anchor-link" href="#parallel-matlab-batch-job-in-local-mode" target="_self" title="">ocal cluster mode</a>, "SalomonPBSPro" profile will not work.</p>
+<p>Â </p>
+<p>Â </p>
+
+
+ </div>
+
+
+ <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
+
+ <div id="plone-discussions">
+ <hr />
+ <b><a id="plone-discussions-href" href="#plone-discussions">Komentáře</a></b>
+ </div>
+
+ <!-- <div id="contact-form" tal:condition="context/isDiscussable">
+ <hr />
+ <b><a id="contact-form-href" href="#contact-form" i18n:translate="">Contact form</a></b>
+ <tal:contactform tal:content="structure python:getattr(context, 'contact-info')()"></tal:contactform>
+ </div> -->
+
+
+
+
+ </div>
+ </content>
+
+ <author>
+
+ <name>jansik</name>
+
+ </author>
+
+ <published>2013-07-24T12:50:00+02:00</published>
+
+ <updated>2016-07-13T16:10:41+02:00</updated>
+
+
+ </entry>
+
+
+
+ <entry>
+ <title>Matlab 2013-2014</title>
+ <link rel="alternate" type="text/html" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab"/>
+
+ <id>urn:syndication:41bf242708954438ac56e1a431788c0e</id>
+
+ <content type="xhtml" xml:base="https://docs.it4i.cz/changelog" xml:lang="cs" xml:space="preserve">
+ <div xmlns="http://www.w3.org/1999/xhtml">
+
+
+
+ <div id="parent-fieldname-text-41bf242708954438ac56e1a431788c0e" class="">
+ <h2 class=" ">Introduction</h2>
+<p class="exclamation">This document relates to the old versions R2013 and R2014. For MATLAB 2015, please use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab">this documentation instead</a>.</p>
+<p>Matlab is available in the latest stable version. There are always two variants of the release:</p>
+<ul>
+<li>Non commercial or so called EDU variant, which can be used for common research and educational purposes.</li>
+<li>Commercial or so called COM variant, which can used also for commercial activities. The licenses for commercial variant are much more expensive, so usually the commercial variant has only subset of features compared to the EDU available.</li>
+</ul>
+<p>Â </p>
+<p>To load the latest version of Matlab load the module</p>
+<pre class=" ">$ module load matlab</pre>
+<p>By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use</p>
+<pre class=" ">$ module avail matlab</pre>
+<p>If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.</p>
+<p>If you require the Matlab GUI, please follow the general informations about <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">running graphical applications</a>.</p>
+<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">here</a>) is recommended.</p>
+<p>To run Matlab with GUI, use</p>
+<pre class=" ">$ matlab</pre>
+<p>To run Matlab in text mode, without the Matlab Desktop GUI environment, use</p>
+<pre class=" ">$ matlab -nodesktop -nosplash</pre>
+<p>plots, images, etc... will be still available.</p>
+<h2 class=" ">Running parallel Matlab using Distributed Computing Toolbox / Engine</h2>
+<p>Recommended parallel mode for running parallel Matlab on Anselm is MPIEXEC mode. In this mode user allocates resources through PBS prior to starting Matlab. Once resources are granted the main Matlab instance is started on the first compute node assigned to job by PBS and workers are started on all remaining nodes. User can use both interactive and non-interactive PBS sessions. This mode guarantees that the data processing is not performed on login nodes, but all processing is on compute nodes.</p>
+<p>Â <img alt="Parallel Matlab" class="image-inline" title="Parallel Matlab" src="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/Matlab.png" /></p>
+<p>For the performance reasons Matlab should use system MPI. On Anselm the supported MPI implementation for Matlab is Intel MPI. To switch to system MPI user has to override default Matlab setting by creating new configuration file in its home directory. The path and file name has to be exactly the same as in the following listing:</p>
+<pre class=" "><strong>$ vim ~/matlab/mpiLibConf.m </strong></pre>
+<pre class=" "><strong>function [lib, extras] = mpiLibConf</strong><br /><strong>%MATLAB MPI Library overloading for Infiniband Networks</strong><br /><br /><strong>mpich = '/opt/intel/impi/4.1.1.036/lib64/';</strong><br /><br /><strong>disp('Using Intel MPI 4.1.1.036 over Infiniband')</strong><br /><br /><strong>lib = strcat(mpich, 'libmpich.so');</strong><br /><strong>mpl = strcat(mpich, 'libmpl.so');</strong><br /><strong>opa = strcat(mpich, 'libopa.so');</strong><br /><br /><strong>extras = {};</strong></pre>
+<p>System MPI library allows Matlab to communicate through 40Gbps Infiniband QDR interconnect instead of slower 1Gb ethernet network.</p>
+<p class="callout">Please note: The path to MPI library in "mpiLibConf.m" has to match with version of loaded Intel MPI module. In this example the version 4.1.1.036 of Iintel MPI is used by Matlab and therefore module impi/4.1.1.036Â has to be loaded prior to starting Matlab.</p>
+<h3 class=" ">Parallel Matlab interactive session</h3>
+<p>Once this file is in place, user can request resources from PBS. Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">this page</a>.</p>
+<pre class=" ">$ xhost +<br />$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=4:ncpus=16:mpiprocs=16 -l walltime=00:30:00 \<br />-l feature__matlab__MATLAB=1 </pre>
+<p>This qsub command example shows how to run Matlab with 32 workers in following configuration: 2 nodes (use all 16 cores per node) and 16 workers = mpirocs per node (-l select=2:ncpus=16:mpiprocs=16). If user requires to run smaller number of workers per node then the "mpiprocs" parameter has to be changed.</p>
+<p>The second part of the command shows how to request all necessary licenses. In this case 1 Matlab-EDU license and 32 Distributed Computing Engines licenses.</p>
+<p>Once the access to compute nodes is granted by PBS, user can load following modules and start Matlab:Â </p>
+<pre class=" ">cn79$ module load matlab/R2013a-EDU<br />cn79$ module load impi/4.1.1.036<br />cn79$ matlab &</pre>
+<h3 class=" ">Parallel Matlab batch job</h3>
+<p>To run matlab in batch mode, write an matlab script, then write a bash jobscript and execute via the qsub command. By default, matlab will execute one matlab worker instance per allocated core.</p>
+<pre class=" ">#!/bin/bash<br />#PBS -A PROJECT ID<br />#PBS -q qprod<br />#PBS -l select=2:ncpus=16:mpiprocs=16:ompthreads=1<br /><br /># change to shared scratch directory<br />SCR=/scratch/$USER/$PBS_JOBID<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/matlabcode.m .<br /><br /># load modules<br />module load matlab/R2013a-EDU<br />module load impi/4.1.1.036<br /><br /># execute the calculation<br />matlab -nodisplay -r matlabcode > output.out<br /><br /># copy output file to home<br />cp output.out $PBS_O_WORKDIR/.</pre>
+<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs and matlab script are in matlabcode.m file, outputs in output.out file. Note the missing .m extension in the matlab -r matlabcodefile call, <strong>the .m must not be included</strong>. Note that the <strong>shared /scratch must be used</strong>. Further, it is <strong>important to include quit</strong> statement at the end of the matlabcode.m script.</p>
+<p>Submit the jobscript using qsub</p>
+<pre class=" ">$ qsub ./jobscript</pre>
+<h3 class=" ">Parallel Matlab program example</h3>
+<p>The last part of the configuration is done directly in the user Matlab script before Distributed Computing Toolbox is started.</p>
+<pre class=" ">sched = findResource('scheduler', 'type', 'mpiexec');<br />set(sched, 'MpiexecFileName', '/apps/intel/impi/4.1.1/bin/mpirun');<br />set(sched, 'EnvironmentSetMethod', 'setenv');</pre>
+<p class=" ">This script creates scheduler object "sched" of type "mpiexec" that starts workers using mpirun tool. To use correct version of mpirun, the second line specifies the path to correct version of system Intel MPI library.</p>
+<p class="callout">Please note: Every Matlab script that needs to initialize/use matlabpool has to contain these three lines prior to calling matlabpool(sched, ...) function. </p>
+<p class=" ">The last step is to start matlabpool with "sched" object and correct number of workers. In this case qsub asked for total number of 32 cores, therefore the number of workers is also set to 32.</p>
+<pre class=" ">matlabpool(sched,32);<br /> <br /> <br />... parallel code ...<br /> <br /> <br />matlabpool close</pre>
+<p>The complete example showing how to use Distributed Computing Toolbox is show here. </p>
+<pre class=" ">sched = findResource('scheduler', 'type', 'mpiexec');<br />set(sched, 'MpiexecFileName', '/apps/intel/impi/4.1.1/bin/mpirun')<br />set(sched, 'EnvironmentSetMethod', 'setenv')<br />set(sched, 'SubmitArguments', '') <br />sched<br /><br />matlabpool(sched,32);<br /><br />n=2000;<br /><br />W = rand(n,n);<br />W = distributed(W);<br />x = (1:n)';<br />x = distributed(x);<br />spmd<br />[~, name] = system('hostname')<br />   <br />   T = W*x; % Calculation performed on labs, in parallel.<br />            % T and W are both codistributed arrays here.<br />end<br />T;<br />whos        % T and W are both distributed arrays here.<br /><br />matlabpool close<br />quit</pre>
+<p>You can copy and paste the example in a .m file and execute. Note that the matlabpool size should correspond to <strong>total number of cores</strong> available on allocated nodes.</p>
+<h3 class=" ">Non-interactive Session and Licenses</h3>
+<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">look here</a>.</p>
+<p>In case of non-interactive session please read the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
+<h3 class=" ">Matlab Distributed Computing Engines start up time</h3>
+<p>Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:</p>
+<table class="plain">
+<tbody>
+<tr><th>compute nodes</th><th>number of workers</th><th>start-up time[s]</th></tr>
+<tr>
+<td>16</td>
+<td>256</td>
+<td>1008</td>
+</tr>
+<tr>
+<td>8</td>
+<td>128</td>
+<td>534</td>
+</tr>
+<tr>
+<td>4</td>
+<td>64</td>
+<td>333</td>
+</tr>
+<tr>
+<td>2</td>
+<td>32</td>
+<td>210</td>
+</tr>
+</tbody>
+</table>
+<p>Â </p>
+<p>Â </p>
+
</div>
<!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
+ <div id="plone-discussions">
+ <hr />
+ <b><a id="plone-discussions-href" href="#plone-discussions">Komentáře</a></b>
+ </div>
+
+ <!-- <div id="contact-form" tal:condition="context/isDiscussable">
+ <hr />
+ <b><a id="contact-form-href" href="#contact-form" i18n:translate="">Contact form</a></b>
+ <tal:contactform tal:content="structure python:getattr(context, 'contact-info')()"></tal:contactform>
+ </div> -->
+
+
+
+
+ </div>
+ </content>
+
+ <author>
+
+ <name>jansik</name>
+
+ </author>
+
+ <published>2013-07-24T12:50:00+02:00</published>
+
+ <updated>2016-07-13T15:41:35+02:00</updated>
+
+
+ </entry>
+
+
+
+ <entry>
+ <title>MATLAB 2015b</title>
+ <link rel="alternate" type="text/html" href="https://docs.it4i.cz/whats-new/news-feed/matlab-2015b"/>
+
+ <id>urn:syndication:9b996ea95ba04f218d1eff951249ac50</id>
+
+ <content type="xhtml" xml:base="https://docs.it4i.cz/changelog" xml:lang="cs" xml:space="preserve">
+ <div xmlns="http://www.w3.org/1999/xhtml">
+
+
+
+
+
+
+
+ <div id="parent-fieldname-text" class="plain">
+ <p>MATLAB 2015b has been installed on Anselm and Salomon. Modules are named MATLAB/2015b-COM and MATLAB/2015b-EDU. Release notes:Â http://www.mathworks.com/help/matlab/release-notes.html#R2015b</p>
+ </div>
+
+
+
+ </div>
+ </content>
+
+ <author>
+
+ <name>sta545</name>
+
+ </author>
+
+ <published>2016-07-13T15:40:00+02:00</published>
+
+ <updated>2016-07-13T15:38:48+02:00</updated>
+
+
+ </entry>
+
+
+
+ <entry>
+ <title>Numerical languages</title>
+ <link rel="alternate" type="text/html" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction"/>
+
+ <id>urn:syndication:6c3faf66932c4ed6aaf3471f0ab0e081</id>
+ <summary>Interpreted languages for numerical computations and analysis</summary>
+ <content type="xhtml" xml:base="https://docs.it4i.cz/changelog" xml:lang="cs" xml:space="preserve">
+ <div xmlns="http://www.w3.org/1999/xhtml">
+
+
+
+ <div id="parent-fieldname-text-6c3faf66932c4ed6aaf3471f0ab0e081" class="">
+ <h2 class=" ">Introduction</h2>
+<p>This section contains a collection of high-level interpreted languages, primarily intended for numerical computations.</p>
+<h2 class=" ">Matlab</h2>
+<p>MATLAB<sup>®</sup> is a high-level language and interactive environment for numerical computation, visualization, and programming.</p>
+<pre class=" ">$ module load MATLAB/2015b-EDU<br />$ matlab</pre>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab">Matlab<span class="internal-link"></span> page</a>.</p>
+<h2 class=" ">Octave</h2>
+<p>GNU Octave is a high-level interpreted language, primarily intended for numerical computations. The Octave language is quite similar to Matlab so that most programs are easily portable.</p>
+<pre class=" ">$ module load Octave<br />$ octave</pre>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave">Octave page</a>.</p>
+<h2 class=" ">R</h2>
+<p>The R is an interpreted language and environment for statistical computing and graphics.</p>
+<pre class=" ">$ module load R<br />$ R</pre>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r">R page</a>.</p>
+
+ </div>
+ <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
+
+ <div id="plone-discussions">
+ <hr />
+ <b><a id="plone-discussions-href" href="#plone-discussions">Komentáře</a></b>
+ </div>
+
<!-- <div id="contact-form" tal:condition="context/isDiscussable">
<hr />
<b><a id="contact-form-href" href="#contact-form" i18n:translate="">Contact form</a></b>
@@ -5437,13 +5448,13 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
<author>
- <name>admin_write_modules_table</name>
+ <name>jansik</name>
</author>
- <published>2016-07-13T02:00:02+02:00</published>
+ <published>2014-02-25T13:25:00+02:00</published>
- <updated>2016-07-13T02:00:02+02:00</updated>
+ <updated>2016-07-13T15:35:37+02:00</updated>
</entry>
@@ -5504,25 +5515,25 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
<h2 class=" ">Introduction</h2>
<p>We provide state of the art programms and tools to develop, profile and debug HPC codes at IT4Innovations.<br />On these pages, we provide an overview of the profiling and debugging tools available on Anslem at IT4I.</p>
<h2 class=" ">Intel debugger</h2>
-<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">X display</a> for running the GUI.</p>
+<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">X display</a> for running the GUI.</p>
<pre class=" ">$ module load intel<br />$ idb</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger">Intel Debugger</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger">Intel Debugger</a> page.</p>
<h2 class=" ">Allinea Forge (DDT/MAP)</h2>
<p>Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel Xeon Phi accelerators. DDT provides all the standard debugging features (stack trace, breakpoints, watches, view variables, threads etc.) for every thread running as part of your program, or for every process - even if these processes are distributed across a cluster using an MPI implementation.</p>
<pre class=" ">$ module load Forge<br />$ forge</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt">Allinea DDT</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt">Allinea DDT</a> page.</p>
<h2 class=" ">Allinea Performance Reports</h2>
<p>Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs. Our license is limited to 64 MPI processes.</p>
<pre class=" ">$ module load PerformanceReports/6.0 <br />$ perf-report mpirun -n 64 ./my_application argument01 argument02</pre>
-<p class=" ">Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports">Allinea Performance Reports</a> page.</p>
+<p class=" ">Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports">Allinea Performance Reports</a> page.</p>
<h2 class=" ">RougeWave Totalview</h2>
<p>TotalView is a source- and machine-level debugger for multi-process, multi-threaded programs. Its wide range of tools provides ways to analyze, organize, and test programs, making it easy to isolate and identify problems in individual threads and processes in programs of great complexity.</p>
<pre class=" ">$ module load totalview<br />$ totalview</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view">Totalview</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view">Totalview</a> page.</p>
<h2 class=" ">Vampir trace analyzer</h2>
<p>Vampir is a GUI trace analyzer for traces in OTF format.</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">Vampir</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">Vampir</a> page.</p>
</div>
@@ -5573,8 +5584,8 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
<div id="parent-fieldname-text-50ee0f8999e14a08822bd423d24de7ef" class="">
- <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
-<h2 class=" "><img title="Vampir screenshot" class="image-inline" alt="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
+ <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
+<h2 class=" "><img alt="Vampir screenshot" class="image-inline" title="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
<h2 class=" ">Installed versions</h2>
<p>Version 8.5.0 is currently installed as module <span class="monospace">Vampir/8.5.0</span> :</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir &</pre>
@@ -5639,25 +5650,25 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
<p>We provide state of the art programms and tools to develop, profile and debug HPC codes at IT4Innovations.<br />On these pages, we provide an overview of the profiling and debugging tools available on Anslem at IT4I.</p>
<h2 class=" ">Intel debugger</h2>
<p class="exclamation">Intel debugger is no longer available since Parallel Studio version 2015</p>
-<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">X display</a> for running the GUI.</p>
+<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">X display</a> for running the GUI.</p>
<pre class=" ">$ module load intel<br />$ idb</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger">Intel Debugger</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger">Intel Debugger</a> page.</p>
<h2 class=" ">Allinea Forge (DDT/MAP)</h2>
<p>Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel Xeon Phi accelerators. DDT provides all the standard debugging features (stack trace, breakpoints, watches, view variables, threads etc.) for every thread running as part of your program, or for every process - even if these processes are distributed across a cluster using an MPI implementation.</p>
<pre class=" ">$ module load Forge<br />$ forge</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt">Allinea DDT</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt">Allinea DDT</a> page.</p>
<h2 class=" ">Allinea Performance Reports</h2>
<p>Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs. Our license is limited to 64 MPI processes.</p>
<pre class=" ">$ module load PerformanceReports/6.0 <br />$ perf-report mpirun -n 64 ./my_application argument01 argument02</pre>
-<p class=" ">Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports">Allinea Performance Reports</a> page.</p>
+<p class=" ">Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports">Allinea Performance Reports</a> page.</p>
<h2 class=" ">RougeWave Totalview</h2>
<p>TotalView is a source- and machine-level debugger for multi-process, multi-threaded programs. Its wide range of tools provides ways to analyze, organize, and test programs, making it easy to isolate and identify problems in individual threads and processes in programs of great complexity.</p>
<pre class=" ">$ module load TotalView/8.15.4-6-linux-x86-64<br />$ totalview</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/total-view">Totalview</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/total-view">Totalview</a> page.</p>
<h2 class=" ">Vampir trace analyzer</h2>
<p>Vampir is a GUI trace analyzer for traces in OTF format.</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">Vampir</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">Vampir</a> page.</p>
</div>
@@ -5708,8 +5719,8 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
<div id="parent-fieldname-text-f6e25102d1244fb4ab355175867747b5" class="">
- <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
-<h2 class=" "><img title="Vampir screenshot" class="image-inline" alt="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
+ <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
+<h2 class=" "><img alt="Vampir screenshot" class="image-inline" title="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
<h2 class=" ">Installed versions</h2>
<p>Version 8.5.0 is currently installed as module <span class="monospace">Vampir/8.5.0</span> :</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir &</pre>
diff --git a/changelog/rss.xml b/docs.it4i.cz/changelog/rss.xml
old mode 100755
new mode 100644
similarity index 97%
rename from changelog/rss.xml
rename to docs.it4i.cz/changelog/rss.xml
index 70bcae583f2a67a7ca99b16942b3418e816db763..9800c62b25e923673b6c469bcbb28b20288b2579
--- a/changelog/rss.xml
+++ b/docs.it4i.cz/changelog/rss.xml
@@ -17,7 +17,7 @@
- <div id="parent-fieldname-text-4dd38593eea94c1081575284a571f1b7" class="">
+ <div id="parent-fieldname-text-afd31d559759479bb0cefe1718fb3b12" class="">
<br />
<div>
<table class="listing">
@@ -456,635 +456,84 @@
]]>
</content:encoded>
- <pubDate>Wed, 13 Jul 2016 20:04:07 +0200</pubDate>
+ <pubDate>Thu, 14 Jul 2016 20:49:24 +0200</pubDate>
<guid>https://docs.it4i.cz/whats-new/downtimes_history</guid>
</item>
<item>
- <title>Matlab</title>
- <description></description>
+ <title>List of Available Modules</title>
+ <description>List of Available Modules on Salomon Cluster</description>
<content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/">
<![CDATA[
- <div id="parent-fieldname-text-73e8cd3babab4da398f316c8d257916d" class="">
- <h2 class=" ">Introduction</h2>
-<p>Matlab is available in versions R2015a and R2015b. There are always two variants of the release:</p>
-<ul>
-<li>Non commercial or so called EDU variant, which can be used for common research and educational purposes.</li>
-<li>Commercial or so called COM variant, which can used also for commercial activities. The licenses for commercial variant are much more expensive, so usually the commercial variant has only subset of features compared to the EDU available.</li>
-</ul>
-<p>Â </p>
-<p>To load the latest version of Matlab load the module</p>
-<pre class=" ">$ module load MATLAB</pre>
-<p>By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use</p>
-<pre class=" ">$ module avail MATLAB</pre>
-<p>If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.</p>
-<p>If you require the Matlab GUI, please follow the general informations about <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">running graphical applications</a>.</p>
-<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">here</a>) is recommended.</p>
-<p>To run Matlab with GUI, use</p>
-<pre class=" ">$ matlab</pre>
-<p>To run Matlab in text mode, without the Matlab Desktop GUI environment, use</p>
-<pre class=" ">$ matlab -nodesktop -nosplash</pre>
-<p>plots, images, etc... will be still available.</p>
-<h2 class=" "><a name="running-parallel-matlab-using-distributed-computing-toolbox---engine"></a>Running parallel Matlab using Distributed Computing Toolbox / Engine</h2>
-<p class="exclamation">Distributed toolbox is available only for the EDU variant</p>
-<p class=" ">The MPIEXEC mode available in previous versions is no longer available in MATLAB 2015. Also, the programming interface has changed. Refer to <a class="external-link" href="http://www.mathworks.com/help/distcomp/release-notes.html#buanp9e-1" target="_self" title="">Release Notes</a>.</p>
-<p class=" ">Delete previously used file mpiLibConf.m, we have observed crashes when using Intel MPI.</p>
-<p class=" ">To use Distributed Computing, you first need to setup a parallel profile. We have provided the profile for you, you can either import it in MATLAB command line:</p>
-<pre class=" ">>> parallel.importProfile('/apps/all/MATLAB/2015a-EDU/SalomonPBSPro.settings')<br /><br />ans = <br /><br />SalomonPBSPro </pre>
-<p class=" ">Or in the GUI, go to tab HOME -> Parallel -> Manage Cluster Profiles..., click Import and navigate to :</p>
-<p class=" ">/apps/all/MATLAB/2015a-EDU/SalomonPBSPro.settings</p>
-<p class=" ">With the new mode, MATLAB itself launches the workers via PBS, so you can either use interactive mode or a batch mode on one node, but the actual parallel processing will be done in a separate job started by MATLAB itself. Alternatively, you can use "local" mode to run parallel code on just a single node.</p>
-<p class="exclamation">The profile is confusingly named Salomon, but you can use it also on Anselm.</p>
-<h3 class=" ">Parallel Matlab interactive session</h3>
-<p>Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">this page</a>.</p>
-<pre class=" ">$ xhost +<br />$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00 \<br />-l feature__matlab__MATLAB=1 </pre>
-<p>This qsub command example shows how to run Matlab on a single node.</p>
-<p>The second part of the command shows how to request all necessary licenses. In this case 1 Matlab-EDU license and 48 Distributed Computing Engines licenses.</p>
-<p>Once the access to compute nodes is granted by PBS, user can load following modules and start Matlab:Â </p>
-<pre class=" ">r1i0n17$ module load MATLAB/2015b-EDU<br />r1i0n17$ matlab &</pre>
-<h3 class=" "><a name="parallel-matlab-batch-job-in-local-mode"></a>Parallel Matlab batch job in Local mode</h3>
-<p>To run matlab in batch mode, write an matlab script, then write a bash jobscript and execute via the qsub command. By default, matlab will execute one matlab worker instance per allocated core.</p>
-<pre class=" ">#!/bin/bash<br />#PBS -A PROJECT ID<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=16:mpiprocs=16:ompthreads=1<br /><br /># change to shared scratch directory<br />SCR=/scratch/work/user/$USER/$PBS_JOBID<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/matlabcode.m .<br /><br /># load modules<br />module load MATLAB/2015a-EDU<br /><br /># execute the calculation<br />matlab -nodisplay -r matlabcode > output.out<br /><br /># copy output file to home<br />cp output.out $PBS_O_WORKDIR/.</pre>
-<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs and matlab script are in matlabcode.m file, outputs in output.out file. Note the missing .m extension in the matlab -r matlabcodefile call, <strong>the .m must not be included</strong>. Note that the <strong>shared /scratch must be used</strong>. Further, it is <strong>important to include quit</strong> statement at the end of the matlabcode.m script.</p>
-<p>Submit the jobscript using qsub</p>
-<pre class=" ">$ qsub ./jobscript</pre>
-<h3 class=" ">Parallel Matlab Local mode program example</h3>
-<p>The last part of the configuration is done directly in the user Matlab script before Distributed Computing Toolbox is started.</p>
-<pre class=" ">cluster = parcluster('local')</pre>
-<p class=" ">This script creates scheduler object "cluster" of type "local" that starts workers locally. </p>
-<p class="callout">Please note: Every Matlab script that needs to initialize/use matlabpool has to contain these three lines prior to calling parpool(sched, ...) function. </p>
-<p class=" ">The last step is to start matlabpool with "cluster" object and correct number of workers. We have 24 cores per node, so we start 24 workers.</p>
-<pre class=" ">parpool(cluster,16);<br /> <br /> <br />... parallel code ...<br /> <br /> <br />parpool close</pre>
-<p>The complete example showing how to use Distributed Computing Toolbox in local mode is shown here. </p>
-<pre class=" ">cluster = parcluster('local');<br />cluster<br /><br />parpool(cluster,24);<br /><br />n=2000;<br /><br />W = rand(n,n);<br />W = distributed(W);<br />x = (1:n)';<br />x = distributed(x);<br />spmd<br />[~, name] = system('hostname')<br />   <br />   T = W*x; % Calculation performed on labs, in parallel.<br />            % T and W are both codistributed arrays here.<br />end<br />T;<br />whos        % T and W are both distributed arrays here.<br /><br />parpool close<br />quit</pre>
-<p>You can copy and paste the example in a .m file and execute. Note that the parpool size should correspond to <strong>total number of cores</strong> available on allocated nodes.</p>
-<h3 class=" ">Parallel Matlab Batch job using PBS mode (workers spawned in a separate job)</h3>
-<p>This mode uses PBS scheduler to launch the parallel pool. It uses the SalomonPBSPro profile that needs to be imported to Cluster Manager, as mentioned before. This methodod uses MATLAB's PBS Scheduler interface - it spawns the workers in a separate job submitted by MATLAB using qsub.</p>
-<p>This is an example of m-script using PBS mode:</p>
-<pre class=" ">cluster = parcluster('SalomonPBSPro');
-set(cluster, 'SubmitArguments', '-A OPEN-0-0');
-set(cluster, 'ResourceTemplate', '-q qprod -l select=10:ncpus=16');
-set(cluster, 'NumWorkers', 160);
-
-pool = parpool(cluster, 160);
-
-n=2000;
-
-W = rand(n,n);
-W = distributed(W);
-x = (1:n)';
-x = distributed(x);
-spmd
-[~, name] = system('hostname')
-
- T = W*x; % Calculation performed on labs, in parallel.
- % T and W are both codistributed arrays here.
-end
-whos % T and W are both distributed arrays here.
-
-% shut down parallel pool
-delete(pool)
-</pre>
-<p class=" ">Note that we first construct a cluster object using the imported profile, then set some important options, namely : SubmitArguments, where you need to specify accounting id, and ResourceTemplate, where you need to specify number of nodes to run the job. </p>
-<p class=" ">You can start this script using batch mode the same way as in Local mode example.</p>
-<h3 class=" ">Parallel Matlab Batch with direct launch (workers spawned within the existing job)</h3>
-<p>This method is a "hack" invented by us to emulate the mpiexec functionality found in previous MATLAB versions. We leverage the MATLAB Generic Scheduler interface, but instead of submitting the workers to PBS, we launch the workers directly within the running job, thus we avoid the issues with master script and workers running in separate jobs (issues with license not available, waiting for the worker's job to spawn etc.)</p>
-<p>Please note that this method is experimental.</p>
-<p>For this method, you need to use SalomonDirect profile, import it using <a class="anchor-link" href="#running-parallel-matlab-using-distributed-computing-toolbox---engine" target="_self" title="">the same way as SalomonPBSPro</a> </p>
-<p>This is an example of m-script using direct mode:</p>
-<pre class=" "><br />parallel.importProfile('/apps/all/MATLAB/2015a-EDU/SalomonDirect.settings')<br />cluster = parcluster('SalomonDirect');
-set(cluster, 'NumWorkers', 48);
-
-pool = parpool(cluster, 48);
-
-n=2000;
-
-W = rand(n,n);
-W = distributed(W);
-x = (1:n)';
-x = distributed(x);
-spmd
-[~, name] = system('hostname')
-
- T = W*x; % Calculation performed on labs, in parallel.
- % T and W are both codistributed arrays here.
-end
-whos % T and W are both distributed arrays here.
-
-% shut down parallel pool
-delete(pool)</pre>
-<h3 class=" ">Non-interactive Session and Licenses</h3>
-<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">look here</a>.</p>
-<p>In case of non-interactive session please read the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
-<h3 class=" ">Matlab Distributed Computing Engines start up time</h3>
-<p>Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:</p>
-<table class="plain">
-<tbody>
-<tr><th>compute nodes</th><th>number of workers</th><th>start-up time[s]</th></tr>
-<tr>
-<td>16</td>
-<td>384</td>
-<td>831</td>
-</tr>
-<tr>
-<td>8</td>
-<td>192</td>
-<td>807</td>
-</tr>
-<tr>
-<td>4</td>
-<td>96</td>
-<td>483</td>
-</tr>
-<tr>
-<td>2</td>
-<td>48</td>
-<td>16</td>
-</tr>
-</tbody>
-</table>
-<h2>MATLAB on UV2000Â </h2>
-<p>UV2000 machine available in queue "qfat" can be used for MATLAB computations. This is a SMP NUMA machine with large amount of RAM, which can be beneficial for certain types of MATLAB jobs. CPU cores are allocated in chunks of 8 for this machine.</p>
-<p>You can use MATLAB on UV2000 in two parallel modes :</p>
-<h3>Threaded mode</h3>
-<p class=" ">Since this is a SMP machine, you can completely avoid using Parallel Toolbox and use only MATLAB's threading. MATLAB will automatically detect the number of cores you have allocated and will set <span class="monospace">maxNumCompThreads </span>accordingly and certain operations, such as <span class="monospace">fft, \, eig, svd</span>, etc. will be automatically run in threads. The advantage of this mode is that you don't need to modify your existing sequential codes.<span class="monospace"><br /></span></p>
-<h3 class=" ">Local cluster mode</h3>
-<p>You can also use Parallel Toolbox on UV2000. Use l<a class="anchor-link" href="#parallel-matlab-batch-job-in-local-mode" target="_self" title="">ocal cluster mode</a>, "SalomonPBSPro" profile will not work.</p>
-<p>Â </p>
-<p>Â </p>
-
-
- </div>
-
-
- <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
-
- <div id="plone-discussions">
- <hr />
- <b><a id="plone-discussions-href" href="#plone-discussions">Komentáře</a></b>
- </div>
+ <div id="parent-fieldname-text-12f4645a6b084b17bca6411df10a8022" class="">
+ <div>
- <!-- <div id="contact-form" tal:condition="context/isDiscussable">
- <hr />
- <b><a id="contact-form-href" href="#contact-form" i18n:translate="">Contact form</a></b>
- <tal:contactform tal:content="structure python:getattr(context, 'contact-info')()"></tal:contactform>
- </div> -->
+ <h2 id="categories">Categories</h2>
-
-
-
- ]]>
- </content:encoded>
- <pubDate>Wed, 24 Jul 2013 12:50:00 +0200</pubDate>
- <guid>https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab</guid>
- </item>
- <item>
- <title>Matlab</title>
- <description></description>
- <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/">
- <![CDATA[
-
-
-
- <div id="parent-fieldname-text-2efd48d0282d45b7b8fb11393c96d853" class="">
- <h2 class=" ">Introduction</h2>
-<p>Matlab is available in versions R2015a and R2015b. There are always two variants of the release:</p>
-<ul>
-<li>Non commercial or so called EDU variant, which can be used for common research and educational purposes.</li>
-<li>Commercial or so called COM variant, which can used also for commercial activities. The licenses for commercial variant are much more expensive, so usually the commercial variant has only subset of features compared to the EDU available.</li>
-</ul>
-<p>Â </p>
-<p>To load the latest version of Matlab load the module</p>
-<pre class=" ">$ module load MATLAB</pre>
-<p>By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use</p>
-<pre class=" ">$ module avail MATLAB</pre>
-<p>If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.</p>
-<p>If you require the Matlab GUI, please follow the general informations about <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">running graphical applications</a>.</p>
-<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">here</a>) is recommended.</p>
-<p>To run Matlab with GUI, use</p>
-<pre class=" ">$ matlab</pre>
-<p>To run Matlab in text mode, without the Matlab Desktop GUI environment, use</p>
-<pre class=" ">$ matlab -nodesktop -nosplash</pre>
-<p>plots, images, etc... will be still available.</p>
-<h2 class=" "><a name="running-parallel-matlab-using-distributed-computing-toolbox---engine"></a>Running parallel Matlab using Distributed Computing Toolbox / Engine</h2>
-<p class="exclamation">Distributed toolbox is available only for the EDU variant</p>
-<p class=" ">The MPIEXEC mode available in previous versions is no longer available in MATLAB 2015. Also, the programming interface has changed. Refer to <a class="external-link" href="http://www.mathworks.com/help/distcomp/release-notes.html#buanp9e-1" target="_self" title="">Release Notes</a>.</p>
-<p class=" ">Delete previously used file mpiLibConf.m, we have observed crashes when using Intel MPI.</p>
-<p class=" ">To use Distributed Computing, you first need to setup a parallel profile. We have provided the profile for you, you can either import it in MATLAB command line:</p>
-<pre class=" ">>> parallel.importProfile('/apps/all/MATLAB/2015b-EDU/SalomonPBSPro.settings')<br /><br />ans = <br /><br />SalomonPBSPro </pre>
-<p class=" ">Or in the GUI, go to tab HOME -> Parallel -> Manage Cluster Profiles..., click Import and navigate to :</p>
-<p class=" ">/apps/all/MATLAB/2015b-EDU/SalomonPBSPro.settings</p>
-<p class=" ">With the new mode, MATLAB itself launches the workers via PBS, so you can either use interactive mode or a batch mode on one node, but the actual parallel processing will be done in a separate job started by MATLAB itself. Alternatively, you can use "local" mode to run parallel code on just a single node.</p>
-<h3 class=" ">Parallel Matlab interactive session</h3>
-<p>Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">this page</a>.</p>
-<pre class=" ">$ xhost +<br />$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00 \<br />-l feature__matlab__MATLAB=1 </pre>
-<p>This qsub command example shows how to run Matlab on a single node.</p>
-<p>The second part of the command shows how to request all necessary licenses. In this case 1 Matlab-EDU license and 48 Distributed Computing Engines licenses.</p>
-<p>Once the access to compute nodes is granted by PBS, user can load following modules and start Matlab:Â </p>
-<pre class=" ">r1i0n17$ module load MATLAB/2015a-EDU<br />r1i0n17$ matlab &</pre>
-<h3 class=" "><a name="parallel-matlab-batch-job-in-local-mode"></a>Parallel Matlab batch job in Local mode</h3>
-<p>To run matlab in batch mode, write an matlab script, then write a bash jobscript and execute via the qsub command. By default, matlab will execute one matlab worker instance per allocated core.</p>
-<pre class=" ">#!/bin/bash<br />#PBS -A PROJECT ID<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=24:mpiprocs=24:ompthreads=1<br /><br /># change to shared scratch directory<br />SCR=/scratch/work/user/$USER/$PBS_JOBID<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/matlabcode.m .<br /><br /># load modules<br />module load MATLAB/2015a-EDU<br /><br /># execute the calculation<br />matlab -nodisplay -r matlabcode > output.out<br /><br /># copy output file to home<br />cp output.out $PBS_O_WORKDIR/.</pre>
-<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs and matlab script are in matlabcode.m file, outputs in output.out file. Note the missing .m extension in the matlab -r matlabcodefile call, <strong>the .m must not be included</strong>. Note that the <strong>shared /scratch must be used</strong>. Further, it is <strong>important to include quit</strong> statement at the end of the matlabcode.m script.</p>
-<p>Submit the jobscript using qsub</p>
-<pre class=" ">$ qsub ./jobscript</pre>
-<h3 class=" ">Parallel Matlab Local mode program example</h3>
-<p>The last part of the configuration is done directly in the user Matlab script before Distributed Computing Toolbox is started.</p>
-<pre class=" ">cluster = parcluster('local')</pre>
-<p class=" ">This script creates scheduler object "cluster" of type "local" that starts workers locally. </p>
-<p class="callout">Please note: Every Matlab script that needs to initialize/use matlabpool has to contain these three lines prior to calling parpool(sched, ...) function. </p>
-<p class=" ">The last step is to start matlabpool with "cluster" object and correct number of workers. We have 24 cores per node, so we start 24 workers.</p>
-<pre class=" ">parpool(cluster,24);<br /> <br /> <br />... parallel code ...<br /> <br /> <br />parpool close</pre>
-<p>The complete example showing how to use Distributed Computing Toolbox in local mode is shown here. </p>
-<pre class=" ">cluster = parcluster('local');<br />cluster<br /><br />parpool(cluster,24);<br /><br />n=2000;<br /><br />W = rand(n,n);<br />W = distributed(W);<br />x = (1:n)';<br />x = distributed(x);<br />spmd<br />[~, name] = system('hostname')<br />   <br />   T = W*x; % Calculation performed on labs, in parallel.<br />            % T and W are both codistributed arrays here.<br />end<br />T;<br />whos        % T and W are both distributed arrays here.<br /><br />parpool close<br />quit</pre>
-<p>You can copy and paste the example in a .m file and execute. Note that the parpool size should correspond to <strong>total number of cores</strong> available on allocated nodes.</p>
-<h3 class=" ">Parallel Matlab Batch job using PBS mode (workers spawned in a separate job)</h3>
-<p>This mode uses PBS scheduler to launch the parallel pool. It uses the SalomonPBSPro profile that needs to be imported to Cluster Manager, as mentioned before. This methodod uses MATLAB's PBS Scheduler interface - it spawns the workers in a separate job submitted by MATLAB using qsub.</p>
-<p>This is an example of m-script using PBS mode:</p>
-<pre class=" ">cluster = parcluster('SalomonPBSPro');
-set(cluster, 'SubmitArguments', '-A OPEN-0-0');
-set(cluster, 'ResourceTemplate', '-q qprod -l select=10:ncpus=24');
-set(cluster, 'NumWorkers', 240);
-
-pool = parpool(cluster,240);
-
-n=2000;
-
-W = rand(n,n);
-W = distributed(W);
-x = (1:n)';
-x = distributed(x);
-spmd
-[~, name] = system('hostname')
-
- T = W*x; % Calculation performed on labs, in parallel.
- % T and W are both codistributed arrays here.
-end
-whos % T and W are both distributed arrays here.
-
-% shut down parallel pool
-delete(pool)
-</pre>
-<p class=" ">Note that we first construct a cluster object using the imported profile, then set some important options, namely : SubmitArguments, where you need to specify accounting id, and ResourceTemplate, where you need to specify number of nodes to run the job. </p>
-<p class=" ">You can start this script using batch mode the same way as in Local mode example.</p>
-<h3 class=" ">Parallel Matlab Batch with direct launch (workers spawned within the existing job)</h3>
-<p>This method is a "hack" invented by us to emulate the mpiexec functionality found in previous MATLAB versions. We leverage the MATLAB Generic Scheduler interface, but instead of submitting the workers to PBS, we launch the workers directly within the running job, thus we avoid the issues with master script and workers running in separate jobs (issues with license not available, waiting for the worker's job to spawn etc.)</p>
-<p>Please note that this method is experimental.</p>
-<p>For this method, you need to use SalomonDirect profile, import it using <a class="anchor-link" href="#running-parallel-matlab-using-distributed-computing-toolbox---engine" target="_self" title="">the same way as SalomonPBSPro</a> </p>
-<p>This is an example of m-script using direct mode:</p>
-<pre class=" "><br />parallel.importProfile('/apps/all/MATLAB/2015b-EDU/SalomonDirect.settings')<br />cluster = parcluster('SalomonDirect');
-set(cluster, 'NumWorkers', 48);
-
-pool = parpool(cluster, 48);
-
-n=2000;
-
-W = rand(n,n);
-W = distributed(W);
-x = (1:n)';
-x = distributed(x);
-spmd
-[~, name] = system('hostname')
-
- T = W*x; % Calculation performed on labs, in parallel.
- % T and W are both codistributed arrays here.
-end
-whos % T and W are both distributed arrays here.
-
-% shut down parallel pool
-delete(pool)</pre>
-<h3 class=" ">Non-interactive Session and Licenses</h3>
-<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">look here</a>.</p>
-<p class="exclamation">The licensing feature of PBS is currently disabled.</p>
-<p>In case of non-interactive session please read the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
-<h3 class=" ">Matlab Distributed Computing Engines start up time</h3>
-<p>Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:</p>
-<table class="plain">
-<tbody>
-<tr><th>compute nodes</th><th>number of workers</th><th>start-up time[s]</th></tr>
-<tr>
-<td>16</td>
-<td>384</td>
-<td>831</td>
-</tr>
-<tr>
-<td>8</td>
-<td>192</td>
-<td>807</td>
-</tr>
-<tr>
-<td>4</td>
-<td>96</td>
-<td>483</td>
-</tr>
-<tr>
-<td>2</td>
-<td>48</td>
-<td>16</td>
-</tr>
-</tbody>
-</table>
-<h2>MATLAB on UV2000Â </h2>
-<p>UV2000 machine available in queue "qfat" can be used for MATLAB computations. This is a SMP NUMA machine with large amount of RAM, which can be beneficial for certain types of MATLAB jobs. CPU cores are allocated in chunks of 8 for this machine.</p>
-<p>You can use MATLAB on UV2000 in two parallel modes :</p>
-<h3>Threaded mode</h3>
-<p class=" ">Since this is a SMP machine, you can completely avoid using Parallel Toolbox and use only MATLAB's threading. MATLAB will automatically detect the number of cores you have allocated and will set <span class="monospace">maxNumCompThreads </span>accordingly and certain operations, such as <span class="monospace">fft, \, eig, svd</span>, etc. will be automatically run in threads. The advantage of this mode is that you don't need to modify your existing sequential codes.<span class="monospace"><br /></span></p>
-<h3 class=" ">Local cluster mode</h3>
-<p>You can also use Parallel Toolbox on UV2000. Use l<a class="anchor-link" href="#parallel-matlab-batch-job-in-local-mode" target="_self" title="">ocal cluster mode</a>, "SalomonPBSPro" profile will not work.</p>
-<p>Â </p>
-<p>Â </p>
-
-
- </div>
-
-
- <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
-
- <div id="plone-discussions">
- <hr />
- <b><a id="plone-discussions-href" href="#plone-discussions">Komentáře</a></b>
- </div>
-
- <!-- <div id="contact-form" tal:condition="context/isDiscussable">
- <hr />
- <b><a id="contact-form-href" href="#contact-form" i18n:translate="">Contact form</a></b>
- <tal:contactform tal:content="structure python:getattr(context, 'contact-info')()"></tal:contactform>
- </div> -->
-
-
-
-
- ]]>
- </content:encoded>
- <pubDate>Wed, 24 Jul 2013 12:50:00 +0200</pubDate>
- <guid>https://docs.it4i.cz/salomon/software/numerical-languages/matlab</guid>
- </item>
- <item>
- <title>Matlab 2013-2014</title>
- <description></description>
- <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/">
- <![CDATA[
-
-
-
- <div id="parent-fieldname-text-41bf242708954438ac56e1a431788c0e" class="">
- <h2 class=" ">Introduction</h2>
-<p class="exclamation">This document relates to the old versions R2013 and R2014. For MATLAB 2015, please use <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab">this documentation instead</a>.</p>
-<p>Matlab is available in the latest stable version. There are always two variants of the release:</p>
-<ul>
-<li>Non commercial or so called EDU variant, which can be used for common research and educational purposes.</li>
-<li>Commercial or so called COM variant, which can used also for commercial activities. The licenses for commercial variant are much more expensive, so usually the commercial variant has only subset of features compared to the EDU available.</li>
-</ul>
-<p>Â </p>
-<p>To load the latest version of Matlab load the module</p>
-<pre class=" ">$ module load matlab</pre>
-<p>By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use</p>
-<pre class=" ">$ module avail matlab</pre>
-<p>If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.</p>
-<p>If you require the Matlab GUI, please follow the general informations about <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">running graphical applications</a>.</p>
-<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">here</a>) is recommended.</p>
-<p>To run Matlab with GUI, use</p>
-<pre class=" ">$ matlab</pre>
-<p>To run Matlab in text mode, without the Matlab Desktop GUI environment, use</p>
-<pre class=" ">$ matlab -nodesktop -nosplash</pre>
-<p>plots, images, etc... will be still available.</p>
-<h2 class=" ">Running parallel Matlab using Distributed Computing Toolbox / Engine</h2>
-<p>Recommended parallel mode for running parallel Matlab on Anselm is MPIEXEC mode. In this mode user allocates resources through PBS prior to starting Matlab. Once resources are granted the main Matlab instance is started on the first compute node assigned to job by PBS and workers are started on all remaining nodes. User can use both interactive and non-interactive PBS sessions. This mode guarantees that the data processing is not performed on login nodes, but all processing is on compute nodes.</p>
-<p>Â <img title="Parallel Matlab" class="image-inline" alt="Parallel Matlab" src="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/Matlab.png" /></p>
-<p>For the performance reasons Matlab should use system MPI. On Anselm the supported MPI implementation for Matlab is Intel MPI. To switch to system MPI user has to override default Matlab setting by creating new configuration file in its home directory. The path and file name has to be exactly the same as in the following listing:</p>
-<pre class=" "><strong>$ vim ~/matlab/mpiLibConf.m </strong></pre>
-<pre class=" "><strong>function [lib, extras] = mpiLibConf</strong><br /><strong>%MATLAB MPI Library overloading for Infiniband Networks</strong><br /><br /><strong>mpich = '/opt/intel/impi/4.1.1.036/lib64/';</strong><br /><br /><strong>disp('Using Intel MPI 4.1.1.036 over Infiniband')</strong><br /><br /><strong>lib = strcat(mpich, 'libmpich.so');</strong><br /><strong>mpl = strcat(mpich, 'libmpl.so');</strong><br /><strong>opa = strcat(mpich, 'libopa.so');</strong><br /><br /><strong>extras = {};</strong></pre>
-<p>System MPI library allows Matlab to communicate through 40Gbps Infiniband QDR interconnect instead of slower 1Gb ethernet network.</p>
-<p class="callout">Please note: The path to MPI library in "mpiLibConf.m" has to match with version of loaded Intel MPI module. In this example the version 4.1.1.036 of Iintel MPI is used by Matlab and therefore module impi/4.1.1.036Â has to be loaded prior to starting Matlab.</p>
-<h3 class=" ">Parallel Matlab interactive session</h3>
-<p>Once this file is in place, user can request resources from PBS. Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">this page</a>.</p>
-<pre class=" ">$ xhost +<br />$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=4:ncpus=16:mpiprocs=16 -l walltime=00:30:00 \<br />-l feature__matlab__MATLAB=1 </pre>
-<p>This qsub command example shows how to run Matlab with 32 workers in following configuration: 2 nodes (use all 16 cores per node) and 16 workers = mpirocs per node (-l select=2:ncpus=16:mpiprocs=16). If user requires to run smaller number of workers per node then the "mpiprocs" parameter has to be changed.</p>
-<p>The second part of the command shows how to request all necessary licenses. In this case 1 Matlab-EDU license and 32 Distributed Computing Engines licenses.</p>
-<p>Once the access to compute nodes is granted by PBS, user can load following modules and start Matlab:Â </p>
-<pre class=" ">cn79$ module load matlab/R2013a-EDU<br />cn79$ module load impi/4.1.1.036<br />cn79$ matlab &</pre>
-<h3 class=" ">Parallel Matlab batch job</h3>
-<p>To run matlab in batch mode, write an matlab script, then write a bash jobscript and execute via the qsub command. By default, matlab will execute one matlab worker instance per allocated core.</p>
-<pre class=" ">#!/bin/bash<br />#PBS -A PROJECT ID<br />#PBS -q qprod<br />#PBS -l select=2:ncpus=16:mpiprocs=16:ompthreads=1<br /><br /># change to shared scratch directory<br />SCR=/scratch/$USER/$PBS_JOBID<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/matlabcode.m .<br /><br /># load modules<br />module load matlab/R2013a-EDU<br />module load impi/4.1.1.036<br /><br /># execute the calculation<br />matlab -nodisplay -r matlabcode > output.out<br /><br /># copy output file to home<br />cp output.out $PBS_O_WORKDIR/.</pre>
-<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs and matlab script are in matlabcode.m file, outputs in output.out file. Note the missing .m extension in the matlab -r matlabcodefile call, <strong>the .m must not be included</strong>. Note that the <strong>shared /scratch must be used</strong>. Further, it is <strong>important to include quit</strong> statement at the end of the matlabcode.m script.</p>
-<p>Submit the jobscript using qsub</p>
-<pre class=" ">$ qsub ./jobscript</pre>
-<h3 class=" ">Parallel Matlab program example</h3>
-<p>The last part of the configuration is done directly in the user Matlab script before Distributed Computing Toolbox is started.</p>
-<pre class=" ">sched = findResource('scheduler', 'type', 'mpiexec');<br />set(sched, 'MpiexecFileName', '/apps/intel/impi/4.1.1/bin/mpirun');<br />set(sched, 'EnvironmentSetMethod', 'setenv');</pre>
-<p class=" ">This script creates scheduler object "sched" of type "mpiexec" that starts workers using mpirun tool. To use correct version of mpirun, the second line specifies the path to correct version of system Intel MPI library.</p>
-<p class="callout">Please note: Every Matlab script that needs to initialize/use matlabpool has to contain these three lines prior to calling matlabpool(sched, ...) function. </p>
-<p class=" ">The last step is to start matlabpool with "sched" object and correct number of workers. In this case qsub asked for total number of 32 cores, therefore the number of workers is also set to 32.</p>
-<pre class=" ">matlabpool(sched,32);<br /> <br /> <br />... parallel code ...<br /> <br /> <br />matlabpool close</pre>
-<p>The complete example showing how to use Distributed Computing Toolbox is show here. </p>
-<pre class=" ">sched = findResource('scheduler', 'type', 'mpiexec');<br />set(sched, 'MpiexecFileName', '/apps/intel/impi/4.1.1/bin/mpirun')<br />set(sched, 'EnvironmentSetMethod', 'setenv')<br />set(sched, 'SubmitArguments', '') <br />sched<br /><br />matlabpool(sched,32);<br /><br />n=2000;<br /><br />W = rand(n,n);<br />W = distributed(W);<br />x = (1:n)';<br />x = distributed(x);<br />spmd<br />[~, name] = system('hostname')<br />   <br />   T = W*x; % Calculation performed on labs, in parallel.<br />            % T and W are both codistributed arrays here.<br />end<br />T;<br />whos        % T and W are both distributed arrays here.<br /><br />matlabpool close<br />quit</pre>
-<p>You can copy and paste the example in a .m file and execute. Note that the matlabpool size should correspond to <strong>total number of cores</strong> available on allocated nodes.</p>
-<h3 class=" ">Non-interactive Session and Licenses</h3>
-<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">look here</a>.</p>
-<p>In case of non-interactive session please read the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
-<h3 class=" ">Matlab Distributed Computing Engines start up time</h3>
-<p>Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:</p>
-<table class="plain">
-<tbody>
-<tr><th>compute nodes</th><th>number of workers</th><th>start-up time[s]</th></tr>
-<tr>
-<td>16</td>
-<td>256</td>
-<td>1008</td>
-</tr>
-<tr>
-<td>8</td>
-<td>128</td>
-<td>534</td>
-</tr>
-<tr>
-<td>4</td>
-<td>64</td>
-<td>333</td>
-</tr>
-<tr>
-<td>2</td>
-<td>32</td>
-<td>210</td>
-</tr>
-</tbody>
-</table>
-<p>Â </p>
-<p>Â </p>
-
-
- </div>
-
-
- <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
-
- <div id="plone-discussions">
- <hr />
- <b><a id="plone-discussions-href" href="#plone-discussions">Komentáře</a></b>
- </div>
-
- <!-- <div id="contact-form" tal:condition="context/isDiscussable">
- <hr />
- <b><a id="contact-form-href" href="#contact-form" i18n:translate="">Contact form</a></b>
- <tal:contactform tal:content="structure python:getattr(context, 'contact-info')()"></tal:contactform>
- </div> -->
-
-
-
-
- ]]>
- </content:encoded>
- <pubDate>Wed, 24 Jul 2013 12:50:00 +0200</pubDate>
- <guid>https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab</guid>
- </item>
- <item>
- <title>MATLAB 2015b</title>
- <description></description>
- <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/">
- <![CDATA[
-
-
-
-
-
-
-
- <div id="parent-fieldname-text" class="plain">
- <p>MATLAB 2015b has been installed on Anselm and Salomon. Modules are named MATLAB/2015b-COM and MATLAB/2015b-EDU. Release notes:Â http://www.mathworks.com/help/matlab/release-notes.html#R2015b</p>
- </div>
-
-
-
- ]]>
- </content:encoded>
- <pubDate>Wed, 13 Jul 2016 15:40:00 +0200</pubDate>
- <guid>https://docs.it4i.cz/whats-new/news-feed/matlab-2015b</guid>
- </item>
- <item>
- <title>Numerical languages</title>
- <description>Interpreted languages for numerical computations and analysis</description>
- <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/">
- <![CDATA[
-
-
-
- <div id="parent-fieldname-text-6c3faf66932c4ed6aaf3471f0ab0e081" class="">
- <h2 class=" ">Introduction</h2>
-<p>This section contains a collection of high-level interpreted languages, primarily intended for numerical computations.</p>
-<h2 class=" ">Matlab</h2>
-<p>MATLAB<sup>®</sup> is a high-level language and interactive environment for numerical computation, visualization, and programming.</p>
-<pre class=" ">$ module load MATLAB/2015b-EDU<br />$ matlab</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab">Matlab<span class="internal-link"></span> page</a>.</p>
-<h2 class=" ">Octave</h2>
-<p>GNU Octave is a high-level interpreted language, primarily intended for numerical computations. The Octave language is quite similar to Matlab so that most programs are easily portable.</p>
-<pre class=" ">$ module load Octave<br />$ octave</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave">Octave page</a>.</p>
-<h2 class=" ">R</h2>
-<p>The R is an interpreted language and environment for statistical computing and graphics.</p>
-<pre class=" ">$ module load R<br />$ R</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r">R page</a>.</p>
-
- </div>
-
-
- <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
-
- <div id="plone-discussions">
- <hr />
- <b><a id="plone-discussions-href" href="#plone-discussions">Komentáře</a></b>
- </div>
-
- <!-- <div id="contact-form" tal:condition="context/isDiscussable">
- <hr />
- <b><a id="contact-form-href" href="#contact-form" i18n:translate="">Contact form</a></b>
- <tal:contactform tal:content="structure python:getattr(context, 'contact-info')()"></tal:contactform>
- </div> -->
-
-
-
-
- ]]>
- </content:encoded>
- <pubDate>Tue, 25 Feb 2014 13:25:00 +0200</pubDate>
- <guid>https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction</guid>
- </item>
- <item>
- <title>List of Available Modules</title>
- <description>List of Available Modules on Salomon Cluster</description>
- <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/">
- <![CDATA[
-
-
-
- <div id="parent-fieldname-text-07f9a79724204a24adc155a93c34b79c" class="">
- <div>
-
- <h2 id="categories">Categories</h2>
-
- <ul>
- <li>
- <a href="#base">base</a><br />
- </li>
- <li>
- <a href="#bio">bio</a><br />
- </li>
- <li>
- <a href="#cae">cae</a><br />
- </li>
- <li>
- <a href="#chem">chem</a><br />
- </li>
- <li>
- <a href="#compiler">compiler</a><br />
- </li>
- <li>
- <a href="#data">data</a><br />
- </li>
- <li>
- <a href="#debugger">debugger</a><br />
- </li>
- <li>
- <a href="#devel">devel</a><br />
- </li>
- <li>
- <a href="#geo">geo</a><br />
- </li>
- <li>
- <a href="#lang">lang</a><br />
- </li>
- <li>
- <a href="#lib">lib</a><br />
- </li>
- <li>
- <a href="#math">math</a><br />
- </li>
- <li>
- <a href="#mpi">mpi</a><br />
- </li>
- <li>
- <a href="#numlib">numlib</a><br />
- </li>
- <li>
- <a href="#perf">perf</a><br />
- </li>
- <li>
- <a href="#phys">phys</a><br />
- </li>
- <li>
- <a href="#system">system</a><br />
- </li>
- <li>
- <a href="#toolchain">toolchain</a><br />
- </li>
- <li>
- <a href="#tools">tools</a><br />
- </li>
- <li>
- <a href="#vis">vis</a><br />
- </li>
- </ul>
+ <ul>
+ <li>
+ <a href="#base">base</a><br />
+ </li>
+ <li>
+ <a href="#bio">bio</a><br />
+ </li>
+ <li>
+ <a href="#cae">cae</a><br />
+ </li>
+ <li>
+ <a href="#chem">chem</a><br />
+ </li>
+ <li>
+ <a href="#compiler">compiler</a><br />
+ </li>
+ <li>
+ <a href="#data">data</a><br />
+ </li>
+ <li>
+ <a href="#debugger">debugger</a><br />
+ </li>
+ <li>
+ <a href="#devel">devel</a><br />
+ </li>
+ <li>
+ <a href="#geo">geo</a><br />
+ </li>
+ <li>
+ <a href="#lang">lang</a><br />
+ </li>
+ <li>
+ <a href="#lib">lib</a><br />
+ </li>
+ <li>
+ <a href="#math">math</a><br />
+ </li>
+ <li>
+ <a href="#mpi">mpi</a><br />
+ </li>
+ <li>
+ <a href="#numlib">numlib</a><br />
+ </li>
+ <li>
+ <a href="#perf">perf</a><br />
+ </li>
+ <li>
+ <a href="#phys">phys</a><br />
+ </li>
+ <li>
+ <a href="#system">system</a><br />
+ </li>
+ <li>
+ <a href="#toolchain">toolchain</a><br />
+ </li>
+ <li>
+ <a href="#tools">tools</a><br />
+ </li>
+ <li>
+ <a href="#vis">vis</a><br />
+ </li>
+ </ul>
<div>
<h2 id="base"><a class="tooltip" title="Go to list of categories..." href="#categories">base</a></h2>
@@ -2486,6 +1935,7 @@ latency hiding, direct access to the protocol, improved threading support, and e
<td>
<ul>
<li style="white-space: nowrap;">1.10-Python-2.7.8</li>
+ <li style="white-space: nowrap;">1.11-Python-2.7.9</li>
<li style="white-space: nowrap;">1.11-foss-2015g-Python-2.7.9</li>
<li style="white-space: nowrap;">1.11-intel-2015b-Python-2.7.9</li>
</ul>
@@ -2767,6 +2217,7 @@ in numerous market categories from gaming and entertainment to scientific and me
<li style="white-space: nowrap;">2.7.11-intel-2015b</li>
<li style="white-space: nowrap;">2.7.8-intel-2015b</li>
<li style="white-space: nowrap;">2.7.8-intel-2016.01</li>
+ <li style="white-space: nowrap;">2.7.9</li>
<li style="white-space: nowrap;">2.7.9-GNU-5.1.0-2.25</li>
<li style="white-space: nowrap;">2.7.9-foss-2015b</li>
<li style="white-space: nowrap;">2.7.9-foss-2015g</li>
@@ -3253,6 +2704,7 @@ latency hiding, direct access to the protocol, improved threading support, and e
<td>
<ul>
<li style="white-space: nowrap;">1.10-Python-2.7.8</li>
+ <li style="white-space: nowrap;">1.11-Python-2.7.9</li>
<li style="white-space: nowrap;">1.11-foss-2015g-Python-2.7.9</li>
<li style="white-space: nowrap;">1.11-intel-2015b-Python-2.7.9</li>
</ul>
@@ -4398,6 +3850,8 @@ is distributed under the GNU General Public License (GPL)</td>
<ul>
<li style="white-space: nowrap;">2015a-COM</li>
<li style="white-space: nowrap;">2015a-EDU</li>
+ <li style="white-space: nowrap;">2015b-COM</li>
+ <li style="white-space: nowrap;">2015b-EDU</li>
</ul>
</td>
</tr>
@@ -4493,6 +3947,7 @@ virtualizer.</td>
<td>Szip compression software, providing lossless compression of scientific data</td>
<td>
<ul>
+ <li style="white-space: nowrap;">2.1</li>
<li style="white-space: nowrap;">2.1-foss-2015b</li>
<li style="white-space: nowrap;">2.1-foss-2015g</li>
<li style="white-space: nowrap;">2.1-ictce-7.3.5</li>
@@ -4701,6 +4156,7 @@ to handle everything from small to very large projects with speed and efficiency
<li style="white-space: nowrap;">2.0.10-GNU-4.9.3-2.25</li>
<li style="white-space: nowrap;">2.0.10-GNU-5.1.0-2.25</li>
<li style="white-space: nowrap;">2.0.10-iccifort-2015.3.187-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">2.0.11</li>
<li style="white-space: nowrap;">2.0.11-GCC-4.9.3-2.25</li>
<li style="white-space: nowrap;">2.0.11-GCC-5.3.0-2.26</li>
<li style="white-space: nowrap;">2.0.9-GCC-4.4.7-system</li>
@@ -4731,6 +4187,7 @@ to handle everything from small to very large projects with speed and efficiency
<td>
<ul>
<li style="white-space: nowrap;">6.18.01-intel-2015b</li>
+ <li style="white-space: nowrap;">6.19.00</li>
</ul>
</td>
</tr>
@@ -5124,6 +4581,7 @@ and documentation</td>
<td>
<ul>
<li style="white-space: nowrap;">1.6.2-Python-2.7.8</li>
+ <li style="white-space: nowrap;">1.6.2-Python-2.7.9</li>
<li style="white-space: nowrap;">1.6.2-foss-2015g-Python-2.7.9</li>
<li style="white-space: nowrap;">1.6.2-intel-2015b-Python-2.7.9</li>
</ul>
@@ -5181,6 +4639,7 @@ useful for allowing clients to interact with the X Display Manager.
<td>
<ul>
<li style="white-space: nowrap;">1.3.2-Python-2.7.8</li>
+ <li style="white-space: nowrap;">1.3.3</li>
<li style="white-space: nowrap;">1.3.3-foss-2015g</li>
<li style="white-space: nowrap;">1.3.3-foss-2015g-Python-2.7.9</li>
<li style="white-space: nowrap;">1.3.3-intel-2015b</li>
@@ -5258,6 +4717,7 @@ useful for allowing clients to interact with the X Display Manager.
<ul>
<li style="white-space: nowrap;">1.1.4-foss-2015g-libX11-1.6.2</li>
<li style="white-space: nowrap;">1.1.4-intel-2015b-libX11-1.6.2</li>
+ <li style="white-space: nowrap;">1.1.4-libX11-1.6.2</li>
<li style="white-space: nowrap;">1.1.5-foss-2015g</li>
</ul>
</td>
@@ -5310,15 +4770,566 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
</table>
</div>
-</div>
+</div>
+
+ </div>
+
+
+ <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
+
+
+
+ <!-- <div id="contact-form" tal:condition="context/isDiscussable">
+ <hr />
+ <b><a id="contact-form-href" href="#contact-form" i18n:translate="">Contact form</a></b>
+ <tal:contactform tal:content="structure python:getattr(context, 'contact-info')()"></tal:contactform>
+ </div> -->
+
+
+
+
+ ]]>
+ </content:encoded>
+ <pubDate>Thu, 14 Jul 2016 02:00:02 +0200</pubDate>
+ <guid>https://docs.it4i.cz/salomon/list_of_modules</guid>
+ </item>
+ <item>
+ <title>Matlab</title>
+ <description></description>
+ <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/">
+ <![CDATA[
+
+
+
+ <div id="parent-fieldname-text-73e8cd3babab4da398f316c8d257916d" class="">
+ <h2 class=" ">Introduction</h2>
+<p>Matlab is available in versions R2015a and R2015b. There are always two variants of the release:</p>
+<ul>
+<li>Non commercial or so called EDU variant, which can be used for common research and educational purposes.</li>
+<li>Commercial or so called COM variant, which can used also for commercial activities. The licenses for commercial variant are much more expensive, so usually the commercial variant has only subset of features compared to the EDU available.</li>
+</ul>
+<p>Â </p>
+<p>To load the latest version of Matlab load the module</p>
+<pre class=" ">$ module load MATLAB</pre>
+<p>By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use</p>
+<pre class=" ">$ module avail MATLAB</pre>
+<p>If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.</p>
+<p>If you require the Matlab GUI, please follow the general informations about <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">running graphical applications</a>.</p>
+<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">here</a>) is recommended.</p>
+<p>To run Matlab with GUI, use</p>
+<pre class=" ">$ matlab</pre>
+<p>To run Matlab in text mode, without the Matlab Desktop GUI environment, use</p>
+<pre class=" ">$ matlab -nodesktop -nosplash</pre>
+<p>plots, images, etc... will be still available.</p>
+<h2 class=" "><a name="running-parallel-matlab-using-distributed-computing-toolbox---engine"></a>Running parallel Matlab using Distributed Computing Toolbox / Engine</h2>
+<p class="exclamation">Distributed toolbox is available only for the EDU variant</p>
+<p class=" ">The MPIEXEC mode available in previous versions is no longer available in MATLAB 2015. Also, the programming interface has changed. Refer to <a class="external-link" href="http://www.mathworks.com/help/distcomp/release-notes.html#buanp9e-1" target="_self" title="">Release Notes</a>.</p>
+<p class=" ">Delete previously used file mpiLibConf.m, we have observed crashes when using Intel MPI.</p>
+<p class=" ">To use Distributed Computing, you first need to setup a parallel profile. We have provided the profile for you, you can either import it in MATLAB command line:</p>
+<pre class=" ">>> parallel.importProfile('/apps/all/MATLAB/2015a-EDU/SalomonPBSPro.settings')<br /><br />ans = <br /><br />SalomonPBSPro </pre>
+<p class=" ">Or in the GUI, go to tab HOME -> Parallel -> Manage Cluster Profiles..., click Import and navigate to :</p>
+<p class=" ">/apps/all/MATLAB/2015a-EDU/SalomonPBSPro.settings</p>
+<p class=" ">With the new mode, MATLAB itself launches the workers via PBS, so you can either use interactive mode or a batch mode on one node, but the actual parallel processing will be done in a separate job started by MATLAB itself. Alternatively, you can use "local" mode to run parallel code on just a single node.</p>
+<p class="exclamation">The profile is confusingly named Salomon, but you can use it also on Anselm.</p>
+<h3 class=" ">Parallel Matlab interactive session</h3>
+<p>Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">this page</a>.</p>
+<pre class=" ">$ xhost +<br />$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00 \<br />-l feature__matlab__MATLAB=1 </pre>
+<p>This qsub command example shows how to run Matlab on a single node.</p>
+<p>The second part of the command shows how to request all necessary licenses. In this case 1 Matlab-EDU license and 48 Distributed Computing Engines licenses.</p>
+<p>Once the access to compute nodes is granted by PBS, user can load following modules and start Matlab:Â </p>
+<pre class=" ">r1i0n17$ module load MATLAB/2015b-EDU<br />r1i0n17$ matlab &</pre>
+<h3 class=" "><a name="parallel-matlab-batch-job-in-local-mode"></a>Parallel Matlab batch job in Local mode</h3>
+<p>To run matlab in batch mode, write an matlab script, then write a bash jobscript and execute via the qsub command. By default, matlab will execute one matlab worker instance per allocated core.</p>
+<pre class=" ">#!/bin/bash<br />#PBS -A PROJECT ID<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=16:mpiprocs=16:ompthreads=1<br /><br /># change to shared scratch directory<br />SCR=/scratch/work/user/$USER/$PBS_JOBID<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/matlabcode.m .<br /><br /># load modules<br />module load MATLAB/2015a-EDU<br /><br /># execute the calculation<br />matlab -nodisplay -r matlabcode > output.out<br /><br /># copy output file to home<br />cp output.out $PBS_O_WORKDIR/.</pre>
+<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs and matlab script are in matlabcode.m file, outputs in output.out file. Note the missing .m extension in the matlab -r matlabcodefile call, <strong>the .m must not be included</strong>. Note that the <strong>shared /scratch must be used</strong>. Further, it is <strong>important to include quit</strong> statement at the end of the matlabcode.m script.</p>
+<p>Submit the jobscript using qsub</p>
+<pre class=" ">$ qsub ./jobscript</pre>
+<h3 class=" ">Parallel Matlab Local mode program example</h3>
+<p>The last part of the configuration is done directly in the user Matlab script before Distributed Computing Toolbox is started.</p>
+<pre class=" ">cluster = parcluster('local')</pre>
+<p class=" ">This script creates scheduler object "cluster" of type "local" that starts workers locally. </p>
+<p class="callout">Please note: Every Matlab script that needs to initialize/use matlabpool has to contain these three lines prior to calling parpool(sched, ...) function. </p>
+<p class=" ">The last step is to start matlabpool with "cluster" object and correct number of workers. We have 24 cores per node, so we start 24 workers.</p>
+<pre class=" ">parpool(cluster,16);<br /> <br /> <br />... parallel code ...<br /> <br /> <br />parpool close</pre>
+<p>The complete example showing how to use Distributed Computing Toolbox in local mode is shown here. </p>
+<pre class=" ">cluster = parcluster('local');<br />cluster<br /><br />parpool(cluster,24);<br /><br />n=2000;<br /><br />W = rand(n,n);<br />W = distributed(W);<br />x = (1:n)';<br />x = distributed(x);<br />spmd<br />[~, name] = system('hostname')<br />   <br />   T = W*x; % Calculation performed on labs, in parallel.<br />            % T and W are both codistributed arrays here.<br />end<br />T;<br />whos        % T and W are both distributed arrays here.<br /><br />parpool close<br />quit</pre>
+<p>You can copy and paste the example in a .m file and execute. Note that the parpool size should correspond to <strong>total number of cores</strong> available on allocated nodes.</p>
+<h3 class=" ">Parallel Matlab Batch job using PBS mode (workers spawned in a separate job)</h3>
+<p>This mode uses PBS scheduler to launch the parallel pool. It uses the SalomonPBSPro profile that needs to be imported to Cluster Manager, as mentioned before. This methodod uses MATLAB's PBS Scheduler interface - it spawns the workers in a separate job submitted by MATLAB using qsub.</p>
+<p>This is an example of m-script using PBS mode:</p>
+<pre class=" ">cluster = parcluster('SalomonPBSPro');
+set(cluster, 'SubmitArguments', '-A OPEN-0-0');
+set(cluster, 'ResourceTemplate', '-q qprod -l select=10:ncpus=16');
+set(cluster, 'NumWorkers', 160);
+
+pool = parpool(cluster, 160);
+
+n=2000;
+
+W = rand(n,n);
+W = distributed(W);
+x = (1:n)';
+x = distributed(x);
+spmd
+[~, name] = system('hostname')
+
+ T = W*x; % Calculation performed on labs, in parallel.
+ % T and W are both codistributed arrays here.
+end
+whos % T and W are both distributed arrays here.
+
+% shut down parallel pool
+delete(pool)
+</pre>
+<p class=" ">Note that we first construct a cluster object using the imported profile, then set some important options, namely : SubmitArguments, where you need to specify accounting id, and ResourceTemplate, where you need to specify number of nodes to run the job. </p>
+<p class=" ">You can start this script using batch mode the same way as in Local mode example.</p>
+<h3 class=" ">Parallel Matlab Batch with direct launch (workers spawned within the existing job)</h3>
+<p>This method is a "hack" invented by us to emulate the mpiexec functionality found in previous MATLAB versions. We leverage the MATLAB Generic Scheduler interface, but instead of submitting the workers to PBS, we launch the workers directly within the running job, thus we avoid the issues with master script and workers running in separate jobs (issues with license not available, waiting for the worker's job to spawn etc.)</p>
+<p>Please note that this method is experimental.</p>
+<p>For this method, you need to use SalomonDirect profile, import it using <a class="anchor-link" href="#running-parallel-matlab-using-distributed-computing-toolbox---engine" target="_self" title="">the same way as SalomonPBSPro</a> </p>
+<p>This is an example of m-script using direct mode:</p>
+<pre class=" "><br />parallel.importProfile('/apps/all/MATLAB/2015a-EDU/SalomonDirect.settings')<br />cluster = parcluster('SalomonDirect');
+set(cluster, 'NumWorkers', 48);
+
+pool = parpool(cluster, 48);
+
+n=2000;
+
+W = rand(n,n);
+W = distributed(W);
+x = (1:n)';
+x = distributed(x);
+spmd
+[~, name] = system('hostname')
+
+ T = W*x; % Calculation performed on labs, in parallel.
+ % T and W are both codistributed arrays here.
+end
+whos % T and W are both distributed arrays here.
+
+% shut down parallel pool
+delete(pool)</pre>
+<h3 class=" ">Non-interactive Session and Licenses</h3>
+<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">look here</a>.</p>
+<p>In case of non-interactive session please read the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
+<h3 class=" ">Matlab Distributed Computing Engines start up time</h3>
+<p>Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:</p>
+<table class="plain">
+<tbody>
+<tr><th>compute nodes</th><th>number of workers</th><th>start-up time[s]</th></tr>
+<tr>
+<td>16</td>
+<td>384</td>
+<td>831</td>
+</tr>
+<tr>
+<td>8</td>
+<td>192</td>
+<td>807</td>
+</tr>
+<tr>
+<td>4</td>
+<td>96</td>
+<td>483</td>
+</tr>
+<tr>
+<td>2</td>
+<td>48</td>
+<td>16</td>
+</tr>
+</tbody>
+</table>
+<h2>MATLAB on UV2000Â </h2>
+<p>UV2000 machine available in queue "qfat" can be used for MATLAB computations. This is a SMP NUMA machine with large amount of RAM, which can be beneficial for certain types of MATLAB jobs. CPU cores are allocated in chunks of 8 for this machine.</p>
+<p>You can use MATLAB on UV2000 in two parallel modes :</p>
+<h3>Threaded mode</h3>
+<p class=" ">Since this is a SMP machine, you can completely avoid using Parallel Toolbox and use only MATLAB's threading. MATLAB will automatically detect the number of cores you have allocated and will set <span class="monospace">maxNumCompThreads </span>accordingly and certain operations, such as <span class="monospace">fft, \, eig, svd</span>, etc. will be automatically run in threads. The advantage of this mode is that you don't need to modify your existing sequential codes.<span class="monospace"><br /></span></p>
+<h3 class=" ">Local cluster mode</h3>
+<p>You can also use Parallel Toolbox on UV2000. Use l<a class="anchor-link" href="#parallel-matlab-batch-job-in-local-mode" target="_self" title="">ocal cluster mode</a>, "SalomonPBSPro" profile will not work.</p>
+<p>Â </p>
+<p>Â </p>
+
+
+ </div>
+
+
+ <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
+
+ <div id="plone-discussions">
+ <hr />
+ <b><a id="plone-discussions-href" href="#plone-discussions">Komentáře</a></b>
+ </div>
+
+ <!-- <div id="contact-form" tal:condition="context/isDiscussable">
+ <hr />
+ <b><a id="contact-form-href" href="#contact-form" i18n:translate="">Contact form</a></b>
+ <tal:contactform tal:content="structure python:getattr(context, 'contact-info')()"></tal:contactform>
+ </div> -->
+
+
+
+
+ ]]>
+ </content:encoded>
+ <pubDate>Wed, 24 Jul 2013 12:50:00 +0200</pubDate>
+ <guid>https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab</guid>
+ </item>
+ <item>
+ <title>Matlab</title>
+ <description></description>
+ <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/">
+ <![CDATA[
+
+
+
+ <div id="parent-fieldname-text-2efd48d0282d45b7b8fb11393c96d853" class="">
+ <h2 class=" ">Introduction</h2>
+<p>Matlab is available in versions R2015a and R2015b. There are always two variants of the release:</p>
+<ul>
+<li>Non commercial or so called EDU variant, which can be used for common research and educational purposes.</li>
+<li>Commercial or so called COM variant, which can used also for commercial activities. The licenses for commercial variant are much more expensive, so usually the commercial variant has only subset of features compared to the EDU available.</li>
+</ul>
+<p>Â </p>
+<p>To load the latest version of Matlab load the module</p>
+<pre class=" ">$ module load MATLAB</pre>
+<p>By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use</p>
+<pre class=" ">$ module avail MATLAB</pre>
+<p>If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.</p>
+<p>If you require the Matlab GUI, please follow the general informations about <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">running graphical applications</a>.</p>
+<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">here</a>) is recommended.</p>
+<p>To run Matlab with GUI, use</p>
+<pre class=" ">$ matlab</pre>
+<p>To run Matlab in text mode, without the Matlab Desktop GUI environment, use</p>
+<pre class=" ">$ matlab -nodesktop -nosplash</pre>
+<p>plots, images, etc... will be still available.</p>
+<h2 class=" "><a name="running-parallel-matlab-using-distributed-computing-toolbox---engine"></a>Running parallel Matlab using Distributed Computing Toolbox / Engine</h2>
+<p class="exclamation">Distributed toolbox is available only for the EDU variant</p>
+<p class=" ">The MPIEXEC mode available in previous versions is no longer available in MATLAB 2015. Also, the programming interface has changed. Refer to <a class="external-link" href="http://www.mathworks.com/help/distcomp/release-notes.html#buanp9e-1" target="_self" title="">Release Notes</a>.</p>
+<p class=" ">Delete previously used file mpiLibConf.m, we have observed crashes when using Intel MPI.</p>
+<p class=" ">To use Distributed Computing, you first need to setup a parallel profile. We have provided the profile for you, you can either import it in MATLAB command line:</p>
+<pre class=" ">>> parallel.importProfile('/apps/all/MATLAB/2015b-EDU/SalomonPBSPro.settings')<br /><br />ans = <br /><br />SalomonPBSPro </pre>
+<p class=" ">Or in the GUI, go to tab HOME -> Parallel -> Manage Cluster Profiles..., click Import and navigate to :</p>
+<p class=" ">/apps/all/MATLAB/2015b-EDU/SalomonPBSPro.settings</p>
+<p class=" ">With the new mode, MATLAB itself launches the workers via PBS, so you can either use interactive mode or a batch mode on one node, but the actual parallel processing will be done in a separate job started by MATLAB itself. Alternatively, you can use "local" mode to run parallel code on just a single node.</p>
+<h3 class=" ">Parallel Matlab interactive session</h3>
+<p>Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">this page</a>.</p>
+<pre class=" ">$ xhost +<br />$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00 \<br />-l feature__matlab__MATLAB=1 </pre>
+<p>This qsub command example shows how to run Matlab on a single node.</p>
+<p>The second part of the command shows how to request all necessary licenses. In this case 1 Matlab-EDU license and 48 Distributed Computing Engines licenses.</p>
+<p>Once the access to compute nodes is granted by PBS, user can load following modules and start Matlab:Â </p>
+<pre class=" ">r1i0n17$ module load MATLAB/2015a-EDU<br />r1i0n17$ matlab &</pre>
+<h3 class=" "><a name="parallel-matlab-batch-job-in-local-mode"></a>Parallel Matlab batch job in Local mode</h3>
+<p>To run matlab in batch mode, write an matlab script, then write a bash jobscript and execute via the qsub command. By default, matlab will execute one matlab worker instance per allocated core.</p>
+<pre class=" ">#!/bin/bash<br />#PBS -A PROJECT ID<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=24:mpiprocs=24:ompthreads=1<br /><br /># change to shared scratch directory<br />SCR=/scratch/work/user/$USER/$PBS_JOBID<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/matlabcode.m .<br /><br /># load modules<br />module load MATLAB/2015a-EDU<br /><br /># execute the calculation<br />matlab -nodisplay -r matlabcode > output.out<br /><br /># copy output file to home<br />cp output.out $PBS_O_WORKDIR/.</pre>
+<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs and matlab script are in matlabcode.m file, outputs in output.out file. Note the missing .m extension in the matlab -r matlabcodefile call, <strong>the .m must not be included</strong>. Note that the <strong>shared /scratch must be used</strong>. Further, it is <strong>important to include quit</strong> statement at the end of the matlabcode.m script.</p>
+<p>Submit the jobscript using qsub</p>
+<pre class=" ">$ qsub ./jobscript</pre>
+<h3 class=" ">Parallel Matlab Local mode program example</h3>
+<p>The last part of the configuration is done directly in the user Matlab script before Distributed Computing Toolbox is started.</p>
+<pre class=" ">cluster = parcluster('local')</pre>
+<p class=" ">This script creates scheduler object "cluster" of type "local" that starts workers locally. </p>
+<p class="callout">Please note: Every Matlab script that needs to initialize/use matlabpool has to contain these three lines prior to calling parpool(sched, ...) function. </p>
+<p class=" ">The last step is to start matlabpool with "cluster" object and correct number of workers. We have 24 cores per node, so we start 24 workers.</p>
+<pre class=" ">parpool(cluster,24);<br /> <br /> <br />... parallel code ...<br /> <br /> <br />parpool close</pre>
+<p>The complete example showing how to use Distributed Computing Toolbox in local mode is shown here. </p>
+<pre class=" ">cluster = parcluster('local');<br />cluster<br /><br />parpool(cluster,24);<br /><br />n=2000;<br /><br />W = rand(n,n);<br />W = distributed(W);<br />x = (1:n)';<br />x = distributed(x);<br />spmd<br />[~, name] = system('hostname')<br />   <br />   T = W*x; % Calculation performed on labs, in parallel.<br />            % T and W are both codistributed arrays here.<br />end<br />T;<br />whos        % T and W are both distributed arrays here.<br /><br />parpool close<br />quit</pre>
+<p>You can copy and paste the example in a .m file and execute. Note that the parpool size should correspond to <strong>total number of cores</strong> available on allocated nodes.</p>
+<h3 class=" ">Parallel Matlab Batch job using PBS mode (workers spawned in a separate job)</h3>
+<p>This mode uses PBS scheduler to launch the parallel pool. It uses the SalomonPBSPro profile that needs to be imported to Cluster Manager, as mentioned before. This methodod uses MATLAB's PBS Scheduler interface - it spawns the workers in a separate job submitted by MATLAB using qsub.</p>
+<p>This is an example of m-script using PBS mode:</p>
+<pre class=" ">cluster = parcluster('SalomonPBSPro');
+set(cluster, 'SubmitArguments', '-A OPEN-0-0');
+set(cluster, 'ResourceTemplate', '-q qprod -l select=10:ncpus=24');
+set(cluster, 'NumWorkers', 240);
+
+pool = parpool(cluster,240);
+
+n=2000;
+
+W = rand(n,n);
+W = distributed(W);
+x = (1:n)';
+x = distributed(x);
+spmd
+[~, name] = system('hostname')
+
+ T = W*x; % Calculation performed on labs, in parallel.
+ % T and W are both codistributed arrays here.
+end
+whos % T and W are both distributed arrays here.
+
+% shut down parallel pool
+delete(pool)
+</pre>
+<p class=" ">Note that we first construct a cluster object using the imported profile, then set some important options, namely : SubmitArguments, where you need to specify accounting id, and ResourceTemplate, where you need to specify number of nodes to run the job. </p>
+<p class=" ">You can start this script using batch mode the same way as in Local mode example.</p>
+<h3 class=" ">Parallel Matlab Batch with direct launch (workers spawned within the existing job)</h3>
+<p>This method is a "hack" invented by us to emulate the mpiexec functionality found in previous MATLAB versions. We leverage the MATLAB Generic Scheduler interface, but instead of submitting the workers to PBS, we launch the workers directly within the running job, thus we avoid the issues with master script and workers running in separate jobs (issues with license not available, waiting for the worker's job to spawn etc.)</p>
+<p>Please note that this method is experimental.</p>
+<p>For this method, you need to use SalomonDirect profile, import it using <a class="anchor-link" href="#running-parallel-matlab-using-distributed-computing-toolbox---engine" target="_self" title="">the same way as SalomonPBSPro</a> </p>
+<p>This is an example of m-script using direct mode:</p>
+<pre class=" "><br />parallel.importProfile('/apps/all/MATLAB/2015b-EDU/SalomonDirect.settings')<br />cluster = parcluster('SalomonDirect');
+set(cluster, 'NumWorkers', 48);
+
+pool = parpool(cluster, 48);
+
+n=2000;
+
+W = rand(n,n);
+W = distributed(W);
+x = (1:n)';
+x = distributed(x);
+spmd
+[~, name] = system('hostname')
+
+ T = W*x; % Calculation performed on labs, in parallel.
+ % T and W are both codistributed arrays here.
+end
+whos % T and W are both distributed arrays here.
+
+% shut down parallel pool
+delete(pool)</pre>
+<h3 class=" ">Non-interactive Session and Licenses</h3>
+<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">look here</a>.</p>
+<p class="exclamation">The licensing feature of PBS is currently disabled.</p>
+<p>In case of non-interactive session please read the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
+<h3 class=" ">Matlab Distributed Computing Engines start up time</h3>
+<p>Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:</p>
+<table class="plain">
+<tbody>
+<tr><th>compute nodes</th><th>number of workers</th><th>start-up time[s]</th></tr>
+<tr>
+<td>16</td>
+<td>384</td>
+<td>831</td>
+</tr>
+<tr>
+<td>8</td>
+<td>192</td>
+<td>807</td>
+</tr>
+<tr>
+<td>4</td>
+<td>96</td>
+<td>483</td>
+</tr>
+<tr>
+<td>2</td>
+<td>48</td>
+<td>16</td>
+</tr>
+</tbody>
+</table>
+<h2>MATLAB on UV2000Â </h2>
+<p>UV2000 machine available in queue "qfat" can be used for MATLAB computations. This is a SMP NUMA machine with large amount of RAM, which can be beneficial for certain types of MATLAB jobs. CPU cores are allocated in chunks of 8 for this machine.</p>
+<p>You can use MATLAB on UV2000 in two parallel modes :</p>
+<h3>Threaded mode</h3>
+<p class=" ">Since this is a SMP machine, you can completely avoid using Parallel Toolbox and use only MATLAB's threading. MATLAB will automatically detect the number of cores you have allocated and will set <span class="monospace">maxNumCompThreads </span>accordingly and certain operations, such as <span class="monospace">fft, \, eig, svd</span>, etc. will be automatically run in threads. The advantage of this mode is that you don't need to modify your existing sequential codes.<span class="monospace"><br /></span></p>
+<h3 class=" ">Local cluster mode</h3>
+<p>You can also use Parallel Toolbox on UV2000. Use l<a class="anchor-link" href="#parallel-matlab-batch-job-in-local-mode" target="_self" title="">ocal cluster mode</a>, "SalomonPBSPro" profile will not work.</p>
+<p>Â </p>
+<p>Â </p>
+
+
+ </div>
+
+
+ <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
+
+ <div id="plone-discussions">
+ <hr />
+ <b><a id="plone-discussions-href" href="#plone-discussions">Komentáře</a></b>
+ </div>
+
+ <!-- <div id="contact-form" tal:condition="context/isDiscussable">
+ <hr />
+ <b><a id="contact-form-href" href="#contact-form" i18n:translate="">Contact form</a></b>
+ <tal:contactform tal:content="structure python:getattr(context, 'contact-info')()"></tal:contactform>
+ </div> -->
+
+
+
+
+ ]]>
+ </content:encoded>
+ <pubDate>Wed, 24 Jul 2013 12:50:00 +0200</pubDate>
+ <guid>https://docs.it4i.cz/salomon/software/numerical-languages/matlab</guid>
+ </item>
+ <item>
+ <title>Matlab 2013-2014</title>
+ <description></description>
+ <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/">
+ <![CDATA[
+
+
+
+ <div id="parent-fieldname-text-41bf242708954438ac56e1a431788c0e" class="">
+ <h2 class=" ">Introduction</h2>
+<p class="exclamation">This document relates to the old versions R2013 and R2014. For MATLAB 2015, please use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab">this documentation instead</a>.</p>
+<p>Matlab is available in the latest stable version. There are always two variants of the release:</p>
+<ul>
+<li>Non commercial or so called EDU variant, which can be used for common research and educational purposes.</li>
+<li>Commercial or so called COM variant, which can used also for commercial activities. The licenses for commercial variant are much more expensive, so usually the commercial variant has only subset of features compared to the EDU available.</li>
+</ul>
+<p>Â </p>
+<p>To load the latest version of Matlab load the module</p>
+<pre class=" ">$ module load matlab</pre>
+<p>By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use</p>
+<pre class=" ">$ module avail matlab</pre>
+<p>If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.</p>
+<p>If you require the Matlab GUI, please follow the general informations about <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">running graphical applications</a>.</p>
+<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">here</a>) is recommended.</p>
+<p>To run Matlab with GUI, use</p>
+<pre class=" ">$ matlab</pre>
+<p>To run Matlab in text mode, without the Matlab Desktop GUI environment, use</p>
+<pre class=" ">$ matlab -nodesktop -nosplash</pre>
+<p>plots, images, etc... will be still available.</p>
+<h2 class=" ">Running parallel Matlab using Distributed Computing Toolbox / Engine</h2>
+<p>Recommended parallel mode for running parallel Matlab on Anselm is MPIEXEC mode. In this mode user allocates resources through PBS prior to starting Matlab. Once resources are granted the main Matlab instance is started on the first compute node assigned to job by PBS and workers are started on all remaining nodes. User can use both interactive and non-interactive PBS sessions. This mode guarantees that the data processing is not performed on login nodes, but all processing is on compute nodes.</p>
+<p>Â <img alt="Parallel Matlab" class="image-inline" title="Parallel Matlab" src="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/Matlab.png" /></p>
+<p>For the performance reasons Matlab should use system MPI. On Anselm the supported MPI implementation for Matlab is Intel MPI. To switch to system MPI user has to override default Matlab setting by creating new configuration file in its home directory. The path and file name has to be exactly the same as in the following listing:</p>
+<pre class=" "><strong>$ vim ~/matlab/mpiLibConf.m </strong></pre>
+<pre class=" "><strong>function [lib, extras] = mpiLibConf</strong><br /><strong>%MATLAB MPI Library overloading for Infiniband Networks</strong><br /><br /><strong>mpich = '/opt/intel/impi/4.1.1.036/lib64/';</strong><br /><br /><strong>disp('Using Intel MPI 4.1.1.036 over Infiniband')</strong><br /><br /><strong>lib = strcat(mpich, 'libmpich.so');</strong><br /><strong>mpl = strcat(mpich, 'libmpl.so');</strong><br /><strong>opa = strcat(mpich, 'libopa.so');</strong><br /><br /><strong>extras = {};</strong></pre>
+<p>System MPI library allows Matlab to communicate through 40Gbps Infiniband QDR interconnect instead of slower 1Gb ethernet network.</p>
+<p class="callout">Please note: The path to MPI library in "mpiLibConf.m" has to match with version of loaded Intel MPI module. In this example the version 4.1.1.036 of Iintel MPI is used by Matlab and therefore module impi/4.1.1.036Â has to be loaded prior to starting Matlab.</p>
+<h3 class=" ">Parallel Matlab interactive session</h3>
+<p>Once this file is in place, user can request resources from PBS. Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">this page</a>.</p>
+<pre class=" ">$ xhost +<br />$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=4:ncpus=16:mpiprocs=16 -l walltime=00:30:00 \<br />-l feature__matlab__MATLAB=1 </pre>
+<p>This qsub command example shows how to run Matlab with 32 workers in following configuration: 2 nodes (use all 16 cores per node) and 16 workers = mpirocs per node (-l select=2:ncpus=16:mpiprocs=16). If user requires to run smaller number of workers per node then the "mpiprocs" parameter has to be changed.</p>
+<p>The second part of the command shows how to request all necessary licenses. In this case 1 Matlab-EDU license and 32 Distributed Computing Engines licenses.</p>
+<p>Once the access to compute nodes is granted by PBS, user can load following modules and start Matlab:Â </p>
+<pre class=" ">cn79$ module load matlab/R2013a-EDU<br />cn79$ module load impi/4.1.1.036<br />cn79$ matlab &</pre>
+<h3 class=" ">Parallel Matlab batch job</h3>
+<p>To run matlab in batch mode, write an matlab script, then write a bash jobscript and execute via the qsub command. By default, matlab will execute one matlab worker instance per allocated core.</p>
+<pre class=" ">#!/bin/bash<br />#PBS -A PROJECT ID<br />#PBS -q qprod<br />#PBS -l select=2:ncpus=16:mpiprocs=16:ompthreads=1<br /><br /># change to shared scratch directory<br />SCR=/scratch/$USER/$PBS_JOBID<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/matlabcode.m .<br /><br /># load modules<br />module load matlab/R2013a-EDU<br />module load impi/4.1.1.036<br /><br /># execute the calculation<br />matlab -nodisplay -r matlabcode > output.out<br /><br /># copy output file to home<br />cp output.out $PBS_O_WORKDIR/.</pre>
+<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs and matlab script are in matlabcode.m file, outputs in output.out file. Note the missing .m extension in the matlab -r matlabcodefile call, <strong>the .m must not be included</strong>. Note that the <strong>shared /scratch must be used</strong>. Further, it is <strong>important to include quit</strong> statement at the end of the matlabcode.m script.</p>
+<p>Submit the jobscript using qsub</p>
+<pre class=" ">$ qsub ./jobscript</pre>
+<h3 class=" ">Parallel Matlab program example</h3>
+<p>The last part of the configuration is done directly in the user Matlab script before Distributed Computing Toolbox is started.</p>
+<pre class=" ">sched = findResource('scheduler', 'type', 'mpiexec');<br />set(sched, 'MpiexecFileName', '/apps/intel/impi/4.1.1/bin/mpirun');<br />set(sched, 'EnvironmentSetMethod', 'setenv');</pre>
+<p class=" ">This script creates scheduler object "sched" of type "mpiexec" that starts workers using mpirun tool. To use correct version of mpirun, the second line specifies the path to correct version of system Intel MPI library.</p>
+<p class="callout">Please note: Every Matlab script that needs to initialize/use matlabpool has to contain these three lines prior to calling matlabpool(sched, ...) function. </p>
+<p class=" ">The last step is to start matlabpool with "sched" object and correct number of workers. In this case qsub asked for total number of 32 cores, therefore the number of workers is also set to 32.</p>
+<pre class=" ">matlabpool(sched,32);<br /> <br /> <br />... parallel code ...<br /> <br /> <br />matlabpool close</pre>
+<p>The complete example showing how to use Distributed Computing Toolbox is show here. </p>
+<pre class=" ">sched = findResource('scheduler', 'type', 'mpiexec');<br />set(sched, 'MpiexecFileName', '/apps/intel/impi/4.1.1/bin/mpirun')<br />set(sched, 'EnvironmentSetMethod', 'setenv')<br />set(sched, 'SubmitArguments', '') <br />sched<br /><br />matlabpool(sched,32);<br /><br />n=2000;<br /><br />W = rand(n,n);<br />W = distributed(W);<br />x = (1:n)';<br />x = distributed(x);<br />spmd<br />[~, name] = system('hostname')<br />   <br />   T = W*x; % Calculation performed on labs, in parallel.<br />            % T and W are both codistributed arrays here.<br />end<br />T;<br />whos        % T and W are both distributed arrays here.<br /><br />matlabpool close<br />quit</pre>
+<p>You can copy and paste the example in a .m file and execute. Note that the matlabpool size should correspond to <strong>total number of cores</strong> available on allocated nodes.</p>
+<h3 class=" ">Non-interactive Session and Licenses</h3>
+<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">look here</a>.</p>
+<p>In case of non-interactive session please read the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
+<h3 class=" ">Matlab Distributed Computing Engines start up time</h3>
+<p>Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:</p>
+<table class="plain">
+<tbody>
+<tr><th>compute nodes</th><th>number of workers</th><th>start-up time[s]</th></tr>
+<tr>
+<td>16</td>
+<td>256</td>
+<td>1008</td>
+</tr>
+<tr>
+<td>8</td>
+<td>128</td>
+<td>534</td>
+</tr>
+<tr>
+<td>4</td>
+<td>64</td>
+<td>333</td>
+</tr>
+<tr>
+<td>2</td>
+<td>32</td>
+<td>210</td>
+</tr>
+</tbody>
+</table>
+<p>Â </p>
+<p>Â </p>
+
</div>
<!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
+ <div id="plone-discussions">
+ <hr />
+ <b><a id="plone-discussions-href" href="#plone-discussions">Komentáře</a></b>
+ </div>
+
+ <!-- <div id="contact-form" tal:condition="context/isDiscussable">
+ <hr />
+ <b><a id="contact-form-href" href="#contact-form" i18n:translate="">Contact form</a></b>
+ <tal:contactform tal:content="structure python:getattr(context, 'contact-info')()"></tal:contactform>
+ </div> -->
+
+
+
+
+ ]]>
+ </content:encoded>
+ <pubDate>Wed, 24 Jul 2013 12:50:00 +0200</pubDate>
+ <guid>https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab</guid>
+ </item>
+ <item>
+ <title>MATLAB 2015b</title>
+ <description></description>
+ <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/">
+ <![CDATA[
+
+
+
+
+
+
+
+ <div id="parent-fieldname-text" class="plain">
+ <p>MATLAB 2015b has been installed on Anselm and Salomon. Modules are named MATLAB/2015b-COM and MATLAB/2015b-EDU. Release notes:Â http://www.mathworks.com/help/matlab/release-notes.html#R2015b</p>
+ </div>
+
+
+
+ ]]>
+ </content:encoded>
+ <pubDate>Wed, 13 Jul 2016 15:40:00 +0200</pubDate>
+ <guid>https://docs.it4i.cz/whats-new/news-feed/matlab-2015b</guid>
+ </item>
+ <item>
+ <title>Numerical languages</title>
+ <description>Interpreted languages for numerical computations and analysis</description>
+ <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/">
+ <![CDATA[
+
+
+
+ <div id="parent-fieldname-text-6c3faf66932c4ed6aaf3471f0ab0e081" class="">
+ <h2 class=" ">Introduction</h2>
+<p>This section contains a collection of high-level interpreted languages, primarily intended for numerical computations.</p>
+<h2 class=" ">Matlab</h2>
+<p>MATLAB<sup>®</sup> is a high-level language and interactive environment for numerical computation, visualization, and programming.</p>
+<pre class=" ">$ module load MATLAB/2015b-EDU<br />$ matlab</pre>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab">Matlab<span class="internal-link"></span> page</a>.</p>
+<h2 class=" ">Octave</h2>
+<p>GNU Octave is a high-level interpreted language, primarily intended for numerical computations. The Octave language is quite similar to Matlab so that most programs are easily portable.</p>
+<pre class=" ">$ module load Octave<br />$ octave</pre>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave">Octave page</a>.</p>
+<h2 class=" ">R</h2>
+<p>The R is an interpreted language and environment for statistical computing and graphics.</p>
+<pre class=" ">$ module load R<br />$ R</pre>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r">R page</a>.</p>
+
+ </div>
+ <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
+
+ <div id="plone-discussions">
+ <hr />
+ <b><a id="plone-discussions-href" href="#plone-discussions">Komentáře</a></b>
+ </div>
+
<!-- <div id="contact-form" tal:condition="context/isDiscussable">
<hr />
<b><a id="contact-form-href" href="#contact-form" i18n:translate="">Contact form</a></b>
@@ -5330,8 +5341,8 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
]]>
</content:encoded>
- <pubDate>Wed, 13 Jul 2016 02:00:02 +0200</pubDate>
- <guid>https://docs.it4i.cz/salomon/list_of_modules</guid>
+ <pubDate>Tue, 25 Feb 2014 13:25:00 +0200</pubDate>
+ <guid>https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction</guid>
</item>
<item>
<title>Vampir installed</title>
@@ -5368,25 +5379,25 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
<h2 class=" ">Introduction</h2>
<p>We provide state of the art programms and tools to develop, profile and debug HPC codes at IT4Innovations.<br />On these pages, we provide an overview of the profiling and debugging tools available on Anslem at IT4I.</p>
<h2 class=" ">Intel debugger</h2>
-<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">X display</a> for running the GUI.</p>
+<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33">X display</a> for running the GUI.</p>
<pre class=" ">$ module load intel<br />$ idb</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger">Intel Debugger</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger">Intel Debugger</a> page.</p>
<h2 class=" ">Allinea Forge (DDT/MAP)</h2>
<p>Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel Xeon Phi accelerators. DDT provides all the standard debugging features (stack trace, breakpoints, watches, view variables, threads etc.) for every thread running as part of your program, or for every process - even if these processes are distributed across a cluster using an MPI implementation.</p>
<pre class=" ">$ module load Forge<br />$ forge</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt">Allinea DDT</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt">Allinea DDT</a> page.</p>
<h2 class=" ">Allinea Performance Reports</h2>
<p>Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs. Our license is limited to 64 MPI processes.</p>
<pre class=" ">$ module load PerformanceReports/6.0 <br />$ perf-report mpirun -n 64 ./my_application argument01 argument02</pre>
-<p class=" ">Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports">Allinea Performance Reports</a> page.</p>
+<p class=" ">Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports">Allinea Performance Reports</a> page.</p>
<h2 class=" ">RougeWave Totalview</h2>
<p>TotalView is a source- and machine-level debugger for multi-process, multi-threaded programs. Its wide range of tools provides ways to analyze, organize, and test programs, making it easy to isolate and identify problems in individual threads and processes in programs of great complexity.</p>
<pre class=" ">$ module load totalview<br />$ totalview</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view">Totalview</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view">Totalview</a> page.</p>
<h2 class=" ">Vampir trace analyzer</h2>
<p>Vampir is a GUI trace analyzer for traces in OTF format.</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">Vampir</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">Vampir</a> page.</p>
</div>
@@ -5421,8 +5432,8 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
<div id="parent-fieldname-text-50ee0f8999e14a08822bd423d24de7ef" class="">
- <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
-<h2 class=" "><img title="Vampir screenshot" class="image-inline" alt="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
+ <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
+<h2 class=" "><img alt="Vampir screenshot" class="image-inline" title="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
<h2 class=" ">Installed versions</h2>
<p>Version 8.5.0 is currently installed as module <span class="monospace">Vampir/8.5.0</span> :</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir &</pre>
@@ -5471,25 +5482,25 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
<p>We provide state of the art programms and tools to develop, profile and debug HPC codes at IT4Innovations.<br />On these pages, we provide an overview of the profiling and debugging tools available on Anslem at IT4I.</p>
<h2 class=" ">Intel debugger</h2>
<p class="exclamation">Intel debugger is no longer available since Parallel Studio version 2015</p>
-<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">X display</a> for running the GUI.</p>
+<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">X display</a> for running the GUI.</p>
<pre class=" ">$ module load intel<br />$ idb</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger">Intel Debugger</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger">Intel Debugger</a> page.</p>
<h2 class=" ">Allinea Forge (DDT/MAP)</h2>
<p>Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel Xeon Phi accelerators. DDT provides all the standard debugging features (stack trace, breakpoints, watches, view variables, threads etc.) for every thread running as part of your program, or for every process - even if these processes are distributed across a cluster using an MPI implementation.</p>
<pre class=" ">$ module load Forge<br />$ forge</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt">Allinea DDT</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt">Allinea DDT</a> page.</p>
<h2 class=" ">Allinea Performance Reports</h2>
<p>Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs. Our license is limited to 64 MPI processes.</p>
<pre class=" ">$ module load PerformanceReports/6.0 <br />$ perf-report mpirun -n 64 ./my_application argument01 argument02</pre>
-<p class=" ">Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports">Allinea Performance Reports</a> page.</p>
+<p class=" ">Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports">Allinea Performance Reports</a> page.</p>
<h2 class=" ">RougeWave Totalview</h2>
<p>TotalView is a source- and machine-level debugger for multi-process, multi-threaded programs. Its wide range of tools provides ways to analyze, organize, and test programs, making it easy to isolate and identify problems in individual threads and processes in programs of great complexity.</p>
<pre class=" ">$ module load TotalView/8.15.4-6-linux-x86-64<br />$ totalview</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/total-view">Totalview</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/total-view">Totalview</a> page.</p>
<h2 class=" ">Vampir trace analyzer</h2>
<p>Vampir is a GUI trace analyzer for traces in OTF format.</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">Vampir</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">Vampir</a> page.</p>
</div>
@@ -5524,8 +5535,8 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
<div id="parent-fieldname-text-f6e25102d1244fb4ab355175867747b5" class="">
- <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
-<h2 class=" "><img title="Vampir screenshot" class="image-inline" alt="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
+ <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
+<h2 class=" "><img alt="Vampir screenshot" class="image-inline" title="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
<h2 class=" ">Installed versions</h2>
<p>Version 8.5.0 is currently installed as module <span class="monospace">Vampir/8.5.0</span> :</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir &</pre>
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<title>Accessing the Clusters — IT4I Docs</title>
- <link rel="canonical" href="shell-access-and-data-transfer.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer" />
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<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="shell-access-and-data-transfer.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="shell-access-and-data-transfer.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
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</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../get-started-with-it4innovations.html">Get Started with IT4Innovations</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations">Get Started with IT4Innovations</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="shell-access-and-data-transfer.html">Accessing the Clusters</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">Accessing the Clusters</a>
<span class="breadcrumbSeparator">
/
@@ -237,11 +234,11 @@
<div id="parent-fieldname-text-d82802a347ff4469bd07c74ab392d72b" class="">
<p>The IT4Innovations clusters are accessed by SSH protocol via login nodes.</p>
-<p class="callout">Read more on <a target="_self" title="" class="internal-link" href="../../salomon/accessing-the-cluster/shell-and-data-access.html">Accessing the Salomon Cluste</a>r or <a target="_self" title="" class="internal-link" href="../../anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access.html">Accessing the Anselm Cluster</a> pages.</p>
+<p class="callout">Read more on <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/accessing-the-cluster">Accessing the Salomon Cluste</a>r or <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">Accessing the Anselm Cluster</a> pages.</p>
<h3 class=" ">PuTTY</h3>
-<p>On <strong>Windows</strong>, use <a target="_self" title="" class="internal-link" href="shell-access-and-data-transfer/putty/putty.html">PuTTY ssh client</a>.</p>
+<p>On <strong>Windows</strong>, use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty">PuTTY ssh client</a>.</p>
<h3 class=" " id="parent-fieldname-title">SSH keys</h3>
-<p>Read more about <a target="_self" title="" class="internal-link" href="shell-access-and-data-transfer/ssh-keys.html">SSH keys management</a>.</p>
+<p>Read more about <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">SSH keys management</a>.</p>
</div>
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<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
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<span>What's New</span>
</a>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../applying-for-resources.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources">
<span>Applying for Resources</span>
</a>
@@ -381,7 +378,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../obtaining-login-credentials.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">
<span>Obtaining Login Credentials</span>
</a>
@@ -397,7 +394,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="shell-access-and-data-transfer.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">
<span>Accessing the Clusters</span>
</a>
@@ -413,7 +410,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="shell-access-and-data-transfer.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer">
<span>Shell access and data transfer</span>
</a>
@@ -429,7 +426,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="shell-access-and-data-transfer/putty.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty">
<span>PuTTY</span>
</a>
@@ -445,7 +442,7 @@
- <a title="" class="state-published contenttype-document" href="shell-access-and-data-transfer/ssh-keys.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">
<span>SSH keys</span>
</a>
@@ -470,7 +467,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="graphical-user-interface.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface">
<span>Graphical User Interface</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
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<span>Anselm Cluster Documentation</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
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- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
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- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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})();
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<div id="portal-footer">
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters.md
new file mode 100644
index 0000000000000000000000000000000000000000..f918d611f7785269ff28f4a45f3bb4999e19d455
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters.md
@@ -0,0 +1,15 @@
+Accessing the Clusters
+======================
+The IT4Innovations clusters are accessed by SSH protocol via login
+nodes.
+Read more on [Accessing the Salomon
+Cluste](https://docs.it4i.cz/salomon/accessing-the-cluster)r
+or [Accessing the Anselm
+Cluster](https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster)
+pages.
+### PuTTY
+On **Windows**, use [PuTTY ssh
+client](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty).
+### SSH keys {#parent-fieldname-title}
+Read more about [SSH keys
+management](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys).
diff --git a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html
old mode 100755
new mode 100644
similarity index 67%
rename from get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html
rename to docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html
index 935ab0fb75cfaf4fecba2155dbb182a2077eb0bc..35cf1ad696acf13ac5c8083c479a130569d074e1
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface" /><!--[if lt IE 7]></base><![endif]-->
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<title> Graphical User Interface — IT4I Docs</title>
- <link rel="canonical" href="graphical-user-interface.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
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<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="graphical-user-interface.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="graphical-user-interface.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<div id="portal-advanced-search" class="hiddenStructure">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../get-started-with-it4innovations.html">Get Started with IT4Innovations</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations">Get Started with IT4Innovations</a>
<span class="breadcrumbSeparator">
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@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="shell-access-and-data-transfer.html">Accessing the Clusters</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">Accessing the Clusters</a>
<span class="breadcrumbSeparator">
/
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<div id="parent-fieldname-text-0088a96108124c8b932ad89062d8b4dd" class="">
<h2 class=" ">X Window System</h2>
<p>The X Window system is a principal way to get GUI access to the clusters.</p>
-<p>Read more about configuring <a target="_self" title="" class="internal-link" href="graphical-user-interface/x-window-system/x-window-and-vnc.html"><b>X Window System</b></a>.</p>
+<p>Read more about configuring <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc"><b>X Window System</b></a>.</p>
<h2>VNC</h2>
<p>The <b>Virtual Network Computing</b> (<b>VNC</b>) is a graphical <span class="link-external"><a href="http://en.wikipedia.org/wiki/Desktop_sharing" title="Desktop sharing">desktop sharing</a></span> system that uses the <span class="link-external"><a href="http://en.wikipedia.org/wiki/RFB_protocol" title="RFB protocol">Remote Frame Buffer protocol (RFB)</a></span> to remotely control another <span class="link-external"><a href="http://en.wikipedia.org/wiki/Computer" title="Computer">computer</a></span>.</p>
-<p>Read more about configuring <strong><a target="_self" title="" class="internal-link" href="graphical-user-interface/vnc.html">VNC</a></strong>.</p>
+<p>Read more about configuring <strong><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc">VNC</a></strong>.</p>
</div>
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+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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<span>Get Started with IT4Innovations</span>
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<span>Applying for Resources</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">
<span>Obtaining Login Credentials</span>
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<span>Graphical User Interface</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="graphical-user-interface/x-window-system.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system">
<span>X Window System</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="graphical-user-interface/vnc.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc">
<span>VNC</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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<span>Anselm Cluster Documentation</span>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.md
new file mode 100644
index 0000000000000000000000000000000000000000..ff3738063f55085dad7cad70901c9102e176ce07
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.md
@@ -0,0 +1,21 @@
+Graphical User Interface
+========================
+
+X Window System
+---------------
+The X Window system is a principal way to get GUI access to the
+clusters.
+Read more about configuring [**X Window
+System**](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc).
+VNC
+---
+The **Virtual Network Computing** (**VNC**) is a graphical <span
+class="link-external">[desktop
+sharing](http://en.wikipedia.org/wiki/Desktop_sharing "Desktop sharing")</span>
+system that uses the <span class="link-external">[Remote Frame Buffer
+protocol
+(RFB)](http://en.wikipedia.org/wiki/RFB_protocol "RFB protocol")</span>
+to remotely control another <span
+class="link-external">[computer](http://en.wikipedia.org/wiki/Computer "Computer")</span>.
+Read more about configuring
+**[VNC](https://docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc)**.
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.html
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+<p>Read more about configuring <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc"><b>X Window System</b></a>.</p>
+<h2>VNC</h2>
+<p>The <b>Virtual Network Computing</b> (<b>VNC</b>) is a graphical <span class="link-external"><a href="http://en.wikipedia.org/wiki/Desktop_sharing" title="Desktop sharing">desktop sharing</a></span> system that uses the <span class="link-external"><a href="http://en.wikipedia.org/wiki/RFB_protocol" title="RFB protocol">Remote Frame Buffer protocol (RFB)</a></span> to remotely control another <span class="link-external"><a href="http://en.wikipedia.org/wiki/Computer" title="Computer">computer</a></span>.</p>
+<p>Read more about configuring <strong><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc">VNC</a></strong>.</p>
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md
new file mode 100644
index 0000000000000000000000000000000000000000..ff3738063f55085dad7cad70901c9102e176ce07
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md
@@ -0,0 +1,21 @@
+Graphical User Interface
+========================
+
+X Window System
+---------------
+The X Window system is a principal way to get GUI access to the
+clusters.
+Read more about configuring [**X Window
+System**](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc).
+VNC
+---
+The **Virtual Network Computing** (**VNC**) is a graphical <span
+class="link-external">[desktop
+sharing](http://en.wikipedia.org/wiki/Desktop_sharing "Desktop sharing")</span>
+system that uses the <span class="link-external">[Remote Frame Buffer
+protocol
+(RFB)](http://en.wikipedia.org/wiki/RFB_protocol "RFB protocol")</span>
+to remotely control another <span
+class="link-external">[computer](http://en.wikipedia.org/wiki/Computer "Computer")</span>.
+Read more about configuring
+**[VNC](https://docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc)**.
diff --git a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/2015-10-02_135128cV.png b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/TightVNC_login.png
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diff --git a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/2015-10-07_120255acV.png b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-compute-nodes-over-vnc.png
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diff --git a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/2015-10-07_121839acV.png b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-terminal.png
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diff --git a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/2015-10-02_135100cV.png b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/putty-tunnel.png
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/vnc.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/vnc.html
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@@ -0,0 +1,736 @@
+
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+ <p>The <b>Virtual Network Computing</b> (<b>VNC</b>) is a graphical <a href="http://en.wikipedia.org/wiki/Desktop_sharing" title="Desktop sharing">desktop sharing</a> system that uses the <a href="http://en.wikipedia.org/wiki/RFB_protocol" title="RFB protocol">Remote Frame Buffer protocol (RFB)</a> to remotely control another <a href="http://en.wikipedia.org/wiki/Computer" title="Computer">computer</a>. It transmits the <a href="http://en.wikipedia.org/wiki/Computer_keyboard" title="Computer keyboard">keyboard</a> and <a class="mw-redirect" href="http://en.wikipedia.org/wiki/Computer_mouse" title="Computer mouse">mouse</a> events from one computer to another, relaying the graphical <a class="mw-redirect" href="http://en.wikipedia.org/wiki/Computer_screen" title="Computer screen">screen</a> updates back in the other direction, over a <a href="http://en.wikipedia.org/wiki/Computer_network" title="Computer network">network</a>.<sup class="reference" id="cite_ref-1"><a href="http://en.wikipedia.org/wiki/Virtual_Network_Computing#cite_note-1"><span>[</span>1<span>]</span></a></sup></p>
+<p>The recommended clients are <a class="external-link" href="http://www.tightvnc.com" target="_self" title="">TightVNC</a> or <a class="external-link" href="http://sourceforge.net/apps/mediawiki/tigervnc/index.php?title=Main_Page" target="_self" title="">TigerVNC</a> (free, open source, available for almost any platform).</p>
+<h2 class=" ">Create VNC password</h2>
+<p class="callout">Local VNC password should be set before the first login. Do use a strong password.</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">~]</span><span class="pln">$ vncpasswd</span><br /><span class="typ">Password</span><span class="pun">:</span><br /><span class="typ">Verify</span><span class="pun">:</span></pre>
+<h2 class=" ">Start vncserver</h2>
+<p class="callout">To access VNC a local vncserver must be started first and also a tunnel using SSH port forwarding must be established.<br /><a class="anchor-link" href="#linux-example-of-creating-a-tunnel" target="_self" title="">See below</a> for the details on SSH tunnels. In this example we use port 61.</p>
+<p class=" ">You can find ports which are already occupied. Here you can see that ports "<span class="pln">/usr/bin/Xvnc :79"</span> and "<span class="pln">/usr/bin/Xvnc :60" are occupied.</span></p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">~]</span><span class="pln">$ </span>ps aux | grep Xvnc<br /><span class="pln"><span class="pln"><span class="pln">username</span></span></span>   5971 0.0 0.0 201072 92564 ?       SN  Sep22  4:19 /usr/bin/Xvnc :79 -desktop login2:79 (<span class="pln"><span class="pln"><span class="pln">username</span></span></span>) -auth /home/gre196/.Xauthority -geometry 1024x768 -rfbwait 30000 -rfbauth /home/<span class="pln"><span class="pln"><span class="pln">username</span></span></span>/.vnc/passwd -rfbport 5979 -fp catalogue:/etc/X11/fontpath.d -pn<br /><span class="pln"><span class="pln"><span class="pln">username</span>   </span>10296 0.0 0.0 131772 21076 pts/29  SN  13:01  0:01 /usr/bin/Xvnc :60 -desktop login2:61 (<span class="pln">username</span>) -auth /home/<span class="pln">username</span>/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/jir13/.vnc/passwd -rfbport 5960 -fp catalogue:/etc/X11/fontpath.d -pn<br />.....<br /></span></pre>
+<p class=" ">Choose free port e.g. 61 and start your VNC server:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">~]</span><span class="pln">$ vncserver </span><span class="pln">:61 </span><span class="pun">-</span><span class="pln">geometry </span><strong><span class="lit">1600</span></strong><span class="lit">x900</span><span class="pln"> </span><span class="pun">-</span><span class="pln">depth </span><span class="lit">16</span><br /><br /><span class="typ">New</span><span class="pln"> </span><span class="str">'login2:1 (username)'</span><span class="pln"> desktop is login2</span><span class="pun">:</span><span class="lit">1</span><br /><br /><span class="typ">Starting</span><span class="pln"> applications specified </span><span class="kwd">in</span><span class="pln"> </span><span class="pun">/</span><span class="pln">home</span><span class="pun">/</span><span class="pln">username</span><span class="pun">/.</span><span class="pln">vnc</span><span class="pun">/</span><span class="pln">xstartup</span><br /><span class="typ">Log</span><span class="pln"> file is </span><span class="pun">/</span><span class="pln">home</span><span class="pun">/</span><span class="pln">username</span><span class="pun">/.</span><span class="pln">vnc</span><span class="pun">/</span><span class="pln">login2</span><span class="pun">:</span><span class="lit">1.log</span><br /><span class="pun"></span></pre>
+<p>Check if VNC server is started on the port (in this example 61):</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ vncserver </span><span class="pun">-</span><span class="pln">list</span><br /><br /><span class="typ">TigerVNC</span><span class="pln"> server sessions</span><span class="pun">:</span><br /><br /><span class="pln">X DISPLAY </span><span class="com">#Â Â Â Â PROCESS ID</span><br /><span class="pun">:<span class="pun"></span><span class="lit">6</span></span><span class="lit">1</span><span class="pln">Â Â Â Â Â Â Â Â Â Â Â Â Â </span><span class="lit">18437</span></pre>
+<p>Another command:<span class="pln"></span></p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ Â ps aux | grep Xvnc<br /><br /><span class="pln">username</span>Â Â Â 10296Â 0.0Â 0.0 131772 21076 pts/29Â Â SNÂ Â 13:01Â Â 0:01 /usr/bin/Xvnc :61 -desktop login2:61 (<span class="pln">username</span>) -auth /home/jir13/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/<span class="pln"><span class="pln">username</span></span>/.vnc/passwd -rfbport 5961 -fp catalogue:/etc/X11/fontpath.d -pn<br /></span></pre>
+<p>To access the VNC server you have to create a tunnel between the login node using TCP <strong>port 5961</strong> and your machine using a free TCP port (for simplicity the very same, in this case).</p>
+<p class="exclamation">The tunnel must point to the same login node where you launched the VNC server, eg. login2. If you use just cluster-name.it4i.cz, the tunnel might point to a different node due to DNS round robin.</p>
+<h3 class=" "><a name="linux-example-of-creating-a-tunnel"></a><a name="linux-example"></a>Linux/Mac OS example of creating a tunnel</h3>
+<p>At your machine, create the tunnel:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="kwd">local</span><span class="pln"> $Â ssh </span><span class="pun">-</span><span class="pln">TN </span><span class="pun">-</span><span class="pln">f username@login2.cluster-name</span><span class="pun">.</span><span class="pln">it4i</span><span class="pun">.</span><span class="pln">cz </span><span class="pun">-</span><span class="pln">L </span><span class="lit">5961</span><span class="pun">:</span><span class="pln">localhost</span><span class="pun">:</span><span class="lit">5961</span></pre>
+<p>Issue the following command to check the tunnel is established (please note the PID 2022 in the last column, you'll need it for closing the tunnel):</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="kwd">local</span><span class="pln"> $ netstat </span><span class="pun">-</span><span class="pln">natp </span><span class="pun">|</span><span class="pln"> grep </span><span class="lit">5961</span><br /><span class="pun">(</span><span class="typ">Not</span><span class="pln"> all processes could be identified</span><span class="pun">,</span><span class="pln"> non</span><span class="pun">-</span><span class="pln">owned process info</span><br /><span class="pln"> will not be shown</span><span class="pun">,</span><span class="pln"> you would have to be root to see it all</span><span class="pun">.)</span><br /><span class="pln">tcp       </span><span class="lit">0</span><span class="pln">     </span><span class="lit">0</span><span class="pln"> </span><span class="lit">127.0</span><span class="pun">.</span><span class="lit">0.1</span><span class="pun">:</span><span class="lit">5961</span><span class="pln">         </span><span class="lit">0.0</span><span class="pun">.</span><span class="lit">0.0</span><span class="pun">:*</span><span class="pln">              LISTEN     </span><span class="lit">2022</span><span class="pun">/</span><span class="pln">ssh       </span><br /><span class="pln">tcp6      </span><span class="lit">0</span><span class="pln">     </span><span class="lit">0</span><span class="pln"> </span><span class="pun">::</span><span class="lit">1</span><span class="pun">:</span><span class="lit">5961</span><span class="pln">               </span><span class="pun">:::*</span><span class="pln">                   LISTEN     </span><span class="lit">2022</span><span class="pun">/</span><span class="pln">ssh </span></pre>
+<p>Or on Mac OS use this command:</p>
+<pre class="prettyprint lang-sh">local-mac $ lsof -n -i4TCP:5961 | grep LISTEN<br />ssh 75890 sta545 7u IPv4 0xfb062b5c15a56a3b 0t0 TCP 127.0.0.1:5961 (LISTEN)</pre>
+<p>Connect with the VNC client:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="kwd">local</span><span class="pln"> $ vncviewer </span><span class="lit">127.0</span><span class="pun">.</span><span class="lit">0.1</span><span class="pun">:</span><span class="lit">5961</span></pre>
+<p>In this example, we connect to VNC server on port 5961, via the ssh tunnel. The connection is encrypted and secured. The VNC server listening on port 5961 provides screen of 1600x900 pixels.</p>
+<p>You have to destroy the SSH tunnel which is still running at the background after you finish the work. Use the following command (PID 2022 in this case, see the netstat command above):</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">kill </span><span class="lit">2022</span></pre>
+<h3 class=" ">Windows example of creating a tunnel</h3>
+<p>Use PuTTY to log in on cluster.</p>
+<p>Start vncserver using command vncserver described above.</p>
+<p>Search for the localhost and port number (in this case 127.0.0.1:5961).<strong><br /></strong></p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ netstat </span><span class="pun">-</span><span class="pln">tanp </span><span class="pun">|</span><span class="pln"> grep </span><span class="typ">Xvnc</span><br /><span class="pun">(</span><span class="typ">Not</span><span class="pln"> all processes could be identified</span><span class="pun">,</span><span class="pln"> non</span><span class="pun">-</span><span class="pln">owned process info</span><br /><span class="pln"> will not be shown</span><span class="pun">,</span><span class="pln"> you would have to be root to see it all</span><span class="pun">.)</span><br /><span class="pln">tcp       </span><span class="lit">0</span><span class="pln">     </span><span class="lit">0</span><span class="pln"> </span><span class="lit">127.0</span><span class="pun">.</span><span class="lit">0.1</span><span class="pun">:</span><span class="lit">5961</span><span class="pln">             </span><span class="lit">0.0</span><span class="pun">.</span><span class="lit">0.0</span><span class="pun">:*</span><span class="pln">                  LISTEN     </span><span class="lit">24031</span><span class="pun">/</span><span class="typ">Xvnc</span></pre>
+<p>On the PuTTY Configuration screen go to Connection->SSH->Tunnels to set up the tunnel.</p>
+<p>Fill the Source port and Destination fields. <strong>Do not forget to click the Add button</strong>.<br /><br /> <a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/putty-tunnel.png"><img alt="PuTTY - Create tunnel" class="image-inline" title="PuTTY Tunnel" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/putty-tunnel.png/@@images/4c66cd51-c858-473b-98c2-8d901aea7118.png" /></a></p>
+<p>Run the VNC client of your choice, select VNC server 127.0.0.1, port 5961 and connect using VNC password.</p>
+<h3 class=" ">Example of starting TigerVNC viewer</h3>
+<p><img alt="TigerVNC vncviewer" class="image-inline" title="Vncviewer" src="https://docs.it4i.cz/anselm-cluster-documentation/vncviewer.png/@@images/bb4cedff-4cb6-402b-ac79-039186fe5df3.png" /></p>
+<p>In this example, we connect to VNC server on port 5961, via the ssh tunnel, using TigerVNC viewer. The connection is encrypted and secured. The VNC server listening on port 5961 provides screen of 1600x900 pixels.</p>
+<h3 class=" ">Example of starting TightVNC Viewer</h3>
+<p>Use your VNC password to log using TightVNC Viewer and start a Gnome Session on the login node.</p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/TightVNC_login.png"><strong><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/TightVNC_login.png/@@images/e53354d8-a2e8-4947-92b3-dd107d498408.png" /></strong></a></p>
+<h2 class=" ">Gnome session</h2>
+<p>You should see after the successful login.</p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/get-started-with-it4innovations/gnome_screen.jpg"><img alt="Default Gnome session" class="image-inline" title="Default Gnome session" src="https://docs.it4i.cz/salomon/gnome_screen.jpg/@@images/7758b792-24eb-48dc-bf72-618cda100fda.png" /></a></p>
+<h3 class=" "><strong>Disable your Gnome session screensaver<br /></strong></h3>
+<p>Open Screensaver preferences dialog:</p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/gnome_screen.jpg"><img alt="Screensaver Preferences" class="image-inline" title="Screensaver Preferences" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmscreensaver.png/@@images/44048cfa-e854-4cb4-902b-c173821c2db1.png" /></a></p>
+<p>Uncheck both options below the slider:</p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png"><img alt="Disable lock screen and screensaver" class="image-inline" title="Disable lock screen and screensaver" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png/@@images/0259b284-18eb-402c-a55c-584562e26b47.png" /></a></p>
+<h3 class=" ">Kill screensaver if locked screen</h3>
+<p>If the screen gets locked you have to kill the screensaver. Do not to forget to disable the screensaver then.</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ ps aux </span><span class="pun">|</span><span class="pln"> grep screen</span><br /><span class="pln">username    </span><span class="lit">1503</span><span class="pln"> </span><span class="lit">0.0</span><span class="pln"> </span><span class="lit">0.0</span><span class="pln"> </span><span class="lit">103244</span><span class="pln">  </span><span class="lit">892</span><span class="pln"> pts</span><span class="pun">/</span><span class="lit">4</span><span class="pln">   S</span><span class="pun">+</span><span class="pln">  </span><span class="lit">14</span><span class="pun">:</span><span class="lit">37</span><span class="pln">  </span><span class="lit">0</span><span class="pun">:</span><span class="lit">00</span><span class="pln"> grep screen</span><br /><span class="pln">username    </span><span class="lit">24316</span><span class="pln"> </span><span class="lit">0.0</span><span class="pln"> </span><span class="lit">0.0</span><span class="pln"> </span><span class="lit">270564</span><span class="pln"> </span><span class="lit">3528</span><span class="pln"> </span><span class="pun">?</span><span class="pln">       </span><span class="typ">Ss</span><span class="pln">  </span><span class="lit">14</span><span class="pun">:</span><span class="lit">12</span><span class="pln">  </span><span class="lit">0</span><span class="pun">:</span><span class="lit">00</span><span class="pln"> gnome</span><span class="pun">-</span><span class="pln">screensaver</span><br /><br /><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ kill </span><span class="lit">24316</span></pre>
+<h3 class=" ">Kill vncserver after finished work</h3>
+<p>You should kill your VNC server using command:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ </span><span class="pln">vncserver -kill :61<br />Killing Xvnc process ID 7074<br />Xvnc process ID 7074 already killed<br /></span><span class="pun"></span></pre>
+<p>Or this way:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$Â p</span><span class="pln">kill vnc</span></pre>
+<h2 class=" ">GUI applications on compute nodes over VNC</h2>
+<p>The very <a title="" class="anchor-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-and-vnc#gui-applications-on-compute-nodes">same methods as described above</a>, may be used to run the GUI applications on compute nodes. However, for <strong>maximum performance</strong>, proceed following these steps:</p>
+<p>Open a Terminal (Applications -> System Tools -> Terminal). Run all the next commands in the terminal.<br /><br /><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-terminal.png"><img alt="gnome-terminal.png" class="image-inline" title="gnome-terminal.png" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-terminal.png/@@images/dc0f0207-c614-49be-9cfb-905a523c5a39.png" /></a></p>
+<p>Allow incoming X11 graphics from the compute nodes at the login node:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">$ xhost </span><span class="pun">+</span></pre>
+<p>Get an interactive session on a compute node (for more detailed info <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">look here</a>). Use the <strong>-v DISPLAY</strong> option to propagate the DISPLAY on the compute node. In this example, we want a complete node (24 cores in this example) from the production queue:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">$ qsub </span><span class="pun">-</span><span class="pln">I </span><span class="pun">-</span><span class="pln">v DISPLAY</span><span class="pun">=</span><span class="pln">$</span><span class="pun">(</span><span class="pln">uname </span><span class="pun">-</span><span class="pln">n</span><span class="pun">):</span><span class="pln">$</span><span class="pun">(</span><span class="pln">echo $DISPLAY </span><span class="pun">|</span><span class="pln"> cut </span><span class="pun">-</span><span class="pln">d </span><span class="str">':'</span><span class="pln"> </span><span class="pun">-</span><span class="pln">f </span><span class="lit">2</span><span class="pun">)</span><span class="pln"> </span><span class="pun">-</span><span class="pln">A PROJECT_ID </span><span class="pun">-</span><span class="pln">q qprod </span><span class="pun">-</span><span class="pln">l select</span><span class="pun">=</span><span class="lit">1</span><span class="pun">:</span><span class="pln">ncpus</span><span class="pun">=24</span><span class="lit"></span></pre>
+<p>Test that the DISPLAY redirection into your VNC session works, by running a X11 application (e. g. XTerm) on the assigned compute node:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">$ xterm<br /></span></pre>
+<p>Example described above:</p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-compute-nodes-over-vnc.png"><img alt="gnome-compute-nodes-over-vnc.png" class="image-inline" title="gnome-compute-nodes-over-vnc.png" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-compute-nodes-over-vnc.png/@@images/d4c9b6b6-6e2c-48c0-84dd-26d291517355.png" /></a></p>
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/vnc.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/vnc.md
new file mode 100644
index 0000000000000000000000000000000000000000..639e7df17d9fb68eae74bd555db95cd03c5a5262
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/vnc.md
@@ -0,0 +1,196 @@
+VNC
+===
+
+The **Virtual Network Computing** (**VNC**) is a graphical [desktop
+sharing](http://en.wikipedia.org/wiki/Desktop_sharing "Desktop sharing")
+system that uses the [Remote Frame Buffer protocol
+(RFB)](http://en.wikipedia.org/wiki/RFB_protocol "RFB protocol") to
+remotely control another
+[computer](http://en.wikipedia.org/wiki/Computer "Computer"). It
+transmits the
+[keyboard](http://en.wikipedia.org/wiki/Computer_keyboard "Computer keyboard")
+and
+[mouse](http://en.wikipedia.org/wiki/Computer_mouse "Computer mouse"){.mw-redirect}
+events from one computer to another, relaying the graphical
+[screen](http://en.wikipedia.org/wiki/Computer_screen "Computer screen"){.mw-redirect}
+updates back in the other direction, over a
+[network](http://en.wikipedia.org/wiki/Computer_network "Computer network").^[<span>[</span>1<span>]</span>](http://en.wikipedia.org/wiki/Virtual_Network_Computing#cite_note-1)^
+The recommended clients are
+[TightVNC](http://www.tightvnc.com) or
+[TigerVNC](http://sourceforge.net/apps/mediawiki/tigervnc/index.php?title=Main_Page)
+(free, open source, available for almost any platform).
+Create VNC password
+-------------------
+Local VNC password should be set before the first login. Do use a strong
+password.
+```
+[username@login2 ~]$ vncpasswd
+Password:
+Verify:
+```
+Start vncserver
+---------------
+To access VNC a local vncserver must be started first and also a tunnel
+using SSH port forwarding must be established.
+[See below](#linux-example-of-creating-a-tunnel) for the
+details on SSH tunnels. In this example we use port 61.
+You can find ports which are already occupied. Here you can see that
+ports "<span class="pln">/usr/bin/Xvnc :79"</span> and "<span
+class="pln">/usr/bin/Xvnc :60" are occupied.</span>
+```
+[username@login2 ~]$ ps aux | grep Xvnc
+username   5971 0.0 0.0 201072 92564 ?       SN  Sep22  4:19 /usr/bin/Xvnc :79 -desktop login2:79 (username) -auth /home/gre196/.Xauthority -geometry 1024x768 -rfbwait 30000 -rfbauth /home/username/.vnc/passwd -rfbport 5979 -fp catalogue:/etc/X11/fontpath.d -pn
+username   10296 0.0 0.0 131772 21076 pts/29  SN  13:01  0:01 /usr/bin/Xvnc :60 -desktop login2:61 (username) -auth /home/username/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/jir13/.vnc/passwd -rfbport 5960 -fp catalogue:/etc/X11/fontpath.d -pn
+.....
+```
+Choose free port e.g. 61 and start your VNC server:
+```
+[username@login2 ~]$ vncserver :61 -geometry 1600x900 -depth 16
+New 'login2:1 (username)' desktop is login2:1
+Starting applications specified in /home/username/.vnc/xstartup
+Log file is /home/username/.vnc/login2:1.log
+```
+Check if VNC server is started on the port (in this example 61):
+```
+[username@login2 .vnc]$ vncserver -list
+TigerVNC server sessions:
+X DISPLAY #Â Â Â Â PROCESS ID
+:61Â Â Â Â Â Â Â Â Â Â Â Â Â 18437
+```
+Another command:<span class="pln"></span>
+```
+[username@login2 .vnc]$ Â ps aux | grep Xvnc
+username   10296 0.0 0.0 131772 21076 pts/29  SN  13:01  0:01 /usr/bin/Xvnc :61 -desktop login2:61 (username) -auth /home/jir13/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/username/.vnc/passwd -rfbport 5961 -fp catalogue:/etc/X11/fontpath.d -pn
+```
+To access the VNC server you have to create a tunnel between the login
+node using TCP **port 5961** and your machine using a free TCP port (for
+simplicity the very same, in this case).
+The tunnel must point to the same login node where you launched the VNC
+server, eg. login2. If you use just cluster-name.it4i.cz, the tunnel
+might point to a different node due to DNS round robin.
+### []()[]()Linux/Mac OS example of creating a tunnel
+At your machine, create the tunnel:
+```
+local $Â ssh -TN -f username@login2.cluster-name.it4i.cz -L 5961:localhost:5961
+```
+Issue the following command to check the tunnel is established (please
+note the PID 2022 in the last column, you'll need it for closing the
+tunnel):
+```
+local $ netstat -natp | grep 5961
+(Not all processes could be identified, non-owned process info
+Â will not be shown, you would have to be root to see it all.)
+tcp       0     0 127.0.0.1:5961         0.0.0.0:*              LISTEN     2022/ssh      Â
+tcp6Â Â Â Â Â Â 0Â Â Â Â Â 0 ::1:5961Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â :::*Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â LISTENÂ Â Â Â Â 2022/ssh
+```
+Or on Mac OS use this command:
+``` {.prettyprint .lang-sh}
+local-mac $ lsof -n -i4TCP:5961 | grep LISTEN
+ssh 75890 sta545 7u IPv4 0xfb062b5c15a56a3b 0t0 TCP 127.0.0.1:5961 (LISTEN)
+```
+Connect with the VNC client:
+```
+local $ vncviewer 127.0.0.1:5961
+```
+In this example, we connect to VNC server on port 5961, via the ssh
+tunnel. The connection is encrypted and secured. The VNC server
+listening on port 5961 provides screen of 1600x900 pixels.
+You have to destroy the SSH tunnel which is still running at the
+background after you finish the work. Use the following command (PID
+2022 in this case, see the netstat command above):
+```
+kill 2022
+```
+### Windows example of creating a tunnel
+Use PuTTY to log in on cluster.
+Start vncserver using command vncserver described above.
+Search for the localhost and port number (in this case
+127.0.0.1:5961).**
+**
+```
+[username@login2 .vnc]$ netstat -tanp | grep Xvnc
+(Not all processes could be identified, non-owned process info
+Â will not be shown, you would have to be root to see it all.)
+tcp       0     0 127.0.0.1:5961             0.0.0.0:*                  LISTEN     24031/Xvnc
+```
+On the PuTTY Configuration screen go to Connection->SSH->Tunnels
+to set up the tunnel.
+Fill the Source port and Destination fields. **Do not forget to click
+the Add button**.
+[](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/putty-tunnel.png)
+Run the VNC client of your choice, select VNC server 127.0.0.1, port
+5961 and connect using VNC password.
+### Example of starting TigerVNC viewer
+
+In this example, we connect to VNC server on port 5961, via the ssh
+tunnel, using TigerVNC viewer. The connection is encrypted and secured.
+The VNC server listening on port 5961 provides screen of 1600x900
+pixels.
+### Example of starting TightVNC Viewer
+Use your VNC password to log using TightVNC Viewer and start a Gnome
+Session on the login node.
+[****](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/TightVNC_login.png)
+Gnome session
+-------------
+You should see after the successful login.
+[](https://docs.it4i.cz/get-started-with-it4innovations/gnome_screen.jpg)
+### **Disable your Gnome session screensaver
+**
+Open Screensaver preferences dialog:
+[](https://docs.it4i.cz/salomon/gnome_screen.jpg)
+Uncheck both options below the slider:
+[](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png)
+### Kill screensaver if locked screen
+If the screen gets locked you have to kill the screensaver. Do not to
+forget to disable the screensaver then.
+```
+[username@login2 .vnc]$ ps aux | grep screen
+username    1503 0.0 0.0 103244  892 pts/4   S+  14:37  0:00 grep screen
+username    24316 0.0 0.0 270564 3528 ?       Ss  14:12  0:00 gnome-screensaver
+[username@login2 .vnc]$ kill 24316
+```
+### Kill vncserver after finished work
+You should kill your VNC server using command:
+```
+[username@login2 .vnc]$ vncserver -kill :61
+Killing Xvnc process ID 7074
+Xvnc process ID 7074 already killed
+```
+Or this way:
+```
+[username@login2 .vnc]$Â pkill vnc
+```
+GUI applications on compute nodes over VNC
+-------------------
+The very [same methods as described
+above](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-and-vnc#gui-applications-on-compute-nodes),
+may be used to run the GUI applications on compute nodes. However, for
+**maximum performance**, proceed following these steps:
+Open a Terminal (Applications -> System Tools -> Terminal). Run
+all the next commands in the terminal.
+[](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-terminal.png)
+Allow incoming X11 graphics from the compute nodes at the login node:
+```
+$ xhost +
+```
+Get an interactive session on a compute node (for more detailed info
+[look
+here](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution)).
+Use the **-v DISPLAY** option to propagate the DISPLAY on the compute
+node. In this example, we want a complete node (24 cores in this
+example) from the production queue:
+```
+$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A PROJECT_ID -q qprod -l select=1:ncpus=24
+```
+Test that the DISPLAY redirection into your VNC session works, by
+running a X11 application (e. g. XTerm) on the assigned compute node:
+```
+$ xterm
+```
+Example described above:
+[](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-compute-nodes-over-vnc.png)
diff --git a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.1.html
old mode 100755
new mode 100644
similarity index 74%
rename from get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html
rename to docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.1.html
index 9e36a09744295efb842f6c8d1ae1ff449860b2fc..186596bb90cb637f820826b7035b1f339da7a78c
--- a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.1.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:02 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc" /><!--[if lt IE 7]></base><![endif]-->
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- <link rel="stylesheet" type="text/css" href="../../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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- <link rel="stylesheet" type="text/css" href="../../../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>X Window System — IT4I Docs</title>
- <link rel="canonical" href="../x-window-system.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="x-window-and-vnc.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="x-window-and-vnc.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../../index.html">
- <img src="../../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../../get-started-with-it4innovations.html">Get Started with IT4Innovations</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations">Get Started with IT4Innovations</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../shell-access-and-data-transfer.html">Accessing the Clusters</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">Accessing the Clusters</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../../graphical-user-interface.html">Graphical User Interface</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface">Graphical User Interface</a>
<span class="breadcrumbSeparator">
/
@@ -250,7 +247,7 @@
<div id="parent-fieldname-text-34157d99bc154332ae72e2c19ea79725" class="">
- <p>The X Window system is a principal way to get GUI access to the clusters. The <b>X Window System</b> (commonly known as <b>X11</b>, based on its current major version being 11, or shortened to simply <b>X</b>, and sometimes informally <b>X-Windows</b>) is a computer software system and network <a class="mw-redirect" href="http://en.wikipedia.org/wiki/Protocol_(computing)" title="Protocol (computing)">protocol</a> that provides a basis for <a href="http://en.wikipedia.org/wiki/Graphical_user_interface" title="Graphical user interface">graphical user interfaces</a> (GUIs) and rich input device capability for <a href="http://en.wikipedia.org/wiki/Computer_network" title="Computer network">networked computers</a>.</p>
+ <p>The X Window system is a principal way to get GUI access to the clusters. The <b>X Window System</b> (commonly known as <b>X11</b>, based on its current major version being 11, or shortened to simply <b>X</b>, and sometimes informally <b>X-Windows</b>) is a computer software system and network <a class="mw-redirect" href="http://en.wikipedia.org/wiki/Protocol_%28computing%29" title="Protocol (computing)">protocol</a> that provides a basis for <a href="http://en.wikipedia.org/wiki/Graphical_user_interface" title="Graphical user interface">graphical user interfaces</a> (GUIs) and rich input device capability for <a href="http://en.wikipedia.org/wiki/Computer_network" title="Computer network">networked computers</a>.</p>
<p class="callout">The X display forwarding must be activated and the X server running on client side</p>
<h3 class=" ">X display</h3>
<p>In order to display graphical user interface GUI of various software tools, you need to enable the X display forwarding. On Linux and Mac, log in using the -X option tho ssh client:</p>
@@ -275,7 +272,7 @@
<td>
<p><a class="external-link" href="http://x.cygwin.com/" target="_self" title="">Install Cygwin</a></p>
<p>Find and execute XWin.exe<br />to start the X server on Windows desktop computer.</p>
-<p><a target="_self" title="" class="internal-link" href="cygwin-and-x11-forwarding.html">If no able to forward X11 using PuTTY to CygwinX</a></p>
+<p><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding">If no able to forward X11 using PuTTY to CygwinX</a></p>
</td>
<td>
<p>Use Xlaunch to configure the Xming.</p>
@@ -391,7 +388,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -407,7 +404,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -423,7 +420,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -439,7 +436,7 @@
- <a title="" class="state-published contenttype-document" href="../../../applying-for-resources.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources">
<span>Applying for Resources</span>
</a>
@@ -455,7 +452,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../obtaining-login-credentials.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">
<span>Obtaining Login Credentials</span>
</a>
@@ -471,7 +468,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../shell-access-and-data-transfer.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">
<span>Accessing the Clusters</span>
</a>
@@ -487,7 +484,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../shell-access-and-data-transfer.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer">
<span>Shell access and data transfer</span>
</a>
@@ -503,7 +500,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../graphical-user-interface.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface">
<span>Graphical User Interface</span>
</a>
@@ -519,7 +516,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="../x-window-system.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system">
<span>X Window System</span>
</a>
@@ -535,7 +532,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="cygwin-and-x11-forwarding.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding">
<span>Cygwin and X11 forwarding</span>
</a>
@@ -560,7 +557,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../vnc.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc">
<span>VNC</span>
</a>
@@ -603,7 +600,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -619,7 +616,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -635,7 +632,7 @@
- <a title="" class="state-published contenttype-document" href="../../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -651,7 +648,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -667,7 +664,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -706,14 +703,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -735,12 +732,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -756,7 +753,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:03 GMT -->
</html>
diff --git a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.1.md
similarity index 66%
rename from get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
rename to docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.1.md
index 4e7c8ba71de3bc66abe9112748e137fce4b6c7ac..bc1a29316f043b469e4b5c1a5ae8a65a3d6ce2be 100644
--- a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.1.md
@@ -1,25 +1,22 @@
-Info
-
X Window System
===============
-
-
+
The X Window system is a principal way to get GUI access to the
clusters. The **X Window System** (commonly known as **X11**, based on
its current major version being 11, or shortened to simply **X**, and
sometimes informally **X-Windows**) is a computer software system and
network
-[protocol](http//en.wikipedia.org/wiki/Protocol_(computing) "Protocol (computing)"){.mw-redirect}
+[protocol](http://en.wikipedia.org/wiki/Protocol_%28computing%29 "Protocol (computing)"){.mw-redirect}
that provides a basis for [graphical user
-interfaces](http//en.wikipedia.org/wiki/Graphical_user_interface "Graphical user interface")
+interfaces](http://en.wikipedia.org/wiki/Graphical_user_interface "Graphical user interface")
(GUIs) and rich input device capability for [networked
-computers](http//en.wikipedia.org/wiki/Computer_network "Computer network").
+computers](http://en.wikipedia.org/wiki/Computer_network "Computer network").
The X display forwarding must be activated and the X server running on
client side
### X display
In order to display graphical user interface GUI of various software
tools, you need to enable the X display forwarding. On Linux and Mac,
-log in using the -X option tho ssh client
+log in using the -X option tho ssh client:
``` {.prettyprint .lang-sh}
local $ ssh -X username@cluster-name.it4i.cz
```
@@ -33,7 +30,7 @@ $ echo $DISPLAY
```
if you receive something like
``` {.prettyprint .lang-sh}
-localhost10.0
+localhost:10.0
```
then the X11 forwarding is enabled.
### X Server
@@ -44,26 +41,40 @@ environment on most Linux distributions. Mac and Windows users need to
install and run the X server on their workstations.
### X Server on OS X
Mac OS users need to install [XQuartz
-server](http//xquartz.macosforge.org/landing/).
+server](http://xquartz.macosforge.org/landing/).
### X Server on Windows
There are variety of X servers available for Windows environment. The
commercial Xwin32 is very stable and rich featured. The Cygwin
environment provides fully featured open-source XWin X server. For
simplicity, we recommend open-source X server by the [Xming
-project](http//sourceforge.net/projects/xming/). For
+project](http://sourceforge.net/projects/xming/). For
stability and full features we recommend the
-[XWin](http//x.cygwin.com/) X server by Cygwin
-How to use Xwin
-How to use Xming
-Install Cygwin
-Find and execute XWin.exe
-to start the X server on Windows desktop computer.
-If no able to forward X11 using PuTTY to CygwinX
-Use Xlaunch to configure the Xming.
-Run Xming
-to start the X server on Windows desktop computer.
+[XWin](http://x.cygwin.com/) X server by Cygwin
+<table>
+<colgroup>
+<col width="50%" />
+<col width="50%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">How to use Xwin</th>
+<th align="left">How to use Xming</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><p><a href="http://x.cygwin.com/" class="external-link">Install Cygwin</a></p>
+<p>Find and execute XWin.exe<br />
+to start the X server on Windows desktop computer.</p>
+<p><a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding" class="internal-link">If no able to forward X11 using PuTTY to CygwinX</a></p></td>
+<td align="left"><p>Use Xlaunch to configure the Xming.</p>
+<p>Run Xming<br />
+to start the X server on Windows desktop computer.</p></td>
+</tr>
+</tbody>
+</table>
Read more on
-[http//www.math.umn.edu/systems_guide/putty_xwin32.html](http//www.math.umn.edu/systems_guide/putty_xwin32.shtml)
+[http://www.math.umn.edu/systems_guide/putty_xwin32.html](http://www.math.umn.edu/systems_guide/putty_xwin32.shtml)
### Running GUI Enabled Applications
Make sure that X forwarding is activated and the X server is running.
Then launch the application as usual. Use the & to run the application
@@ -80,7 +91,7 @@ then start the graphical gvim editor.
### []()GUI Applications on Compute Nodes
Allocate the compute nodes using -X option on the qsub command
``` {.prettyprint .lang-sh}
-$ qsub -q qexp -l select=2ncpus=24 -X -I
+$ qsub -q qexp -l select=2:ncpus=24 -X -I
```
In this example, we allocate 2 nodes via qexp queue, interactively. We
request X11 forwarding with the -X option. It will be possible to run
@@ -99,28 +110,28 @@ recommend to use separate X server window for displaying the Gnome
environment.
### Gnome on Linux and OS X
To run the remote Gnome session in a window on Linux/OS X computer, you
-need to install Xephyr. Ubuntu package is
-class="monospace">xserver-xephyr, on OS X it is part of
-[XQuartz](http//xquartz.macosforge.org/landing/).
-First, launch Xephyr on local machine
+need to install Xephyr. Ubuntu package is <span
+class="monospace">xserver-xephyr</span>, on OS X it is part of
+[XQuartz](http://xquartz.macosforge.org/landing/).
+First, launch Xephyr on local machine:
``` {.prettyprint .lang-sh}
-local $ Xephyr -ac -screen 1024x768 -br -reset -terminate 1 &
+local $ Xephyr -ac -screen 1024x768 -br -reset -terminate :1 &
```
-This will open a new X window with size 1024x768 at DISPLAY 1. Next,
+This will open a new X window with size 1024x768 at DISPLAY :1. Next,
ssh to the cluster with DISPLAY environment variable set and launch
-gnome-session
- local $ DISPLAY=1.0 ssh -XC yourname@cluster-name.it4i.cz -i ~/.ssh/path_to_your_key
+<span class="monospace">gnome-session</span>
+ local $ DISPLAY=:1.0 ssh -XC yourname@cluster-name.it4i.cz -i ~/.ssh/path_to_your_key
... cluster-name MOTD...
yourname@login1.cluster-namen.it4i.cz $Â gnome-session &
On older systems where Xephyr is not available, you may also try Xnest
instead of Xephyr. Another option is to launch a new X server in a
-separate console, via
+separate console, via:
```
-xinit /usr/bin/ssh -XT -i .ssh/path_to_your_key yourname@cluster-namen.it4i.cz gnome-session -- 1 vt12
+xinit /usr/bin/ssh -XT -i .ssh/path_to_your_key yourname@cluster-namen.it4i.cz gnome-session -- :1 vt12
```
However this method does not seem to work with recent Linux
-distributions and you will need to manually source
-class="monospace">/etc/profile to properly set environment
+distributions and you will need to manually source <span
+class="monospace">/etc/profile</span> to properly set environment
variables for PBS.
### Gnome on Windows**
**
@@ -134,15 +145,3 @@ $ gnome-session &
In this way, we run remote gnome session on the cluster, displaying it
in the local X server
Use System->Log Out to close the gnome-session
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
diff --git a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding.html
old mode 100755
new mode 100644
similarity index 66%
rename from get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.html
rename to docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding.html
index 4d107dee8ec3d0f95b83e07bc212a776505ed692..9e5ca917be125b5123b1885af1a731c05d155f12
--- a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.html
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:19:02 GMT -->
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Cygwin and X11 forwarding — IT4I Docs</title>
- <link rel="canonical" href="../cygwin-and-x11-forwarding.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="cygwin-and-x11-forwarding.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="cygwin-and-x11-forwarding.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../../../index.html">
- <img src="../../../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../../../get-started-with-it4innovations.html">Get Started with IT4Innovations</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations">Get Started with IT4Innovations</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../../shell-access-and-data-transfer.html">Accessing the Clusters</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">Accessing the Clusters</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../../../graphical-user-interface.html">Graphical User Interface</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface">Graphical User Interface</a>
<span class="breadcrumbSeparator">
/
@@ -183,7 +180,7 @@
</span>
<span id="breadcrumbs-4" dir="ltr">
- <a href="../../x-window-system.html">X Window System</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system">X Window System</a>
<span class="breadcrumbSeparator">
/
@@ -260,8 +257,8 @@
<pre class="prettyprint lang-sh"><span style="text-align: left; float: none; ">[usename@login1.anselm ~]$ gnome-session &<br />[1] 23691<br />[<span style="text-align: left; float: none; ">usename</span>@login1.anselm ~]$ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused<br />PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused<br /><br />** (gnome-session:23691): WARNING **: Cannot open display:<br /></span></pre>
<p><span style="text-align: left; float: none; ">Â </span></p>
<ol>
-<li><span style="text-align: left; float: none; ">Locate and modify <span style="text-align: left; float: none; ">Cygwin shortcut that uses<span class="Apple-converted-space">Â </span></span><a href="http://x.cygwin.com/docs/man1/startxwin.1.html" rel="nofollow" style="text-align: left; ">startxwin</a><br />locate<br />C:\cygwin64\bin\XWin.exe<br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">change it to</span></span></span><br />C:\<i class="moz-txt-slash">cygwin64\bin\XWin.exe -listen tcp</i><br /><br /><img title="XWin-listen-tcp.png" class="image-inline" alt="XWin-listen-tcp.png" src="XWin-listen-tcp.png" /><br /></span><br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span></span></li>
-<li><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">Check Putty settings:<br /><span style="text-align: left; float: none; ">Enable X11 forwarding</span><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span><span class="Apple-converted-space"><br /></span></span><br /><a target="_self" title="" class="internal-link" href="cygwin-and-x11-forwarding.html"><img title="" class="image-inline" alt="" src="cygwinX11forwarding.png/%40%40images/0f5b58e3-253c-4f87-a3b2-16f75cbf090f.30b" /></a><br /></span></span></li>
+<li><span style="text-align: left; float: none; ">Locate and modify <span style="text-align: left; float: none; ">Cygwin shortcut that uses<span class="Apple-converted-space">Â </span></span><a href="http://x.cygwin.com/docs/man1/startxwin.1.html" rel="nofollow" style="text-align: left; ">startxwin</a><br />locate<br />C:\cygwin64\bin\XWin.exe<br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">change it to</span></span></span><br />C:\<i class="moz-txt-slash">cygwin64\bin\XWin.exe -listen tcp</i><br /><br /><img alt="XWin-listen-tcp.png" class="image-inline" title="XWin-listen-tcp.png" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/XWinlistentcp.png" /><br /></span><br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span></span></li>
+<li><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">Check Putty settings:<br /><span style="text-align: left; float: none; ">Enable X11 forwarding</span><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span><span class="Apple-converted-space"><br /></span></span><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding"><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwinX11forwarding.png/@@images/0f5b58e3-253c-4f87-a3b2-16f75cbf090f.png" /></a><br /></span></span></li>
</ol>
<p>Â </p>
@@ -339,7 +336,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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@@ -355,7 +352,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -371,7 +368,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -387,7 +384,7 @@
- <a title="" class="state-published contenttype-document" href="../../../../applying-for-resources.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources">
<span>Applying for Resources</span>
</a>
@@ -403,7 +400,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../obtaining-login-credentials.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">
<span>Obtaining Login Credentials</span>
</a>
@@ -419,7 +416,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../shell-access-and-data-transfer.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">
<span>Accessing the Clusters</span>
</a>
@@ -435,7 +432,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../shell-access-and-data-transfer.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer">
<span>Shell access and data transfer</span>
</a>
@@ -451,7 +448,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../graphical-user-interface.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface">
<span>Graphical User Interface</span>
</a>
@@ -467,7 +464,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../x-window-system.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system">
<span>X Window System</span>
</a>
@@ -483,7 +480,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="../cygwin-and-x11-forwarding.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding">
<span>Cygwin and X11 forwarding</span>
</a>
@@ -508,7 +505,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../vnc.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc">
<span>VNC</span>
</a>
@@ -551,7 +548,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -567,7 +564,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -583,7 +580,7 @@
- <a title="" class="state-published contenttype-document" href="../../../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -599,7 +596,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -615,7 +612,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</div>
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</html>
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding.md
new file mode 100644
index 0000000000000000000000000000000000000000..355972864bb013b33ff322dbcbc308557f0d6c78
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding.md
@@ -0,0 +1,37 @@
+Cygwin and X11 forwarding
+=========================
+### If <span style="text-alignleft; floatnone; ">no able to forward X11 using PuTTY to CygwinX</span>
+``` {.prettyprint .lang-sh}
+[usename@login1.anselm ~]$ gnome-session &
+[1] 23691
+[usename@login1.anselm ~]$ PuTTY X11 proxyunable to connect to forwarded X serverNetwork errorConnection refused
+PuTTY X11 proxyunable to connect to forwarded X serverNetwork errorConnection refused
+** (gnome-session:23691)WARNING **Cannot open display:
+```
+<span style="text-alignleft; floatnone; ">Â </span>
+1. <span style="text-alignleft; floatnone; ">Locate and modify
+ <span style="text-alignleft; floatnone; ">Cygwin shortcut that
+ uses<span
+ class="Apple-converted-space">Â </span></span>[startxwin](http://x.cygwin.com/docs/man1/startxwin.1.html)
+ locate
+ C:cygwin64binXWin.exe
+ <span style="text-alignleft; floatnone; "><span
+ style="text-alignleft; floatnone; "><span
+ style="text-alignleft; floatnone; ">change it
+ to</span></span></span>
+ C:*cygwin64binXWin.exe -listen tcp*
+
+ 
+ </span>
+ <span style="text-alignleft; floatnone; "><span
+ style="text-alignleft; floatnone; "></span></span>
+2. <span style="text-alignleft; floatnone; "><span
+ style="text-alignleft; floatnone; ">Check Putty settings:
+ <span style="text-alignleft; floatnone; ">Enable X11
+ forwarding</span><span style="text-alignleft; floatnone; "><span
+ style="text-alignleft; floatnone; "></span><span
+ class="Apple-converted-space">
+ </span></span>
+ [](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding)
+ </span></span>
+Â
diff --git a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/XWin-listen-tcp.png b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/XWinlistentcp.png
old mode 100755
new mode 100644
similarity index 100%
rename from get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/XWin-listen-tcp.png
rename to docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/XWinlistentcp.png
diff --git a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.html
old mode 100755
new mode 100644
similarity index 66%
rename from get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding.html
rename to docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.html
index 9a504bf03c64c57f819d5120b44919a1c751789c..e393aca6cfaa81b75ca18e592735ab9da82b3c6f
--- a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding.html
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:47 GMT -->
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ <base href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding" /><!--[if lt IE 7]></base><![endif]-->
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- <link rel="stylesheet" type="text/css" href="../../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Cygwin and X11 forwarding — IT4I Docs</title>
- <link rel="canonical" href="cygwin-and-x11-forwarding.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="cygwin-and-x11-forwarding.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="cygwin-and-x11-forwarding.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
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-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../../index.html">
- <img src="../../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../../get-started-with-it4innovations.html">Get Started with IT4Innovations</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations">Get Started with IT4Innovations</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../shell-access-and-data-transfer.html">Accessing the Clusters</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">Accessing the Clusters</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../../graphical-user-interface.html">Graphical User Interface</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface">Graphical User Interface</a>
<span class="breadcrumbSeparator">
/
@@ -183,7 +180,7 @@
</span>
<span id="breadcrumbs-4" dir="ltr">
- <a href="../x-window-system.html">X Window System</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system">X Window System</a>
<span class="breadcrumbSeparator">
/
@@ -260,8 +257,8 @@
<pre class="prettyprint lang-sh"><span style="text-align: left; float: none; ">[usename@login1.anselm ~]$ gnome-session &<br />[1] 23691<br />[<span style="text-align: left; float: none; ">usename</span>@login1.anselm ~]$ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused<br />PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused<br /><br />** (gnome-session:23691): WARNING **: Cannot open display:<br /></span></pre>
<p><span style="text-align: left; float: none; ">Â </span></p>
<ol>
-<li><span style="text-align: left; float: none; ">Locate and modify <span style="text-align: left; float: none; ">Cygwin shortcut that uses<span class="Apple-converted-space">Â </span></span><a href="http://x.cygwin.com/docs/man1/startxwin.1.html" rel="nofollow" style="text-align: left; ">startxwin</a><br />locate<br />C:\cygwin64\bin\XWin.exe<br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">change it to</span></span></span><br />C:\<i class="moz-txt-slash">cygwin64\bin\XWin.exe -listen tcp</i><br /><br /><img title="XWin-listen-tcp.png" class="image-inline" alt="XWin-listen-tcp.png" src="cygwin-and-x11-forwarding/XWin-listen-tcp.png" /><br /></span><br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span></span></li>
-<li><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">Check Putty settings:<br /><span style="text-align: left; float: none; ">Enable X11 forwarding</span><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span><span class="Apple-converted-space"><br /></span></span><br /><a target="_self" title="" class="internal-link" href="cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.html"><img title="" class="image-inline" alt="" src="cygwin-and-x11-forwarding/cygwinX11forwarding.png/%40%40images/0f5b58e3-253c-4f87-a3b2-16f75cbf090f.30b" /></a><br /></span></span></li>
+<li><span style="text-align: left; float: none; ">Locate and modify <span style="text-align: left; float: none; ">Cygwin shortcut that uses<span class="Apple-converted-space">Â </span></span><a href="http://x.cygwin.com/docs/man1/startxwin.1.html" rel="nofollow" style="text-align: left; ">startxwin</a><br />locate<br />C:\cygwin64\bin\XWin.exe<br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">change it to</span></span></span><br />C:\<i class="moz-txt-slash">cygwin64\bin\XWin.exe -listen tcp</i><br /><br /><img alt="XWin-listen-tcp.png" class="image-inline" title="XWin-listen-tcp.png" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/XWinlistentcp.png" /><br /></span><br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span></span></li>
+<li><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">Check Putty settings:<br /><span style="text-align: left; float: none; ">Enable X11 forwarding</span><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span><span class="Apple-converted-space"><br /></span></span><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding"><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwinX11forwarding.png/@@images/0f5b58e3-253c-4f87-a3b2-16f75cbf090f.png" /></a><br /></span></span></li>
</ol>
<p>Â </p>
@@ -339,7 +336,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
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@@ -355,7 +352,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -371,7 +368,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -387,7 +384,7 @@
- <a title="" class="state-published contenttype-document" href="../../../applying-for-resources.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources">
<span>Applying for Resources</span>
</a>
@@ -403,7 +400,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../obtaining-login-credentials.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">
<span>Obtaining Login Credentials</span>
</a>
@@ -419,7 +416,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../shell-access-and-data-transfer.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">
<span>Accessing the Clusters</span>
</a>
@@ -435,7 +432,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../shell-access-and-data-transfer.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer">
<span>Shell access and data transfer</span>
</a>
@@ -451,7 +448,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../graphical-user-interface.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface">
<span>Graphical User Interface</span>
</a>
@@ -467,7 +464,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../x-window-system.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system">
<span>X Window System</span>
</a>
@@ -483,7 +480,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="cygwin-and-x11-forwarding.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding">
<span>Cygwin and X11 forwarding</span>
</a>
@@ -508,7 +505,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../vnc.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc">
<span>VNC</span>
</a>
@@ -551,7 +548,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -567,7 +564,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -583,7 +580,7 @@
- <a title="" class="state-published contenttype-document" href="../../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -599,7 +596,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -615,7 +612,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -654,14 +651,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -683,12 +680,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -704,7 +701,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:48 GMT -->
</html>
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.md
new file mode 100644
index 0000000000000000000000000000000000000000..355972864bb013b33ff322dbcbc308557f0d6c78
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.md
@@ -0,0 +1,37 @@
+Cygwin and X11 forwarding
+=========================
+### If <span style="text-alignleft; floatnone; ">no able to forward X11 using PuTTY to CygwinX</span>
+``` {.prettyprint .lang-sh}
+[usename@login1.anselm ~]$ gnome-session &
+[1] 23691
+[usename@login1.anselm ~]$ PuTTY X11 proxyunable to connect to forwarded X serverNetwork errorConnection refused
+PuTTY X11 proxyunable to connect to forwarded X serverNetwork errorConnection refused
+** (gnome-session:23691)WARNING **Cannot open display:
+```
+<span style="text-alignleft; floatnone; ">Â </span>
+1. <span style="text-alignleft; floatnone; ">Locate and modify
+ <span style="text-alignleft; floatnone; ">Cygwin shortcut that
+ uses<span
+ class="Apple-converted-space">Â </span></span>[startxwin](http://x.cygwin.com/docs/man1/startxwin.1.html)
+ locate
+ C:cygwin64binXWin.exe
+ <span style="text-alignleft; floatnone; "><span
+ style="text-alignleft; floatnone; "><span
+ style="text-alignleft; floatnone; ">change it
+ to</span></span></span>
+ C:*cygwin64binXWin.exe -listen tcp*
+
+ 
+ </span>
+ <span style="text-alignleft; floatnone; "><span
+ style="text-alignleft; floatnone; "></span></span>
+2. <span style="text-alignleft; floatnone; "><span
+ style="text-alignleft; floatnone; ">Check Putty settings:
+ <span style="text-alignleft; floatnone; ">Enable X11
+ forwarding</span><span style="text-alignleft; floatnone; "><span
+ style="text-alignleft; floatnone; "></span><span
+ class="Apple-converted-space">
+ </span></span>
+ [](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding)
+ </span></span>
+Â
diff --git a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwinX11forwarding.png/@@images/0f5b58e3-253c-4f87-a3b2-16f75cbf090f.30b b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwinX11forwarding.png/@@images/0f5b58e3-253c-4f87-a3b2-16f75cbf090f.png
old mode 100755
new mode 100644
similarity index 100%
rename from get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwinX11forwarding.png/@@images/0f5b58e3-253c-4f87-a3b2-16f75cbf090f.30b
rename to docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwinX11forwarding.png/@@images/0f5b58e3-253c-4f87-a3b2-16f75cbf090f.png
diff --git a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html
old mode 100755
new mode 100644
similarity index 74%
rename from get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.html
rename to docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html
index 9d5a42cc864fb2b6f726a83700b01a1263308fe9..711161ee8a7d49eaeb5d4053ec7235db3ae437a8
--- a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.html
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:18 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc" /><!--[if lt IE 7]></base><![endif]-->
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/IEFixes-cachekey-ec9b60024fd235ff2c883b4b54db91cb.css" />
<![endif]-->
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>X Window System — IT4I Docs</title>
- <link rel="canonical" href="x-window-system.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="x-window-system.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="x-window-system.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../get-started-with-it4innovations.html">Get Started with IT4Innovations</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations">Get Started with IT4Innovations</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../shell-access-and-data-transfer.html">Accessing the Clusters</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">Accessing the Clusters</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../graphical-user-interface.html">Graphical User Interface</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface">Graphical User Interface</a>
<span class="breadcrumbSeparator">
/
@@ -250,7 +247,7 @@
<div id="parent-fieldname-text-34157d99bc154332ae72e2c19ea79725" class="">
- <p>The X Window system is a principal way to get GUI access to the clusters. The <b>X Window System</b> (commonly known as <b>X11</b>, based on its current major version being 11, or shortened to simply <b>X</b>, and sometimes informally <b>X-Windows</b>) is a computer software system and network <a class="mw-redirect" href="http://en.wikipedia.org/wiki/Protocol_(computing)" title="Protocol (computing)">protocol</a> that provides a basis for <a href="http://en.wikipedia.org/wiki/Graphical_user_interface" title="Graphical user interface">graphical user interfaces</a> (GUIs) and rich input device capability for <a href="http://en.wikipedia.org/wiki/Computer_network" title="Computer network">networked computers</a>.</p>
+ <p>The X Window system is a principal way to get GUI access to the clusters. The <b>X Window System</b> (commonly known as <b>X11</b>, based on its current major version being 11, or shortened to simply <b>X</b>, and sometimes informally <b>X-Windows</b>) is a computer software system and network <a class="mw-redirect" href="http://en.wikipedia.org/wiki/Protocol_%28computing%29" title="Protocol (computing)">protocol</a> that provides a basis for <a href="http://en.wikipedia.org/wiki/Graphical_user_interface" title="Graphical user interface">graphical user interfaces</a> (GUIs) and rich input device capability for <a href="http://en.wikipedia.org/wiki/Computer_network" title="Computer network">networked computers</a>.</p>
<p class="callout">The X display forwarding must be activated and the X server running on client side</p>
<h3 class=" ">X display</h3>
<p>In order to display graphical user interface GUI of various software tools, you need to enable the X display forwarding. On Linux and Mac, log in using the -X option tho ssh client:</p>
@@ -275,7 +272,7 @@
<td>
<p><a class="external-link" href="http://x.cygwin.com/" target="_self" title="">Install Cygwin</a></p>
<p>Find and execute XWin.exe<br />to start the X server on Windows desktop computer.</p>
-<p><a target="_self" title="" class="internal-link" href="x-window-system/cygwin-and-x11-forwarding.html">If no able to forward X11 using PuTTY to CygwinX</a></p>
+<p><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding">If no able to forward X11 using PuTTY to CygwinX</a></p>
</td>
<td>
<p>Use Xlaunch to configure the Xming.</p>
@@ -391,7 +388,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -407,7 +404,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -423,7 +420,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -439,7 +436,7 @@
- <a title="" class="state-published contenttype-document" href="../../applying-for-resources.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources">
<span>Applying for Resources</span>
</a>
@@ -455,7 +452,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../obtaining-login-credentials.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">
<span>Obtaining Login Credentials</span>
</a>
@@ -471,7 +468,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../shell-access-and-data-transfer.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">
<span>Accessing the Clusters</span>
</a>
@@ -487,7 +484,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../shell-access-and-data-transfer.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer">
<span>Shell access and data transfer</span>
</a>
@@ -503,7 +500,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../graphical-user-interface.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface">
<span>Graphical User Interface</span>
</a>
@@ -519,7 +516,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="x-window-system.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system">
<span>X Window System</span>
</a>
@@ -535,7 +532,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="x-window-system/cygwin-and-x11-forwarding.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding">
<span>Cygwin and X11 forwarding</span>
</a>
@@ -560,7 +557,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="vnc.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc">
<span>VNC</span>
</a>
@@ -603,7 +600,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -619,7 +616,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -635,7 +632,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -651,7 +648,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -667,7 +664,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -706,14 +703,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -735,12 +732,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -756,7 +753,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.md
similarity index 66%
rename from get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.md
rename to docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.md
index f539613e9d2c83183c2f79e8a4c2e59026e0b20b..bc1a29316f043b469e4b5c1a5ae8a65a3d6ce2be 100644
--- a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.md
@@ -1,25 +1,22 @@
-Info
-
X Window System
===============
-
-
+
The X Window system is a principal way to get GUI access to the
clusters. The **X Window System** (commonly known as **X11**, based on
its current major version being 11, or shortened to simply **X**, and
sometimes informally **X-Windows**) is a computer software system and
network
-[protocol](http//en.wikipedia.org/wiki/Protocol_(computing) "Protocol (computing)"){.mw-redirect}
+[protocol](http://en.wikipedia.org/wiki/Protocol_%28computing%29 "Protocol (computing)"){.mw-redirect}
that provides a basis for [graphical user
-interfaces](http//en.wikipedia.org/wiki/Graphical_user_interface "Graphical user interface")
+interfaces](http://en.wikipedia.org/wiki/Graphical_user_interface "Graphical user interface")
(GUIs) and rich input device capability for [networked
-computers](http//en.wikipedia.org/wiki/Computer_network "Computer network").
+computers](http://en.wikipedia.org/wiki/Computer_network "Computer network").
The X display forwarding must be activated and the X server running on
client side
### X display
In order to display graphical user interface GUI of various software
tools, you need to enable the X display forwarding. On Linux and Mac,
-log in using the -X option tho ssh client
+log in using the -X option tho ssh client:
``` {.prettyprint .lang-sh}
local $ ssh -X username@cluster-name.it4i.cz
```
@@ -33,7 +30,7 @@ $ echo $DISPLAY
```
if you receive something like
``` {.prettyprint .lang-sh}
-localhost10.0
+localhost:10.0
```
then the X11 forwarding is enabled.
### X Server
@@ -44,26 +41,40 @@ environment on most Linux distributions. Mac and Windows users need to
install and run the X server on their workstations.
### X Server on OS X
Mac OS users need to install [XQuartz
-server](http//xquartz.macosforge.org/landing/).
+server](http://xquartz.macosforge.org/landing/).
### X Server on Windows
There are variety of X servers available for Windows environment. The
commercial Xwin32 is very stable and rich featured. The Cygwin
environment provides fully featured open-source XWin X server. For
simplicity, we recommend open-source X server by the [Xming
-project](http//sourceforge.net/projects/xming/). For
+project](http://sourceforge.net/projects/xming/). For
stability and full features we recommend the
-[XWin](http//x.cygwin.com/) X server by Cygwin
-How to use Xwin
-How to use Xming
-Install Cygwin
-Find and execute XWin.exe
-to start the X server on Windows desktop computer.
-If no able to forward X11 using PuTTY to CygwinX
-Use Xlaunch to configure the Xming.
-Run Xming
-to start the X server on Windows desktop computer.
+[XWin](http://x.cygwin.com/) X server by Cygwin
+<table>
+<colgroup>
+<col width="50%" />
+<col width="50%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">How to use Xwin</th>
+<th align="left">How to use Xming</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><p><a href="http://x.cygwin.com/" class="external-link">Install Cygwin</a></p>
+<p>Find and execute XWin.exe<br />
+to start the X server on Windows desktop computer.</p>
+<p><a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding" class="internal-link">If no able to forward X11 using PuTTY to CygwinX</a></p></td>
+<td align="left"><p>Use Xlaunch to configure the Xming.</p>
+<p>Run Xming<br />
+to start the X server on Windows desktop computer.</p></td>
+</tr>
+</tbody>
+</table>
Read more on
-[http//www.math.umn.edu/systems_guide/putty_xwin32.html](http//www.math.umn.edu/systems_guide/putty_xwin32.shtml)
+[http://www.math.umn.edu/systems_guide/putty_xwin32.html](http://www.math.umn.edu/systems_guide/putty_xwin32.shtml)
### Running GUI Enabled Applications
Make sure that X forwarding is activated and the X server is running.
Then launch the application as usual. Use the & to run the application
@@ -80,7 +91,7 @@ then start the graphical gvim editor.
### []()GUI Applications on Compute Nodes
Allocate the compute nodes using -X option on the qsub command
``` {.prettyprint .lang-sh}
-$ qsub -q qexp -l select=2ncpus=24 -X -I
+$ qsub -q qexp -l select=2:ncpus=24 -X -I
```
In this example, we allocate 2 nodes via qexp queue, interactively. We
request X11 forwarding with the -X option. It will be possible to run
@@ -99,28 +110,28 @@ recommend to use separate X server window for displaying the Gnome
environment.
### Gnome on Linux and OS X
To run the remote Gnome session in a window on Linux/OS X computer, you
-need to install Xephyr. Ubuntu package is
-class="monospace">xserver-xephyr, on OS X it is part of
-[XQuartz](http//xquartz.macosforge.org/landing/).
-First, launch Xephyr on local machine
+need to install Xephyr. Ubuntu package is <span
+class="monospace">xserver-xephyr</span>, on OS X it is part of
+[XQuartz](http://xquartz.macosforge.org/landing/).
+First, launch Xephyr on local machine:
``` {.prettyprint .lang-sh}
-local $ Xephyr -ac -screen 1024x768 -br -reset -terminate 1 &
+local $ Xephyr -ac -screen 1024x768 -br -reset -terminate :1 &
```
-This will open a new X window with size 1024x768 at DISPLAY 1. Next,
+This will open a new X window with size 1024x768 at DISPLAY :1. Next,
ssh to the cluster with DISPLAY environment variable set and launch
-gnome-session
- local $ DISPLAY=1.0 ssh -XC yourname@cluster-name.it4i.cz -i ~/.ssh/path_to_your_key
+<span class="monospace">gnome-session</span>
+ local $ DISPLAY=:1.0 ssh -XC yourname@cluster-name.it4i.cz -i ~/.ssh/path_to_your_key
... cluster-name MOTD...
yourname@login1.cluster-namen.it4i.cz $Â gnome-session &
On older systems where Xephyr is not available, you may also try Xnest
instead of Xephyr. Another option is to launch a new X server in a
-separate console, via
+separate console, via:
```
-xinit /usr/bin/ssh -XT -i .ssh/path_to_your_key yourname@cluster-namen.it4i.cz gnome-session -- 1 vt12
+xinit /usr/bin/ssh -XT -i .ssh/path_to_your_key yourname@cluster-namen.it4i.cz gnome-session -- :1 vt12
```
However this method does not seem to work with recent Linux
-distributions and you will need to manually source
-class="monospace">/etc/profile to properly set environment
+distributions and you will need to manually source <span
+class="monospace">/etc/profile</span> to properly set environment
variables for PBS.
### Gnome on Windows**
**
@@ -134,15 +145,3 @@ $ gnome-session &
In this way, we run remote gnome session on the cluster, displaying it
in the local X server
Use System->Log Out to close the gnome-session
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
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@@ -0,0 +1,658 @@
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+<p class="callout">Read more on <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/accessing-the-cluster">Accessing the Salomon Cluste</a>r or <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">Accessing the Anselm Cluster</a> pages.</p>
+<h3 class=" ">PuTTY</h3>
+<p>On <strong>Windows</strong>, use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty">PuTTY ssh client</a>.</p>
+<h3 class=" " id="parent-fieldname-title">SSH keys</h3>
+<p>Read more about <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">SSH keys management</a>.</p>
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/accessing-the-clusters.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/accessing-the-clusters.md
new file mode 100644
index 0000000000000000000000000000000000000000..f918d611f7785269ff28f4a45f3bb4999e19d455
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/accessing-the-clusters.md
@@ -0,0 +1,15 @@
+Accessing the Clusters
+======================
+The IT4Innovations clusters are accessed by SSH protocol via login
+nodes.
+Read more on [Accessing the Salomon
+Cluste](https://docs.it4i.cz/salomon/accessing-the-cluster)r
+or [Accessing the Anselm
+Cluster](https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster)
+pages.
+### PuTTY
+On **Windows**, use [PuTTY ssh
+client](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty).
+### SSH keys {#parent-fieldname-title}
+Read more about [SSH keys
+management](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys).
diff --git a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.1.html
old mode 100755
new mode 100644
similarity index 60%
rename from get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html
rename to docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.1.html
index 5da0bb52c93344cc5157de4eb89d031d507e2de6..477405acd3b1c01c488008c13ba111d88b420955
--- a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.1.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:58 GMT -->
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<title>PuTTY — IT4I Docs</title>
- <link rel="canonical" href="../putty.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../../favicon.ico" />
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+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="putty.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="putty.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
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-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../../index.html">
- <img src="../../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
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@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../../get-started-with-it4innovations.html">Get Started with IT4Innovations</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations">Get Started with IT4Innovations</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../shell-access-and-data-transfer.html">Accessing the Clusters</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">Accessing the Clusters</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../../shell-access-and-data-transfer.html">Shell access and data transfer</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer">Shell access and data transfer</a>
<span class="breadcrumbSeparator">
/
@@ -255,21 +252,21 @@
<p>We recommned you to download "<b style="text-align: start; ">A Windows installer for everything except PuTTYtel</b>" with <strong><em>Pageant</em> </strong>(SSH authentication agent) and <strong>PuTTYgen</strong> (PuTTY key generator) which is available <a class="external-link" href="http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html" target="_self" title="">here</a>.</p>
<p class="callout"><span class="internal-link">After installation you can proceed directly to private keys authentication using <a class="internal-link" href="#putty" target="_self" title="">"Putty"</a>.</span><br />"Change Password for Existing Private Key" is optional.<br />"Generate a New Public/Private key pair" is intended for users without Public/Private key in the initial email containing login credentials.<br />"Pageant" is optional.</p>
<h3 class=" ">PuTTYgen</h3>
-<p>PuTTYgen is the PuTTY key generator. Read more how to load in an existing private key and change your passphrase or generate a new public/private key pair using <a target="_self" title="" class="internal-link" href="puttygen.html">PuTTYgen</a> if needed.</p>
+<p>PuTTYgen is the PuTTY key generator. Read more how to load in an existing private key and change your passphrase or generate a new public/private key pair using <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen">PuTTYgen</a> if needed.</p>
<h3 class=" ">Pageant SSH agent</h3>
-<p><a target="_self" title="" class="internal-link" href="pageant.html">Pageant</a> holds your private key in memory without needing to retype a passphrase on every login. We recommend its usage.</p>
+<p><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant">Pageant</a> holds your private key in memory without needing to retype a passphrase on every login. We recommend its usage.</p>
<h2 class=" "><a name="putty"></a>PuTTY - how to connect to the IT4Innovations cluster</h2>
<ul>
<li>Run PuTTY</li>
-<li>Enter Host name and Save session fields with <a target="_self" title="" class="internal-link" href="../../../../salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html">Login address</a> and browse Connection - > SSH -> Auth menu.<br />The <em>Host Name</em> input may be in the format <strong>"username@clustername.it4i.cz"</strong> so you don't have to type your login each time.<br />In this example we will connect to the Salomon cluster using  <strong>"salomon.it4i.cz"</strong>.<br /><br /><a target="_self" title="" class="internal-link" href="PuTTY_host_SalomonV.png"><img title="" class="image-inline" alt="" src="PuTTY_host_Salomon.png/%40%40images/c24acdc5-21eb-47aa-b412-75849ccd2e82.png" /></a></li>
+<li>Enter Host name and Save session fields with <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access">Login address</a> and browse Connection - > SSH -> Auth menu.<br />The <em>Host Name</em> input may be in the format <strong>"username@clustername.it4i.cz"</strong> so you don't have to type your login each time.<br />In this example we will connect to the Salomon cluster using  <strong>"salomon.it4i.cz"</strong>.<br /><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_host_Salomon.png"><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_host_Salomon.png/@@images/c24acdc5-21eb-47aa-b412-75849ccd2e82.png" /></a></li>
</ul>
<p class=" ">Â </p>
<ul>
-<li>Category -> Connection - > SSH -> Auth:<br />Select Attempt authentication using Pageant.<br />Select Allow agent forwarding.<br />Browse and select your <a target="_self" title="" class="internal-link" href="../ssh-keys.html">private key</a> file.<br /><br /><a target="_self" title="" class="internal-link" href="PuTTY_keyV.png"><img title="PuttyKey" class="image-inline" alt="PuttyKey" src="PuTTY_keyV.png/%40%40images/9f161548-31a6-42a7-ad61-4e885e4b4664.png" /></a><br /><br /></li>
-<li>Return to Session page and Save selected configuration with <em>Save</em> button.<br /><br /><a target="_self" title="" class="internal-link" href="PuTTY_save_SalomonV.png"><img title="" class="image-inline" alt="" src="PuTTY_save_Salomon.png/%40%40images/0eeeb971-b295-4780-88e7-7557da05a1cb.png" /></a><br /><br /></li>
-<li>Now you can log in using <em>Open</em> button.<br /><br /><a target="_self" title="" class="internal-link" href="PuTTY_open_SalomonV.png"><img title="" class="image-inline" alt="" src="PuTTY_open_Salomon.png/%40%40images/741d3e56-d9b3-48fd-838f-90ad6c1bf8eb.png" /></a><br /><br /></li>
+<li>Category -> Connection - > SSH -> Auth:<br />Select Attempt authentication using Pageant.<br />Select Allow agent forwarding.<br />Browse and select your <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">private key</a> file.<br /><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_keyV.png"><img alt="PuttyKey" class="image-inline" title="PuttyKey" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_keyV.png/@@images/9f161548-31a6-42a7-ad61-4e885e4b4664.png" /></a><br /><br /></li>
+<li>Return to Session page and Save selected configuration with <em>Save</em> button.<br /><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_save_Salomon.png"><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_save_Salomon.png/@@images/0eeeb971-b295-4780-88e7-7557da05a1cb.png" /></a><br /><br /></li>
+<li>Now you can log in using <em>Open</em> button.<br /><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_open_Salomon.png"><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_open_Salomon.png/@@images/741d3e56-d9b3-48fd-838f-90ad6c1bf8eb.png" /></a><br /><br /></li>
<li>Enter your username if the <em>Host Name</em> input is not in the format "username@salomon.it4i.cz".<br /><br /></li>
-<li>Enter passphrase for selected <a target="_self" title="" class="internal-link" href="../ssh-keys.html">private key</a> file if Pageant <strong></strong>SSH authentication agent is not used.<br /><br /></li>
+<li>Enter passphrase for selected <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">private key</a> file if Pageant <strong></strong>SSH authentication agent is not used.<br /><br /></li>
</ul>
<h2 class=" ">Another PuTTY Settings</h2>
<ul>
@@ -354,7 +351,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -370,7 +367,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -386,7 +383,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -402,7 +399,7 @@
- <a title="" class="state-published contenttype-document" href="../../../applying-for-resources.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources">
<span>Applying for Resources</span>
</a>
@@ -418,7 +415,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../obtaining-login-credentials.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">
<span>Obtaining Login Credentials</span>
</a>
@@ -434,7 +431,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../shell-access-and-data-transfer.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">
<span>Accessing the Clusters</span>
</a>
@@ -450,7 +447,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../shell-access-and-data-transfer.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer">
<span>Shell access and data transfer</span>
</a>
@@ -466,7 +463,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="../putty.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty">
<span>PuTTY</span>
</a>
@@ -482,7 +479,7 @@
- <a title="" class="state-published contenttype-document" href="pageant.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant">
<span>Pageant SSH agent</span>
</a>
@@ -498,7 +495,7 @@
- <a title="" class="state-published contenttype-document" href="puttygen.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen">
<span>PuTTY key generator</span>
</a>
@@ -523,7 +520,7 @@
- <a title="" class="state-published contenttype-document" href="../ssh-keys.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">
<span>SSH keys</span>
</a>
@@ -548,7 +545,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../graphical-user-interface.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface">
<span>Graphical User Interface</span>
</a>
@@ -582,7 +579,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -598,7 +595,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -614,7 +611,7 @@
- <a title="" class="state-published contenttype-document" href="../../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -630,7 +627,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -646,7 +643,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -685,14 +682,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -714,12 +711,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -735,7 +732,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:00 GMT -->
</html>
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.1.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.1.md
new file mode 100644
index 0000000000000000000000000000000000000000..61311b4df8d471a634be11891872d209f9fc1fa9
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.1.md
@@ -0,0 +1,75 @@
+PuTTY
+=====
+
+PuTTY -<span class="Apple-converted-space"> </span>before we start SSH connection {#putty---before-we-start-ssh-connection style="text-alignstart; "}
+------------
+### Windows PuTTY Installer
+We recommned you to download "**A Windows installer for everything
+except PuTTYtel**" with ***Pageant*** (SSH authentication agent) and
+**PuTTYgen** (PuTTY key generator) which is available
+[here](http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html).
+<span class="internal-link">After installation you can proceed directly
+to private keys authentication using
+["Putty"](#putty).</span>
+"Change Password for Existing Private Key" is optional.
+"Generate a New Public/Private key pair" is intended for users without
+Public/Private key in the initial email containing login credentials.
+"Pageant" is optional.
+### PuTTYgen
+PuTTYgen is the PuTTY key generator. Read more how to load in an
+existing private key and change your passphrase or generate a new
+public/private key pair using
+[PuTTYgen](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen)
+if needed.
+### Pageant SSH agent
+[Pageant](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant)
+holds your private key in memory without needing to retype a passphrase
+on every login. We recommend its usage.
+[]()PuTTY - how to connect to the IT4Innovations cluster
+----------
+- Run PuTTY
+- Enter Host name and Save session fields with [Login
+ address](https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access)
+ and browse Connection - > SSH -> Auth menu.
+ The *Host Name* input may be in the format
+ **"username@clustername.it4i.cz"** so you don't have to type your
+ login each time.
+ In this example we will connect to the Salomon cluster using
+ Â **"salomon.it4i.cz"**.
+
+ [](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_host_Salomon.png)
+Â
+- Category -> Connection - > SSH -> Auth:
+ Select Attempt authentication using Pageant.
+ Select Allow agent forwarding.
+ Browse and select your [private
+ key](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys)
+ file.
+
+ [](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_keyV.png)
+
+- Return to Session page and Save selected configuration with *Save*
+ button.
+
+ [](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_save_Salomon.png)
+
+- Now you can log in using *Open* button.
+
+ [](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_open_Salomon.png)
+
+- Enter your username if the *Host Name* input is not in the format
+ "username@salomon.it4i.cz".
+
+- Enter passphrase for selected [private
+ key](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys)
+ file if Pageant ****SSH authentication agent is not used.
+
+Another PuTTY Settings
+----------------------
+- Category -> Windows -> Translation -> Remote character set
+ and select **UTF-8**.
+<!-- -->
+- Category -> Terminal -> Features and select **Disable
+ application keypad mode** (enable numpad)
+- Save your configuration on Session page in to Default Settings with
+ *Save* button .
diff --git a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/2015-03-12_143443V.png b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/20150312_143443.png
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rename to docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/20150312_143443.png
diff --git a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PageantV.png.txt b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PageantV.png
old mode 100755
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rename from get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PageantV.png.txt
rename to docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PageantV.png
diff --git a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_host_SalomonV.png b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_host_Salomon.png
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rename to docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_host_Salomon.png
diff --git a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_keyV.png.txt b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_keyV.png
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<title>Pageant SSH agent — IT4I Docs</title>
- <link rel="canonical" href="pageant.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant" />
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- <a accesskey="6" href="pageant.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<li>Run Pageant.</li>
<li>On Pageant Key List press <em>Add key</em> and select your private key (id_rsa.ppk).</li>
<li>Enter your passphrase.</li>
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<span>PuTTY</span>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -724,7 +721,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:46 GMT -->
</html>
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant.md
new file mode 100644
index 0000000000000000000000000000000000000000..03cd2bbce4d30e078c087bcb5f72181ccc4a013c
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant.md
@@ -0,0 +1,14 @@
+Pageant SSH agent
+=================
+
+Pageant holds your private key in memory without needing to retype a
+passphrase on every login.
+- Run Pageant.
+- On Pageant Key List press *Add key* and select your private
+ key (id_rsa.ppk).
+- Enter your passphrase.
+- Now you have your private key in memory without needing to retype a
+ passphrase on every login.
+
+ [](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PageantV.png)
+Â
diff --git a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html
old mode 100755
new mode 100644
similarity index 60%
rename from get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.html
rename to docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html
index df37fd6f911a8b486e5fee267ff472d1affa1ab1..b7254088f15e47d3d4d736a405ca2c611b5613be
--- a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.html
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:01 GMT -->
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>PuTTY — IT4I Docs</title>
- <link rel="canonical" href="putty.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="putty.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="putty.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../get-started-with-it4innovations.html">Get Started with IT4Innovations</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations">Get Started with IT4Innovations</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../shell-access-and-data-transfer.html">Accessing the Clusters</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">Accessing the Clusters</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../shell-access-and-data-transfer.html">Shell access and data transfer</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer">Shell access and data transfer</a>
<span class="breadcrumbSeparator">
/
@@ -255,21 +252,21 @@
<p>We recommned you to download "<b style="text-align: start; ">A Windows installer for everything except PuTTYtel</b>" with <strong><em>Pageant</em> </strong>(SSH authentication agent) and <strong>PuTTYgen</strong> (PuTTY key generator) which is available <a class="external-link" href="http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html" target="_self" title="">here</a>.</p>
<p class="callout"><span class="internal-link">After installation you can proceed directly to private keys authentication using <a class="internal-link" href="#putty" target="_self" title="">"Putty"</a>.</span><br />"Change Password for Existing Private Key" is optional.<br />"Generate a New Public/Private key pair" is intended for users without Public/Private key in the initial email containing login credentials.<br />"Pageant" is optional.</p>
<h3 class=" ">PuTTYgen</h3>
-<p>PuTTYgen is the PuTTY key generator. Read more how to load in an existing private key and change your passphrase or generate a new public/private key pair using <a target="_self" title="" class="internal-link" href="putty/puttygen.html">PuTTYgen</a> if needed.</p>
+<p>PuTTYgen is the PuTTY key generator. Read more how to load in an existing private key and change your passphrase or generate a new public/private key pair using <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen">PuTTYgen</a> if needed.</p>
<h3 class=" ">Pageant SSH agent</h3>
-<p><a target="_self" title="" class="internal-link" href="putty/pageant.html">Pageant</a> holds your private key in memory without needing to retype a passphrase on every login. We recommend its usage.</p>
+<p><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant">Pageant</a> holds your private key in memory without needing to retype a passphrase on every login. We recommend its usage.</p>
<h2 class=" "><a name="putty"></a>PuTTY - how to connect to the IT4Innovations cluster</h2>
<ul>
<li>Run PuTTY</li>
-<li>Enter Host name and Save session fields with <a target="_self" title="" class="internal-link" href="../../../salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html">Login address</a> and browse Connection - > SSH -> Auth menu.<br />The <em>Host Name</em> input may be in the format <strong>"username@clustername.it4i.cz"</strong> so you don't have to type your login each time.<br />In this example we will connect to the Salomon cluster using  <strong>"salomon.it4i.cz"</strong>.<br /><br /><a target="_self" title="" class="internal-link" href="putty/PuTTY_host_SalomonV.png"><img title="" class="image-inline" alt="" src="putty/PuTTY_host_Salomon.png/%40%40images/c24acdc5-21eb-47aa-b412-75849ccd2e82.png" /></a></li>
+<li>Enter Host name and Save session fields with <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access">Login address</a> and browse Connection - > SSH -> Auth menu.<br />The <em>Host Name</em> input may be in the format <strong>"username@clustername.it4i.cz"</strong> so you don't have to type your login each time.<br />In this example we will connect to the Salomon cluster using  <strong>"salomon.it4i.cz"</strong>.<br /><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_host_Salomon.png"><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_host_Salomon.png/@@images/c24acdc5-21eb-47aa-b412-75849ccd2e82.png" /></a></li>
</ul>
<p class=" ">Â </p>
<ul>
-<li>Category -> Connection - > SSH -> Auth:<br />Select Attempt authentication using Pageant.<br />Select Allow agent forwarding.<br />Browse and select your <a target="_self" title="" class="internal-link" href="ssh-keys.html">private key</a> file.<br /><br /><a target="_self" title="" class="internal-link" href="putty/PuTTY_keyV.png"><img title="PuttyKey" class="image-inline" alt="PuttyKey" src="putty/PuTTY_keyV.png/%40%40images/9f161548-31a6-42a7-ad61-4e885e4b4664.png" /></a><br /><br /></li>
-<li>Return to Session page and Save selected configuration with <em>Save</em> button.<br /><br /><a target="_self" title="" class="internal-link" href="putty/PuTTY_save_SalomonV.png"><img title="" class="image-inline" alt="" src="putty/PuTTY_save_Salomon.png/%40%40images/0eeeb971-b295-4780-88e7-7557da05a1cb.png" /></a><br /><br /></li>
-<li>Now you can log in using <em>Open</em> button.<br /><br /><a target="_self" title="" class="internal-link" href="putty/PuTTY_open_SalomonV.png"><img title="" class="image-inline" alt="" src="putty/PuTTY_open_Salomon.png/%40%40images/741d3e56-d9b3-48fd-838f-90ad6c1bf8eb.png" /></a><br /><br /></li>
+<li>Category -> Connection - > SSH -> Auth:<br />Select Attempt authentication using Pageant.<br />Select Allow agent forwarding.<br />Browse and select your <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">private key</a> file.<br /><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_keyV.png"><img alt="PuttyKey" class="image-inline" title="PuttyKey" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_keyV.png/@@images/9f161548-31a6-42a7-ad61-4e885e4b4664.png" /></a><br /><br /></li>
+<li>Return to Session page and Save selected configuration with <em>Save</em> button.<br /><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_save_Salomon.png"><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_save_Salomon.png/@@images/0eeeb971-b295-4780-88e7-7557da05a1cb.png" /></a><br /><br /></li>
+<li>Now you can log in using <em>Open</em> button.<br /><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_open_Salomon.png"><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_open_Salomon.png/@@images/741d3e56-d9b3-48fd-838f-90ad6c1bf8eb.png" /></a><br /><br /></li>
<li>Enter your username if the <em>Host Name</em> input is not in the format "username@salomon.it4i.cz".<br /><br /></li>
-<li>Enter passphrase for selected <a target="_self" title="" class="internal-link" href="ssh-keys.html">private key</a> file if Pageant <strong></strong>SSH authentication agent is not used.<br /><br /></li>
+<li>Enter passphrase for selected <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">private key</a> file if Pageant <strong></strong>SSH authentication agent is not used.<br /><br /></li>
</ul>
<h2 class=" ">Another PuTTY Settings</h2>
<ul>
@@ -354,7 +351,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -370,7 +367,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -386,7 +383,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -402,7 +399,7 @@
- <a title="" class="state-published contenttype-document" href="../../applying-for-resources.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources">
<span>Applying for Resources</span>
</a>
@@ -418,7 +415,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../obtaining-login-credentials.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">
<span>Obtaining Login Credentials</span>
</a>
@@ -434,7 +431,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../shell-access-and-data-transfer.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">
<span>Accessing the Clusters</span>
</a>
@@ -450,7 +447,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../shell-access-and-data-transfer.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer">
<span>Shell access and data transfer</span>
</a>
@@ -466,7 +463,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="putty.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty">
<span>PuTTY</span>
</a>
@@ -482,7 +479,7 @@
- <a title="" class="state-published contenttype-document" href="putty/pageant.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant">
<span>Pageant SSH agent</span>
</a>
@@ -498,7 +495,7 @@
- <a title="" class="state-published contenttype-document" href="putty/puttygen.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen">
<span>PuTTY key generator</span>
</a>
@@ -523,7 +520,7 @@
- <a title="" class="state-published contenttype-document" href="ssh-keys.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">
<span>SSH keys</span>
</a>
@@ -548,7 +545,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../graphical-user-interface.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface">
<span>Graphical User Interface</span>
</a>
@@ -582,7 +579,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -598,7 +595,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -614,7 +611,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -630,7 +627,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -646,7 +643,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -685,14 +682,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -714,12 +711,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -735,7 +732,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:01 GMT -->
</html>
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.md
new file mode 100644
index 0000000000000000000000000000000000000000..61311b4df8d471a634be11891872d209f9fc1fa9
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.md
@@ -0,0 +1,75 @@
+PuTTY
+=====
+
+PuTTY -<span class="Apple-converted-space"> </span>before we start SSH connection {#putty---before-we-start-ssh-connection style="text-alignstart; "}
+------------
+### Windows PuTTY Installer
+We recommned you to download "**A Windows installer for everything
+except PuTTYtel**" with ***Pageant*** (SSH authentication agent) and
+**PuTTYgen** (PuTTY key generator) which is available
+[here](http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html).
+<span class="internal-link">After installation you can proceed directly
+to private keys authentication using
+["Putty"](#putty).</span>
+"Change Password for Existing Private Key" is optional.
+"Generate a New Public/Private key pair" is intended for users without
+Public/Private key in the initial email containing login credentials.
+"Pageant" is optional.
+### PuTTYgen
+PuTTYgen is the PuTTY key generator. Read more how to load in an
+existing private key and change your passphrase or generate a new
+public/private key pair using
+[PuTTYgen](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen)
+if needed.
+### Pageant SSH agent
+[Pageant](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant)
+holds your private key in memory without needing to retype a passphrase
+on every login. We recommend its usage.
+[]()PuTTY - how to connect to the IT4Innovations cluster
+----------
+- Run PuTTY
+- Enter Host name and Save session fields with [Login
+ address](https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access)
+ and browse Connection - > SSH -> Auth menu.
+ The *Host Name* input may be in the format
+ **"username@clustername.it4i.cz"** so you don't have to type your
+ login each time.
+ In this example we will connect to the Salomon cluster using
+ Â **"salomon.it4i.cz"**.
+
+ [](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_host_Salomon.png)
+Â
+- Category -> Connection - > SSH -> Auth:
+ Select Attempt authentication using Pageant.
+ Select Allow agent forwarding.
+ Browse and select your [private
+ key](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys)
+ file.
+
+ [](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_keyV.png)
+
+- Return to Session page and Save selected configuration with *Save*
+ button.
+
+ [](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_save_Salomon.png)
+
+- Now you can log in using *Open* button.
+
+ [](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_open_Salomon.png)
+
+- Enter your username if the *Host Name* input is not in the format
+ "username@salomon.it4i.cz".
+
+- Enter passphrase for selected [private
+ key](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys)
+ file if Pageant ****SSH authentication agent is not used.
+
+Another PuTTY Settings
+----------------------
+- Category -> Windows -> Translation -> Remote character set
+ and select **UTF-8**.
+<!-- -->
+- Category -> Terminal -> Features and select **Disable
+ application keypad mode** (enable numpad)
+- Save your configuration on Session page in to Default Settings with
+ *Save* button .
diff --git a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.html
old mode 100755
new mode 100644
similarity index 57%
rename from get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.html
rename to docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.html
index 6bf4c9bb7c685934e81b2752319001e7871a20c1..60b52be64cf454fc56e1954dcf082315e1a9514d
--- a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.html
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:11 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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- <link rel="stylesheet" type="text/css" href="../../../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="../../../../portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
- <script type="text/javascript" src="../../../../portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
- <script type="text/javascript" src="../../../../portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
- <script type="text/javascript" src="../../../../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="../../../../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>PuTTY key generator — IT4I Docs</title>
- <link rel="canonical" href="puttygen.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="puttygen.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="puttygen.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../../index.html">
- <img src="../../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../../get-started-with-it4innovations.html">Get Started with IT4Innovations</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations">Get Started with IT4Innovations</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../shell-access-and-data-transfer.html">Accessing the Clusters</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">Accessing the Clusters</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../../shell-access-and-data-transfer.html">Shell access and data transfer</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer">Shell access and data transfer</a>
<span class="breadcrumbSeparator">
/
@@ -183,7 +180,7 @@
</span>
<span id="breadcrumbs-4" dir="ltr">
- <a href="../putty.html">PuTTY</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty">PuTTY</a>
<span class="breadcrumbSeparator">
/
@@ -264,23 +261,23 @@
<h3 class=" ">Change Password for Existing Private Key</h3>
<p>You can change the password of your SSH key with "PuTTY Key Generator". Make sure to backup the key.</p>
<ul>
-<li>Load your <a target="_self" title="" class="internal-link" href="../ssh-keys.html">private key</a> file with <em>Load</em> button.</li>
+<li>Load your <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">private key</a> file with <em>Load</em> button.</li>
<li>Enter your current passphrase.</li>
<li>Change key passphrase.</li>
<li>Confirm key passphrase.</li>
-<li>Save your private key with <em>Save private key</em> button.<br /><br /><a target="_self" title="" class="internal-link" href="PuttyKeygeneratorV.png"><img title="PuttyKeygenerator" class="image-inline" alt="PuttyKeygenerator" src="PuttyKeygeneratorV.png/%40%40images/22954eec-6127-4d42-b159-9bebacb3223d.png" /></a></li>
+<li>Save your private key with <em>Save private key</em> button.<br /><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygeneratorV.png"><img alt="PuttyKeygenerator" class="image-inline" title="PuttyKeygenerator" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygeneratorV.png/@@images/22954eec-6127-4d42-b159-9bebacb3223d.png" /></a></li>
</ul>
<p>Â </p>
<h3 class=" ">Generate a New Public/Private key pair</h3>
<p>You can generate an additional public/private key pair and insert public key into authorized_keys file for authentication with your own private <span>key. </span></p>
<ul>
-<li>Start with <em>Generate</em> button.<br /><br /><a target="_self" title="" class="internal-link" href="PuttyKeygenerator_001V.png"><img title="PuttyKeygenerator_001" class="image-inline" alt="PuttyKeygenerator_001" src="PuttyKeygenerator_001V.png/%40%40images/f7c1889f-605f-4c5c-8904-d962ec4531a2.png" /></a><br /><br /></li>
-<li>Generate some randomness.<br /><br /><a target="_self" title="" class="internal-link" href="PuttyKeygenerator_002V.png"><img title="PuttyKeygenerator_002" class="image-inline" alt="PuttyKeygenerator_002" src="PuttyKeygenerator_002V.png/%40%40images/13b88922-8c1d-47b2-b3e6-043c18b11d86.png" /></a><br /><br /></li>
-<li>Wait.<br /><br /><a target="_self" title="" class="internal-link" href="2015-03-12_143443V.png"><img title="PuttyKeygenerator_003" class="image-inline" alt="PuttyKeygenerator_003" src="20150312_143443.png/%40%40images/29ff0f89-8203-4777-9a00-c068d3188fd0.png" /></a><br /><br /></li>
-<li>Enter a <em>comment</em> for your key using format 'username@organization.example.com'.<br />Enter key passphrase.<br />Confirm key passphrase.<br />Save your new private key <code>in "*.ppk" </code>format with <em>Save private key</em> button.<br /><br /><a target="_self" title="" class="internal-link" href="PuttyKeygenerator_004V.png"><img title="PuttyKeygenerator_004" class="image-inline" alt="PuttyKeygenerator_004" src="PuttyKeygenerator_004V.png/%40%40images/8ef00e6b-0155-4dc2-82e6-7141a15f282c.png" /></a><br /><br /></li>
-<li>Save the public key with <em>Save public key</em> button.<br />You can copy public key out of the â€Public key for pasting into authorized_keys file’ box.<br /><br /><a target="_self" title="" class="internal-link" href="PuttyKeygenerator_005V.png"><img title="PuttyKeygenerator_005" class="image-inline" alt="PuttyKeygenerator_005" src="PuttyKeygenerator_005V.png/%40%40images/929621fe-45f7-45c8-9ed0-c34d430d65f4.png" /></a><br /><br /></li>
-<li>Export private key in OpenSSH format "id_rsa" using Conversion -> Export OpenSSH key<br /><br /><a target="_self" title="" class="internal-link" href="PuttyKeygenerator_006V.png"><img title="PuttyKeygenerator_006" class="image-inline" alt="PuttyKeygenerator_006" src="PuttyKeygenerator_006V.png/%40%40images/de851079-6ed4-440a-b270-77dd6a0a950c.png" /></a><br /><br /></li>
-<li>Now you can insert additional public key into authorized_keys file for authentication with your own private <span>key. <br />You must log in using ssh key received after registration. Then proceed to <a target="_self" title="" class="internal-link" href="../ssh-keys.html">How to add your own key</a>.<br /></span></li>
+<li>Start with <em>Generate</em> button.<br /><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_001V.png"><img alt="PuttyKeygenerator_001" class="image-inline" title="PuttyKeygenerator_001" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_001V.png/@@images/f7c1889f-605f-4c5c-8904-d962ec4531a2.png" /></a><br /><br /></li>
+<li>Generate some randomness.<br /><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_002V.png"><img alt="PuttyKeygenerator_002" class="image-inline" title="PuttyKeygenerator_002" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_002V.png/@@images/13b88922-8c1d-47b2-b3e6-043c18b11d86.png" /></a><br /><br /></li>
+<li>Wait.<br /><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/20150312_143443.png"><img alt="PuttyKeygenerator_003" class="image-inline" title="PuttyKeygenerator_003" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/20150312_143443.png/@@images/29ff0f89-8203-4777-9a00-c068d3188fd0.png" /></a><br /><br /></li>
+<li>Enter a <em>comment</em> for your key using format 'username@organization.example.com'.<br />Enter key passphrase.<br />Confirm key passphrase.<br />Save your new private key <code>in "*.ppk" </code>format with <em>Save private key</em> button.<br /><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_004V.png"><img alt="PuttyKeygenerator_004" class="image-inline" title="PuttyKeygenerator_004" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_004V.png/@@images/8ef00e6b-0155-4dc2-82e6-7141a15f282c.png" /></a><br /><br /></li>
+<li>Save the public key with <em>Save public key</em> button.<br />You can copy public key out of the â€Public key for pasting into authorized_keys file’ box.<br /><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_005V.png"><img alt="PuttyKeygenerator_005" class="image-inline" title="PuttyKeygenerator_005" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_005V.png/@@images/929621fe-45f7-45c8-9ed0-c34d430d65f4.png" /></a><br /><br /></li>
+<li>Export private key in OpenSSH format "id_rsa" using Conversion -> Export OpenSSH key<br /><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_006V.png"><img alt="PuttyKeygenerator_006" class="image-inline" title="PuttyKeygenerator_006" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_006V.png/@@images/de851079-6ed4-440a-b270-77dd6a0a950c.png" /></a><br /><br /></li>
+<li>Now you can insert additional public key into authorized_keys file for authentication with your own private <span>key. <br />You must log in using ssh key received after registration. Then proceed to <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">How to add your own key</a>.<br /></span></li>
</ul>
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<dt class="portletHeader hiddenStructure">
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+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -389,7 +386,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -405,7 +402,7 @@
- <a title="" class="state-published contenttype-document" href="../../../applying-for-resources.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources">
<span>Applying for Resources</span>
</a>
@@ -421,7 +418,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../obtaining-login-credentials.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">
<span>Obtaining Login Credentials</span>
</a>
@@ -437,7 +434,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../shell-access-and-data-transfer.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">
<span>Accessing the Clusters</span>
</a>
@@ -453,7 +450,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../shell-access-and-data-transfer.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer">
<span>Shell access and data transfer</span>
</a>
@@ -469,7 +466,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../putty.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty">
<span>PuTTY</span>
</a>
@@ -485,7 +482,7 @@
- <a title="" class="state-published contenttype-document" href="pageant.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant">
<span>Pageant SSH agent</span>
</a>
@@ -501,7 +498,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="puttygen.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen">
<span>PuTTY key generator</span>
</a>
@@ -526,7 +523,7 @@
- <a title="" class="state-published contenttype-document" href="../ssh-keys.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">
<span>SSH keys</span>
</a>
@@ -551,7 +548,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../graphical-user-interface.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface">
<span>Graphical User Interface</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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<span>Anselm Cluster Documentation</span>
</a>
@@ -617,7 +614,7 @@
- <a title="" class="state-published contenttype-document" href="../../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -633,7 +630,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -649,7 +646,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</html>
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.md
new file mode 100644
index 0000000000000000000000000000000000000000..7716b5024c56dd5ecb97dae506452a006dc20905
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.md
@@ -0,0 +1,61 @@
+PuTTY key generator
+===================
+
+PuTTYgen is the PuTTY key generator. You can load in an existing private
+key and change your passphrase or generate a new public/private key
+pair.
+### Change Password for Existing Private Key
+You can change the password of your SSH key with "PuTTY Key Generator".
+Make sure to backup the key.
+- Load your [private
+ key](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys)
+ file with *Load* button.
+- Enter your current passphrase.
+- Change key passphrase.
+- Confirm key passphrase.
+- Save your private key with *Save private key* button.
+
+ [](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygeneratorV.png)
+Â
+### Generate a New Public/Private key pair
+You can generate an additional public/private key pair and insert public
+key into authorized_keys file for authentication with your own private
+<span>key. </span>
+- Start with *Generate* button.
+
+ [](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_001V.png)
+
+- Generate some randomness.
+
+ [](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_002V.png)
+
+- Wait.
+
+ [](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/20150312_143443.png)
+
+- Enter a *comment* for your key using formatÂ
+ 'username@organization.example.com'.
+ Enter key passphrase.
+ Confirm key passphrase.
+ Save your new private key `in "*.ppk" `format with *Save private
+ key* button.
+
+ [](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_004V.png)
+
+- Save the public key with *Save public key* button.
+ You can copy public key out of the â€Public key for pasting into
+ authorized_keys file’ box.
+
+ [](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_005V.png)
+
+- Export private key in OpenSSH format "id_rsa" using Conversion
+ -> Export OpenSSH key
+
+ [](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_006V.png)
+
+- Now you can insert additional public key into authorized_keys file
+ for authentication with your own private <span>key.
+ You must log in using ssh key received after registration. Then
+ proceed to [How to add your own
+ key](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys).
+ </span>
diff --git a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html
old mode 100755
new mode 100644
similarity index 75%
rename from get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html
rename to docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html
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--- a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html
@@ -10,45 +10,42 @@
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-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:00 GMT -->
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys" /><!--[if lt IE 7]></base><![endif]-->
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
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<title>SSH keys — IT4I Docs</title>
- <link rel="canonical" href="ssh-keys.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="ssh-keys.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="ssh-keys.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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@@ -153,7 +150,7 @@
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@@ -163,7 +160,7 @@
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+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">Accessing the Clusters</a>
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@@ -173,7 +170,7 @@
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- <a href="../shell-access-and-data-transfer.html">Shell access and data transfer</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer">Shell access and data transfer</a>
<span class="breadcrumbSeparator">
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@@ -263,7 +260,7 @@
<pre class=" ">cd /home/username/<br />chmod 700 .ssh/<br />chmod 644 .ssh/authorized_keys<br />chmod 644 .ssh/id_rsa.pub<br />chmod 644 .ssh/<span style="text-align: left; float: none; "><span style="text-align: left; float: none; "><span class="Apple-converted-space">known_hosts</span></span></span><br />chmod 600 .ssh/id_rsa<br />chmod 600Â .ssh/id_rsa.ppk</pre>
<h2 class=" ">Private key</h2>
<p class="exclamation">The path to a private key is usually /home/username/.ssh/</p>
-<p>Private key file in "id_rsa" or <code>"*.ppk" </code>format is used to authenticate with the servers. <span style="text-align: start; float: none; ">Private key is present locally on local side and used for example in SSH agent <a target="_self" title="" class="internal-link" href="putty/PageantV.png">Pageant (for Windows users)</a>. The private key should always be kept in a safe place.</span></p>
+<p>Private key file in "id_rsa" or <code>"*.ppk" </code>format is used to authenticate with the servers. <span style="text-align: start; float: none; ">Private key is present locally on local side and used for example in SSH agent <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PageantV.png">Pageant (for Windows users)</a>. The private key should always be kept in a safe place.</span></p>
<p><span style="text-align: start; float: none; ">An example of private key format:</span></p>
<pre class=" "><span style="text-align: start; float: none; ">-----BEGIN RSA PRIVATE KEY-----<br />MIIEpAIBAAKCAQEAqbo7jokygnBpG2wYa5NB45ns6+UKTNLMLHF0BO3zmRtKEElE<br />aGqXfbYwvXlcuRb2d9/Y5dVpCZHV0kbY3NhtVOcEIe+1ROaiU9BEsUAhMNEvgiLV<br />gSql4QvRO4BWPlM8+WAWXDp3oeoBh8glXyuh9teb8yq98fv1r1peYGRrW3/s4V+q<br />O1SQ0XY2T7rWCYRLIP6rTMXArTI35v3WU513mn7nm1fJ7oN0QgVH5b0W9V1Kyc4l<br />9vILHeMXxvz+i/5jTEfLOJpiRGYZYcaYrE4dIiHPl3IlbV7hlkK23Xb1US8QJr5G<br />ADxp1VTkHjY+mKagEfxl1hQIb42JLHhKMEGqNQIDAQABAoIBAQCkypPuxZjL+vai<br />UGa5dAWiRZ46P2yrwHPKpvEdpCdDPbLAc1K/CtdBkHZsUPxNHVV6eFWweW99giIY<br />Av+mFWC58X8asBHQ7xkmxW0cqAZRzpkRAl9IBS9/fKjO28Fgy/p+suOi8oWbKIgJ<br />3LMkX0nnT9oz1AkOfTNC6Tv+3SE7eTj1RPcMjur4W1Cd1N3EljLszdVk4tLxlXBS<br /><span style="text-align: start; float: none; ">yl9NzVnJJbJR4t01l45VfFECgYEAno1WJSB/SwdZvS9GkfhvmZd3r4vyV9Bmo3dn<br /></span>XZAh8HRW13imOnpklDR4FRe98D9A7V3yh9h60Co4oAUd6N+Oc68/qnv/8O9efA+M<br />/neI9ANYFo8F0+yFCp4Duj7zPV3aWlN/pd8TNzLqecqh10uZNMy8rAjCxybeZjWd<br />DyhgywXhAoGBAN3BCazNefYpLbpBQzwes+f2oStvwOYKDqySWsYVXeVgUI+OWTVZ<br />eZ26Y86E8MQO+q0TIxpwou+TEaUgOSqCX40Q37rGSl9K+rjnboJBYNCmwVp9bfyj<br />kCLL/3g57nTSqhgHNa1xwemePvgNdn6FZteA8sXiCg5ZzaISqWAffek5AoGBAMPw<br />V/vwQ96C8E3l1cH5cUbmBCCcfXM2GLv74bb1V3SvCiAKgOrZ8gEgUiQ0+TfcbAbe<br />7MM20vRNQjaLTBpai/BTbmqM1Q+r1KNjq8k5bfTdAoGANgzlNM9omM10rd9WagL5<br />yuJcal/03p048mtB4OI4Xr5ZJISHze8fK4jQ5veUT9Vu2Fy/w6QMsuRf+qWeCXR5<br /><span style="text-align: start; float: none; ">RPC2H0JzkS+2uZp8BOHk1iDPqbxWXJE9I57CxBV9C/tfzo2IhtOOcuJ4LY+sw+y/<br /></span>ocKpJbdLTWrTLdqLHwicdn8OxeWot1mOukyK2l0UeDkY6H5pYPtHTpAZvRBd7ETL<br />Zs2RP3KFFvho6aIDGrY0wee740/jWotx7fbxxKwPyDRsbH3+1Wx/eX2RND4OGdkH<br />gejJEzpk/7y/P/hCad7bSDdHZwO+Z03HIRC0E8yQz+JYatrqckaRCtd7cXryTmTR<br />FbvLJmECgYBDpfno2CzcFJCTdNBZFi34oJRiDb+HdESXepk58PcNcgK3R8PXf+au<br />OqDBtZIuFv9U1WAg0gzGwt/0Y9u2c8m0nXziUS6AePxy5sBHs7g9C9WeZRz/nCWK<br />+cHIm7XOwBEzDKz5f9eBqRGipm0skDZNKl8X/5QMTT5K3Eci2n+lTw==<br />-----END RSA PRIVATE KEY-----</span></pre>
<h2 class=" ">Public key</h2>
@@ -355,7 +352,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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@@ -371,7 +368,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -387,7 +384,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -403,7 +400,7 @@
- <a title="" class="state-published contenttype-document" href="../../applying-for-resources.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources">
<span>Applying for Resources</span>
</a>
@@ -419,7 +416,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../obtaining-login-credentials.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">
<span>Obtaining Login Credentials</span>
</a>
@@ -435,7 +432,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../shell-access-and-data-transfer.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">
<span>Accessing the Clusters</span>
</a>
@@ -451,7 +448,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../shell-access-and-data-transfer.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer">
<span>Shell access and data transfer</span>
</a>
@@ -467,7 +464,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="putty.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty">
<span>PuTTY</span>
</a>
@@ -483,7 +480,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="ssh-keys.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">
<span>SSH keys</span>
</a>
@@ -508,7 +505,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../graphical-user-interface.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface">
<span>Graphical User Interface</span>
</a>
@@ -542,7 +539,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -558,7 +555,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -574,7 +571,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -590,7 +587,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -606,7 +603,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -645,14 +642,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -674,12 +671,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -695,7 +692,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:01 GMT -->
</html>
diff --git a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
similarity index 60%
rename from get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
rename to docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
index 816a1093ece93a66432b49d9cbe5a20548052966..38516c776631b328200c599013ba3715fdd2c36e 100644
--- a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
@@ -1,50 +1,48 @@
-Info
-
SSH keys
========
-
-
-Key management
--------------------------------------------------------------------
+
+<span id="Key_management" class="mw-headline">Key management</span>
+---------------------
After logging in, you can see .ssh/ directory with SSH keys and
-authorized_keys file
+authorized_keys file:
$ cd /home/username/
$ ls -la .ssh/
total 24
- drwx------ 2 username username 4096 May 13 1512 .
- drwxr-x---22 username username 4096 May 13 0722 ..
+ drwx------ 2 username username 4096 May 13 15:12 .
+ drwxr-x---22 username username 4096 May 13 07:22 ..
-rw-r--r-- 1 username username 392 May 21 2014 authorized_keys
-rw------- 1 username username 1675 May 21Â 2014 id_rsa
-rw------- 1 username username 1460 May 21Â 2014 id_rsa.ppk
-rw-r--r-- 1 username username 392 May 21 2014 id_rsa.pub
-Please note that private keys in
+<span class="visualHighlight"></span>Please note that private keys in
.ssh directory are without passphrase and allow you to connect within
the cluster.
### Access privileges on .ssh folder
-- `.ssh`{style="text-align left; "}
- style="text-align left; float none; ">
- class="Apple-converted-space">Â directory
- style="text-align left; float none; ">700 (drwx------)
--
- style="text-align left; float none; ">Authorized_keys,Â
- style="text-align left; float none; ">
- style="text-align left; float none; ">
- class="Apple-converted-space">known_hosts and
- public keyÂ
- style="text-align left; float none; ">(`.pub`{style="text-align left; "}
- style="text-align left; float none; ">
- class="Apple-converted-space">Â file)Â
+- `.ssh`{style="text-alignleft; "}<span
+ style="text-alignleft; floatnone; "><span
+ class="Apple-converted-space">Â </span>directory:</span> <span
+ style="text-alignleft; floatnone; ">700 (drwx------)</span>
+- <span
+ style="text-alignleft; floatnone; ">Authorized_keys, <span
+ style="text-alignleft; floatnone; "><span
+ style="text-alignleft; floatnone; "><span
+ class="Apple-converted-space">known_hosts</span></span></span> and
+ <span style="text-alignleft; floatnone; ">public key <span
+ style="text-alignleft; floatnone; ">(</span>`.pub`{style="text-alignleft; "}<span
+ style="text-alignleft; floatnone; "><span
+ class="Apple-converted-space">Â </span>file):Â <span
class="Apple-converted-space">
- `644 (-rw-r--r--)`{style="text-align left; "}
--
- style="text-align left; float none; ">``{style="text-align left; "}
- class="Apple-converted-space">
- style="text-align left; float none; ">Private key
- (`id_rsa/id_rsa.ppk`{style="text-align left; "}
- style="text-align left; float none; ">)
- class="Apple-converted-space">`600 (-rw-------)`{style="text-align left; "}
-
-
+ </span></span>`644 (-rw-r--r--)`{style="text-alignleft; "}</span></span>
+- <span style="text-alignleft; floatnone; "><span
+ style="text-alignleft; floatnone; ">``{style="text-alignleft; "}<span
+ class="Apple-converted-space"> <span
+ style="text-alignleft; floatnone; ">Private key
+ (</span>`id_rsa/id_rsa.ppk`{style="text-alignleft; "}<span
+ style="text-alignleft; floatnone; ">)<span
+ class="Apple-converted-space"></span></span>`600 (-rw-------)`{style="text-alignleft; "}
+ </span></span>
+ </span>
+<!-- -->
cd /home/username/
chmod 700 .ssh/
chmod 644 .ssh/authorized_keys
@@ -56,13 +54,13 @@ Private key
-----------
The path to a private key is usually /home/username/.ssh/
Private key file in "id_rsa" or `"*.ppk" `format is used to
-authenticate with the servers.
-style="text-align start; float none; ">Private key is present locally
+authenticate with the servers. <span
+style="text-alignstart; floatnone; ">Private key is present locally
on local side and used for example in SSH agent [Pageant (for Windows
-users)](putty/PageantV.png). The private key should
-always be kept in a safe place.
-An example of private key
-format
+users)](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PageantV.png).
+The private key should always be kept in a safe place.</span>
+<span style="text-alignstart; floatnone; ">An example of private key
+format:</span>
-----BEGIN RSA PRIVATE KEY-----
MIIEpAIBAAKCAQEAqbo7jokygnBpG2wYa5NB45ns6+UKTNLMLHF0BO3zmRtKEElE
aGqXfbYwvXlcuRb2d9/Y5dVpCZHV0kbY3NhtVOcEIe+1ROaiU9BEsUAhMNEvgiLV
@@ -92,25 +90,25 @@ format
-----END RSA PRIVATE KEY-----
Public key
----------
-Public key file in "*.pub" format is used to
-style="text-align start; float none; ">verify a
-class="Apple-converted-space">Â
-style="text-align start; ">digital signature. Public
-style="text-align start; float none; ">key is present on the remote
-side and allows access to
-the owner of the matching private key.
-An example of public key
-format
+Public key file in "*.pub" format is used to <span
+style="text-alignstart; floatnone; ">verify a<span
+class="Apple-converted-space">Â </span></span><span
+style="text-alignstart; ">digital signature</span>. Public <span
+style="text-alignstart; floatnone; ">key is present on the remote
+side and <span style="text-alignstart; floatnone; ">allows access to
+the owner of the matching private key</span>.</span>
+<span style="text-alignstart; floatnone; ">An example of public key
+format:</span>
ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCpujuOiTKCcGkbbBhrk0Hjmezr5QpM0swscXQE7fOZG0oQSURoapd9tjC9eVy5FvZ339jl1WkJkdXSRtjc2G1U5wQh77VE5qJT0ESxQCEw0S+CItWBKqXhC9E7gFY+UyP5YBZcOneh6gGHyCVfK6H215vzKr3x+/WvWl5gZGtbf+zhX6o4RJDRdjZPutYJhEsg/qtMxcCtMjfm/dZTnXeafuebV8nug3RCBUflvRb1XUrJuiX28gsd4xfG/P6L/mNMR8s4kmJEZhlhxpj8Th0iIc+XciVtXuGWQrbddcVRLxAmvkYAPGnVVOQeNj69pqAR/GXaFAhvjYkseEowQao1 username@organization.example.com
### How to add your own key
-First, generate a new keypair of your public and private key
+First, generate a new keypair of your public and private key:
local $ ssh-keygen -C 'username@organization.example.com' -f additional_key
Please, enter **strong** **passphrase** for securing your private key.
You can insert additional public key into authorized_keys file for
-authentication with your own private key. Additional records in
-authorized_keys file must be delimited by new line. Users are
+authentication with your own private <span>key. Additional records in
+authorized_keys file must be delimited by new line</span>. Users are
not advised to remove the default public key from authorized_keys file.
-Example
+Example:
$ cat additional_key.pub >> ~/.ssh/authorized_keys
In this example, we add an additional public key, stored in file
additional_key.pub into the authorized_keys. Next time we log in, we
@@ -119,12 +117,3 @@ will be able to use the private addtional_key key to log in.
Removing your key from authorized_keys can be done simply by deleting
the corresponding public key which can be identified by a comment at the
end of line (eg. username@organization.example.com).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
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- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
diff --git a/get-started-with-it4innovations/applying-for-resources.html b/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.html
old mode 100755
new mode 100644
similarity index 72%
rename from get-started-with-it4innovations/applying-for-resources.html
rename to docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.html
index 47c30190316a20db34581fa5ea9f3c4d5859ad7f..4abe6eb2629b060aa84ce2512e417865ac5f7ce1
--- a/get-started-with-it4innovations/applying-for-resources.html
+++ b/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.html
@@ -10,45 +10,42 @@
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Applying for Resources — IT4I Docs</title>
- <link rel="canonical" href="applying-for-resources.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="applying-for-resources.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="applying-for-resources.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../index.html">
- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../get-started-with-it4innovations.html">Get Started with IT4Innovations</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations">Get Started with IT4Innovations</a>
<span class="breadcrumbSeparator">
/
@@ -234,7 +231,7 @@
<p>Academic researchers can apply for computational resources via <a class="external-link" href="http://www.it4i.cz/open-access-competition/?lang=en&lang=en" target="_self" title="">Open Access Competitions</a>.</p>
<p>Anyone is welcomed to apply via the <a class="external-link" href="http://www.it4i.cz/obtaining-computational-resources-through-directors-discretion/?lang=en&lang=en" target="_self" title="">Directors Discretion.</a></p>
<p>Foreign (mostly European) users can obtain computational resources via the <a class="external-link" href="http://www.prace-ri.eu/DECI-Projects" target="_self" title="">PRACE (DECI) program</a>.</p>
-<p>In all cases, IT4Innovations’ access mechanisms are aimed at distributing computational resources while taking into account the development and application of supercomputing methods and their benefits and usefulness for society. The applicants are expected to submit a proposal. In the proposal, the applicants <em><strong>apply for a particular amount of core-hours</strong></em> of computational resources. The requested core-hours should be substantiated by scientific excellence of the proposal, its computational maturity and expected impacts. <span>Proposals do undergo a scientific, technical and economic evaluation.</span> The allocation decisions are based on this evaluation. More information at <a class="external-link" href="http://www.it4i.cz/computing-resources-allocation/?lang=en" target="_self" title="">Computing resources allocation</a> and <a target="_self" title="" class="internal-link" href="obtaining-login-credentials.html">Obtaining Login Credentials</a> page.</p>
+<p>In all cases, IT4Innovations’ access mechanisms are aimed at distributing computational resources while taking into account the development and application of supercomputing methods and their benefits and usefulness for society. The applicants are expected to submit a proposal. In the proposal, the applicants <em><strong>apply for a particular amount of core-hours</strong></em> of computational resources. The requested core-hours should be substantiated by scientific excellence of the proposal, its computational maturity and expected impacts. <span>Proposals do undergo a scientific, technical and economic evaluation.</span> The allocation decisions are based on this evaluation. More information at <a class="external-link" href="http://www.it4i.cz/computing-resources-allocation/?lang=en" target="_self" title="">Computing resources allocation</a> and <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">Obtaining Login Credentials</a> page.</p>
<p>Â </p>
</div>
@@ -311,7 +308,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -327,7 +324,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -343,7 +340,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -359,7 +356,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="applying-for-resources.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources">
<span>Applying for Resources</span>
</a>
@@ -375,7 +372,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="obtaining-login-credentials.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">
<span>Obtaining Login Credentials</span>
</a>
@@ -391,7 +388,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-clusters/shell-access-and-data-transfer.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">
<span>Accessing the Clusters</span>
</a>
@@ -416,7 +413,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -432,7 +429,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -448,7 +445,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -464,7 +461,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -480,7 +477,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -519,14 +516,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -548,12 +545,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -569,7 +566,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations/applying-for-resources by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:15:55 GMT -->
</html>
diff --git a/get-started-with-it4innovations/applying-for-resources.md b/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.md
similarity index 56%
rename from get-started-with-it4innovations/applying-for-resources.md
rename to docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.md
index daaba7fc06225a93c6e3c97e637a2417a75668bb..373340cca4967fdfe27d4c79164c8f04ac36c535 100644
--- a/get-started-with-it4innovations/applying-for-resources.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.md
@@ -1,15 +1,18 @@
+Applying for Resources
+======================
+
Computational resources may be allocated by any of the following
[Computing resources
-allocation](http//www.it4i.cz/computing-resources-allocation/?lang=en)
+allocation](http://www.it4i.cz/computing-resources-allocation/?lang=en)
mechanisms.
Academic researchers can apply for computational resources via [Open
Access
-Competitions](http//www.it4i.cz/open-access-competition/?lang=en&lang=en).
+Competitions](http://www.it4i.cz/open-access-competition/?lang=en&lang=en).
Anyone is welcomed to apply via the [Directors
-Discretion.](http//www.it4i.cz/obtaining-computational-resources-through-directors-discretion/?lang=en&lang=en)
+Discretion.](http://www.it4i.cz/obtaining-computational-resources-through-directors-discretion/?lang=en&lang=en)
Foreign (mostly European) users can obtain computational resources via
the [PRACE (DECI)
-program](http//www.prace-ri.eu/DECI-Projects).
+program](http://www.prace-ri.eu/DECI-Projects).
In all cases, IT4Innovations’ access mechanisms are aimed at
distributing computational resources while taking into account the
development and application of supercomputing methods and their benefits
@@ -18,6 +21,11 @@ proposal. In the proposal, the applicants ***apply for a particular
amount of core-hours*** of computational resources. The requested
core-hours should be substantiated by scientific excellence of the
proposal, its computational maturity and expected impacts.
-Proposals do undergo a scientific, technical and economic
-evaluation. The allocation decisions are based on this
+<span>Proposals do undergo a scientific, technical and economic
+evaluation.</span> The allocation decisions are based on this
evaluation. More information at [Computing resources
+allocation](http://www.it4i.cz/computing-resources-allocation/?lang=en)
+and [Obtaining Login
+Credentials](https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials)
+page.
+Â
diff --git a/get-started-with-it4innovations/changelog.html b/docs.it4i.cz/get-started-with-it4innovations/changelog.html
old mode 100755
new mode 100644
similarity index 70%
rename from get-started-with-it4innovations/changelog.html
rename to docs.it4i.cz/get-started-with-it4innovations/changelog.html
index d955d18d2e63562bdea18fc13dfd38ea5c864b50..b34d2173b3460028eadac1d1448b717cda94ac8f
--- a/get-started-with-it4innovations/changelog.html
+++ b/docs.it4i.cz/get-started-with-it4innovations/changelog.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
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<title>Changelog — IT4I Docs</title>
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- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
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- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
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- <a accesskey="6" href="changelog.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/get-started-with-it4innovations/changelog#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
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<td class="listing-body-Title">
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<td class="listing-body-Title">
- <a href="../anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.html" title="Matlab">Matlab</a>
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<td class="listing-body-Title">
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+ <a href="https://docs.it4i.cz/whats-new/news-feed/intel-vtune-amplifier-support-for-xeon-phi-on-salomon" title="Intel VTune Amplifier support for Xeon Phi on Salomon">Intel VTune Amplifier support for Xeon Phi on Salomon</a>
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<span>Changelog</span>
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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diff --git a/whats-new/news-feed/vampir-installed.md b/docs.it4i.cz/get-started-with-it4innovations/changelog.md
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<title>Documentation — IT4I Docs</title>
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- <a accesskey="6" href="introduction.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
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</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../index.html">
- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -220,7 +217,7 @@
<div id="parent-fieldname-text-7c82cccbb7c34932b6b2a934ad0f971a" class="">
- <p>Welcome to IT4Innovations documentation pages. The IT4Innovations national supercomputing center operates supercomputers <a target="_self" title="" class="internal-link" href="../salomon.html">Salomon</a> and <a target="_self" title="" class="internal-link" href="../anselm-cluster-documentation.html">Anselm</a>. The supercomputers are <a target="_self" title="" class="internal-link" href="applying-for-resources.html"><span class="external-link">available</span></a> to academic community within the Czech Republic and Europe and industrial community worldwide. The purpose of these pages is to provide a comprehensive documentation on hardware, software and usage of the computers.</p>
+ <p>Welcome to IT4Innovations documentation pages. The IT4Innovations national supercomputing center operates supercomputers <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon">Salomon</a> and <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm</a>. The supercomputers are <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources"><span class="external-link">available</span></a> to academic community within the Czech Republic and Europe and industrial community worldwide. The purpose of these pages is to provide a comprehensive documentation on hardware, software and usage of the computers.</p>
<h2><span class="link-external"><span class="WYSIWYG_LINK">How to read the documentation</span></span></h2>
<ol>
<li>Read the list in the left column. Select the subject of interest. Alternatively, use the Search box in the upper right corner.</li>
@@ -232,7 +229,7 @@
<p class="callout">The call-out. Â Focus on the call-outs before reading full details.</p>
<p>Â </p>
<ul>
-<li>Read the <a target="_self" title="" class="external-link" href="changelog.html">Changelog</a> to keep up to date.</li>
+<li>Read the <a title="" class="external-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/changelog">Changelog</a> to keep up to date.</li>
</ul>
<h2 class=" ">Getting Help and Support</h2>
<p class="callout" title="">Contact <a class="email-link" href="mailto:support%20[at]%20it4i.cz" target="_self" title="">support [at] it4i.cz</a> for help and support regarding the cluster technology at IT4Innovations.<br />Please use <strong>Czech</strong>, <strong>Slovak</strong> or <strong>English</strong> language for communication with us.<br />Follow the status of your request to IT4Innovations at <a class="external-link" href="http://support.it4i.cz/rt" target="_self" title="">support.it4i.cz/rt</a>.</p>
@@ -245,7 +242,7 @@
<p>Â </p>
<p class="callout">Learn how to parallelize your code!</p>
<p>Â </p>
-<p>In many cases, you will run your own code on the cluster. In order to fully exploit the cluster, you will need to carefully consider how to utilize all the cores available on the node and how to use multiple nodes at the same time. You need to <b>parallelize</b> your code. Proficieny in MPI, OpenMP, CUDA, UPC or GPI2 programming may be gained via the <a class="external-link" href="http://prace.it4i.cz/" target="_self" title="">training provided by IT4Innovations.</a></p>
+<p>In many cases, you will run your own code on the cluster. In order to fully exploit the cluster, you will need to carefully consider how to utilize all the cores available on the node and how to use multiple nodes at the same time. You need to <b>parallelize</b> your code. Proficieny in MPI, OpenMP, CUDA, UPC or GPI2 programming may be gained via the <a class="external-link" href="http://prace.it4i.cz" target="_self" title="">training provided by IT4Innovations.</a></p>
<h2 class=" ">Terminology Frequently Used on These Pages</h2>
<ul>
<ul>
@@ -327,7 +324,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -343,7 +340,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -359,7 +356,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -375,7 +372,7 @@
- <a title="" class="state-published contenttype-document" href="applying-for-resources.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources">
<span>Applying for Resources</span>
</a>
@@ -391,7 +388,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="obtaining-login-credentials.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">
<span>Obtaining Login Credentials</span>
</a>
@@ -407,7 +404,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-clusters/shell-access-and-data-transfer.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">
<span>Accessing the Clusters</span>
</a>
@@ -432,7 +429,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -448,7 +445,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -464,7 +461,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -480,7 +477,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -496,7 +493,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -535,14 +532,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -564,12 +561,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -585,7 +582,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations/introduction by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:11 GMT -->
</html>
diff --git a/get-started-with-it4innovations.md b/docs.it4i.cz/get-started-with-it4innovations/introduction.md
similarity index 59%
rename from get-started-with-it4innovations.md
rename to docs.it4i.cz/get-started-with-it4innovations/introduction.md
index 2c598aac6c8b70d2efce96b0abd5bec236d98f39..2fadd6e75b803ba9888700875e5380c7026bf290 100644
--- a/get-started-with-it4innovations.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/introduction.md
@@ -1,14 +1,18 @@
+Documentation
+=============
+
+Welcome to IT4Innovations documentation pages. The IT4Innovations
national supercomputing center operates supercomputers
-[Salomon](salomon.html) and
-[Anselm](anselm-cluster-documentation.html). The
-supercomputers are [
-class="external-link">available](get-started-with-it4innovations/applying-for-resources.html)
+[Salomon](https://docs.it4i.cz/salomon) and
+[Anselm](https://docs.it4i.cz/anselm-cluster-documentation).
+The supercomputers are [<span
+class="external-link">available</span>](https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources)
to academic community within the Czech Republic and Europe and
industrial community worldwide. The purpose of these pages is to provide
a comprehensive documentation on hardware, software and usage of the
computers.
-How to read the documentation
---------------------------------------------------------------------------------------------------
+<span class="link-external"><span class="WYSIWYG_LINK">How to read the documentation</span></span>
+------
1. Read the list in the left column. Select the subject of interest.
Alternatively, use the Search box in the upper right corner.
2. Read the CONTENTS in the upper right corner.
@@ -19,31 +23,31 @@ How to read the documentation
The call-out. Â Focus on the call-outs before reading full details.
Â
- Read the
- [Changelog](get-started-with-it4innovations/changelog.html)
+ [Changelog](https://docs.it4i.cz/get-started-with-it4innovations/changelog)
to keep up to date.
Getting Help and Support
-------------------------
+-
Contact [support [at]
-it4i.cz](mailtosupport%20%5Bat%5D%20it4i.cz){.email-link} for help and
+it4i.cz](mailto:support%20%5Bat%5D%20it4i.cz){.email-link} for help and
support regarding the cluster technology at IT4Innovations.
Please use **Czech**, **Slovak** or **English** language for
communication with us.
Follow the status of your request to IT4Innovations at
-[support.it4i.cz/rt](http//support.it4i.cz/rt).
+[support.it4i.cz/rt](http://support.it4i.cz/rt).
Â
Use your IT4Innotations username and password to log in to the
-[support](http//support.it4i.cz/) portal.
+[support](http://support.it4i.cz/) portal.
Required Proficiency
--------------------
You need basic proficiency in Linux environment.
Â
In order to use the system for your calculations, you need basic
proficiency in Linux environment. To gain the proficiency, we recommend
-you reading the [introduction to
-Linux](http//www.tldp.org/LDP/intro-linux/html/)
+you reading the [<span class="WYSIWYG_LINK">introduction to
+Linux</span>](http://www.tldp.org/LDP/intro-linux/html/)
operating system environment and installing a Linux distribution on your
-personal computer. A good choice might be the [
-class="WYSIWYG_LINK">Fedora](http//fedoraproject.org/)
+personal computer. A good choice might be the [<span
+class="WYSIWYG_LINK">Fedora</span>](http://fedoraproject.org/)
distribution, as it is similar to systems on the clusters at
IT4Innovations. It's easy to install and use. In fact, any distribution
would do.
@@ -56,40 +60,39 @@ utilize all the cores available on the node and how to use multiple
nodes at the same time. You need to **parallelize** your code.
Proficieny in MPI, OpenMP, CUDA, UPC or GPI2 programming may be gained
via the [training provided by
-IT4Innovations.](http//prace.it4i.cz/)
+IT4Innovations.](http://prace.it4i.cz)
Terminology Frequently Used on These Pages
-------------------------------------------
-- **node** a computer, interconnected by network to other computers -
+-------------------
+- **node:** a computer, interconnected by network to other computers -
Computational nodes are powerful computers, designed and dedicated
for executing demanding scientific computations.
-- **core** processor core, a unit of processor, executing
+- **core:** processor core, a unit of processor, executing
computations
-- **corehours** wall clock hours of processor core time - Each node
+- **corehours:** wall clock hours of processor core time - Each node
is equipped with **X** processor cores, provides **X** corehours per
1 wall clock hour.
-- **[]()job** a calculation running on the supercomputer - The job
+- **[]()job:** a calculation running on the supercomputer - The job
allocates and utilizes resources of the supercomputer for
certain time.
-- **HPC** High Performance Computing
-- []()**HPC (computational) resources** corehours, storage capacity,
+- **HPC:** High Performance Computing
+- []()**HPC (computational) resources:** corehours, storage capacity,
software licences
-- **code** a program
-- **primary investigator (PI)** a person responsible for execution of
+- **code:** a program
+- **primary investigator (PI):** a person responsible for execution of
computational project and utilization of computational resources
allocated to that project
-- **collaborator** a person participating on execution of
+- **collaborator:** a person participating on execution of
computational project and utilization of computational resources
allocated to that project
-- **[]()project** a computational project under investigation by the
+- **[]()project:** a computational project under investigation by the
PI - The project is identified by the project ID. The computational
resources are allocated and charged per project.
-- **[]()jobscript** a script to be executed by the PBS Professional
+- **[]()jobscript:** a script to be executed by the PBS Professional
workload manager
Conventions
-----------
In this documentation, you will find a number of pages containing
-examples. We use the following conventions
-
+examples. We use the following conventions:
 Cluster command prompt
``` {.prettyprint .lang-sh}
$
@@ -103,3 +106,9 @@ local $
Although we have taken every care to ensure the accuracy of our content,
mistakes do happen. If you find a mistake in the text or the code we
would be grateful if you would report this to us. By doing so, you can
+save other readers from frustration and help us improve subsequent
+versions of this documentation. If you find any errata, please report
+them by visiting http://support.it4i.cz/rt, creating a new ticket, and
+entering the details of your errata. Once your errata are verified, your
+submission will be accepted and the errata will be uploaded on our
+website.
diff --git a/get-started-with-it4innovations/obtaining-login-credentials.html b/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials.html
old mode 100755
new mode 100644
similarity index 67%
rename from get-started-with-it4innovations/obtaining-login-credentials.html
rename to docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials.html
index 78aab2db5328367448e8373d561bc66bedcd50c6..4e09c8e99af669c084a02b15cae9a50f6c9381d5
--- a/get-started-with-it4innovations/obtaining-login-credentials.html
+++ b/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:38 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Obtaining Login Credentials — IT4I Docs</title>
- <link rel="canonical" href="obtaining-login-credentials.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="obtaining-login-credentials.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="obtaining-login-credentials.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../index.html">
- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials.md b/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials.md
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<title>Certificates FAQ — IT4I Docs</title>
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- <a accesskey="6" href="certificates-faq.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
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<dt class="portletHeader hiddenStructure">
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g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
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-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -684,12 +681,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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@@ -705,7 +702,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
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diff --git a/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md b/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
similarity index 80%
rename from get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
rename to docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
index fe105fff17bad31e455199c492520da7158f4a3a..ff56a00ae127392d17f469d57f5f1b8992972f9a 100644
--- a/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
@@ -1,59 +1,62 @@
+Certificates FAQ
================
FAQ about certificates in general
-
-
-Q What are certificates?
--------------------------
+
+QWhat are certificates?
+--
IT4Innovations employs X.509 certificates for secure communication (e.
g. credentials exchange) and for grid services related to PRACE, as they
present a single method of authentication for all PRACE services, where
only one password is required.
There are different kinds of certificates, each with a different scope
-of use. We mention here
+of use. We mention here:
- User (Private) certificates
+<!-- -->
- Certificate Authority (CA) certificates
+<!-- -->
- Host certificates
+<!-- -->
- Service certificates
Â
However, users need only manage User and CA certificates. Note that your
user certificate is protected by an associated private key, and this
**private key must never be disclosed**.
-Q Which X.509 certificates are recognised by IT4Innovations?
--------------------------------------------------------------
+QWhich X.509 certificates are recognised by IT4Innovations?
+---------------
Any certificate that has been issued by a Certification Authority (CA)
-from a member of the IGTF ([httpwww.igtf.net](http//www.igtf.net/)) is
-recognised by IT4Innovations European certificates are issued by
+from a member of the IGTF ([http:www.igtf.net](http://www.igtf.net/)) is
+recognised by IT4InnovationsEuropean certificates are issued by
members of the EUGridPMA
-([https//www.eugridmpa.org](https//www.eugridpma.org/)), which is part
+([https://www.eugridmpa.org](https://www.eugridpma.org/)), which is part
of the IGTF and coordinates the trust fabric for e-Science Grid
authentication within Europe. Further the Czech *"Qualified certificate"
-(Kvalifikovaný certifikát)* (provided by or
-), that is used in
+(Kvalifikovaný certifikát)* (provided by <http://www.postsignum.cz/> or
+<http://www.ica.cz/Kvalifikovany-certifikat.aspx>), that is used in
electronic contact with Czech public authorities is accepted.
-Q How do I get a User Certificate that can be used with IT4Innovations?
-------------------------------------------------------------------------
+QHow do I get a User Certificate that can be used with IT4Innovations?
+---
To get a certificate, you must make a request to your local, IGTF
approved, Certificate Authority (CA). Usually you then must visit, in
person, your nearest Registration Authority (RA) to verify your
affiliation and identity (photo identification is required). Usually,
you will then be emailed details on how to retrieve your certificate,
although procedures can vary between CAs. If you are in Europe, you can
-locate your trusted CA via .
+locate your trusted CA via <http://www.eugridpma.org/members/worldmap>.
In some countries certificates can also be retrieved using the TERENA
Certificate Service, see the FAQ below for the link.
-Q Does IT4Innovations support short lived certificates (SLCS)?
----------------------------------------------------------------
+QDoes IT4Innovations support short lived certificates (SLCS)?
+-----------------
Yes, provided that the CA which provides this service is also a member
of IGTF.
-Q Does IT4Innovations support the TERENA certificate service?
---------------------------------------------------------------
+QDoes IT4Innovations support the TERENA certificate service?
+----------------
Yes, ITInnovations supports TERENA eScience personal certificates. For
more information, please visit
-[https//tcs-escience-portal.terena.org](https//tcs-escience-portal.terena.org/){.spip_url
+[https://tcs-escience-portal.terena.org](https://tcs-escience-portal.terena.org/){.spip_url
.spip_out}, where you also can find if your organisation/country can use
this service
-Q What format should my certificate take?
-------------------------------------------
+QWhat format should my certificate take?
+-------------------
User Certificates come in many formats, the three most common being the
’PKCS12’, ’PEM’ and the JKS formats.
The PKCS12 (often abbreviated to ’p12’) format stores your user
@@ -74,8 +77,8 @@ form of your certificate can be used by grid services like DART and
UNICORE6.
To convert your Certificate from p12 to JKS, IT4Innovations recommends
using the keytool utiliy (see separate FAQ entry).
-Q What are CA certificates?
-----------------------------
+QWhat are CA certificates?
+-----
Certification Authority (CA) certificates are used to verify the link
between your user certificate and the authority which issued it. They
are also used to verify the link between the host certificate of a
@@ -87,7 +90,7 @@ To assist users, SURFsara (a member of PRACE) provides a complete and
up-to-date bundle of all the CA certificates that any PRACE user (or
IT4Innovations grid services user) will require. Bundle of certificates,
in either p12, PEM or JKS formats, are available from
-.
+<http://winnetou.sara.nl/prace/certs/>.
It is worth noting that gsissh-term and DART automatically updates their
CA certificates from this SURFsara website. In other cases, if you
receive a warning that a server’s certificate can not be validated (not
@@ -101,9 +104,9 @@ If you run this command as ’root’, then it will install the certificates
into /etc/grid-security/certificates. If you run this not as ’root’,
then the certificates will be installed into
$HOME/.globus/certificates. For Globus, you can download the
-globuscerts.tar.gz packet from .
-Q What is a DN and how do I find mine?
----------------------------------------
+globuscerts.tar.gz packet from <http://winnetou.sara.nl/prace/certs/>.
+QWhat is a DN and how do I find mine?
+----------------
DN stands for Distinguished Name and is part of your user certificate.
IT4Innovations needs to know your DN to enable your account to use the
grid services. You may use openssl (see below) to determine your DN or,
@@ -116,28 +119,27 @@ For users running Firefox under Windows, the DN is referred to as the
"subject" of your certificate.
Tools->Options->Advanced->Encryption->View Certificates.
Highlight your name and then Click View->Details->Subject.
-Q How do I use the openssl tool?
----------------------------------
+QHow do I use the openssl tool?
+----------
The following examples are for Unix/Linux operating systems only.
-To convert from PEM to p12, enter the following command
+To convert from PEM to p12, enter the following command:
openssl pkcs12 -export -in usercert.pem -inkey userkey.pem -out
username.p12
-To convert from p12 to PEM, type the following *four* commands
+To convert from p12 to PEM, type the following *four* commands:
openssl pkcs12 -in username.p12 -out usercert.pem -clcerts -nokeys
openssl pkcs12 -in username.p12 -out userkey.pem -nocerts
chmod 444 usercert.pem
chmod 400 userkey.pem
-To check your Distinguished Name (DN), enter the following command
+To check your Distinguished Name (DN), enter the following command:
openssl x509 -in usercert.pem -noout -subject -nameopt
RFC2253
To check your certificate (e.g., DN, validity, issuer, public key
-algorithm, etc.), enter the following command
+algorithm, etc.), enter the following command:
openssl x509 -in usercert.pem -text -noout
To download openssl for both Linux and Windows, please visit
-. On Macintosh Mac OS X
+<http://www.openssl.org/related/binaries.html>. On Macintosh Mac OS X
computers openssl is already pre-installed and can be used immediately.
-Q How do I create and then manage a keystore?
-----------------------------------------------
+QHow do I create and then manage a keystore?
IT4innovations recommends the java based keytool utility to create and
manage keystores, which themselves are stores of keys and certificates.
For example if you want to convert your pkcs12 formatted key pair into a
@@ -150,14 +152,13 @@ $my_keystore is the name that you give to your new java keystore and
$my_nickname is the alias name that the p12 certificate was given and
is used also for the new keystore.
You also can import CA certificates into your java keystore with the
-tool, e.g.
+tool, e.g.:
keytool -import -trustcacerts -alias $mydomain -file $mydomain.crt -keystore $my_keystore
where $mydomain.crt is the certificate of a trusted signing authority
(CA) and $mydomain is the alias name that you give to the entry.
More information on the tool can be found
-at
-Q How do I use my certificate to access the different grid Services?
----------------------------------------------------------------------
+at:<http://docs.oracle.com/javase/7/docs/technotes/tools/solaris/keytool.html>
+QHow do I use my certificate to access the different grid Services?
Most grid services require the use of your certificate; however, the
format of your certificate depends on the grid Service you wish to
employ.
@@ -167,7 +168,7 @@ service automatically installs up-to-date PRACE CA certificates.
If the grid service is UNICORE, then you bind your certificate, in
either the p12 format or JKS, to UNICORE during the installation of the
client on your local machine. For more information, please visit
-[UNICORE6 in PRACE](http//www.prace-ri.eu/UNICORE6-in-PRACE){.spip_in
+[UNICORE6 in PRACE](http://www.prace-ri.eu/UNICORE6-in-PRACE){.spip_in
.external-link}
If the grid service is part of Globus, such as GSI-SSH, GriFTP or GRAM5,
then the certificates can be in either p12 or PEM format and must reside
@@ -182,8 +183,8 @@ directory is either $HOME/.globus/certificates or
%HOMEPATH%.globuscertificates. (If you are using GSISSH-Term from
prace-ri.eu then you do not have to create the .globus directory nor
install CA certificates to use this tool alone).
-Q How do I manually import my certificate into my browser?
------------------------------------------------------------
+QHow do I manually import my certificate into my browser?
+-------------
If you employ the Firefox browser, then you can import your certificate
by first choosing the "Preferences" window. For Windows, this is
Tools->Options. For Linux, this is Edit->Preferences. For Mac,
@@ -204,8 +205,8 @@ Password box, type your password. NB you may be prompted multiple times
for your password. In the "Certificate File To Import" box, type the
filename of the certificate you wish to import, and then click OK. Click
Close, and then click OK.
-Q What is a proxy certificate?
--------------------------------
+QWhat is a proxy certificate?
+--------
A proxy certificate is a short-lived certificate which may be employed
by UNICORE and the Globus services. The proxy certificate consists of a
new user certificate and a newly generated proxy private key. This proxy
@@ -213,9 +214,9 @@ typically has a rather short lifetime (normally 12 hours) and often only
allows a limited delegation of rights. Its default location, for
Unix/Linux, is /tmp/x509_u*uid* but can be set via the
$X509_USER_PROXY environment variable.
-Q What is the MyProxy service?
--------------------------------
-[The MyProxy Service](http//grid.ncsa.illinois.edu/myproxy/){.spip_in
+QWhat is the MyProxy service?
+--------
+[The MyProxy Service](http://grid.ncsa.illinois.edu/myproxy/){.spip_in
.external-link}, can be employed by gsissh-term and Globus tools, and is
an online repository that allows users to store long lived proxy
certificates remotely, which can then be retrieved for use at a later
@@ -224,11 +225,9 @@ time of storage. This is beneficial to Globus users as they do not have
to carry their private keys and certificates when travelling; nor do
users have to install private keys and certificates on possibly insecure
computers.
-Q Someone may have copied or had access to the private key of my certificate either in a separate file or in the browser. What should I do?
---------------------------------------------------------------------------------------------------------------------------------------------
+QSomeone may have copied or had access to the private key of my certificate either in a separate file or in the browser. What should I do?
+--
Please ask the CA that issued your certificate to revoke this certifcate
and to supply you with a new one. In addition, please report this to
IT4Innovations by contacting [the support
-team](https//support.it4i.cz/rt).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
+team](https://support.it4i.cz/rt).
diff --git a/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html b/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html
old mode 100755
new mode 100644
similarity index 74%
rename from get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html
rename to docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html
index dc6ca6f296871d6c6c4033d59c486e14a9221cde..9fb013b2d1a18b067b39888dbb8795629d562019
--- a/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html
+++ b/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:08 GMT -->
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Obtaining Login Credentials — IT4I Docs</title>
- <link rel="canonical" href="obtaining-login-credentials.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="obtaining-login-credentials.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="obtaining-login-credentials.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../get-started-with-it4innovations.html">Get Started with IT4Innovations</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations">Get Started with IT4Innovations</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../obtaining-login-credentials.html">Obtaining Login Credentials</a>
+ <a href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">Obtaining Login Credentials</a>
<span class="breadcrumbSeparator">
/
@@ -241,17 +238,17 @@
<div id="parent-fieldname-text-4d37670923054a0bb9d85a3979c2301a" class="">
<h2 class=" ">Obtaining Authorization</h2>
-<p>The computational resources of IT4I  are allocated by the Allocation Committee to a <a target="_self" title="" class="internal-link" href="../introduction.html">Project</a>, investigated by a Primary Investigator. By allocating the computational resources, the Allocation Committee is authorizing the PI to access and use the clusters. The PI may decide to authorize a number of her/his Collaborators to access and use the clusters, to consume the resources allocated to her/his Project. These collaborators will be associated to the Project. The Figure below is depicting the authorization chain:</p>
+<p>The computational resources of IT4I  are allocated by the Allocation Committee to a <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/introduction">Project</a>, investigated by a Primary Investigator. By allocating the computational resources, the Allocation Committee is authorizing the PI to access and use the clusters. The PI may decide to authorize a number of her/his Collaborators to access and use the clusters, to consume the resources allocated to her/his Project. These collaborators will be associated to the Project. The Figure below is depicting the authorization chain:</p>
<div class="wide-view-wrapper">
-<p><img title="Authorization chain" class="image-inline" alt="The Authorization chain for access and utilization of computational resources on Anselm" src="../../anselm-cluster-documentation/Authorization_chain.png" /></p>
+<p><img alt="The Authorization chain for access and utilization of computational resources on Anselm" class="image-inline" title="Authorization chain" src="https://docs.it4i.cz/anselm-cluster-documentation/Authorization_chain.png" /></p>
</div>
-<p class="callout">Â You need to either <a target="_self" title="" class="internal-link" href="../applying-for-resources.html">become the PI</a> or <a class="anchor-link" href="#authorization-of-collaborator-by-pi" target="_self" title="">be named as a collaborator</a> by a PI in order to access and use the clusters.</p>
+<p class="callout">Â You need to either <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources">become the PI</a> or <a class="anchor-link" href="#authorization-of-collaborator-by-pi" target="_self" title="">be named as a collaborator</a> by a PI in order to access and use the clusters.</p>
<p>Head of Supercomputing Services acts as a PI of a project DD-13-5. Joining this project, you may <strong>access and explore the clusters</strong>, use software, development environment and computers via the qexp and qfree queues. You may use these resources for own education/research, no paperwork is required. All IT4I employees may contact the Head of Supercomputing Services in order to obtain <strong>free access to the clusters</strong>.</p>
<h3 class=" "><a name="authorization-of-collaborator-by-pi"></a>Authorization of PI by Allocation Committee</h3>
<p>The PI is authorized to use the clusters by the allocation decision issued by the Allocation Committee.The PI will be informed by IT4I about the Allocation Committee decision.</p>
<h3 class=" ">Authorization by web</h3>
<p class="callout">This is a preferred way of granting access to project resources.<br />Please, use this method whenever it's possible.</p>
-<p>Log in to the <a class="external-link" href="https://extranet.it4i.cz/" target="_self" title="">IT4I Extranet portal</a> using IT4I credentials and go to the <strong>Projects</strong> section.</p>
+<p>Log in to the <a class="external-link" href="https://extranet.it4i.cz" target="_self" title="">IT4I Extranet portal</a> using IT4I credentials and go to the <strong>Projects</strong> section.</p>
<ul>
<li><strong>Users:</strong> Please, submit your requests for becoming a project member.</li>
<li><strong>Primary Investigators:</strong> Please, approve or deny users' requests in the same section.</li>
@@ -287,11 +284,11 @@
<li>ssh private key and private key passphrase</li>
<li>system password</li>
</ol>
-<p class="callout">The clusters are accessed by the <a target="_self" title="" class="internal-link" href="../accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html">private key</a> and username.<br />Username and password is used for login to the information systems listed on <a class="external-link" href="http://support.it4i.cz/" target="_self" title="">http://support.it4i.cz/</a>.</p>
+<p class="callout">The clusters are accessed by the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">private key</a> and username.<br />Username and password is used for login to the information systems listed on <a class="external-link" href="http://support.it4i.cz/" target="_self" title="">http://support.it4i.cz/</a>.</p>
<h3 class=" ">Change Passphrase</h3>
<p>On Linux, use</p>
<pre class="prettyprint lang-sh prettyprinted"><span class="kwd">local</span><span class="pln"> $ </span><span class="pln"><span style="text-align: start; float: none; ">ssh-keygen -f id_rsa -p</span></span></pre>
-<p>On Windows, use <a target="_self" title="" class="internal-link" href="../accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.html">PuTTY Key Generator</a>.</p>
+<p>On Windows, use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen">PuTTY Key Generator</a>.</p>
<h3 class=" ">Change Password</h3>
<p>Change password in your user profile at <a class="external-link" href="https://extranet.it4i.cz/user/" target="_self" title="extranet.it4i.cz/user/">https://extranet.it4i.cz/user/</a></p>
<h2 class=" "><a name="the-certificates-for-digital-signatures"></a>The Certificates for Digital Signatures</h2>
@@ -301,7 +298,7 @@
<li><a class="external-link" href="http://idoc.vsb.cz/xwiki/wiki/infra/view/uzivatel/moz-cert-gen" target="_self" title="">How to generate a personal TCS certificate in Mozilla Firefox web browser (in Czech)</a></li>
</ul>
<p>Â </p>
-<p>A FAQ about certificates can be found here: <span><a target="_self" title="" class="internal-link" href="certificates-faq.html">Certificates FAQ</a>.</span></p>
+<p>A FAQ about certificates can be found here: <span><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq">Certificates FAQ</a>.</span></p>
<h2 class=" "><a name="alternative-way-of-getting-personal-certificate"></a>Alternative Way to Personal Certificate</h2>
<p class="callout">Follow these steps <strong>only</strong> if you can not obtain your certificate in a standard way.<br />In case you choose this procedure, please attach a <strong>scan of photo ID</strong> (personal ID or passport or drivers license) when applying for <a class="anchor-link" href="#the-login-credentials" target="_self" title="">login credentials</a>.</p>
<ol>
@@ -411,7 +408,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -427,7 +424,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -443,7 +440,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -459,7 +456,7 @@
- <a title="" class="state-published contenttype-document" href="../applying-for-resources.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources">
<span>Applying for Resources</span>
</a>
@@ -475,7 +472,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../obtaining-login-credentials.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">
<span>Obtaining Login Credentials</span>
</a>
@@ -491,7 +488,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="obtaining-login-credentials.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials">
<span>Obtaining Login Credentials</span>
</a>
@@ -507,7 +504,7 @@
- <a title="FAQ about certificates in general" class="state-published contenttype-document" href="certificates-faq.html">
+ <a class="state-published contenttype-document" title="FAQ about certificates in general" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq">
<span>Certificates FAQ</span>
</a>
@@ -532,7 +529,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-clusters/shell-access-and-data-transfer.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">
<span>Accessing the Clusters</span>
</a>
@@ -557,7 +554,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -573,7 +570,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -589,7 +586,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -605,7 +602,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -621,7 +618,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -660,14 +657,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -689,12 +686,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -710,7 +707,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:09 GMT -->
</html>
diff --git a/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md b/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
similarity index 74%
rename from get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
rename to docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
index 5e19073355c7c5b7631817df7f3c344438f430cc..b5da24e46f2786c2b817b3855b760c5a85fa7dc1 100644
--- a/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
@@ -1,22 +1,22 @@
Obtaining Login Credentials
===========================
-
-
+
Obtaining Authorization
------------------------
The computational resources of IT4I Â are allocated by the Allocation
-Committee to a [Project](../introduction.html),
+Committee to a
+[Project](https://docs.it4i.cz/get-started-with-it4innovations/introduction),
investigated by a Primary Investigator. By allocating the computational
resources, the Allocation Committee is authorizing the PI to access and
use the clusters. The PI may decide to authorize a number of her/his
Collaborators to access and use the clusters, to consume the resources
allocated to her/his Project. These collaborators will be associated to
-the Project. The Figure below is depicting the authorization chain
+the Project. The Figure below is depicting the authorization chain:
+Anselm](https://docs.it4i.cz/anselm-cluster-documentation/Authorization_chain.png "Authorization chain")
 You need to either [become the
-PI](../applying-for-resources.html) or [be named as a
+PI](https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources)
+or [be named as a
collaborator](#authorization-of-collaborator-by-pi) by a
PI in order to access and use the clusters.
Head of Supercomputing Services acts as a PI of a project DD-13-5.
@@ -34,18 +34,18 @@ the Allocation Committee decision.
This is a preferred way of granting access to project resources.
Please, use this method whenever it's possible.
Log in to the [IT4I Extranet
-portal](https//extranet.it4i.cz/) using IT4I
-credentials and go to the **Projects** section.
-- **Users** Please, submit your requests for becoming a
+portal](https://extranet.it4i.cz) using IT4I credentials
+and go to the **Projects** section.
+- **Users:** Please, submit your requests for becoming a
project member.
-- **Primary Investigators** Please, approve or deny users' requests
+- **Primary Investigators:** Please, approve or deny users' requests
in the same section.
### Authorization by e-mail (an alternative approach)
 In order to authorize a Collaborator to utilize the allocated
resources, the PI should contact the [IT4I
-support](https//support.it4i.cz/rt/) (E-mail [support
-[at] it4i.cz](mailtosupport%20%5Bat%5D%20it4i.cz)) and provide
-following information
+support](https://support.it4i.cz/rt/) (E-mail[support
+[at] it4i.cz](mailto:support%20%5Bat%5D%20it4i.cz)) and provide
+following information:
1. Identify your project by project ID
2. Provide list of people, including himself, who are authorized to use
the resources allocated to the project. The list must include full
@@ -53,8 +53,8 @@ following information
collaborator login access already exists on the IT4I systems.
3. Include "Authorization to IT4Innovations" into the subject line.
Example (except the subject line which must be in English, you may use
-Czech or Slovak language for communication with us)
- Subject Authorization to IT4Innovations
+Czech or Slovak language for communication with us):
+ SubjectAuthorization to IT4Innovations
Dear support,
Please include my collaborators to project OPEN-0-0.
John Smith, john.smith@myemail.com, Department of Chemistry, MIT, US
@@ -68,16 +68,16 @@ be** digitally signed. Read more on [digital
signatures](#the-certificates-for-digital-signatures)
below.
[]()The Login Credentials
--------------------------
+--
Once authorized by PI, every person (PI or Collaborator) wishing to
access the clusters, should contact the [IT4I
-support](https//support.it4i.cz/rt/) (E-mail [support
-[at] it4i.cz](mailtosupport%20%5Bat%5D%20it4i.cz)) providing
-following information
+support](https://support.it4i.cz/rt/) (E-mail[support
+[at] it4i.cz](mailto:support%20%5Bat%5D%20it4i.cz)) providing
+following information:
1. Project ID
2. Full name and affiliation
3. Statement that you have read and accepted the [Acceptable use policy
- document](http//www.it4i.cz/acceptable-use-policy.pdf) (AUP).
+ document](http://www.it4i.cz/acceptable-use-policy.pdf) (AUP).
4. Attach the AUP file.
5. Your preferred username, max 8 characters long. The preferred
username must associate your surname and name or be otherwise
@@ -88,13 +88,13 @@ following information
a **scan of photo ID** (personal ID or passport or driver license)
is required
Example (except the subject line which must be in English, you may use
-Czech or Slovak language for communication with us)
- Subject Access to IT4Innovations
+Czech or Slovak language for communication with us):
+ SubjectAccess to IT4Innovations
Dear support,
Please open the user account for me and attach the account to OPEN-0-0
- Name and affiliation John Smith, john.smith@myemail.com, Department of Chemistry, MIT, US
+ Name and affiliationJohn Smith, john.smith@myemail.com, Department of Chemistry, MIT, US
I have read and accept the Acceptable use policy document (attached)
- Preferred username johnsm
+ Preferred usernamejohnsm
Thank you,
John Smith
(Digitally signed)
@@ -109,57 +109,57 @@ sensitive information such as login credentials. After receiving your
signed e-mail with the requested information, we will send you your
login credentials (user name, key, passphrase and password) to access
the IT4I systems.
-
We accept certificates issued by any widely respected certification
authority.
**For various reasons we do not accept PGP keys.** Please, use only
X.509 PKI certificates for communication with us.
You will receive your personal login credentials by protected e-mail.
-The login credentials include
+The login credentials include:
1. username
2. ssh private key and private key passphrase
3. system password
The clusters are accessed by the [private
-key](../accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+key](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys)
and username.
Username and password is used for login to the information systems
-listed on .
+listed on <http://support.it4i.cz/>.
### Change Passphrase
On Linux, use
```
local $ ssh-keygen -f id_rsa -p
```
On Windows, use [PuTTY Key
-Generator](../accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.html).
+Generator](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen).
### Change Password
Change password in your user profile atÂ
+<https://extranet.it4i.cz/user/>
[]()The Certificates for Digital Signatures
--------------------------------------------
+--------------------
We accept personal certificates issued by any widely respected
certification authority (CA). This includes certificates by CAs
organized in International Grid Trust Federation
-(), its European branch EUGridPMA -
- and its member organizations, e.g. the
-CESNET certification authority - . The
+(<http://www.igtf.net/>), its European branch EUGridPMA -
+<https://www.eugridpma.org/> and its member organizations, e.g. the
+CESNET certification authority - <https://tcs-p.cesnet.cz/confusa/>. The
Czech *"Qualified certificate" (Kvalifikovaný certifikát)* (provided by
- or
-), that is used in
+<http://www.postsignum.cz/> or
+<http://www.ica.cz/Kvalifikovany-certifikat.aspx>), that is used in
electronic contact with Czech authorities is accepted as well.
-Certificate generation process is well-described here
+Certificate generation process is well-described here:
- [How to generate a personal TCS certificate in Mozilla Firefox web
browser
- (in Czech)](http//idoc.vsb.cz/xwiki/wiki/infra/view/uzivatel/moz-cert-gen)
+ (in Czech)](http://idoc.vsb.cz/xwiki/wiki/infra/view/uzivatel/moz-cert-gen)
Â
-A FAQ about certificates can be found here [Certificates
-FAQ](certificates-faq.html).
+A FAQ about certificates can be found here<span>[Certificates
+FAQ](https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq).</span>
[]()Alternative Way to Personal Certificate
--------------------------------------------
+--------------------
Follow these steps **only** if you can not obtain your certificate in a
standard way.
In case you choose this procedure, please attach a **scan of photo ID**
(personal ID or passport or drivers license) when applying for [login
credentials](#the-login-credentials).
-1. Go to .
+1. Go to <https://www.cacert.org/>.
- If there's a security warning, just acknowledge it.
2. Click *Join*.
3. Fill in the form and submit it by the *Next* button.
@@ -177,27 +177,27 @@ credentials](#the-login-credentials).
- Simultaneously you'll get an e-mail with a link to
the certificate.
Installation of the Certificate Into Your Mail Client
------------------------------------------------------
-The procedure is similar to the following guides
+-------
+The procedure is similar to the following guides:
- MS Outlook 2010
- [How to Remove, Import, and Export Digital
- Certificates](http//support.microsoft.com/kb/179380)
+ Certificates](http://support.microsoft.com/kb/179380)
- [Importing a PKCS #12 certificate
- (in Czech)](http//idoc.vsb.cz/xwiki/wiki/infra/view/uzivatel/outl-cert-imp)
+ (in Czech)](http://idoc.vsb.cz/xwiki/wiki/infra/view/uzivatel/outl-cert-imp)
- Mozilla Thudnerbird
- [Installing an SMIME
- certificate](http//kb.mozillazine.org/Installing_an_SMIME_certificate)
+ certificate](http://kb.mozillazine.org/Installing_an_SMIME_certificate)
- [Importing a PKCS #12 certificate
- (in Czech)](http//idoc.vsb.cz/xwiki/wiki/infra/view/uzivatel/moz-cert-imp)
+ (in Czech)](http://idoc.vsb.cz/xwiki/wiki/infra/view/uzivatel/moz-cert-imp)
End of User Account Lifecycle
------------------------------
+------
User accounts are supported by membership in active Project(s) or by
affiliation to IT4Innovations. User accounts, that loose the support
(meaning, are not attached to an active project and are not affiliated
with IT4I), will be deleted 1 year after the last project to which they
were attached expires.
User will get 3 automatically generated warning e-mail messages of the
-pending removal.
+pending removal:.
- First message will be sent 3 months before the removal
- Second message will be sent 1 month before the removal
- Third message will be sent 1 week before the removal.
diff --git a/heartbleed-bug.html b/docs.it4i.cz/heartbleed-bug.html
old mode 100755
new mode 100644
similarity index 76%
rename from heartbleed-bug.html
rename to docs.it4i.cz/heartbleed-bug.html
index 9c2e66364164c7b9f0a4d3936a3609b7490bcfa0..a12ed2497445248aaf45ca68a3da530304889286
--- a/heartbleed-bug.html
+++ b/docs.it4i.cz/heartbleed-bug.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/heartbleed-bug by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:03 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/heartbleed-bug" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/IEFixes-cachekey-ec9b60024fd235ff2c883b4b54db91cb.css" />
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- <link rel="stylesheet" type="text/css" href="portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
- <script type="text/javascript" src="portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
- <script type="text/javascript" src="portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
- <script type="text/javascript" src="portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Heartbleed bug — IT4I Docs</title>
- <link rel="canonical" href="heartbleed-bug.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/heartbleed-bug" />
- <link rel="shortcut icon" type="image/x-icon" href="favicon.ico" />
- <link rel="apple-touch-icon" href="touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="heartbleed-bug.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/heartbleed-bug#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="heartbleed-bug.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/heartbleed-bug#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="index.html">
- <img src="logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -314,7 +311,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -330,7 +327,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -346,7 +343,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -362,7 +359,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -378,7 +375,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -394,7 +391,7 @@
- <a title="" class="state-published contenttype-document" href="links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -410,7 +407,7 @@
- <a title="" class="state-published contenttype-collection" href="changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -426,7 +423,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -442,7 +439,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="heartbleed-bug.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/heartbleed-bug">
<span>Heartbleed bug</span>
</a>
@@ -481,14 +478,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -510,12 +507,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -531,7 +528,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/heartbleed-bug by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:03 GMT -->
</html>
diff --git a/heartbleed-bug.md b/docs.it4i.cz/heartbleed-bug.md
similarity index 50%
rename from heartbleed-bug.md
rename to docs.it4i.cz/heartbleed-bug.md
index 06e0c7ac8030aaed60f79bf4d267c6d7ce8b5e32..04dcdb6db0002f21d5597606595417fce82bfb6b 100644
--- a/heartbleed-bug.md
+++ b/docs.it4i.cz/heartbleed-bug.md
@@ -1,31 +1,39 @@
+Heartbleed bug
+==============
+
+Last update2014-04-16 12:20:32
+Introduction
+------------
A serious bug in the OpenSSL library, known as the "Heartbleed bug" has
been recently discovered.
The bug in OpenSSL library affected many sites worldwide for nearly two
-years. Although the Anselm cluster itself was exposed only for two
+years.<span> Although the Anselm cluster itself was exposed only for two
weeks and other systems for approximately three months, IT4I didn't take
this situation lightly and with full responsibility responded
-immediately. At this moment, there is no evidence that any abuse
+immediately.</span> At this moment, there is no evidence that any abuse
of data took place at IT4I.
-For more information about the Heartbleed bug, please see
+<span>For more information about the Heartbleed bug, please see:
+<http://heartbleed.com/></span>
Response
--------
-### OpenSSL fix
-IT4I has taken all necessary steps to fix the OpenSSL library on
-all it's systems.
-### Server keys change
+### <span>OpenSSL fix
+</span>
+<span>IT4I has taken all necessary steps to fix the OpenSSL library on
+all it's systems.</span>
+### <span>Server keys change</span>
Due to a safety preventive action, the fingerprint of Anselm login nodes
has changed.
You are advised to remove the deprecated fingerprint from your local SSH
-known_hosts file
+known_hosts file:
local $ ssh-keygen -R anselm.it4i.cz
local $ ssh-keygen -R login1.anselm.it4i.cz
local $ ssh-keygen -R login2.anselm.it4i.cz
local $ ssh-keygen -R 195.113.250.82
local $ ssh-keygen -R 195.113.250.83
-new fingerprints for both login nodes are
-
-class="monospace">29b3f464b073f56fa7850fe00dbe76bf (DSA)
-d46f5c18f43f70efbcfccc2bfd1336b7Â (RSA)
+new fingerprints for both login nodes are:
+<span
+class="monospace">29:b3:f4:64:b0:73:f5:6f:a7:85:0f:e0:0d:be:76:bf (DSA)
+d4:6f:5c:18:f4:3f:70:ef:bc:fc:cc:2b:fd:13:36:b7Â (RSA)</span>
You have to reconnect on Anselm to apply this change.
### Login credentials change
There is no evidence that any abuse of data took place at IT4I, however
@@ -35,3 +43,12 @@ In order to ensure the security and integrity of IT4I systems, all users
will be issued new login credentials, including password and ssh kyes.
We will use your original digital signatures to deliver the login
credential in a secure way.
+In case that you're using a new digital signature since getting access
+to Anselm, please let us know by writing to <span
+class="moz-txt-link-abbreviated">[support [at]
+it4i.cz](mailto:support%20%5Bat%5D%20it4i.cz){.email-link}</span> .
+Don't forget to digitally sign your message and please include the
+string "**Digital Signature Change**" in the subject line.
+We'll be collecting new digital signatures till Friday, 18th April.
+<span>[](http://heartbleed.com/){.moz-txt-link-freetext}</span>
+Â
diff --git a/get-started-with-it4innovations.html b/docs.it4i.cz/index.html
old mode 100755
new mode 100644
similarity index 74%
rename from get-started-with-it4innovations.html
rename to docs.it4i.cz/index.html
index b8d68e6f1fddac5570dc9b71ce12d7c9032e6ed5..c23de28b32b87cedea94bc7e173bed7d6f650b65
--- a/get-started-with-it4innovations.html
+++ b/docs.it4i.cz/index.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/get-started-with-it4innovations/introduction" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/IEFixes-cachekey-ec9b60024fd235ff2c883b4b54db91cb.css" />
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- <link rel="stylesheet" type="text/css" href="portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
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- <script type="text/javascript" src="portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
- <script type="text/javascript" src="portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Documentation — IT4I Docs</title>
- <link rel="canonical" href="get-started-with-it4innovations.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/get-started-with-it4innovations" />
- <link rel="shortcut icon" type="image/x-icon" href="favicon.ico" />
- <link rel="apple-touch-icon" href="touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="get-started-with-it4innovations.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/get-started-with-it4innovations#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="get-started-with-it4innovations.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/get-started-with-it4innovations#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="index.html">
- <img src="logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -220,7 +217,7 @@
<div id="parent-fieldname-text-7c82cccbb7c34932b6b2a934ad0f971a" class="">
- <p>Welcome to IT4Innovations documentation pages. The IT4Innovations national supercomputing center operates supercomputers <a target="_self" title="" class="internal-link" href="salomon.html">Salomon</a> and <a target="_self" title="" class="internal-link" href="anselm-cluster-documentation.html">Anselm</a>. The supercomputers are <a target="_self" title="" class="internal-link" href="get-started-with-it4innovations/applying-for-resources.html"><span class="external-link">available</span></a> to academic community within the Czech Republic and Europe and industrial community worldwide. The purpose of these pages is to provide a comprehensive documentation on hardware, software and usage of the computers.</p>
+ <p>Welcome to IT4Innovations documentation pages. The IT4Innovations national supercomputing center operates supercomputers <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon">Salomon</a> and <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation">Anselm</a>. The supercomputers are <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources"><span class="external-link">available</span></a> to academic community within the Czech Republic and Europe and industrial community worldwide. The purpose of these pages is to provide a comprehensive documentation on hardware, software and usage of the computers.</p>
<h2><span class="link-external"><span class="WYSIWYG_LINK">How to read the documentation</span></span></h2>
<ol>
<li>Read the list in the left column. Select the subject of interest. Alternatively, use the Search box in the upper right corner.</li>
@@ -232,7 +229,7 @@
<p class="callout">The call-out. Â Focus on the call-outs before reading full details.</p>
<p>Â </p>
<ul>
-<li>Read the <a target="_self" title="" class="external-link" href="get-started-with-it4innovations/changelog.html">Changelog</a> to keep up to date.</li>
+<li>Read the <a title="" class="external-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/changelog">Changelog</a> to keep up to date.</li>
</ul>
<h2 class=" ">Getting Help and Support</h2>
<p class="callout" title="">Contact <a class="email-link" href="mailto:support%20[at]%20it4i.cz" target="_self" title="">support [at] it4i.cz</a> for help and support regarding the cluster technology at IT4Innovations.<br />Please use <strong>Czech</strong>, <strong>Slovak</strong> or <strong>English</strong> language for communication with us.<br />Follow the status of your request to IT4Innovations at <a class="external-link" href="http://support.it4i.cz/rt" target="_self" title="">support.it4i.cz/rt</a>.</p>
@@ -245,7 +242,7 @@
<p>Â </p>
<p class="callout">Learn how to parallelize your code!</p>
<p>Â </p>
-<p>In many cases, you will run your own code on the cluster. In order to fully exploit the cluster, you will need to carefully consider how to utilize all the cores available on the node and how to use multiple nodes at the same time. You need to <b>parallelize</b> your code. Proficieny in MPI, OpenMP, CUDA, UPC or GPI2 programming may be gained via the <a class="external-link" href="http://prace.it4i.cz/" target="_self" title="">training provided by IT4Innovations.</a></p>
+<p>In many cases, you will run your own code on the cluster. In order to fully exploit the cluster, you will need to carefully consider how to utilize all the cores available on the node and how to use multiple nodes at the same time. You need to <b>parallelize</b> your code. Proficieny in MPI, OpenMP, CUDA, UPC or GPI2 programming may be gained via the <a class="external-link" href="http://prace.it4i.cz" target="_self" title="">training provided by IT4Innovations.</a></p>
<h2 class=" ">Terminology Frequently Used on These Pages</h2>
<ul>
<ul>
@@ -327,7 +324,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -343,7 +340,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -359,7 +356,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="get-started-with-it4innovations.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -375,7 +372,7 @@
- <a title="" class="state-published contenttype-document" href="get-started-with-it4innovations/applying-for-resources.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources">
<span>Applying for Resources</span>
</a>
@@ -391,7 +388,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="get-started-with-it4innovations/obtaining-login-credentials.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">
<span>Obtaining Login Credentials</span>
</a>
@@ -407,7 +404,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">
<span>Accessing the Clusters</span>
</a>
@@ -432,7 +429,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -448,7 +445,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -464,7 +461,7 @@
- <a title="" class="state-published contenttype-document" href="links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -480,7 +477,7 @@
- <a title="" class="state-published contenttype-collection" href="changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -496,7 +493,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -535,14 +532,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -564,12 +561,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -585,7 +582,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/get-started-with-it4innovations by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:15:25 GMT -->
</html>
diff --git a/get-started-with-it4innovations/introduction.md b/docs.it4i.cz/index.md
similarity index 57%
rename from get-started-with-it4innovations/introduction.md
rename to docs.it4i.cz/index.md
index ee46a991d6bc5546055712bc52441934a47bdf76..2fadd6e75b803ba9888700875e5380c7026bf290 100644
--- a/get-started-with-it4innovations/introduction.md
+++ b/docs.it4i.cz/index.md
@@ -1,13 +1,18 @@
-[Salomon](../salomon.html) and
-[Anselm](../anselm-cluster-documentation.html). The
-supercomputers are [
-class="external-link">available](applying-for-resources.html)
+Documentation
+=============
+
+Welcome to IT4Innovations documentation pages. The IT4Innovations
+national supercomputing center operates supercomputers
+[Salomon](https://docs.it4i.cz/salomon) and
+[Anselm](https://docs.it4i.cz/anselm-cluster-documentation).
+The supercomputers are [<span
+class="external-link">available</span>](https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources)
to academic community within the Czech Republic and Europe and
industrial community worldwide. The purpose of these pages is to provide
a comprehensive documentation on hardware, software and usage of the
computers.
-How to read the documentation
---------------------------------------------------------------------------------------------------
+<span class="link-external"><span class="WYSIWYG_LINK">How to read the documentation</span></span>
+------
1. Read the list in the left column. Select the subject of interest.
Alternatively, use the Search box in the upper right corner.
2. Read the CONTENTS in the upper right corner.
@@ -17,31 +22,32 @@ How to read the documentation
Â
The call-out. Â Focus on the call-outs before reading full details.
Â
-- Read the [Changelog](changelog.html) to keep up
- to date.
+- Read the
+ [Changelog](https://docs.it4i.cz/get-started-with-it4innovations/changelog)
+ to keep up to date.
Getting Help and Support
-------------------------
+-
Contact [support [at]
-it4i.cz](mailtosupport%20%5Bat%5D%20it4i.cz){.email-link} for help and
+it4i.cz](mailto:support%20%5Bat%5D%20it4i.cz){.email-link} for help and
support regarding the cluster technology at IT4Innovations.
Please use **Czech**, **Slovak** or **English** language for
communication with us.
Follow the status of your request to IT4Innovations at
-[support.it4i.cz/rt](http//support.it4i.cz/rt).
+[support.it4i.cz/rt](http://support.it4i.cz/rt).
Â
Use your IT4Innotations username and password to log in to the
-[support](http//support.it4i.cz/) portal.
+[support](http://support.it4i.cz/) portal.
Required Proficiency
--------------------
You need basic proficiency in Linux environment.
Â
In order to use the system for your calculations, you need basic
proficiency in Linux environment. To gain the proficiency, we recommend
-you reading the [introduction to
-Linux](http//www.tldp.org/LDP/intro-linux/html/)
+you reading the [<span class="WYSIWYG_LINK">introduction to
+Linux</span>](http://www.tldp.org/LDP/intro-linux/html/)
operating system environment and installing a Linux distribution on your
-personal computer. A good choice might be the [
-class="WYSIWYG_LINK">Fedora](http//fedoraproject.org/)
+personal computer. A good choice might be the [<span
+class="WYSIWYG_LINK">Fedora</span>](http://fedoraproject.org/)
distribution, as it is similar to systems on the clusters at
IT4Innovations. It's easy to install and use. In fact, any distribution
would do.
@@ -54,40 +60,39 @@ utilize all the cores available on the node and how to use multiple
nodes at the same time. You need to **parallelize** your code.
Proficieny in MPI, OpenMP, CUDA, UPC or GPI2 programming may be gained
via the [training provided by
-IT4Innovations.](http//prace.it4i.cz/)
+IT4Innovations.](http://prace.it4i.cz)
Terminology Frequently Used on These Pages
-------------------------------------------
-- **node** a computer, interconnected by network to other computers -
+-------------------
+- **node:** a computer, interconnected by network to other computers -
Computational nodes are powerful computers, designed and dedicated
for executing demanding scientific computations.
-- **core** processor core, a unit of processor, executing
+- **core:** processor core, a unit of processor, executing
computations
-- **corehours** wall clock hours of processor core time - Each node
+- **corehours:** wall clock hours of processor core time - Each node
is equipped with **X** processor cores, provides **X** corehours per
1 wall clock hour.
-- **[]()job** a calculation running on the supercomputer - The job
+- **[]()job:** a calculation running on the supercomputer - The job
allocates and utilizes resources of the supercomputer for
certain time.
-- **HPC** High Performance Computing
-- []()**HPC (computational) resources** corehours, storage capacity,
+- **HPC:** High Performance Computing
+- []()**HPC (computational) resources:** corehours, storage capacity,
software licences
-- **code** a program
-- **primary investigator (PI)** a person responsible for execution of
+- **code:** a program
+- **primary investigator (PI):** a person responsible for execution of
computational project and utilization of computational resources
allocated to that project
-- **collaborator** a person participating on execution of
+- **collaborator:** a person participating on execution of
computational project and utilization of computational resources
allocated to that project
-- **[]()project** a computational project under investigation by the
+- **[]()project:** a computational project under investigation by the
PI - The project is identified by the project ID. The computational
resources are allocated and charged per project.
-- **[]()jobscript** a script to be executed by the PBS Professional
+- **[]()jobscript:** a script to be executed by the PBS Professional
workload manager
Conventions
-----------
In this documentation, you will find a number of pages containing
-examples. We use the following conventions
-
+examples. We use the following conventions:
 Cluster command prompt
``` {.prettyprint .lang-sh}
$
@@ -101,3 +106,9 @@ local $
Although we have taken every care to ensure the accuracy of our content,
mistakes do happen. If you find a mistake in the text or the code we
would be grateful if you would report this to us. By doing so, you can
+save other readers from frustration and help us improve subsequent
+versions of this documentation. If you find any errata, please report
+them by visiting http://support.it4i.cz/rt, creating a new ticket, and
+entering the details of your errata. Once your errata are verified, your
+submission will be accepted and the errata will be uploaded on our
+website.
diff --git a/links.html b/docs.it4i.cz/links.html
old mode 100755
new mode 100644
similarity index 71%
rename from links.html
rename to docs.it4i.cz/links.html
index 7d67720efc0e5f57f4d8603c1c7893410b17d299..972bdd725a44cc60825254ca3791cd0ac075ad07
--- a/links.html
+++ b/docs.it4i.cz/links.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/links by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:39 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/links" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/IEFixes-cachekey-ec9b60024fd235ff2c883b4b54db91cb.css" />
<![endif]-->
- <style type="text/css" media="screen">@import url(portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
- <link rel="stylesheet" type="text/css" href="portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
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- <script type="text/javascript" src="portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
- <script type="text/javascript" src="portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Links — IT4I Docs</title>
- <link rel="canonical" href="links.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/links" />
- <link rel="shortcut icon" type="image/x-icon" href="favicon.ico" />
- <link rel="apple-touch-icon" href="touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="links.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/links#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="links.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/links#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="index.html">
- <img src="logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -222,9 +219,9 @@
<div id="parent-fieldname-text-793e3fd3bf314b3dbab91a34e2cfc22e" class="">
<ul>
<li><span class="WYSIWYG_LINK"><a class="external-link" href="http://www.it4i.cz/?lang=en" target="_self" title="">IT4Innovations</a></span></li>
-<li><span class="WYSIWYG_LINK"><a class="external-link" href="http://www.vsb.cz/" target="_self" title="">VSB-Technical university of Ostrava</a><br /></span></li>
-<li><span class="WYSIWYG_LINK"><a class="external-link" href="http://www.prace-ri.eu/" target="_self" title="">PRACE</a></span></li>
-<li><span class="WYSIWYG_LINK"><a class="external-link" href="http://www.cesnet.cz/" target="_self" title="">CESNET</a><br /></span></li>
+<li><span class="WYSIWYG_LINK"><a class="external-link" href="http://www.vsb.cz" target="_self" title="">VSB-Technical university of Ostrava</a><br /></span></li>
+<li><span class="WYSIWYG_LINK"><a class="external-link" href="http://www.prace-ri.eu" target="_self" title="">PRACE</a></span></li>
+<li><span class="WYSIWYG_LINK"><a class="external-link" href="http://www.cesnet.cz" target="_self" title="">CESNET</a><br /></span></li>
<li><a class="external-link" href="http://www.tldp.org/LDP/intro-linux/html/" target="_self" title=""><span class="WYSIWYG_LINK">Introduction to Linux</span></a> <a class="external-link" href="http://www.tldp.org/LDP/intro-linux/html/" target="_self" title=""><span class="WYSIWYG_LINK">(TLDP</span></a>)</li>
</ul>
<p><span class="WYSIWYG_LINK"><br /></span></p>
@@ -303,7 +300,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -319,7 +316,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -335,7 +332,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -351,7 +348,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -367,7 +364,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -383,7 +380,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="links.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -399,7 +396,7 @@
- <a title="" class="state-published contenttype-collection" href="changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -415,7 +412,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -454,14 +451,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -483,12 +480,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -504,7 +501,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/docs.it4i.cz/links.md b/docs.it4i.cz/links.md
new file mode 100644
index 0000000000000000000000000000000000000000..45bd97354f9de1bea558c8b300d7f30d0a8f8538
--- /dev/null
+++ b/docs.it4i.cz/links.md
@@ -0,0 +1,19 @@
+Links
+=====
+
+- <span
+ class="WYSIWYG_LINK">[IT4Innovations](http://www.it4i.cz/?lang=en)</span>
+- <span class="WYSIWYG_LINK">[VSB-Technical university of
+ Ostrava](http://www.vsb.cz)
+ </span>
+- <span
+ class="WYSIWYG_LINK">[PRACE](http://www.prace-ri.eu)</span>
+- <span
+ class="WYSIWYG_LINK">[CESNET](http://www.cesnet.cz)
+ </span>
+- [<span class="WYSIWYG_LINK">Introduction to
+ Linux</span>](http://www.tldp.org/LDP/intro-linux/html/)
+ [<span
+ class="WYSIWYG_LINK">(TLDP</span>](http://www.tldp.org/LDP/intro-linux/html/))
+<span class="WYSIWYG_LINK">
+</span>
diff --git a/login.js b/docs.it4i.cz/login.js
old mode 100755
new mode 100644
similarity index 100%
rename from login.js
rename to docs.it4i.cz/login.js
diff --git a/logo.png b/docs.it4i.cz/logo.png
old mode 100755
new mode 100644
similarity index 100%
rename from logo.png
rename to docs.it4i.cz/logo.png
diff --git a/pbspro-documentation.html b/docs.it4i.cz/pbspro-documentation.html
old mode 100755
new mode 100644
similarity index 66%
rename from pbspro-documentation.html
rename to docs.it4i.cz/pbspro-documentation.html
index c184ab07e704fd5a4c3d9a67308457a27e5b9d0d..c09f03eccd6c2f36db95a498effa7cb621cab1bc
--- a/pbspro-documentation.html
+++ b/docs.it4i.cz/pbspro-documentation.html
@@ -10,45 +10,42 @@
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-<!-- Mirrored from docs.it4i.cz/pbspro-documentation by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:39 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/pbspro-documentation/" /><!--[if lt IE 7]></base><![endif]-->
<meta content="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" name="description" />
- <link rel="stylesheet" type="text/css" media="screen" href="portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>PBSPro Documentation — IT4I Docs</title>
- <link rel="canonical" href="pbspro-documentation.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/pbspro-documentation" />
- <link rel="shortcut icon" type="image/x-icon" href="favicon.ico" />
- <link rel="apple-touch-icon" href="touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="pbspro-documentation.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/pbspro-documentation#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="pbspro-documentation.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/pbspro-documentation#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
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</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="index.html">
- <img src="logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -228,8 +225,8 @@
<dt class="">
<span class="summary">
- <img width="16" height="16" src="pdf.png" alt="Soubor" />
- <a href="pbspro-documentation/pbspro-programmers-guide/view.html" class="contenttype-file state-missing-value url">PBSPro Programmer's Guide</a>
+ <img width="16" height="16" src="https://docs.it4i.cz/pdf.png" alt="Soubor" />
+ <a href="https://docs.it4i.cz/pbspro-documentation/pbspro-programmers-guide/view" class="contenttype-file state-missing-value url">PBSPro Programmer's Guide</a>
</span>
<span class="documentByLine">
@@ -254,8 +251,8 @@
<dt class="">
<span class="summary">
- <img width="16" height="16" src="pdf.png" alt="Soubor" />
- <a href="pbspro-documentation/pbspro-quick-start-guide/view.html" class="contenttype-file state-missing-value url">PBSPro Quick Start Guide</a>
+ <img width="16" height="16" src="https://docs.it4i.cz/pdf.png" alt="Soubor" />
+ <a href="https://docs.it4i.cz/pbspro-documentation/pbspro-quick-start-guide/view" class="contenttype-file state-missing-value url">PBSPro Quick Start Guide</a>
</span>
<span class="documentByLine">
@@ -280,8 +277,8 @@
<dt class="">
<span class="summary">
- <img width="16" height="16" src="pdf.png" alt="Soubor" />
- <a href="pbspro-documentation/pbspro-reference-guide/view.html" class="contenttype-file state-missing-value url">PBSPro Reference Guide</a>
+ <img width="16" height="16" src="https://docs.it4i.cz/pdf.png" alt="Soubor" />
+ <a href="https://docs.it4i.cz/pbspro-documentation/pbspro-reference-guide/view" class="contenttype-file state-missing-value url">PBSPro Reference Guide</a>
</span>
<span class="documentByLine">
@@ -306,8 +303,8 @@
<dt class="">
<span class="summary">
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- <a href="pbspro-documentation/pbspro-users-guide/view.html" class="contenttype-file state-missing-value url">PBSPro User's Guide</a>
+ <img width="16" height="16" src="https://docs.it4i.cz/pdf.png" alt="Soubor" />
+ <a href="https://docs.it4i.cz/pbspro-documentation/pbspro-users-guide/view" class="contenttype-file state-missing-value url">PBSPro User's Guide</a>
</span>
<span class="documentByLine">
@@ -392,7 +389,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -408,7 +405,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -424,7 +421,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -440,7 +437,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -456,7 +453,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -472,7 +469,7 @@
- <a title="" class="state-published contenttype-document" href="links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -488,7 +485,7 @@
- <a title="" class="state-published contenttype-collection" href="changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -504,7 +501,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="pbspro-documentation.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -520,8 +517,8 @@
- <a title="Version 12." class="state-missing-value contenttype-file" href="pbspro-documentation/pbspro-programmers-guide/view.html">
- <img width="16" height="16" src="pdf.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="Version 12." href="https://docs.it4i.cz/pbspro-documentation/pbspro-programmers-guide/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/pdf.png" alt="Soubor" />
<span>PBSPro Programmer's Guide</span>
</a>
@@ -536,8 +533,8 @@
- <a title="Version 12." class="state-missing-value contenttype-file" href="pbspro-documentation/pbspro-quick-start-guide/view.html">
- <img width="16" height="16" src="pdf.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="Version 12." href="https://docs.it4i.cz/pbspro-documentation/pbspro-quick-start-guide/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/pdf.png" alt="Soubor" />
<span>PBSPro Quick Start Guide</span>
</a>
@@ -552,8 +549,8 @@
- <a title="Version 12." class="state-missing-value contenttype-file" href="pbspro-documentation/pbspro-reference-guide/view.html">
- <img width="16" height="16" src="pdf.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="Version 12." href="https://docs.it4i.cz/pbspro-documentation/pbspro-reference-guide/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/pdf.png" alt="Soubor" />
<span>PBSPro Reference Guide</span>
</a>
@@ -568,8 +565,8 @@
- <a title="Version 12." class="state-missing-value contenttype-file" href="pbspro-documentation/pbspro-users-guide/view.html">
- <img width="16" height="16" src="pdf.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="Version 12." href="https://docs.it4i.cz/pbspro-documentation/pbspro-users-guide/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/pdf.png" alt="Soubor" />
<span>PBSPro User's Guide</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
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+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -645,12 +642,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -666,8 +663,6 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
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</html>
diff --git a/docs.it4i.cz/pbspro-documentation.md b/docs.it4i.cz/pbspro-documentation.md
new file mode 100644
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old mode 100755
new mode 100644
similarity index 100%
rename from pbspro-documentation/PBSProProgramGuide12.pdf
rename to docs.it4i.cz/pbspro-documentation/pbspro-programmers-guide.1
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old mode 100755
new mode 100644
similarity index 100%
rename from pbspro-documentation/pbspro-programmers-guide/at_download/PBSProProgramGuide12.pdf
rename to docs.it4i.cz/pbspro-documentation/pbspro-programmers-guide/at_download/file
diff --git a/pbspro-documentation/pbspro-programmers-guide/view.html b/docs.it4i.cz/pbspro-documentation/pbspro-programmers-guide/view.html
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<title>PBSPro Quick Start Guide — IT4I Docs</title>
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- <a accesskey="6" href="view.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
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- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
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@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../pbspro-documentation.html">PBSPro Documentation</a>
+ <a href="https://docs.it4i.cz/pbspro-documentation">PBSPro Documentation</a>
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/
@@ -232,8 +229,8 @@
- <a href="at_download/PBSProQuickStartGuide12.pdf">
- <img src="../../pdf.png" alt="PDF document icon" />
+ <a href="https://docs.it4i.cz/pbspro-documentation/pbspro-quick-start-guide/at_download/file">
+ <img src="https://docs.it4i.cz/pdf.png" alt="PDF document icon" />
PBSProQuickStartGuide12.pdf
</a>
<span class="discreet">
@@ -295,7 +292,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -311,7 +308,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -327,7 +324,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -343,7 +340,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -359,7 +356,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -375,7 +372,7 @@
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<span>Links</span>
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@@ -391,7 +388,7 @@
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+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
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- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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+ <img width="16" height="16" src="https://docs.it4i.cz/pdf.png" alt="Soubor" />
<span>PBSPro Programmer's Guide</span>
</a>
@@ -439,8 +436,8 @@
- <a title="Version 12." class="state-missing-value navTreeCurrentItem navTreeCurrentNode contenttype-file" href="view.html">
- <img width="16" height="16" src="../../pdf.png" alt="Soubor" />
+ <a class="state-missing-value navTreeCurrentItem navTreeCurrentNode contenttype-file" title="Version 12." href="https://docs.it4i.cz/pbspro-documentation/pbspro-quick-start-guide/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/pdf.png" alt="Soubor" />
<span>PBSPro Quick Start Guide</span>
</a>
@@ -455,8 +452,8 @@
- <a title="Version 12." class="state-missing-value contenttype-file" href="../pbspro-reference-guide/view.html">
- <img width="16" height="16" src="../../pdf.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="Version 12." href="https://docs.it4i.cz/pbspro-documentation/pbspro-reference-guide/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/pdf.png" alt="Soubor" />
<span>PBSPro Reference Guide</span>
</a>
@@ -471,8 +468,8 @@
- <a title="Version 12." class="state-missing-value contenttype-file" href="../pbspro-users-guide/view.html">
- <img width="16" height="16" src="../../pdf.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="Version 12." href="https://docs.it4i.cz/pbspro-documentation/pbspro-users-guide/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/pdf.png" alt="Soubor" />
<span>PBSPro User's Guide</span>
</a>
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_paq.push(['enableLinkTracking']);
(function() {
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</html>
diff --git a/docs.it4i.cz/pbspro-documentation/pbspro-quick-start-guide/view.md b/docs.it4i.cz/pbspro-documentation/pbspro-quick-start-guide/view.md
new file mode 100644
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diff --git a/pbspro-documentation/PBSProRefGuide12.pdf b/docs.it4i.cz/pbspro-documentation/pbspro-reference-guide.1
old mode 100755
new mode 100644
similarity index 100%
rename from pbspro-documentation/PBSProRefGuide12.pdf
rename to docs.it4i.cz/pbspro-documentation/pbspro-reference-guide.1
diff --git a/pbspro-documentation/pbspro-reference-guide/at_download/PBSProRefGuide12.pdf b/docs.it4i.cz/pbspro-documentation/pbspro-reference-guide/at_download/file
old mode 100755
new mode 100644
similarity index 100%
rename from pbspro-documentation/pbspro-reference-guide/at_download/PBSProRefGuide12.pdf
rename to docs.it4i.cz/pbspro-documentation/pbspro-reference-guide/at_download/file
diff --git a/pbspro-documentation/pbspro-reference-guide/view.html b/docs.it4i.cz/pbspro-documentation/pbspro-reference-guide/view.html
old mode 100755
new mode 100644
similarity index 66%
rename from pbspro-documentation/pbspro-reference-guide/view.html
rename to docs.it4i.cz/pbspro-documentation/pbspro-reference-guide/view.html
index 7dec111d833904ad51c09d7aafdecbea71fbdb5b..1249d057b2259d29621a3fa3fb23562e5ba0ea17
--- a/pbspro-documentation/pbspro-reference-guide/view.html
+++ b/docs.it4i.cz/pbspro-documentation/pbspro-reference-guide/view.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/pbspro-documentation/pbspro-reference-guide" /><!--[if lt IE 7]></base><![endif]-->
<meta content="Version 12." name="description" />
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<title>PBSPro Reference Guide — IT4I Docs</title>
- <link rel="canonical" href="../PBSProRefGuide12.pdf" />
+ <link rel="canonical" href="https://docs.it4i.cz/pbspro-documentation/pbspro-reference-guide" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="view.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/pbspro-documentation/pbspro-reference-guide/view#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="view.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/pbspro-documentation/pbspro-reference-guide/view#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
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- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../pbspro-documentation.html">PBSPro Documentation</a>
+ <a href="https://docs.it4i.cz/pbspro-documentation">PBSPro Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -232,8 +229,8 @@
- <a href="at_download/PBSProRefGuide12.pdf">
- <img src="../../pdf.png" alt="PDF document icon" />
+ <a href="https://docs.it4i.cz/pbspro-documentation/pbspro-reference-guide/at_download/file">
+ <img src="https://docs.it4i.cz/pdf.png" alt="PDF document icon" />
PBSProRefGuide12.pdf
</a>
<span class="discreet">
@@ -295,7 +292,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -311,7 +308,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -327,7 +324,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -343,7 +340,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -359,7 +356,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -375,7 +372,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -391,7 +388,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
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- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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- <a title="Version 12." class="state-missing-value contenttype-file" href="../pbspro-programmers-guide/view.html">
- <img width="16" height="16" src="../../pdf.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="Version 12." href="https://docs.it4i.cz/pbspro-documentation/pbspro-programmers-guide/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/pdf.png" alt="Soubor" />
<span>PBSPro Programmer's Guide</span>
</a>
@@ -439,8 +436,8 @@
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- <img width="16" height="16" src="../../pdf.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="Version 12." href="https://docs.it4i.cz/pbspro-documentation/pbspro-quick-start-guide/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/pdf.png" alt="Soubor" />
<span>PBSPro Quick Start Guide</span>
</a>
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- <a title="Version 12." class="state-missing-value navTreeCurrentItem navTreeCurrentNode contenttype-file" href="view.html">
- <img width="16" height="16" src="../../pdf.png" alt="Soubor" />
+ <a class="state-missing-value navTreeCurrentItem navTreeCurrentNode contenttype-file" title="Version 12." href="https://docs.it4i.cz/pbspro-documentation/pbspro-reference-guide/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/pdf.png" alt="Soubor" />
<span>PBSPro Reference Guide</span>
</a>
@@ -471,8 +468,8 @@
- <a title="Version 12." class="state-missing-value contenttype-file" href="../pbspro-users-guide/view.html">
- <img width="16" height="16" src="../../pdf.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="Version 12." href="https://docs.it4i.cz/pbspro-documentation/pbspro-users-guide/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/pdf.png" alt="Soubor" />
<span>PBSPro User's Guide</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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<title>PBSPro User's Guide — IT4I Docs</title>
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-144px}.ui-icon-bullet{background-position:-80px -144px}.ui-icon-radio-on{background-position:-96px -144px}.ui-icon-radio-off{background-position:-112px -144px}.ui-icon-pin-w{background-position:-128px -144px}.ui-icon-pin-s{background-position:-144px -144px}.ui-icon-play{background-position:0 -160px}.ui-icon-pause{background-position:-16px -160px}.ui-icon-seek-next{background-position:-32px -160px}.ui-icon-seek-prev{background-position:-48px -160px}.ui-icon-seek-end{background-position:-64px -160px}.ui-icon-seek-start{background-position:-80px -160px}.ui-icon-seek-first{background-position:-80px -160px}.ui-icon-stop{background-position:-96px -160px}.ui-icon-eject{background-position:-112px -160px}.ui-icon-volume-off{background-position:-128px -160px}.ui-icon-volume-on{background-position:-144px -160px}.ui-icon-power{background-position:0 -176px}.ui-icon-signal-diag{background-position:-16px -176px}.ui-icon-signal{background-position:-32px -176px}.ui-icon-battery-0{background-position:-48px -176px}.ui-icon-battery-1{background-position:-64px -176px}.ui-icon-battery-2{background-position:-80px -176px}.ui-icon-battery-3{background-position:-96px -176px}.ui-icon-circle-plus{background-position:0 -192px}.ui-icon-circle-minus{background-position:-16px -192px}.ui-icon-circle-close{background-position:-32px -192px}.ui-icon-circle-triangle-e{background-position:-48px -192px}.ui-icon-circle-triangle-s{background-position:-64px -192px}.ui-icon-circle-triangle-w{background-position:-80px -192px}.ui-icon-circle-triangle-n{background-position:-96px -192px}.ui-icon-circle-arrow-e{background-position:-112px -192px}.ui-icon-circle-arrow-s{background-position:-128px -192px}.ui-icon-circle-arrow-w{background-position:-144px -192px}.ui-icon-circle-arrow-n{background-position:-160px -192px}.ui-icon-circle-zoomin{background-position:-176px -192px}.ui-icon-circle-zoomout{background-position:-192px -192px}.ui-icon-circle-check{background-position:-208px -192px}.ui-icon-circlesmall-plus{background-position:0 -208px}.ui-icon-circlesmall-minus{background-position:-16px -208px}.ui-icon-circlesmall-close{background-position:-32px -208px}.ui-icon-squaresmall-plus{background-position:-48px -208px}.ui-icon-squaresmall-minus{background-position:-64px -208px}.ui-icon-squaresmall-close{background-position:-80px -208px}.ui-icon-grip-dotted-vertical{background-position:0 -224px}.ui-icon-grip-dotted-horizontal{background-position:-16px -224px}.ui-icon-grip-solid-vertical{background-position:-32px -224px}.ui-icon-grip-solid-horizontal{background-position:-48px -224px}.ui-icon-gripsmall-diagonal-se{background-position:-64px -224px}.ui-icon-grip-diagonal-se{background-position:-80px -224px}.ui-corner-all,.ui-corner-top,.ui-corner-left,.ui-corner-tl{border-top-left-radius:5px}.ui-corner-all,.ui-corner-top,.ui-corner-right,.ui-corner-tr{border-top-right-radius:5px}.ui-corner-all,.ui-corner-bottom,.ui-corner-left,.ui-corner-bl{border-bottom-left-radius:5px}.ui-corner-all,.ui-corner-bottom,.ui-corner-right,.ui-corner-br{border-bottom-right-radius:5px}.ui-widget-overlay{background:#aaa url(/++resource++jquery-ui-themes/sunburst/images/ui-bg_flat_75_aaaaaa_40x100.png) 50% 50% repeat-x;opacity:.3;filter:Alpha(Opacity=30)}.ui-widget-shadow{margin:5px 0 0 5px;padding:0;background:#999 url(/++resource++jquery-ui-themes/sunburst/images/ui-bg_flat_55_999999_40x100.png) 50% 50% repeat-x;opacity:.45;filter:Alpha(Opacity=45);border-radius:5px}
/* */
#content .ui-state-default a, #content .ui-state-default a:link, #content .ui-state-default a:visited,
dl.portlet .ui-state-default a, dl.portlet .ui-state-default a:link, dl.portlet .ui-state-default a:visited,
diff --git a/portal_css/Sunburst Theme/contenttypes-sprite.png b/docs.it4i.cz/portal_css/Sunburst Theme/contenttypes-sprite.png
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diff --git a/portal_css/Sunburst Theme/link_icon.png b/docs.it4i.cz/portal_css/Sunburst Theme/link_icon.png
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diff --git a/portal_css/Sunburst Theme/link_icon_external.png b/docs.it4i.cz/portal_css/Sunburst Theme/link_icon_external.png
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rename from portal_css/Sunburst Theme/link_icon_external.png
rename to docs.it4i.cz/portal_css/Sunburst Theme/link_icon_external.png
diff --git a/portal_css/Sunburst Theme/pb_close.png b/docs.it4i.cz/portal_css/Sunburst Theme/pb_close.png
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rename from portal_css/Sunburst Theme/pb_close.png
rename to docs.it4i.cz/portal_css/Sunburst Theme/pb_close.png
diff --git a/portal_css/Sunburst Theme/polaroid-multi.png b/docs.it4i.cz/portal_css/Sunburst Theme/polaroid-multi.png
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rename to docs.it4i.cz/portal_css/Sunburst Theme/polaroid-multi.png
diff --git a/portal_css/Sunburst Theme/polaroid-single.png b/docs.it4i.cz/portal_css/Sunburst Theme/polaroid-single.png
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diff --git a/portal_css/Sunburst Theme/required.png b/docs.it4i.cz/portal_css/Sunburst Theme/required.png
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diff --git a/portal_css/Sunburst Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css b/docs.it4i.cz/portal_css/Sunburst Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css
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rename to docs.it4i.cz/portal_css/Sunburst Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css
diff --git a/portal_css/Sunburst Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css b/docs.it4i.cz/portal_css/Sunburst Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css
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rename to docs.it4i.cz/portal_css/Sunburst Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css
diff --git a/docs.it4i.cz/portal_css/Sunburst Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css b/docs.it4i.cz/portal_css/Sunburst Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css
new file mode 100644
index 0000000000000000000000000000000000000000..4a0605e49f3cb300a2e74ec50d762e1bc9c1c192
--- /dev/null
+++ b/docs.it4i.cz/portal_css/Sunburst Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css
@@ -0,0 +1,395 @@
+
+/* - ++resource++it4i.portal.common/jquery.dataTables.min.css - */
+@media screen {
+table.dataTable{width:100%;margin:0 auto;clear:both;border-collapse:separate;border-spacing:0}table.dataTable thead th,table.dataTable tfoot th{font-weight:bold}table.dataTable thead th,table.dataTable thead td{padding:10px 18px;border-bottom:1px solid #111}table.dataTable thead th:active,table.dataTable thead td:active{outline:none}table.dataTable tfoot th,table.dataTable tfoot td{padding:10px 18px 6px 18px;border-top:1px solid #111}table.dataTable thead .sorting_asc,table.dataTable thead .sorting_desc,table.dataTable thead .sorting{cursor:pointer;*cursor:hand}table.dataTable thead .sorting{background:url("../images/sort_both.png") no-repeat center right}table.dataTable thead .sorting_asc{background:url("../images/sort_asc.png") no-repeat center right}table.dataTable thead .sorting_desc{background:url("../images/sort_desc.png") no-repeat center right}table.dataTable thead .sorting_asc_disabled{background:url("../images/sort_asc_disabled.png") no-repeat center right}table.dataTable thead .sorting_desc_disabled{background:url("../images/sort_desc_disabled.png") no-repeat center right}table.dataTable tbody tr{background-color:#fff}table.dataTable tbody tr.selected{background-color:#b0bed9}table.dataTable tbody th,table.dataTable tbody td{padding:8px 10px}table.dataTable.row-border tbody th,table.dataTable.row-border tbody td,table.dataTable.display tbody th,table.dataTable.display tbody td{border-top:1px solid #ddd}table.dataTable.row-border tbody tr:first-child th,table.dataTable.row-border tbody tr:first-child td,table.dataTable.display tbody tr:first-child th,table.dataTable.display tbody tr:first-child td{border-top:none}table.dataTable.cell-border tbody th,table.dataTable.cell-border tbody td{border-top:1px solid #ddd;border-right:1px solid #ddd}table.dataTable.cell-border tbody tr th:first-child,table.dataTable.cell-border tbody tr td:first-child{border-left:1px solid #ddd}table.dataTable.cell-border tbody tr:first-child th,table.dataTable.cell-border tbody tr:first-child td{border-top:none}table.dataTable.stripe tbody tr.odd,table.dataTable.display tbody tr.odd{background-color:#f9f9f9}table.dataTable.stripe tbody tr.odd.selected,table.dataTable.display tbody tr.odd.selected{background-color:#abb9d3}table.dataTable.hover tbody tr:hover,table.dataTable.hover tbody tr.odd:hover,table.dataTable.hover tbody tr.even:hover,table.dataTable.display tbody tr:hover,table.dataTable.display tbody tr.odd:hover,table.dataTable.display tbody tr.even:hover{background-color:#f5f5f5}table.dataTable.hover tbody tr:hover.selected,table.dataTable.hover tbody tr.odd:hover.selected,table.dataTable.hover tbody tr.even:hover.selected,table.dataTable.display tbody tr:hover.selected,table.dataTable.display tbody tr.odd:hover.selected,table.dataTable.display tbody tr.even:hover.selected{background-color:#a9b7d1}table.dataTable.order-column tbody tr>.sorting_1,table.dataTable.order-column tbody tr>.sorting_2,table.dataTable.order-column tbody tr>.sorting_3,table.dataTable.display tbody tr>.sorting_1,table.dataTable.display tbody tr>.sorting_2,table.dataTable.display tbody tr>.sorting_3{background-color:#f9f9f9}table.dataTable.order-column tbody tr.selected>.sorting_1,table.dataTable.order-column tbody tr.selected>.sorting_2,table.dataTable.order-column tbody tr.selected>.sorting_3,table.dataTable.display tbody tr.selected>.sorting_1,table.dataTable.display tbody tr.selected>.sorting_2,table.dataTable.display tbody tr.selected>.sorting_3{background-color:#acbad4}table.dataTable.display tbody tr.odd>.sorting_1,table.dataTable.order-column.stripe tbody tr.odd>.sorting_1{background-color:#f1f1f1}table.dataTable.display tbody tr.odd>.sorting_2,table.dataTable.order-column.stripe tbody tr.odd>.sorting_2{background-color:#f3f3f3}table.dataTable.display tbody tr.odd>.sorting_3,table.dataTable.order-column.stripe tbody tr.odd>.sorting_3{background-color:#f5f5f5}table.dataTable.display tbody tr.odd.selected>.sorting_1,table.dataTable.order-column.stripe tbody tr.odd.selected>.sorting_1{background-color:#a6b3cd}table.dataTable.display tbody tr.odd.selected>.sorting_2,table.dataTable.order-column.stripe tbody tr.odd.selected>.sorting_2{background-color:#a7b5ce}table.dataTable.display tbody tr.odd.selected>.sorting_3,table.dataTable.order-column.stripe tbody tr.odd.selected>.sorting_3{background-color:#a9b6d0}table.dataTable.display tbody tr.even>.sorting_1,table.dataTable.order-column.stripe tbody tr.even>.sorting_1{background-color:#f9f9f9}table.dataTable.display tbody tr.even>.sorting_2,table.dataTable.order-column.stripe tbody tr.even>.sorting_2{background-color:#fbfbfb}table.dataTable.display tbody tr.even>.sorting_3,table.dataTable.order-column.stripe tbody tr.even>.sorting_3{background-color:#fdfdfd}table.dataTable.display tbody tr.even.selected>.sorting_1,table.dataTable.order-column.stripe tbody tr.even.selected>.sorting_1{background-color:#acbad4}table.dataTable.display tbody tr.even.selected>.sorting_2,table.dataTable.order-column.stripe tbody tr.even.selected>.sorting_2{background-color:#adbbd6}table.dataTable.display tbody tr.even.selected>.sorting_3,table.dataTable.order-column.stripe tbody tr.even.selected>.sorting_3{background-color:#afbdd8}table.dataTable.display tbody tr:hover>.sorting_1,table.dataTable.display tbody tr.odd:hover>.sorting_1,table.dataTable.display tbody tr.even:hover>.sorting_1,table.dataTable.order-column.hover tbody tr:hover>.sorting_1,table.dataTable.order-column.hover tbody tr.odd:hover>.sorting_1,table.dataTable.order-column.hover tbody tr.even:hover>.sorting_1{background-color:#eaeaea}table.dataTable.display tbody tr:hover>.sorting_2,table.dataTable.display tbody tr.odd:hover>.sorting_2,table.dataTable.display tbody tr.even:hover>.sorting_2,table.dataTable.order-column.hover tbody tr:hover>.sorting_2,table.dataTable.order-column.hover tbody tr.odd:hover>.sorting_2,table.dataTable.order-column.hover tbody tr.even:hover>.sorting_2{background-color:#ebebeb}table.dataTable.display tbody tr:hover>.sorting_3,table.dataTable.display tbody tr.odd:hover>.sorting_3,table.dataTable.display tbody tr.even:hover>.sorting_3,table.dataTable.order-column.hover tbody tr:hover>.sorting_3,table.dataTable.order-column.hover tbody tr.odd:hover>.sorting_3,table.dataTable.order-column.hover tbody tr.even:hover>.sorting_3{background-color:#eee}table.dataTable.display tbody tr:hover.selected>.sorting_1,table.dataTable.display tbody tr.odd:hover.selected>.sorting_1,table.dataTable.display tbody tr.even:hover.selected>.sorting_1,table.dataTable.order-column.hover tbody tr:hover.selected>.sorting_1,table.dataTable.order-column.hover tbody tr.odd:hover.selected>.sorting_1,table.dataTable.order-column.hover tbody tr.even:hover.selected>.sorting_1{background-color:#a1aec7}table.dataTable.display tbody tr:hover.selected>.sorting_2,table.dataTable.display tbody tr.odd:hover.selected>.sorting_2,table.dataTable.display tbody tr.even:hover.selected>.sorting_2,table.dataTable.order-column.hover tbody tr:hover.selected>.sorting_2,table.dataTable.order-column.hover tbody tr.odd:hover.selected>.sorting_2,table.dataTable.order-column.hover tbody tr.even:hover.selected>.sorting_2{background-color:#a2afc8}table.dataTable.display tbody tr:hover.selected>.sorting_3,table.dataTable.display tbody tr.odd:hover.selected>.sorting_3,table.dataTable.display tbody tr.even:hover.selected>.sorting_3,table.dataTable.order-column.hover tbody tr:hover.selected>.sorting_3,table.dataTable.order-column.hover tbody tr.odd:hover.selected>.sorting_3,table.dataTable.order-column.hover tbody tr.even:hover.selected>.sorting_3{background-color:#a4b2cb}table.dataTable.no-footer{border-bottom:1px solid #111}table.dataTable.nowrap th,table.dataTable.nowrap td{white-space:nowrap}table.dataTable.compact thead th,table.dataTable.compact thead td{padding:5px 9px}table.dataTable.compact tfoot th,table.dataTable.compact tfoot td{padding:5px 9px 3px 9px}table.dataTable.compact tbody th,table.dataTable.compact tbody td{padding:4px 5px}table.dataTable th.dt-left,table.dataTable td.dt-left{text-align:left}table.dataTable th.dt-center,table.dataTable td.dt-center,table.dataTable td.dataTables_empty{text-align:center}table.dataTable th.dt-right,table.dataTable td.dt-right{text-align:right}table.dataTable th.dt-justify,table.dataTable td.dt-justify{text-align:justify}table.dataTable th.dt-nowrap,table.dataTable td.dt-nowrap{white-space:nowrap}table.dataTable thead th.dt-head-left,table.dataTable thead td.dt-head-left,table.dataTable tfoot th.dt-head-left,table.dataTable tfoot td.dt-head-left{text-align:left}table.dataTable thead th.dt-head-center,table.dataTable thead td.dt-head-center,table.dataTable tfoot th.dt-head-center,table.dataTable tfoot td.dt-head-center{text-align:center}table.dataTable thead th.dt-head-right,table.dataTable thead td.dt-head-right,table.dataTable tfoot th.dt-head-right,table.dataTable tfoot td.dt-head-right{text-align:right}table.dataTable thead th.dt-head-justify,table.dataTable thead td.dt-head-justify,table.dataTable tfoot th.dt-head-justify,table.dataTable tfoot td.dt-head-justify{text-align:justify}table.dataTable thead th.dt-head-nowrap,table.dataTable thead td.dt-head-nowrap,table.dataTable tfoot th.dt-head-nowrap,table.dataTable tfoot td.dt-head-nowrap{white-space:nowrap}table.dataTable tbody th.dt-body-left,table.dataTable tbody td.dt-body-left{text-align:left}table.dataTable tbody th.dt-body-center,table.dataTable tbody td.dt-body-center{text-align:center}table.dataTable tbody th.dt-body-right,table.dataTable tbody td.dt-body-right{text-align:right}table.dataTable tbody th.dt-body-justify,table.dataTable tbody td.dt-body-justify{text-align:justify}table.dataTable tbody th.dt-body-nowrap,table.dataTable tbody td.dt-body-nowrap{white-space:nowrap}table.dataTable,table.dataTable th,table.dataTable td{-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box}.dataTables_wrapper{position:relative;clear:both;*zoom:1;zoom:1}.dataTables_wrapper .dataTables_length{float:left}.dataTables_wrapper .dataTables_filter{float:right;text-align:right}.dataTables_wrapper .dataTables_filter input{margin-left:0.5em}.dataTables_wrapper .dataTables_info{clear:both;float:left;padding-top:0.755em}.dataTables_wrapper .dataTables_paginate{float:right;text-align:right;padding-top:0.25em}.dataTables_wrapper .dataTables_paginate .paginate_button{box-sizing:border-box;display:inline-block;min-width:1.5em;padding:0.5em 1em;margin-left:2px;text-align:center;text-decoration:none !important;cursor:pointer;*cursor:hand;color:#333 !important;border:1px solid transparent}.dataTables_wrapper .dataTables_paginate .paginate_button.current,.dataTables_wrapper .dataTables_paginate .paginate_button.current:hover{color:#333 !important;border:1px solid #cacaca;background-color:#fff;background:-webkit-gradient(linear, left top, left bottom, color-stop(0%, #fff), color-stop(100%, #dcdcdc));background:-webkit-linear-gradient(top, #fff 0%, #dcdcdc 100%);background:-moz-linear-gradient(top, #fff 0%, #dcdcdc 100%);background:-ms-linear-gradient(top, #fff 0%, #dcdcdc 100%);background:-o-linear-gradient(top, #fff 0%, #dcdcdc 100%);background:linear-gradient(to bottom, #fff 0%, #dcdcdc 100%)}.dataTables_wrapper .dataTables_paginate .paginate_button.disabled,.dataTables_wrapper .dataTables_paginate .paginate_button.disabled:hover,.dataTables_wrapper .dataTables_paginate .paginate_button.disabled:active{cursor:default;color:#666 !important;border:1px solid transparent;background:transparent;box-shadow:none}.dataTables_wrapper .dataTables_paginate .paginate_button:hover{color:white !important;border:1px solid #111;background-color:#585858;background:-webkit-gradient(linear, left top, left bottom, color-stop(0%, #585858), color-stop(100%, #111));background:-webkit-linear-gradient(top, #585858 0%, #111 100%);background:-moz-linear-gradient(top, #585858 0%, #111 100%);background:-ms-linear-gradient(top, #585858 0%, #111 100%);background:-o-linear-gradient(top, #585858 0%, #111 100%);background:linear-gradient(to bottom, #585858 0%, #111 100%)}.dataTables_wrapper .dataTables_paginate .paginate_button:active{outline:none;background-color:#2b2b2b;background:-webkit-gradient(linear, left top, left bottom, color-stop(0%, #2b2b2b), color-stop(100%, #0c0c0c));background:-webkit-linear-gradient(top, #2b2b2b 0%, #0c0c0c 100%);background:-moz-linear-gradient(top, #2b2b2b 0%, #0c0c0c 100%);background:-ms-linear-gradient(top, #2b2b2b 0%, #0c0c0c 100%);background:-o-linear-gradient(top, #2b2b2b 0%, #0c0c0c 100%);background:linear-gradient(to bottom, #2b2b2b 0%, #0c0c0c 100%);box-shadow:inset 0 0 3px #111}.dataTables_wrapper .dataTables_processing{position:absolute;top:50%;left:50%;width:100%;height:40px;margin-left:-50%;margin-top:-25px;padding-top:20px;text-align:center;font-size:1.2em;background-color:white;background:-webkit-gradient(linear, left top, right top, color-stop(0%, rgba(255,255,255,0)), color-stop(25%, rgba(255,255,255,0.9)), color-stop(75%, rgba(255,255,255,0.9)), color-stop(100%, rgba(255,255,255,0)));background:-webkit-linear-gradient(left, rgba(255,255,255,0) 0%, rgba(255,255,255,0.9) 25%, rgba(255,255,255,0.9) 75%, rgba(255,255,255,0) 100%);background:-moz-linear-gradient(left, rgba(255,255,255,0) 0%, rgba(255,255,255,0.9) 25%, rgba(255,255,255,0.9) 75%, rgba(255,255,255,0) 100%);background:-ms-linear-gradient(left, rgba(255,255,255,0) 0%, rgba(255,255,255,0.9) 25%, rgba(255,255,255,0.9) 75%, rgba(255,255,255,0) 100%);background:-o-linear-gradient(left, rgba(255,255,255,0) 0%, rgba(255,255,255,0.9) 25%, rgba(255,255,255,0.9) 75%, rgba(255,255,255,0) 100%);background:linear-gradient(to right, rgba(255,255,255,0) 0%, rgba(255,255,255,0.9) 25%, rgba(255,255,255,0.9) 75%, rgba(255,255,255,0) 100%)}.dataTables_wrapper .dataTables_length,.dataTables_wrapper .dataTables_filter,.dataTables_wrapper .dataTables_info,.dataTables_wrapper .dataTables_processing,.dataTables_wrapper .dataTables_paginate{color:#333}.dataTables_wrapper .dataTables_scroll{clear:both}.dataTables_wrapper .dataTables_scroll div.dataTables_scrollBody{*margin-top:-1px;-webkit-overflow-scrolling:touch}.dataTables_wrapper .dataTables_scroll div.dataTables_scrollBody th>div.dataTables_sizing,.dataTables_wrapper .dataTables_scroll div.dataTables_scrollBody td>div.dataTables_sizing{height:0;overflow:hidden;margin:0 !important;padding:0 !important}.dataTables_wrapper.no-footer .dataTables_scrollBody{border-bottom:1px solid #111}.dataTables_wrapper.no-footer div.dataTables_scrollHead table,.dataTables_wrapper.no-footer div.dataTables_scrollBody table{border-bottom:none}.dataTables_wrapper:after{visibility:hidden;display:block;content:"";clear:both;height:0}@media screen and (max-width: 767px){.dataTables_wrapper .dataTables_info,.dataTables_wrapper .dataTables_paginate{float:none;text-align:center}.dataTables_wrapper .dataTables_paginate{margin-top:0.5em}}@media screen and (max-width: 640px){.dataTables_wrapper .dataTables_length,.dataTables_wrapper .dataTables_filter{float:none;text-align:center}.dataTables_wrapper .dataTables_filter{margin-top:0.5em}}
+
+}
+
+
+/* - ++resource++it4i.portal.common/prettify.css - */
+@media screen {
+.pln{color:#000}@media screen{.str{color:#080}.kwd{color:#008}.com{color:#800}.typ{color:#606}.lit{color:#066}.pun,.opn,.clo{color:#660}.tag{color:#008}.atn{color:#606}.atv{color:#080}.dec,.var{color:#606}.fun{color:red}}@media print,projection{.str{color:#060}.kwd{color:#006;font-weight:bold}.com{color:#600;font-style:italic}.typ{color:#404;font-weight:bold}.lit{color:#044}.pun,.opn,.clo{color:#440}.tag{color:#006;font-weight:bold}.atn{color:#404}.atv{color:#060}}pre.prettyprint{padding:2px;border:1px solid #888}ol.linenums{margin-top:0;margin-bottom:0}li.L0,li.L1,li.L2,li.L3,li.L5,li.L6,li.L7,li.L8{list-style-type:none}li.L1,li.L3,li.L5,li.L7,li.L9{background:#eee}
+}
+
+
+/* - ++resource++it4i.portal.common/base.css - */
+@media screen {
+/*
+ *
+ * base.css
+ * IT4I Portal-wide base CSS library
+ *
+ */
+
+body {
+ /* background if any */
+ background: url('/background.png');
+ min-height: 100%;
+ position: absolute;
+ width: 100%;
+}
+
+/* wow effect */
+a {
+ transition: color 0.2s linear 0s, background 0.1s linear 0s;
+}
+
+div#portal-columns {
+ margin-bottom: 60px;
+}
+
+/* official colours */
+div#portal-columns a, div#portal-columns a:visited {
+ color: #C0081F;
+}
+
+div#portal-columns a:hover {
+ color: #00A0EE;
+}
+
+ul#portal-globalnav {
+ background-color: #00A0EE;
+}
+
+ul#portal-globalnav>li>a {
+ border-top: none;
+}
+
+ul#portal-globalnav li a:after {
+ content: " →";
+}
+
+ul#portal-globalnav li a.plain {
+ background-color: #00A0EE;
+ color: #fff;
+}
+
+ul#portal-globalnav li.selected a, ul#portal-globalnav li.selected a:hover, ul#portal-globalnav li a:hover {
+ background-color: #11134F;
+ color: #e6e6e6;
+}
+
+/* portal footer */
+div#portal-footer-wrapper {
+ bottom: 0px;
+ position: absolute;
+ text-align: right;
+}
+
+#portal-footer {
+ color: #e6e6e6;
+ background-color: #00A0EE;
+ margin: 0;
+ padding: 0;
+}
+
+#portal-footer a {
+ color: #fff;
+ line-height: 225%;
+ padding: 0.5em 1em;
+ white-space: nowrap;
+}
+
+#portal-footer a:not(:last-child) {
+ border-right: 1px dotted white;
+}
+
+#portal-footer p {
+ line-height: 1.5em;
+ padding: 1em;
+}
+
+.hidden {
+ display: none;
+}
+
+/* breadcrumbs alignment */
+div#portal-breadcrumbs {
+ text-align: right;
+}
+
+#LSResult {
+ z-index: 1;
+}
+
+dl.actionMenu.activated dd {
+ min-width: inherit;
+}
+
+/*
+ *
+ * Pretty printing styles. Used with prettify.js.
+ * BEGIN
+ *
+*/
+
+/* Vim sunburst theme by David Leibovic */
+
+pre .str, code .str { color: #65B042; } /* string - green */
+pre .kwd, code .kwd { color: #E28964; } /* keyword - dark pink */
+pre .com, code .com { color: #AEAEAE; font-style: italic; } /* comment - gray */
+pre .typ, code .typ { color: #89bdff; } /* type - light blue */
+pre .lit, code .lit { color: #3387CC; } /* literal - blue */
+pre .pun, code .pun { color: #fff; } /* punctuation - white */
+pre .pln, code .pln { color: #fff; } /* plaintext - white */
+pre .tag, code .tag { color: #89bdff; } /* html/xml tag - light blue */
+pre .atn, code .atn { color: #bdb76b; } /* html/xml attribute name - khaki */
+pre .atv, code .atv { color: #65B042; } /* html/xml attribute value - green */
+pre .dec, code .dec { color: #3387CC; } /* decimal - blue */
+
+pre.prettyprint, code.prettyprint {
+ background-color: #000;
+ -moz-border-radius: 8px;
+ -webkit-border-radius: 8px;
+ -o-border-radius: 8px;
+ -ms-border-radius: 8px;
+ -khtml-border-radius: 8px;
+ border-radius: 8px;
+}
+
+pre.prettyprint {
+ width: 95%;
+ margin: 1em auto;
+ padding: 1em;
+ white-space: pre-wrap;
+}
+
+/* Specify class=linenums on a pre to get line numbering */
+ol.linenums { margin-top: 0; margin-bottom: 0; color: #AEAEAE; } /* IE indents via margin-left */
+li.L0,li.L1,li.L2,li.L3,li.L5,li.L6,li.L7,li.L8 { list-style-type: none }
+/* Alternate shading for lines */
+li.L1,li.L3,li.L5,li.L7,li.L9 { }
+
+@media print {
+ pre .str, code .str { color: #060; }
+ pre .kwd, code .kwd { color: #006; font-weight: bold; }
+ pre .com, code .com { color: #600; font-style: italic; }
+ pre .typ, code .typ { color: #404; font-weight: bold; }
+ pre .lit, code .lit { color: #044; }
+ pre .pun, code .pun { color: #440; }
+ pre .pln, code .pln { color: #000; }
+ pre .tag, code .tag { color: #006; font-weight: bold; }
+ pre .atn, code .atn { color: #404; }
+ pre .atv, code .atv { color: #060; }
+}
+
+/*
+ *
+ * Pretty printing styles. Used with prettify.js.
+ * END
+ *
+*/
+
+}
+
+
+/* - ploneCustom.css - */
+@media all {
+/* https://docs.it4i.cz/portal_css/ploneCustom.css?original=1 */
+/* */
+/* */
+/* */
+/* */
+/* */
+/* */
+
+}
+
+
+/* - custom.css - */
+@media screen {
+body {
+ font-size: 110%;
+}
+
+h1 {
+ color: #000;
+}
+
+h2, h3 {
+ color: #000;
+ margin-top: 1.25em;
+ margin-bottom: 0.6em;
+}
+
+#portal-header {
+ border-bottom: 0.1em dotted #aaa;
+}
+
+dl.portlet ul.navTreeLevel0 > .navTreeItem {
+ border-bottom: 0.1em dotted #aaa;
+}
+
+#portal-column-content {
+ margin-top: 0.6em;
+}
+
+dl.toc {
+ margin: 0em 0em 2.5em 2.5em;
+}
+
+dl.portlet ul.navTreeLevel1 .navTreeItem {
+ line-height: 2em;
+ padding-left: 2em;
+}
+
+dl.portlet ul.navTree .navTreeCurrentItem {
+ padding-right: 2em;
+}
+
+table.filled,
+table.filled td,
+table.filled th {
+ border: 1px solid #777;
+ background: #ddd;
+ padding: 0.5em;
+ border-collapse: collapse;
+}
+
+#big-picture-of-cluster td {
+ vertical-align: middle;
+}
+
+#big-picture-of-cluster {
+ border: 2px solid #777;
+}
+
+table#blade-chassis {
+ height: 120px;
+ font-size: 80%;
+ width: 100%;
+}
+
+#blade-chassis td {
+ width: 10%;
+ padding: 0em;
+ text-align: center;
+ background-color: transparent;
+ -webkit-transform: rotate(270deg);
+ -moz-transform: rotate(270deg);
+ -ms-transform: rotate(270deg);
+ -o-transform: rotate(270deg);
+ transform: rotate(270deg);
+ filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=3);
+}
+
+#blade-chassis td[colspan^="2"] {
+ width: 20% !important;
+}
+
+.monospace {
+ font-family: "Courier New";
+}
+
+.searchField, .searchButton {
+ font-size: 130%;
+}
+
+#content .callout {
+ background: url("data:image/png;base64,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") no-repeat scroll 8px 50% #EEEEEE;
+ border-left: 1em solid #CCCCCC;
+ clear: both;
+ padding: 8px 0 8px 54px;
+ min-height: 42px;
+}
+
+#content .exclamation {
+ background: url("data:image/png;base64,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") no-repeat scroll 8px 50% #EEEEEE;
+ border-left: 1em solid #CCCCCC;
+ clear: both;
+ padding: 8px 0 8px 54px;
+ min-height: 42px;
+}
+
+pre code {
+ background-color: transparent;
+}
+
+/*
+ *
+ * Pretty printing styles. Used with prettify.js.
+ * BEGIN
+ *
+*/
+
+/* Vim sunburst theme by David Leibovic */
+
+pre .str, code .str { color: #65B042; } /* string - green */
+pre .kwd, code .kwd { color: #E28964; } /* keyword - dark pink */
+pre .com, code .com { color: #AEAEAE; font-style: italic; } /* comment - gray */
+pre .typ, code .typ { color: #89bdff; } /* type - light blue */
+pre .lit, code .lit { color: #3387CC; } /* literal - blue */
+pre .pun, code .pun { color: #fff; } /* punctuation - white */
+pre .pln, code .pln { color: #fff; } /* plaintext - white */
+pre .tag, code .tag { color: #89bdff; } /* html/xml tag - light blue */
+pre .atn, code .atn { color: #bdb76b; } /* html/xml attribute name - khaki */
+pre .atv, code .atv { color: #65B042; } /* html/xml attribute value - green */
+pre .dec, code .dec { color: #3387CC; } /* decimal - blue */
+
+pre.prettyprint, code.prettyprint {
+ background-color: #000;
+ -moz-border-radius: 8px;
+ -webkit-border-radius: 8px;
+ -o-border-radius: 8px;
+ -ms-border-radius: 8px;
+ -khtml-border-radius: 8px;
+ border-radius: 8px;
+}
+
+pre.prettyprint {
+ width: 95%;
+ margin: 1em auto;
+ padding: 1em;
+ white-space: pre-wrap;
+}
+
+/* Specify class=linenums on a pre to get line numbering */
+ol.linenums { margin-top: 0; margin-bottom: 0; color: #AEAEAE; } /* IE indents via margin-left */
+li.L0,li.L1,li.L2,li.L3,li.L5,li.L6,li.L7,li.L8 { list-style-type: none }
+/* Alternate shading for lines */
+li.L1,li.L3,li.L5,li.L7,li.L9 { }
+
+@media print {
+ pre .str, code .str { color: #060; }
+ pre .kwd, code .kwd { color: #006; font-weight: bold; }
+ pre .com, code .com { color: #600; font-style: italic; }
+ pre .typ, code .typ { color: #404; font-weight: bold; }
+ pre .lit, code .lit { color: #044; }
+ pre .pun, code .pun { color: #440; }
+ pre .pln, code .pln { color: #000; }
+ pre .tag, code .tag { color: #006; font-weight: bold; }
+ pre .atn, code .atn { color: #404; }
+ pre .atv, code .atv { color: #060; }
+}
+
+/*
+ *
+ * Pretty printing styles. Used with prettify.js.
+ * END
+ *
+*/
+
+p.hiddenForView {
+ display: none;
+}
+
+html>body>p.hiddenForView {
+ display: inline;
+ background-color: yellow;
+}
+
+#content span.link-external a {
+ background: transparent url("link_icon_external.png") no-repeat right 0px top 1px;
+ background-size: 12px;
+ padding: 1px 16px 1px 0px;
+}
+
+#content a#plone-discussions-href {
+ border-bottom: 0;
+}
+
+div#viewlet-below-content {
+ display: none;
+}
+}
+
diff --git a/portal_css/Sunburst Theme/treeCollapsed.png b/docs.it4i.cz/portal_css/Sunburst Theme/treeCollapsed.png
old mode 100755
new mode 100644
similarity index 100%
rename from portal_css/Sunburst Theme/treeCollapsed.png
rename to docs.it4i.cz/portal_css/Sunburst Theme/treeCollapsed.png
diff --git a/portal_css/Sunburst Theme/treeExpanded.png b/docs.it4i.cz/portal_css/Sunburst Theme/treeExpanded.png
old mode 100755
new mode 100644
similarity index 100%
rename from portal_css/Sunburst Theme/treeExpanded.png
rename to docs.it4i.cz/portal_css/Sunburst Theme/treeExpanded.png
diff --git a/portal_javascripts/Sunburst Theme/++resource++it4i.portal.common/exporting.js b/docs.it4i.cz/portal_javascripts/Sunburst Theme/++resource++it4i.portal.common/exporting.js
old mode 100755
new mode 100644
similarity index 100%
rename from portal_javascripts/Sunburst Theme/++resource++it4i.portal.common/exporting.js
rename to docs.it4i.cz/portal_javascripts/Sunburst Theme/++resource++it4i.portal.common/exporting.js
diff --git a/portal_javascripts/Sunburst Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js b/docs.it4i.cz/portal_javascripts/Sunburst Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js
old mode 100755
new mode 100644
similarity index 100%
rename from portal_javascripts/Sunburst Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js
rename to docs.it4i.cz/portal_javascripts/Sunburst Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js
diff --git a/portal_javascripts/Sunburst Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js b/docs.it4i.cz/portal_javascripts/Sunburst Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js
old mode 100755
new mode 100644
similarity index 99%
rename from portal_javascripts/Sunburst Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js
rename to docs.it4i.cz/portal_javascripts/Sunburst Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js
index c442d1abc5128182c24c5d079a29899ffde602d3..e87dd491fd69bf95c50cbfec873417c245349cc9
--- a/portal_javascripts/Sunburst Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js
+++ b/docs.it4i.cz/portal_javascripts/Sunburst Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js
@@ -28,7 +28,7 @@ V.LN10))}function nb(a,b,c,d){var e,c=p(c,1);e=a/c;b||(b=[1,2,2.5,5,10],d===!1&&
function Pa(a,b){for(var c in a)a[c]&&a[c]!==b&&a[c].destroy&&a[c].destroy(),delete a[c]}function Qa(a){db||(db=$(Ka));a&&db.appendChild(a);db.innerHTML=""}function ea(a){return parseFloat(a.toPrecision(14))}function Ra(a,b){va=p(a,b.animation)}function Bb(){var a=E.global.useUTC,b=a?"getUTC":"get",c=a?"setUTC":"set";Da=E.global.Date||window.Date;Sa=(a&&E.global.timezoneOffset||0)*6E4;eb=a?Da.UTC:function(a,b,c,g,h,i){return(new Da(a,b,p(c,1),p(g,0),p(h,0),p(i,0))).getTime()};pb=b+"Minutes";qb=b+
"Hours";rb=b+"Day";Xa=b+"Date";fb=b+"Month";gb=b+"FullYear";Cb=c+"Minutes";Db=c+"Hours";sb=c+"Date";Eb=c+"Month";Fb=c+"FullYear"}function S(){}function Ta(a,b,c,d){this.axis=a;this.pos=b;this.type=c||"";this.isNew=!0;!c&&!d&&this.addLabel()}function na(){this.init.apply(this,arguments)}function Ya(){this.init.apply(this,arguments)}function Gb(a,b,c,d,e){var f=a.chart.inverted;this.axis=a;this.isNegative=c;this.options=b;this.x=d;this.total=null;this.points={};this.stack=e;this.alignOptions={align:b.align||
(f?c?"left":"right":"center"),verticalAlign:b.verticalAlign||(f?"middle":c?"bottom":"top"),y:p(b.y,f?4:c?14:-6),x:p(b.x,f?c?-6:6:0)};this.textAlign=b.textAlign||(f?c?"right":"left":"center")}var u,x=document,G=window,V=Math,v=V.round,U=V.floor,La=V.ceil,t=V.max,L=V.min,Q=V.abs,aa=V.cos,fa=V.sin,oa=V.PI,Ea=oa*2/360,wa=navigator.userAgent,Hb=G.opera,Aa=/msie/i.test(wa)&&!Hb,hb=x.documentMode===8,tb=/AppleWebKit/.test(wa),Ua=/Firefox/.test(wa),Ib=/(Mobile|Android|Windows Phone)/.test(wa),xa="http://www.w3.org/2000/svg",
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diff --git a/portal_javascripts/Sunburst Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js b/docs.it4i.cz/portal_javascripts/Sunburst Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js
old mode 100755
new mode 100644
similarity index 100%
rename from portal_javascripts/Sunburst Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js
rename to docs.it4i.cz/portal_javascripts/Sunburst Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js
diff --git a/portal_javascripts/Sunburst Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js b/docs.it4i.cz/portal_javascripts/Sunburst Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js
old mode 100755
new mode 100644
similarity index 93%
rename from portal_javascripts/Sunburst Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js
rename to docs.it4i.cz/portal_javascripts/Sunburst Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js
index 7885fd2c3467f72d1af24aa7f754427619d62c82..4fdfbf69cdc3ed2deb800687285b86c340590ec0
--- a/portal_javascripts/Sunburst Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js
+++ b/docs.it4i.cz/portal_javascripts/Sunburst Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js
@@ -21,10 +21,10 @@ function getContentArea(){var node=jQuery('#region-content,#content');return nod
/* - plone_javascript_variables.js - */
// https://docs.it4i.cz/portal_javascripts/plone_javascript_variables.js?original=1
-var portal_url='index.html';var form_modified_message='Your form has not been saved. All changes you have made will be lost.';var form_resubmit_message='You already clicked the submit button. Do you really want to submit this form again?';var external_links_open_new_window='false';var mark_special_links='true';var ajax_noresponse_message='No response from server. Please try again later.';
+var portal_url='https://docs.it4i.cz';var form_modified_message='Formulář nebyl uloĹľen. Všechny provedenĂ© zmÄ›ny budou ztraceny.';var form_resubmit_message='TlaÄŤĂtko pro odeslánĂ formuláře jiĹľ bylo stisknuto. Opravdu chcete tento formulář odeslat znovu?';var external_links_open_new_window='false';var mark_special_links='true';var ajax_noresponse_message='Od serveru nepĹ™išla žádná odezva. Zkuste to prosĂm pozdÄ›ji.';
/* - ++resource++plone.app.jquerytools.js - */
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conf=this.getConf(),w=$(window);conf.fixed||(pos.top+=w.scrollTop(),pos.left+=w.scrollLeft()),pos.position=conf.fixed?"fixed":"absolute",this.getOverlay().css(pos).fadeIn(conf.speed,onLoad)},function(onClose){this.getOverlay().fadeOut(this.getConf().closeSpeed,onClose)}),$.fn.overlay=function(conf){var el=this.data("overlay");return el?el:($.isFunction(conf)&&(conf={onBeforeLoad:conf}),conf=$.extend(!0,{},$.tools.overlay.conf,conf),this.each(function(){el=new Overlay($(this),conf),instances.push(el),$(this).data("overlay",el)}),conf.api?el:this)}}(jQuery),function($){function find(root,query){var el=$(query);return el.length<2?el:root.parent().find(query)}function Scrollable(root,conf){var self=this,fire=root.add(self),itemWrap=root.children(),index=0,vertical=conf.vertical;if(current||(current=self),itemWrap.length>1&&(itemWrap=$(conf.items,root)),conf.size>1&&(conf.circular=!1),$.extend(self,{getConf:function(){return conf},getIndex:function(){return index},getSize:function(){return 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diff --git a/docs.it4i.cz/robots.txt b/docs.it4i.cz/robots.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0edfaee6b28a81c447fa50bde0dffa5c3072a996
--- /dev/null
+++ b/docs.it4i.cz/robots.txt
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+# already accessible to anonymous users
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+# Add Googlebot-specific syntax extension to exclude forms
+# that are repeated for each piece of content in the site
+# the wildcard is only supported by Googlebot
+# http://www.google.com/support/webmasters/bin/answer.py?answer=40367&ctx=sibling
+
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+Disallow: /*sendto_form$
+Disallow: /*folder_factories$
\ No newline at end of file
diff --git a/rss.xml b/docs.it4i.cz/rss.xml
old mode 100755
new mode 100644
similarity index 95%
rename from rss.xml
rename to docs.it4i.cz/rss.xml
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<div id="parent-fieldname-text-50ee0f8999e14a08822bd423d24de7ef" class="">
- <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
-<h2 class=" "><img title="Vampir screenshot" class="image-inline" alt="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
+ <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
+<h2 class=" "><img alt="Vampir screenshot" class="image-inline" title="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
<h2 class=" ">Installed versions</h2>
<p>Version 8.5.0 is currently installed as module <span class="monospace">Vampir/8.5.0</span> :</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir &</pre>
@@ -87,8 +87,8 @@
<div id="parent-fieldname-text-f6e25102d1244fb4ab355175867747b5" class="">
- <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
-<h2 class=" "><img title="Vampir screenshot" class="image-inline" alt="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
+ <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
+<h2 class=" "><img alt="Vampir screenshot" class="image-inline" title="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
<h2 class=" ">Installed versions</h2>
<p>Version 8.5.0 is currently installed as module <span class="monospace">Vampir/8.5.0</span> :</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir &</pre>
@@ -205,8 +205,8 @@
<pre class="prettyprint lang-sh"><span style="text-align: left; float: none; ">[usename@login1.anselm ~]$ gnome-session &<br />[1] 23691<br />[<span style="text-align: left; float: none; ">usename</span>@login1.anselm ~]$ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused<br />PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused<br /><br />** (gnome-session:23691): WARNING **: Cannot open display:<br /></span></pre>
<p><span style="text-align: left; float: none; ">Â </span></p>
<ol>
-<li><span style="text-align: left; float: none; ">Locate and modify <span style="text-align: left; float: none; ">Cygwin shortcut that uses<span class="Apple-converted-space">Â </span></span><a href="http://x.cygwin.com/docs/man1/startxwin.1.html" rel="nofollow" style="text-align: left; ">startxwin</a><br />locate<br />C:\cygwin64\bin\XWin.exe<br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">change it to</span></span></span><br />C:\<i class="moz-txt-slash">cygwin64\bin\XWin.exe -listen tcp</i><br /><br /><img title="XWin-listen-tcp.png" class="image-inline" alt="XWin-listen-tcp.png" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/XWinlistentcp.png" /><br /></span><br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span></span></li>
-<li><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">Check Putty settings:<br /><span style="text-align: left; float: none; ">Enable X11 forwarding</span><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span><span class="Apple-converted-space"><br /></span></span><br /><a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding"><img title="" class="image-inline" alt="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwinX11forwarding.png/@@images/0f5b58e3-253c-4f87-a3b2-16f75cbf090f.png" /></a><br /></span></span></li>
+<li><span style="text-align: left; float: none; ">Locate and modify <span style="text-align: left; float: none; ">Cygwin shortcut that uses<span class="Apple-converted-space">Â </span></span><a href="http://x.cygwin.com/docs/man1/startxwin.1.html" rel="nofollow" style="text-align: left; ">startxwin</a><br />locate<br />C:\cygwin64\bin\XWin.exe<br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">change it to</span></span></span><br />C:\<i class="moz-txt-slash">cygwin64\bin\XWin.exe -listen tcp</i><br /><br /><img alt="XWin-listen-tcp.png" class="image-inline" title="XWin-listen-tcp.png" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/XWinlistentcp.png" /><br /></span><br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span></span></li>
+<li><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">Check Putty settings:<br /><span style="text-align: left; float: none; ">Enable X11 forwarding</span><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span><span class="Apple-converted-space"><br /></span></span><br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding"><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwinX11forwarding.png/@@images/0f5b58e3-253c-4f87-a3b2-16f75cbf090f.png" /></a><br /></span></span></li>
</ol>
<p>Â </p>
@@ -259,7 +259,7 @@
<div id="parent-fieldname-text" class="plain">
- <p>We have implemented a new way to run parallel MATLAB jobs. Unlike the previously documented method, it does not submit a separate new job to run the workers, all is done within a single job. Read about it here:Â <a target="_self" title="" class="external-link" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6">https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6</a></p>
+ <p>We have implemented a new way to run parallel MATLAB jobs. Unlike the previously documented method, it does not submit a separate new job to run the workers, all is done within a single job. Read about it here:Â <a title="" class="external-link" target="_self" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6">https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6</a></p>
</div>
@@ -538,13 +538,13 @@
<pre class="prettyprint lang-sh">$ module load phono3py/0.9.14-ictce-7.3.5-Python-2.7.9</pre>
<h2>Example of calculating thermal conductivity of Si using VASP code.</h2>
<h3>Calculating force constants</h3>
-<p>One needs to calculate second order and third order force constants using the diamond structure of silicon stored in <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/poscar-si">POSCAR</a>Â (the same form as in VASP) using single displacement calculations within supercell.</p>
+<p>One needs to calculate second order and third order force constants using the diamond structure of silicon stored in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/poscar-si">POSCAR</a>Â (the same form as in VASP) using single displacement calculations within supercell.</p>
<pre class="prettyprint lang-sh">$ cat POSCAR<br />Â Si<br />Â Â 1.0<br />Â Â Â Â 5.4335600309153529Â Â Â 0.0000000000000000Â Â Â 0.0000000000000000<br />Â Â Â Â 0.0000000000000000Â Â Â 5.4335600309153529Â Â Â 0.0000000000000000<br />Â Â Â Â 0.0000000000000000Â Â Â 0.0000000000000000Â Â Â 5.4335600309153529<br />Â Si<br />Â Â 8<br />Direct<br />Â Â 0.8750000000000000Â 0.8750000000000000Â 0.8750000000000000<br />Â Â 0.8750000000000000Â 0.3750000000000000Â 0.3750000000000000<br />Â Â 0.3750000000000000Â 0.8750000000000000Â 0.3750000000000000<br />Â Â 0.3750000000000000Â 0.3750000000000000Â 0.8750000000000000<br />Â Â 0.1250000000000000Â 0.1250000000000000Â 0.1250000000000000<br />Â Â 0.1250000000000000Â 0.6250000000000000Â 0.6250000000000000<br />Â Â 0.6250000000000000Â 0.1250000000000000Â 0.6250000000000000<br />Â Â 0.6250000000000000Â 0.6250000000000000Â 0.1250000000000000<br /><br /></pre>
<h3>Generating displacement using 2x2x2 supercell for both second and third order force constants</h3>
<pre class="prettyprint lang-sh">$ <span class="n">phono3py</span> <span class="o">-</span><span class="n">d</span> <span class="o">--</span><span class="n">dim</span><span class="o">=</span><span class="s2">"2 2 2"</span> <span class="o">-</span><span class="n">c</span> <span class="n">POSCAR</span><span class="o"></span><span class="n"></span></pre>
<p class=" "><span class="n">111 displacements is created stored in <span class="n">disp_fc3.yaml</span>, and the structure input files with this displacements are POSCAR-00XXX, where the XXX=111.<br /></span></p>
<pre class="prettyprint lang-sh"><span class="n">disp_fc3.yaml POSCAR-00008 POSCAR-00017 POSCAR-00026 POSCAR-00035 POSCAR-00044 POSCAR-00053 POSCAR-00062 POSCAR-00071 POSCAR-00080 POSCAR-00089 POSCAR-00098 POSCAR-00107<br />POSCAR        POSCAR-00009 POSCAR-00018 POSCAR-00027 POSCAR-00036 POSCAR-00045 POSCAR-00054 POSCAR-00063 POSCAR-00072 POSCAR-00081 POSCAR-00090 POSCAR-00099 POSCAR-00108<br />POSCAR-00001  POSCAR-00010 POSCAR-00019 POSCAR-00028 POSCAR-00037 POSCAR-00046 POSCAR-00055 POSCAR-00064 POSCAR-00073 POSCAR-00082 POSCAR-00091 POSCAR-00100 POSCAR-00109<br />POSCAR-00002  POSCAR-00011 POSCAR-00020 POSCAR-00029 POSCAR-00038 POSCAR-00047 POSCAR-00056 POSCAR-00065 POSCAR-00074 POSCAR-00083 POSCAR-00092 POSCAR-00101 POSCAR-00110<br />POSCAR-00003  POSCAR-00012 POSCAR-00021 POSCAR-00030 POSCAR-00039 POSCAR-00048 POSCAR-00057 POSCAR-00066 POSCAR-00075 POSCAR-00084 POSCAR-00093 POSCAR-00102 POSCAR-00111<br />POSCAR-00004  POSCAR-00013 POSCAR-00022 POSCAR-00031 POSCAR-00040 POSCAR-00049 POSCAR-00058 POSCAR-00067 POSCAR-00076 POSCAR-00085 POSCAR-00094 POSCAR-00103<br />POSCAR-00005  POSCAR-00014 POSCAR-00023 POSCAR-00032 POSCAR-00041 POSCAR-00050 POSCAR-00059 POSCAR-00068 POSCAR-00077 POSCAR-00086 POSCAR-00095 POSCAR-00104<br />POSCAR-00006  POSCAR-00015 POSCAR-00024 POSCAR-00033 POSCAR-00042 POSCAR-00051 POSCAR-00060 POSCAR-00069 POSCAR-00078 POSCAR-00087 POSCAR-00096 POSCAR-00105<br />POSCAR-00007  POSCAR-00016 POSCAR-00025 POSCAR-00034 POSCAR-00043 POSCAR-00052 POSCAR-00061 POSCAR-00070 POSCAR-00079 POSCAR-00088 POSCAR-00097 POSCAR-00106</span></pre>
-<p class=" "><span class="n"> For each displacement the forces needs to be calculated, i.e. in form of the output file of VASP (vasprun.xml). For a single VASP calculations one needs <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/KPOINTS">KPOINTS</a>, <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/POTCAR">POTCAR</a>, <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/INCAR">INCAR</a> in your case directory (where you have POSCARS) and those 111 displacements calculations can be generated by <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/prepare.sh">prepare.sh</a> script. Then each of the single 111 calculations is submitted <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/run.sh">run.sh</a> by <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/submit.sh">submit.sh</a>.</span></p>
+<p class=" "><span class="n"> For each displacement the forces needs to be calculated, i.e. in form of the output file of VASP (vasprun.xml). For a single VASP calculations one needs <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/KPOINTS">KPOINTS</a>, <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/POTCAR">POTCAR</a>, <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/INCAR">INCAR</a> in your case directory (where you have POSCARS) and those 111 displacements calculations can be generated by <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/prepare.sh">prepare.sh</a> script. Then each of the single 111 calculations is submitted <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/run.sh">run.sh</a> by <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/submit.sh">submit.sh</a>.</span></p>
<pre class="prettyprint lang-sh"><span class="n">$./prepare.sh<br />$ls<br />disp-00001Â disp-00009Â disp-00017Â disp-00025Â disp-00033Â disp-00041Â disp-00049Â disp-00057Â disp-00065Â disp-00073Â disp-00081Â disp-00089Â disp-00097Â disp-00105Â Â Â Â INCAR<br />disp-00002Â disp-00010Â disp-00018Â disp-00026Â disp-00034Â disp-00042Â disp-00050Â disp-00058Â disp-00066Â disp-00074Â disp-00082Â disp-00090Â disp-00098Â disp-00106Â Â Â Â KPOINTS<br />disp-00003Â disp-00011Â disp-00019Â disp-00027Â disp-00035Â disp-00043Â disp-00051Â disp-00059Â disp-00067Â disp-00075Â disp-00083Â disp-00091Â disp-00099Â disp-00107Â Â Â Â POSCAR<br />disp-00004Â disp-00012Â disp-00020Â disp-00028Â disp-00036Â disp-00044Â disp-00052Â disp-00060Â disp-00068Â disp-00076Â disp-00084Â disp-00092Â disp-00100Â disp-00108Â Â Â Â POTCAR<br />disp-00005Â disp-00013Â disp-00021Â disp-00029Â disp-00037Â disp-00045Â disp-00053Â disp-00061Â disp-00069Â disp-00077Â disp-00085Â disp-00093Â disp-00101Â disp-00109Â Â Â Â prepare.sh<br />disp-00006Â disp-00014Â disp-00022Â disp-00030Â disp-00038Â disp-00046Â disp-00054Â disp-00062Â disp-00070Â disp-00078Â disp-00086Â disp-00094Â disp-00102Â disp-00110Â Â Â Â run.sh<br />disp-00007Â disp-00015Â disp-00023Â disp-00031Â disp-00039Â disp-00047Â disp-00055Â disp-00063Â disp-00071Â disp-00079Â disp-00087Â disp-00095Â disp-00103Â disp-00111Â Â Â Â submit.sh<br />disp-00008Â disp-00016Â disp-00024Â disp-00032Â disp-00040Â disp-00048Â disp-00056Â disp-00064Â disp-00072Â disp-00080Â disp-00088Â disp-00096Â disp-00104Â disp_fc3.yaml<br /></span></pre>
<p class=" "><span class="n">Taylor your run.sh script to fit into your project and other needs and submit all 111 calculations using submit.sh script</span></p>
<pre class="prettyprint lang-sh"><span class="n">$ ./submit.sh</span></pre>
@@ -561,7 +561,7 @@
<pre class="prettyprint lang-sh">$ grep grid_point ir_grid_points.yaml<br />num_reduced_ir_grid_points: 35<br />ir_grid_points:Â # [address, weight]<br />- grid_point: 0<br />- grid_point: 1<br />- grid_point: 2<br />- grid_point: 3<br />- grid_point: 4<br />- grid_point: 10<br />- grid_point: 11<br />- grid_point: 12<br />- grid_point: 13<br />- grid_point: 20<br />- grid_point: 21<br />- grid_point: 22<br />- grid_point: 30<br />- grid_point: 31<br />- grid_point: 40<br />- grid_point: 91<br />- grid_point: 92<br />- grid_point: 93<br />- grid_point: 94<br />- grid_point: 101<br />- grid_point: 102<br />- grid_point: 103<br />- grid_point: 111<br />- grid_point: 112<br />- grid_point: 121<br />- grid_point: 182<br />- grid_point: 183<br />- grid_point: 184<br />- grid_point: 192<br />- grid_point: 193<br />- grid_point: 202<br />- grid_point: 273<br />- grid_point: 274<br />- grid_point: 283<br />- grid_point: 364</pre>
<p>one finds which grid points needed to be calculated, for instance using following</p>
<pre class="prettyprint lang-sh"><span class="n">$ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCARÂ --sigma 0.1 --br --write-gamma --gp="0 1 2</span></pre>
-<p><span class="n">one calculates grid points 0, 1, 2. To automize one can use for instance scripts to submit 5 points in series, see <a target="_self" title="" class="internal-link" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/gofree-cond1.sh">gofree-cond1.sh </a></span></p>
+<p><span class="n">one calculates grid points 0, 1, 2. To automize one can use for instance scripts to submit 5 points in series, see <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/gofree-cond1.sh">gofree-cond1.sh </a></span></p>
<pre class="prettyprint lang-sh"><span class="n">$ qsub gofree-cond1.sh</span></pre>
<p><span class="n">Finally the thermal conductivity result is produced by grouping single conductivity per grid calculations using </span></p>
<pre class="prettyprint lang-sh"><span class="n">$ <span class="n">phono3py</span> <span class="o">--</span><span class="n">fc3</span> <span class="o">--</span><span class="n">fc2</span> <span class="o">--</span><span class="n">dim</span><span class="o">=</span><span class="s2">"2 2 2"</span> <span class="o">--</span><span class="n">mesh</span><span class="o">=</span><span class="s2">"</span>9 9 9" <span class="o">--</span><span class="n">br</span> <span class="o">--</span><span class="n">read_gamma</span></span></pre>
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<div id="parent-fieldname-text-fd059ba857eb4bd39efbd852b0776d08" class="">
- <p>Welcome to Salomon supercomputer cluster. The Salomon cluster consists of 1008 compute nodes, totaling 24192 compute cores with 129TB RAM and giving over 2 Pflop/s theoretical peak performance. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 24 cores, at least 128GB RAM. Nodes are interconnected by 7D Enhanced hypercube Infiniband network and equipped with Intel Xeon E5-2680v3 processors. The Salomon cluster consists of 576 nodes without accelerators and 432 nodes equipped with Intel Xeon Phi MIC accelerators. Read more in <a target="_self" title="" class="internal-link" href="salomon/hardware-overview-1/hardware-overview.html">Hardware Overview</a>.</p>
+ <p>Welcome to Salomon supercomputer cluster. The Salomon cluster consists of 1008 compute nodes, totaling 24192 compute cores with 129TB RAM and giving over 2 Pflop/s theoretical peak performance. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 24 cores, at least 128GB RAM. Nodes are interconnected by 7D Enhanced hypercube Infiniband network and equipped with Intel Xeon E5-2680v3 processors. The Salomon cluster consists of 576 nodes without accelerators and 432 nodes equipped with Intel Xeon Phi MIC accelerators. Read more in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/hardware-overview-1/hardware-overview">Hardware Overview</a>.</p>
<p>The cluster runs CentOS Linux <a class="external-link" href="http://www.bull.com/bullx-logiciels/systeme-exploitation.html" target="_self" title=""><span class="WYSIWYG_LINK"></span></a><span class="internal-link">operating system</span>, which is compatible with the <span class="WYSIWYG_LINK">RedHat</span> <a class="external-link" href="http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg" target="_self" title=""><span class="WYSIWYG_LINK">Linux family.</span></a></p>
<p style="padding-left: 30px; "><strong>Water-cooled Compute Nodes With MIC Accelerator</strong></p>
-<p style="padding-left: 30px; "><a target="_self" title="" class="internal-link" href="salomon/salomon_1.jpg"><img title="Salomon" class="image-inline" alt="Salomon" src="salomon/salomon/%40%40images/8fe6c2ad-25f3-48cf-abbb-6f8ba653b93e.jpg" /></a></p>
-<p style="padding-left: 30px; "><img title="Salomon" class="image-inline" alt="Salomon" src="salomon/salomon-1/%40%40images/ba2c321e-1554-4826-b6ec-3c68d370cd9f.jpg" /></p>
+<p style="padding-left: 30px; "><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/salomon"><img alt="Salomon" class="image-inline" title="Salomon" src="https://docs.it4i.cz/salomon/salomon/@@images/8fe6c2ad-25f3-48cf-abbb-6f8ba653b93e.jpeg" /></a></p>
+<p style="padding-left: 30px; "><img alt="Salomon" class="image-inline" title="Salomon" src="https://docs.it4i.cz/salomon/salomon-1/@@images/ba2c321e-1554-4826-b6ec-3c68d370cd9f.jpeg" /></p>
<p style="padding-left: 30px; "><strong>Tape Library T950B</strong></p>
-<p style="padding-left: 30px; "><img title="Salomon" class="image-inline" alt="Salomon" src="salomon/salomon-3/%40%40images/d2a6de55-62fc-454f-adda-a6a25e3f44dd.jpg" /></p>
-<p style="padding-left: 30px; "><img title="Salomon" class="image-inline" alt="Salomon" src="salomon/salomon-4/%40%40images/82997462-cd88-49eb-aad5-71d77903d903.jpg" /></p>
+<p style="padding-left: 30px; "><img alt="Salomon" class="image-inline" title="Salomon" src="https://docs.it4i.cz/salomon/salomon-3/@@images/d2a6de55-62fc-454f-adda-a6a25e3f44dd.jpeg" /></p>
+<p style="padding-left: 30px; "><img alt="Salomon" class="image-inline" title="Salomon" src="https://docs.it4i.cz/salomon/salomon-4/@@images/82997462-cd88-49eb-aad5-71d77903d903.jpeg" /></p>
</div>
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<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
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+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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@@ -315,7 +312,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -331,7 +328,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -347,7 +344,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="salomon.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -363,7 +360,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="salomon/hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -379,7 +376,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="salomon/accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -395,7 +392,7 @@
- <a title="" class="state-published contenttype-document" href="salomon/environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -411,7 +408,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="salomon/list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -427,7 +424,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="salomon/resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -443,7 +440,7 @@
- <a title="" class="state-published contenttype-document" href="salomon/compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -459,7 +456,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="salomon/storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -475,7 +472,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="salomon/network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -491,10 +488,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="salomon/software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -510,7 +507,7 @@
- <a title="" class="state-published contenttype-document" href="salomon/prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -535,7 +532,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -551,7 +548,7 @@
- <a title="" class="state-published contenttype-document" href="links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -567,7 +564,7 @@
- <a title="" class="state-published contenttype-collection" href="changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -583,7 +580,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -651,12 +648,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -672,7 +669,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:15:49 GMT -->
</html>
diff --git a/docs.it4i.cz/salomon.md b/docs.it4i.cz/salomon.md
new file mode 100644
index 0000000000000000000000000000000000000000..ffd19820cf1814a49ec480289d02d1f3836e4f39
--- /dev/null
+++ b/docs.it4i.cz/salomon.md
@@ -0,0 +1,24 @@
+Introduction
+============
+Welcome to Salomon supercomputer cluster. The Salomon cluster consists
+of 1008 compute nodes, totaling 24192 compute cores with 129TB RAM and
+giving over 2 Pflop/s theoretical peak performance. Each node is a <span
+class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 24
+cores, at least 128GB RAM. Nodes are interconnected by 7D Enhanced
+hypercube Infiniband network and equipped with Intel Xeon E5-2680v3
+processors. The Salomon cluster consists of 576 nodes without
+accelerators and 432 nodes equipped with Intel Xeon Phi MIC
+accelerators. Read more in [Hardware
+Overview](https://docs.it4i.cz/salomon/hardware-overview-1/hardware-overview).
+The cluster runs CentOS Linux [<span
+class="WYSIWYG_LINK"></span>](http://www.bull.com/bullx-logiciels/systeme-exploitation.html)<span
+class="internal-link">operating system</span>, which is compatible with
+the <span class="WYSIWYG_LINK">RedHat</span> [<span
+class="WYSIWYG_LINK">Linux
+family.</span>](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
+**Water-cooled Compute Nodes With MIC Accelerator**
+[](https://docs.it4i.cz/salomon/salomon)
+
+**Tape Library T950B**
+
+
diff --git a/salomon/accessing-the-cluster/shell-and-data-access.html b/docs.it4i.cz/salomon/accessing-the-cluster.html
old mode 100755
new mode 100644
similarity index 71%
rename from salomon/accessing-the-cluster/shell-and-data-access.html
rename to docs.it4i.cz/salomon/accessing-the-cluster.html
index c39d28d282b33b37bf905053504137c538e43499..5c5b4b9611778ee8090f067f9657515c7a3d53db
--- a/salomon/accessing-the-cluster/shell-and-data-access.html
+++ b/docs.it4i.cz/salomon/accessing-the-cluster.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:41 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/IEFixes-cachekey-ec9b60024fd235ff2c883b4b54db91cb.css" />
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- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Shell access and data transfer — IT4I Docs</title>
- <link rel="canonical" href="shell-and-data-access.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="shell-and-data-access.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="shell-and-data-access.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="shell-and-data-access.html">Accessing the Cluster</a>
+ <a href="https://docs.it4i.cz/salomon/accessing-the-cluster">Accessing the Cluster</a>
<span class="breadcrumbSeparator">
/
@@ -278,7 +275,7 @@
</tr>
</tbody>
</table>
-<p>The authentication is by the <a target="_self" title="" class="internal-link" href="../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html">private key</a></p>
+<p>The authentication is by the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">private key</a></p>
<p class="callout">Please verify SSH fingerprints during the first logon. They are identical on all login nodes:<span class="monospace"><br />f6:28:98:e4:f9:b2:a6:8f:f2:f4:2d:0a:09:67:69:80 (DSA)<br />70:01:c9:9a:5d:88:91:c7:1b:c0:84:d1:fa:4e:83:5c (RSA)</span></p>
<p>Â </p>
<p>Private keys authentication:</p>
@@ -286,10 +283,10 @@
<pre class="prettyprint lang-sh">local $ ssh -i /path/to/id_rsa username@salomon.it4i.cz</pre>
<p>If you see warning message "UNPROTECTED PRIVATE KEY FILE!", use this command to set lower permissions to private key file.</p>
<pre class="prettyprint lang-sh">local $ chmod 600 /path/to/id_rsa</pre>
-<p>On <strong>Windows</strong>, use <a target="_self" title="" class="internal-link" href="../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html">PuTTY ssh client</a>.</p>
+<p>On <strong>Windows</strong>, use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty">PuTTY ssh client</a>.</p>
<p>After logging in, you will see the command prompt:</p>
<pre class=" ">Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â _____Â Â Â Â Â Â _Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â <br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â / ____|Â Â Â Â | |Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â <br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â | (___Â Â __ _| | ___Â _ __ ___Â Â ___Â _ __ Â <br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â \___ \ / _` | |/ _ \| '_ ` _ \ / _ \| '_ \ <br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â ____) | (_| | | (_) | | | | | | (_) | | | |<br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â |_____/ \__,_|_|\___/|_| |_| |_|\___/|_| |_|<br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â <br /><br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â http://www.it4i.cz/?lang=en<br /><br /><br />Last login: Tue Jul 9 15:57:38 2013 from your-host.example.com<br />[username@login2.salomon ~]$</pre>
-<p class="callout">The environment is <strong>not</strong> shared between login nodes, except for <a target="_self" title="" class="internal-link" href="../storage/storage.html">shared filesystems</a>.</p>
+<p class="callout">The environment is <strong>not</strong> shared between login nodes, except for <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/storage/storage">shared filesystems</a>.</p>
<h2 class=" ">Data Transfer</h2>
<p>Data in and out of the system may be transferred by the <a class="external-link" href="http://en.wikipedia.org/wiki/Secure_copy" target="_self" title="">scp</a> and sftp protocols.</p>
<p class="hiddenForView">In case large volumes of data are transferred, use dedicated data mover nodes cedge[1-3].salomon.it4i.cz for increased performance.</p>
@@ -325,7 +322,7 @@
</tr>
</tbody>
</table>
-<p>Â The authentication is by the <a target="_self" title="" class="internal-link" href="../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html">private key</a></p>
+<p>Â The authentication is by the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">private key</a></p>
<p class="hiddenForView">HTML commented section #2 (ssh transfer performance data need to be verified)</p>
<p>On linux or Mac, use scp or sftp client to transfer the data to Salomon:</p>
@@ -339,7 +336,7 @@
<p>Learn more on ssh, scp and sshfs by reading the manpages</p>
<pre class="prettyprint lang-sh">$ man ssh<br />$ man scp<br />$ man sshfs</pre>
<p><span>On Windows</span>, use <a class="external-link" href="http://winscp.net/eng/download.php" target="_self" title="">WinSCP client</a> to transfer the data. The <a class="external-link" href="http://code.google.com/p/win-sshfs/" target="_self" title="">win-sshfs client</a> provides a way to mount the Salomon filesystems directly as an external disc.</p>
-<p>More information about the shared file systems is available <a target="_self" title="" class="internal-link" href="../storage/storage.html">here</a>.</p>
+<p>More information about the shared file systems is available <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/storage/storage">here</a>.</p>
</div>
@@ -416,7 +413,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -432,7 +429,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -448,7 +445,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -464,7 +461,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -480,7 +477,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -496,7 +493,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="shell-and-data-access.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -512,7 +509,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="shell-and-data-access.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access">
<span>Shell access and data transfer</span>
</a>
@@ -528,7 +525,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface">
<span>Graphical User Interface</span>
</a>
@@ -544,7 +541,7 @@
- <a title="" class="state-published contenttype-document" href="vpn-access.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/vpn-access">
<span>VPN Access</span>
</a>
@@ -560,7 +557,7 @@
- <a title="" class="state-published contenttype-document" href="outgoing-connections.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections">
<span>Outgoing connections</span>
</a>
@@ -585,7 +582,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -601,7 +598,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -617,7 +614,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -633,7 +630,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -649,7 +646,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -665,7 +662,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -681,10 +678,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -700,7 +697,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -725,7 +722,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -741,7 +738,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -757,7 +754,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -773,7 +770,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -812,14 +809,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -841,12 +838,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -862,7 +859,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:42 GMT -->
</html>
diff --git a/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md b/docs.it4i.cz/salomon/accessing-the-cluster.md
similarity index 60%
rename from salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
rename to docs.it4i.cz/salomon/accessing-the-cluster.md
index d215ce9a0b52c3bd2efb21057356bccb88ed137a..db82c44a3fd9611f54757a8dde3e776d15d7e67f 100644
--- a/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
+++ b/docs.it4i.cz/salomon/accessing-the-cluster.md
@@ -1,29 +1,30 @@
-
-
+Shell access and data transfer
+==============================
+
Interactive Login
-----------------
The Salomon cluster is accessed by SSH protocol via login nodes login1,
login2, login3 and login4 at address salomon.it4i.cz. The login nodes
may be addressed specifically, by prepending the login node name to the
address.
-The alias salomon.it4i.cz is currently not available through VPN
+The alias <span>salomon.it4i.cz is currently not available through VPN
connection. Please use loginX.salomon.it4i.cz when connected to
-VPN.
+VPN.</span>
Login address Port Protocol Login node
- ------------------------ ------ ---------- -----------------------------------------
+ - ------ ---------- ------------------
salomon.it4i.cz 22 ssh round-robin DNS record for login[1-4]
login1.salomon.it4i.cz 22 ssh login1
login2.salomon.it4i.cz 22 ssh login2
login3.salomon.it4i.cz 22 ssh login3
login4.salomon.it4i.cz 22 ssh login4
The authentication is by the [private
-key](../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+key](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys)
Please verify SSH fingerprints during the first logon. They are
-identical on all login nodes
-f62898e4f9b2a68ff2f42d0a09676980Â (DSA)
-7001c99a5d8891c71bc084d1fa4e835c (RSA)
+identical on all login nodes:<span class="monospace">
+f6:28:98:e4:f9:b2:a6:8f:f2:f4:2d:0a:09:67:69:80Â (DSA)
+70:01:c9:9a:5d:88:91:c7:1b:c0:84:d1:fa:4e:83:5c (RSA)</span>
Â
-Private keys authentication
+Private keys authentication:
On **Linux** or **Mac**, use
``` {.prettyprint .lang-sh}
local $ ssh -i /path/to/id_rsa username@salomon.it4i.cz
@@ -34,8 +35,8 @@ command to set lower permissions to private key file.
local $ chmod 600 /path/to/id_rsa
```
On **Windows**, use [PuTTY ssh
-client](../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
-After logging in, you will see the command prompt
+client](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty).
+After logging in, you will see the command prompt:
                   _____      _                           Â
                  / ____|    | |                          Â
                 | (___  __ _| | ___ _ __ ___  ___ _ __ Â
@@ -43,37 +44,38 @@ After logging in, you will see the command prompt
                  ____) | (_| | | (_) | | | | | | (_) | | | |
                 |_____/ __,_|_|___/|_| |_| |_|___/|_| |_|
                Â
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â http//www.it4i.cz/?lang=en
- Last login Tue Jul 9 155738 2013 from your-host.example.com
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â http://www.it4i.cz/?lang=en
+ Last loginTue Jul 9 15:57:38 2013 from your-host.example.com
[username@login2.salomon ~]$
The environment is **not** shared between login nodes, except for
-[shared filesystems](../../storage/storage.html).
+[shared
+filesystems](https://docs.it4i.cz/salomon/storage/storage).
Data Transfer
-------------
Data in and out of the system may be transferred by the
-[scp](http//en.wikipedia.org/wiki/Secure_copy) and sftp
+[scp](http://en.wikipedia.org/wiki/Secure_copy) and sftp
protocols.
In case large volumes of data are transferred, use dedicated data mover
nodes cedge[1-3].salomon.it4i.cz for increased performance.
Â
HTML commented section #1 (removed cedge servers from the table)
Address Port Protocol
- ------------------------------------------------------ ------ -----------------------------------------
+ -------- ------ ------------------
salomon.it4i.cz 22 scp, sftp
login1.salomon.it4i.cz 22 scp, sftp
login2.salomon.it4i.cz 22 scp, sftp
- login3.salomon.it4i.cz 22 scp, sftp
+ <span class="discreet"></span>login3.salomon.it4i.cz 22 <span class="discreet"></span>scp, sftp
login4.salomon.it4i.cz 22 scp, sftp
 The authentication is by the [private
-key](../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+key](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys)
HTML commented section #2 (ssh transfer performance data need to be
verified)
-On linux or Mac, use scp or sftp client to transfer the data to Salomon
+On linux or Mac, use scp or sftp client to transfer the data to Salomon:
``` {.prettyprint .lang-sh}
-local $ scp -i /path/to/id_rsa my-local-file username@salomon.it4i.czdirectory/file
+local $ scp -i /path/to/id_rsa my-local-file username@salomon.it4i.cz:directory/file
```
``` {.prettyprint .lang-sh}
-local $ scp -i /path/to/id_rsa -r my-local-dir username@salomon.it4i.czdirectory
+local $ scp -i /path/to/id_rsa -r my-local-dir username@salomon.it4i.cz:directory
```
> or
``` {.prettyprint .lang-sh}
@@ -81,9 +83,9 @@ local $ sftp -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz
```
Very convenient way to transfer files in and out of the Salomon computer
is via the fuse filesystem
-[sshfs](http//linux.die.net/man/1/sshfs)
+[sshfs](http://linux.die.net/man/1/sshfs)
``` {.prettyprint .lang-sh}
-local $ sshfs -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz. mountpoint
+local $ sshfs -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz:. mountpoint
```
Using sshfs, the users Salomon home directory will be mounted on your
local computer, just like an external disk.
@@ -93,37 +95,10 @@ $ man ssh
$ man scp
$ man sshfs
```
-On Windows, use [WinSCP
-client](http//winscp.net/eng/download.php) to transfer
+<span>On Windows</span>, use [WinSCP
+client](http://winscp.net/eng/download.php) to transfer
the data. The [win-sshfs
-client](http//code.google.com/p/win-sshfs/) provides a
+client](http://code.google.com/p/win-sshfs/) provides a
way to mount the Salomon filesystems directly as an external disc.
More information about the shared file systems is available
-[here](../../storage/storage.html).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../shell-and-data-access.html)
-
- - [Shell access and data
- transfer](../shell-and-data-access.html)
-
-
- - [Graphical User
+[here](https://docs.it4i.cz/salomon/storage/storage).
diff --git a/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface.html b/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface.html
new file mode 100644
index 0000000000000000000000000000000000000000..35cf1ad696acf13ac5c8083c479a130569d074e1
--- /dev/null
+++ b/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface.html
@@ -0,0 +1,662 @@
+
+<!DOCTYPE html>
+
+<html xmlns="http://www.w3.org/1999/xhtml" lang="cs">
+
+
+
+
+
+
+
+
+<head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+
+ <base href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface" /><!--[if lt IE 7]></base><![endif]-->
+
+
+
+
+
+
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <!--[if lt IE 8]>
+
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/IEFixes-cachekey-ec9b60024fd235ff2c883b4b54db91cb.css" />
+ <![endif]-->
+
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+
+
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+<p>Read more about configuring <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc"><b>X Window System</b></a>.</p>
+<h2>VNC</h2>
+<p>The <b>Virtual Network Computing</b> (<b>VNC</b>) is a graphical <span class="link-external"><a href="http://en.wikipedia.org/wiki/Desktop_sharing" title="Desktop sharing">desktop sharing</a></span> system that uses the <span class="link-external"><a href="http://en.wikipedia.org/wiki/RFB_protocol" title="RFB protocol">Remote Frame Buffer protocol (RFB)</a></span> to remotely control another <span class="link-external"><a href="http://en.wikipedia.org/wiki/Computer" title="Computer">computer</a></span>.</p>
+<p>Read more about configuring <strong><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc">VNC</a></strong>.</p>
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diff --git a/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface.md b/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface.md
new file mode 100644
index 0000000000000000000000000000000000000000..ff3738063f55085dad7cad70901c9102e176ce07
--- /dev/null
+++ b/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface.md
@@ -0,0 +1,21 @@
+Graphical User Interface
+========================
+
+X Window System
+---------------
+The X Window system is a principal way to get GUI access to the
+clusters.
+Read more about configuring [**X Window
+System**](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc).
+VNC
+---
+The **Virtual Network Computing** (**VNC**) is a graphical <span
+class="link-external">[desktop
+sharing](http://en.wikipedia.org/wiki/Desktop_sharing "Desktop sharing")</span>
+system that uses the <span class="link-external">[Remote Frame Buffer
+protocol
+(RFB)](http://en.wikipedia.org/wiki/RFB_protocol "RFB protocol")</span>
+to remotely control another <span
+class="link-external">[computer](http://en.wikipedia.org/wiki/Computer "Computer")</span>.
+Read more about configuring
+**[VNC](https://docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc)**.
diff --git a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.html b/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc.html
old mode 100755
new mode 100644
similarity index 74%
rename from get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.html
rename to docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc.html
index 88ed23c5ad4d1137778e074d2ad0231b1ca41150..9b1ddb1cfe46a417466040ebce7c3d51eb3c3ca3
--- a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.html
+++ b/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc.html
@@ -10,45 +10,42 @@
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<div id="parent-fieldname-text-5739e5d4b93b40a6b3d987bd4047d4e0" class="">
<p>The <b>Virtual Network Computing</b> (<b>VNC</b>) is a graphical <a href="http://en.wikipedia.org/wiki/Desktop_sharing" title="Desktop sharing">desktop sharing</a> system that uses the <a href="http://en.wikipedia.org/wiki/RFB_protocol" title="RFB protocol">Remote Frame Buffer protocol (RFB)</a> to remotely control another <a href="http://en.wikipedia.org/wiki/Computer" title="Computer">computer</a>. It transmits the <a href="http://en.wikipedia.org/wiki/Computer_keyboard" title="Computer keyboard">keyboard</a> and <a class="mw-redirect" href="http://en.wikipedia.org/wiki/Computer_mouse" title="Computer mouse">mouse</a> events from one computer to another, relaying the graphical <a class="mw-redirect" href="http://en.wikipedia.org/wiki/Computer_screen" title="Computer screen">screen</a> updates back in the other direction, over a <a href="http://en.wikipedia.org/wiki/Computer_network" title="Computer network">network</a>.<sup class="reference" id="cite_ref-1"><a href="http://en.wikipedia.org/wiki/Virtual_Network_Computing#cite_note-1"><span>[</span>1<span>]</span></a></sup></p>
-<p>The recommended clients are <a class="external-link" href="http://www.tightvnc.com/" target="_self" title="">TightVNC</a> or <a class="external-link" href="http://sourceforge.net/apps/mediawiki/tigervnc/index.php?title=Main_Page" target="_self" title="">TigerVNC</a> (free, open source, available for almost any platform).</p>
+<p>The recommended clients are <a class="external-link" href="http://www.tightvnc.com" target="_self" title="">TightVNC</a> or <a class="external-link" href="http://sourceforge.net/apps/mediawiki/tigervnc/index.php?title=Main_Page" target="_self" title="">TigerVNC</a> (free, open source, available for almost any platform).</p>
<h2 class=" ">Create VNC password</h2>
<p class="callout">Local VNC password should be set before the first login. Do use a strong password.</p>
<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">~]</span><span class="pln">$ vncpasswd</span><br /><span class="typ">Password</span><span class="pun">:</span><br /><span class="typ">Verify</span><span class="pun">:</span></pre>
@@ -285,22 +282,22 @@
<p>Search for the localhost and port number (in this case 127.0.0.1:5961).<strong><br /></strong></p>
<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ netstat </span><span class="pun">-</span><span class="pln">tanp </span><span class="pun">|</span><span class="pln"> grep </span><span class="typ">Xvnc</span><br /><span class="pun">(</span><span class="typ">Not</span><span class="pln"> all processes could be identified</span><span class="pun">,</span><span class="pln"> non</span><span class="pun">-</span><span class="pln">owned process info</span><br /><span class="pln"> will not be shown</span><span class="pun">,</span><span class="pln"> you would have to be root to see it all</span><span class="pun">.)</span><br /><span class="pln">tcp       </span><span class="lit">0</span><span class="pln">     </span><span class="lit">0</span><span class="pln"> </span><span class="lit">127.0</span><span class="pun">.</span><span class="lit">0.1</span><span class="pun">:</span><span class="lit">5961</span><span class="pln">             </span><span class="lit">0.0</span><span class="pun">.</span><span class="lit">0.0</span><span class="pun">:*</span><span class="pln">                  LISTEN     </span><span class="lit">24031</span><span class="pun">/</span><span class="typ">Xvnc</span></pre>
<p>On the PuTTY Configuration screen go to Connection->SSH->Tunnels to set up the tunnel.</p>
-<p>Fill the Source port and Destination fields. <strong>Do not forget to click the Add button</strong>.<br /><br /> <a target="_blank" title="" class="internal-link" href="vnc/2015-10-02_135100cV.png"><img title="PuTTY Tunnel" class="image-inline" alt="PuTTY - Create tunnel" src="vnc/putty-tunnel.png/%40%40images/4c66cd51-c858-473b-98c2-8d901aea7118.png" /></a></p>
+<p>Fill the Source port and Destination fields. <strong>Do not forget to click the Add button</strong>.<br /><br /> <a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/putty-tunnel.png"><img alt="PuTTY - Create tunnel" class="image-inline" title="PuTTY Tunnel" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/putty-tunnel.png/@@images/4c66cd51-c858-473b-98c2-8d901aea7118.png" /></a></p>
<p>Run the VNC client of your choice, select VNC server 127.0.0.1, port 5961 and connect using VNC password.</p>
<h3 class=" ">Example of starting TigerVNC viewer</h3>
-<p><img title="Vncviewer" class="image-inline" alt="TigerVNC vncviewer" src="../../../anselm-cluster-documentation/vncviewer.png/%40%40images/bb4cedff-4cb6-402b-ac79-039186fe5df3.png" /></p>
+<p><img alt="TigerVNC vncviewer" class="image-inline" title="Vncviewer" src="https://docs.it4i.cz/anselm-cluster-documentation/vncviewer.png/@@images/bb4cedff-4cb6-402b-ac79-039186fe5df3.png" /></p>
<p>In this example, we connect to VNC server on port 5961, via the ssh tunnel, using TigerVNC viewer. The connection is encrypted and secured. The VNC server listening on port 5961 provides screen of 1600x900 pixels.</p>
<h3 class=" ">Example of starting TightVNC Viewer</h3>
<p>Use your VNC password to log using TightVNC Viewer and start a Gnome Session on the login node.</p>
-<p><a target="_blank" title="" class="internal-link" href="vnc/2015-10-02_135128cV.png"><strong><img title="" class="image-inline" alt="" src="vnc/TightVNC_login.png/%40%40images/e53354d8-a2e8-4947-92b3-dd107d498408.png" /></strong></a></p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/TightVNC_login.png"><strong><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/TightVNC_login.png/@@images/e53354d8-a2e8-4947-92b3-dd107d498408.png" /></strong></a></p>
<h2 class=" ">Gnome session</h2>
<p>You should see after the successful login.</p>
-<p><a target="_blank" title="" class="internal-link" href="../../gnome_screen.html"><img title="Default Gnome session" class="image-inline" alt="Default Gnome session" src="../../../salomon/gnome_screen.jpg/%40%40images/7758b792-24eb-48dc-bf72-618cda100fda.png" /></a></p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/get-started-with-it4innovations/gnome_screen.jpg"><img alt="Default Gnome session" class="image-inline" title="Default Gnome session" src="https://docs.it4i.cz/salomon/gnome_screen.jpg/@@images/7758b792-24eb-48dc-bf72-618cda100fda.png" /></a></p>
<h3 class=" "><strong>Disable your Gnome session screensaver<br /></strong></h3>
<p>Open Screensaver preferences dialog:</p>
-<p><a target="_blank" title="" class="internal-link" href="../../../salomon/salomon-gdm.png"><img title="Screensaver Preferences" class="image-inline" alt="Screensaver Preferences" src="vnc/gdmscreensaver.png/%40%40images/8e80a92f-f691-4d92-8e62-344128dcc00b.png" /></a></p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/gnome_screen.jpg"><img alt="Screensaver Preferences" class="image-inline" title="Screensaver Preferences" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmscreensaver.png/@@images/44048cfa-e854-4cb4-902b-c173821c2db1.png" /></a></p>
<p>Uncheck both options below the slider:</p>
-<p><a target="_blank" title="" class="internal-link" href="vnc/gdm-disable-screensaver-acV.png"><img title="Disable lock screen and screensaver" class="image-inline" alt="Disable lock screen and screensaver" src="vnc/gdmdisablescreensaver.png/%40%40images/0259b284-18eb-402c-a55c-584562e26b47.png" /></a></p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png"><img alt="Disable lock screen and screensaver" class="image-inline" title="Disable lock screen and screensaver" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png/@@images/0259b284-18eb-402c-a55c-584562e26b47.png" /></a></p>
<h3 class=" ">Kill screensaver if locked screen</h3>
<p>If the screen gets locked you have to kill the screensaver. Do not to forget to disable the screensaver then.</p>
<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ ps aux </span><span class="pun">|</span><span class="pln"> grep screen</span><br /><span class="pln">username    </span><span class="lit">1503</span><span class="pln"> </span><span class="lit">0.0</span><span class="pln"> </span><span class="lit">0.0</span><span class="pln"> </span><span class="lit">103244</span><span class="pln">  </span><span class="lit">892</span><span class="pln"> pts</span><span class="pun">/</span><span class="lit">4</span><span class="pln">   S</span><span class="pun">+</span><span class="pln">  </span><span class="lit">14</span><span class="pun">:</span><span class="lit">37</span><span class="pln">  </span><span class="lit">0</span><span class="pun">:</span><span class="lit">00</span><span class="pln"> grep screen</span><br /><span class="pln">username    </span><span class="lit">24316</span><span class="pln"> </span><span class="lit">0.0</span><span class="pln"> </span><span class="lit">0.0</span><span class="pln"> </span><span class="lit">270564</span><span class="pln"> </span><span class="lit">3528</span><span class="pln"> </span><span class="pun">?</span><span class="pln">       </span><span class="typ">Ss</span><span class="pln">  </span><span class="lit">14</span><span class="pun">:</span><span class="lit">12</span><span class="pln">  </span><span class="lit">0</span><span class="pun">:</span><span class="lit">00</span><span class="pln"> gnome</span><span class="pun">-</span><span class="pln">screensaver</span><br /><br /><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ kill </span><span class="lit">24316</span></pre>
@@ -310,16 +307,16 @@
<p>Or this way:</p>
<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$Â p</span><span class="pln">kill vnc</span></pre>
<h2 class=" ">GUI applications on compute nodes over VNC</h2>
-<p>The very <a target="_self" title="" class="anchor-link" href="x-window-and-vnc.html#gui-applications-on-compute-nodes">same methods as described above</a>, may be used to run the GUI applications on compute nodes. However, for <strong>maximum performance</strong>, proceed following these steps:</p>
-<p>Open a Terminal (Applications -> System Tools -> Terminal). Run all the next commands in the terminal.<br /><br /><a target="_blank" title="" class="internal-link" href="vnc/2015-10-07_121839acV.png"><img title="gnome-terminal.png" class="image-inline" alt="gnome-terminal.png" src="vnc/gnome-terminal.png/%40%40images/b44f5d8c-156d-4041-9bb0-973996413834.png" /></a></p>
+<p>The very <a title="" class="anchor-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-and-vnc#gui-applications-on-compute-nodes">same methods as described above</a>, may be used to run the GUI applications on compute nodes. However, for <strong>maximum performance</strong>, proceed following these steps:</p>
+<p>Open a Terminal (Applications -> System Tools -> Terminal). Run all the next commands in the terminal.<br /><br /><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-terminal.png"><img alt="gnome-terminal.png" class="image-inline" title="gnome-terminal.png" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-terminal.png/@@images/dc0f0207-c614-49be-9cfb-905a523c5a39.png" /></a></p>
<p>Allow incoming X11 graphics from the compute nodes at the login node:</p>
<pre class="prettyprint lang-sh prettyprinted"><span class="pln">$ xhost </span><span class="pun">+</span></pre>
-<p>Get an interactive session on a compute node (for more detailed info <a target="_self" title="" class="internal-link" href="../../../anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.html">look here</a>). Use the <strong>-v DISPLAY</strong> option to propagate the DISPLAY on the compute node. In this example, we want a complete node (24 cores in this example) from the production queue:</p>
+<p>Get an interactive session on a compute node (for more detailed info <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">look here</a>). Use the <strong>-v DISPLAY</strong> option to propagate the DISPLAY on the compute node. In this example, we want a complete node (24 cores in this example) from the production queue:</p>
<pre class="prettyprint lang-sh prettyprinted"><span class="pln">$ qsub </span><span class="pun">-</span><span class="pln">I </span><span class="pun">-</span><span class="pln">v DISPLAY</span><span class="pun">=</span><span class="pln">$</span><span class="pun">(</span><span class="pln">uname </span><span class="pun">-</span><span class="pln">n</span><span class="pun">):</span><span class="pln">$</span><span class="pun">(</span><span class="pln">echo $DISPLAY </span><span class="pun">|</span><span class="pln"> cut </span><span class="pun">-</span><span class="pln">d </span><span class="str">':'</span><span class="pln"> </span><span class="pun">-</span><span class="pln">f </span><span class="lit">2</span><span class="pun">)</span><span class="pln"> </span><span class="pun">-</span><span class="pln">A PROJECT_ID </span><span class="pun">-</span><span class="pln">q qprod </span><span class="pun">-</span><span class="pln">l select</span><span class="pun">=</span><span class="lit">1</span><span class="pun">:</span><span class="pln">ncpus</span><span class="pun">=24</span><span class="lit"></span></pre>
<p>Test that the DISPLAY redirection into your VNC session works, by running a X11 application (e. g. XTerm) on the assigned compute node:</p>
<pre class="prettyprint lang-sh prettyprinted"><span class="pln">$ xterm<br /></span></pre>
<p>Example described above:</p>
-<p><a target="_blank" title="" class="internal-link" href="vnc/2015-10-07_120255acV.png"><img title="gnome-compute-nodes-over-vnc.png" class="image-inline" alt="gnome-compute-nodes-over-vnc.png" src="vnc/gnome-compute-nodes-over-vnc.png/%40%40images/d4c9b6b6-6e2c-48c0-84dd-26d291517355.png" /></a></p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-compute-nodes-over-vnc.png"><img alt="gnome-compute-nodes-over-vnc.png" class="image-inline" title="gnome-compute-nodes-over-vnc.png" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-compute-nodes-over-vnc.png/@@images/d4c9b6b6-6e2c-48c0-84dd-26d291517355.png" /></a></p>
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@@ -395,7 +392,7 @@
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+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
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@@ -411,7 +408,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
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@@ -427,7 +424,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources">
<span>Applying for Resources</span>
</a>
@@ -459,7 +456,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../obtaining-login-credentials.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">
<span>Obtaining Login Credentials</span>
</a>
@@ -475,7 +472,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../shell-access-and-data-transfer.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">
<span>Accessing the Clusters</span>
</a>
@@ -491,7 +488,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../shell-access-and-data-transfer.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer">
<span>Shell access and data transfer</span>
</a>
@@ -507,7 +504,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../graphical-user-interface.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface">
<span>Graphical User Interface</span>
</a>
@@ -523,7 +520,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="x-window-system.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system">
<span>X Window System</span>
</a>
@@ -539,7 +536,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="vnc.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc">
<span>VNC</span>
</a>
@@ -582,7 +579,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -630,7 +627,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -646,7 +643,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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<div id="portal-footer">
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
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- <a href="https://extranet.it4i.cz/">Extranet</a>
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+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
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diff --git a/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc.md b/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc.md
new file mode 100644
index 0000000000000000000000000000000000000000..639e7df17d9fb68eae74bd555db95cd03c5a5262
--- /dev/null
+++ b/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc.md
@@ -0,0 +1,196 @@
+VNC
+===
+
+The **Virtual Network Computing** (**VNC**) is a graphical [desktop
+sharing](http://en.wikipedia.org/wiki/Desktop_sharing "Desktop sharing")
+system that uses the [Remote Frame Buffer protocol
+(RFB)](http://en.wikipedia.org/wiki/RFB_protocol "RFB protocol") to
+remotely control another
+[computer](http://en.wikipedia.org/wiki/Computer "Computer"). It
+transmits the
+[keyboard](http://en.wikipedia.org/wiki/Computer_keyboard "Computer keyboard")
+and
+[mouse](http://en.wikipedia.org/wiki/Computer_mouse "Computer mouse"){.mw-redirect}
+events from one computer to another, relaying the graphical
+[screen](http://en.wikipedia.org/wiki/Computer_screen "Computer screen"){.mw-redirect}
+updates back in the other direction, over a
+[network](http://en.wikipedia.org/wiki/Computer_network "Computer network").^[<span>[</span>1<span>]</span>](http://en.wikipedia.org/wiki/Virtual_Network_Computing#cite_note-1)^
+The recommended clients are
+[TightVNC](http://www.tightvnc.com) or
+[TigerVNC](http://sourceforge.net/apps/mediawiki/tigervnc/index.php?title=Main_Page)
+(free, open source, available for almost any platform).
+Create VNC password
+-------------------
+Local VNC password should be set before the first login. Do use a strong
+password.
+```
+[username@login2 ~]$ vncpasswd
+Password:
+Verify:
+```
+Start vncserver
+---------------
+To access VNC a local vncserver must be started first and also a tunnel
+using SSH port forwarding must be established.
+[See below](#linux-example-of-creating-a-tunnel) for the
+details on SSH tunnels. In this example we use port 61.
+You can find ports which are already occupied. Here you can see that
+ports "<span class="pln">/usr/bin/Xvnc :79"</span> and "<span
+class="pln">/usr/bin/Xvnc :60" are occupied.</span>
+```
+[username@login2 ~]$ ps aux | grep Xvnc
+username   5971 0.0 0.0 201072 92564 ?       SN  Sep22  4:19 /usr/bin/Xvnc :79 -desktop login2:79 (username) -auth /home/gre196/.Xauthority -geometry 1024x768 -rfbwait 30000 -rfbauth /home/username/.vnc/passwd -rfbport 5979 -fp catalogue:/etc/X11/fontpath.d -pn
+username   10296 0.0 0.0 131772 21076 pts/29  SN  13:01  0:01 /usr/bin/Xvnc :60 -desktop login2:61 (username) -auth /home/username/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/jir13/.vnc/passwd -rfbport 5960 -fp catalogue:/etc/X11/fontpath.d -pn
+.....
+```
+Choose free port e.g. 61 and start your VNC server:
+```
+[username@login2 ~]$ vncserver :61 -geometry 1600x900 -depth 16
+New 'login2:1 (username)' desktop is login2:1
+Starting applications specified in /home/username/.vnc/xstartup
+Log file is /home/username/.vnc/login2:1.log
+```
+Check if VNC server is started on the port (in this example 61):
+```
+[username@login2 .vnc]$ vncserver -list
+TigerVNC server sessions:
+X DISPLAY #Â Â Â Â PROCESS ID
+:61Â Â Â Â Â Â Â Â Â Â Â Â Â 18437
+```
+Another command:<span class="pln"></span>
+```
+[username@login2 .vnc]$ Â ps aux | grep Xvnc
+username   10296 0.0 0.0 131772 21076 pts/29  SN  13:01  0:01 /usr/bin/Xvnc :61 -desktop login2:61 (username) -auth /home/jir13/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/username/.vnc/passwd -rfbport 5961 -fp catalogue:/etc/X11/fontpath.d -pn
+```
+To access the VNC server you have to create a tunnel between the login
+node using TCP **port 5961** and your machine using a free TCP port (for
+simplicity the very same, in this case).
+The tunnel must point to the same login node where you launched the VNC
+server, eg. login2. If you use just cluster-name.it4i.cz, the tunnel
+might point to a different node due to DNS round robin.
+### []()[]()Linux/Mac OS example of creating a tunnel
+At your machine, create the tunnel:
+```
+local $Â ssh -TN -f username@login2.cluster-name.it4i.cz -L 5961:localhost:5961
+```
+Issue the following command to check the tunnel is established (please
+note the PID 2022 in the last column, you'll need it for closing the
+tunnel):
+```
+local $ netstat -natp | grep 5961
+(Not all processes could be identified, non-owned process info
+Â will not be shown, you would have to be root to see it all.)
+tcp       0     0 127.0.0.1:5961         0.0.0.0:*              LISTEN     2022/ssh      Â
+tcp6Â Â Â Â Â Â 0Â Â Â Â Â 0 ::1:5961Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â :::*Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â LISTENÂ Â Â Â Â 2022/ssh
+```
+Or on Mac OS use this command:
+``` {.prettyprint .lang-sh}
+local-mac $ lsof -n -i4TCP:5961 | grep LISTEN
+ssh 75890 sta545 7u IPv4 0xfb062b5c15a56a3b 0t0 TCP 127.0.0.1:5961 (LISTEN)
+```
+Connect with the VNC client:
+```
+local $ vncviewer 127.0.0.1:5961
+```
+In this example, we connect to VNC server on port 5961, via the ssh
+tunnel. The connection is encrypted and secured. The VNC server
+listening on port 5961 provides screen of 1600x900 pixels.
+You have to destroy the SSH tunnel which is still running at the
+background after you finish the work. Use the following command (PID
+2022 in this case, see the netstat command above):
+```
+kill 2022
+```
+### Windows example of creating a tunnel
+Use PuTTY to log in on cluster.
+Start vncserver using command vncserver described above.
+Search for the localhost and port number (in this case
+127.0.0.1:5961).**
+**
+```
+[username@login2 .vnc]$ netstat -tanp | grep Xvnc
+(Not all processes could be identified, non-owned process info
+Â will not be shown, you would have to be root to see it all.)
+tcp       0     0 127.0.0.1:5961             0.0.0.0:*                  LISTEN     24031/Xvnc
+```
+On the PuTTY Configuration screen go to Connection->SSH->Tunnels
+to set up the tunnel.
+Fill the Source port and Destination fields. **Do not forget to click
+the Add button**.
+[](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/putty-tunnel.png)
+Run the VNC client of your choice, select VNC server 127.0.0.1, port
+5961 and connect using VNC password.
+### Example of starting TigerVNC viewer
+
+In this example, we connect to VNC server on port 5961, via the ssh
+tunnel, using TigerVNC viewer. The connection is encrypted and secured.
+The VNC server listening on port 5961 provides screen of 1600x900
+pixels.
+### Example of starting TightVNC Viewer
+Use your VNC password to log using TightVNC Viewer and start a Gnome
+Session on the login node.
+[****](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/TightVNC_login.png)
+Gnome session
+-------------
+You should see after the successful login.
+[](https://docs.it4i.cz/get-started-with-it4innovations/gnome_screen.jpg)
+### **Disable your Gnome session screensaver
+**
+Open Screensaver preferences dialog:
+[](https://docs.it4i.cz/salomon/gnome_screen.jpg)
+Uncheck both options below the slider:
+[](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png)
+### Kill screensaver if locked screen
+If the screen gets locked you have to kill the screensaver. Do not to
+forget to disable the screensaver then.
+```
+[username@login2 .vnc]$ ps aux | grep screen
+username    1503 0.0 0.0 103244  892 pts/4   S+  14:37  0:00 grep screen
+username    24316 0.0 0.0 270564 3528 ?       Ss  14:12  0:00 gnome-screensaver
+[username@login2 .vnc]$ kill 24316
+```
+### Kill vncserver after finished work
+You should kill your VNC server using command:
+```
+[username@login2 .vnc]$ vncserver -kill :61
+Killing Xvnc process ID 7074
+Xvnc process ID 7074 already killed
+```
+Or this way:
+```
+[username@login2 .vnc]$Â pkill vnc
+```
+GUI applications on compute nodes over VNC
+-------------------
+The very [same methods as described
+above](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-and-vnc#gui-applications-on-compute-nodes),
+may be used to run the GUI applications on compute nodes. However, for
+**maximum performance**, proceed following these steps:
+Open a Terminal (Applications -> System Tools -> Terminal). Run
+all the next commands in the terminal.
+[](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-terminal.png)
+Allow incoming X11 graphics from the compute nodes at the login node:
+```
+$ xhost +
+```
+Get an interactive session on a compute node (for more detailed info
+[look
+here](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution)).
+Use the **-v DISPLAY** option to propagate the DISPLAY on the compute
+node. In this example, we want a complete node (24 cores in this
+example) from the production queue:
+```
+$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A PROJECT_ID -q qprod -l select=1:ncpus=24
+```
+Test that the DISPLAY redirection into your VNC session works, by
+running a X11 application (e. g. XTerm) on the assigned compute node:
+```
+$ xterm
+```
+Example described above:
+[](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-compute-nodes-over-vnc.png)
diff --git a/salomon/accessing-the-cluster/outgoing-connections.html b/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.html
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rename to docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.html
index df83558498b53219870a1d65d6740b5c0c3f9062..368313735421f49ef8dad2556867f33df33f6fe9
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<title>Outgoing connections — IT4I Docs</title>
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</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="shell-and-data-access.html">Accessing the Cluster</a>
+ <a href="https://docs.it4i.cz/salomon/accessing-the-cluster">Accessing the Cluster</a>
<span class="breadcrumbSeparator">
/
@@ -366,7 +363,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -382,7 +379,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -398,7 +395,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -414,7 +411,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -430,7 +427,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -446,7 +443,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="shell-and-data-access.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -462,7 +459,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access">
<span>Shell access and data transfer</span>
</a>
@@ -478,7 +475,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface">
<span>Graphical User Interface</span>
</a>
@@ -494,7 +491,7 @@
- <a title="" class="state-published contenttype-document" href="vpn-access.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/vpn-access">
<span>VPN Access</span>
</a>
@@ -510,7 +507,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="outgoing-connections.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections">
<span>Outgoing connections</span>
</a>
@@ -535,7 +532,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -551,7 +548,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -567,7 +564,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -583,7 +580,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -599,7 +596,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -615,7 +612,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -631,10 +628,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -650,7 +647,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -675,7 +672,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -691,7 +688,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -707,7 +704,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -723,7 +720,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -762,14 +759,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -791,12 +788,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -812,7 +809,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:17 GMT -->
</html>
diff --git a/salomon/accessing-the-cluster/outgoing-connections.md b/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.md
similarity index 57%
rename from salomon/accessing-the-cluster/outgoing-connections.md
rename to docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.md
index d958397c2f9bda8c61cb828d4a594b77d065b7d3..1f497c593dfc58be589659a3781714ef1df145a1 100644
--- a/salomon/accessing-the-cluster/outgoing-connections.md
+++ b/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.md
@@ -1,8 +1,9 @@
-
+Outgoing connections
+====================
+
Connection restrictions
------------------------
Outgoing connections, from Salomon Cluster login nodes to the outside
-world, are restricted to following ports
+world, are restricted to following ports:
Port Protocol
------ ----------
22 ssh
@@ -22,25 +23,25 @@ arbitrary remote host and port.
It works by tunneling the connection from Salomon back to users
workstation and forwarding from the workstation to the remote host.
Pick some unused port on Salomon login node (for example 6000) and
-establish the port forwarding
+establish the port forwarding:
```
-local $ ssh -R 6000remote.host.com1234 salomon.it4i.cz
+local $ ssh -R 6000:remote.host.com:1234 salomon.it4i.cz
```
In this example, we establish port forwarding between port 6000 on
Salomon and port 1234 on the remote.host.com. By accessing
-localhost6000 on Salomon, an application will see response of
-remote.host.com1234. The traffic will run via users local workstation.
+localhost:6000 on Salomon, an application will see response of
+remote.host.com:1234. The traffic will run via users local workstation.
Port forwarding may be done **using PuTTY** as well. On the PuTTY
Configuration screen, load your Salomon configuration first. Then go to
Connection->SSH->Tunnels to set up the port forwarding. Click
Remote radio button. Insert 6000 to Source port textbox. Insert
-remote.host.com1234. Click Add button, then Open.
+remote.host.com:1234. Click Add button, then Open.
Port forwarding may be established directly to the remote host. However,
this requires that user has ssh access to remote.host.com
```
-$ ssh -L 6000localhost1234 remote.host.com
+$ ssh -L 6000:localhost:1234 remote.host.com
```
-Note Port number 6000 is chosen as an example only. Pick any free port.
+NotePort number 6000 is chosen as an example only. Pick any free port.
### []()Port forwarding from compute nodes
Remote port forwarding from compute nodes allows applications running on
the compute nodes to access hosts outside Salomon Cluster.
@@ -49,12 +50,12 @@ First, establish the remote port forwarding form the login node, as
Second, invoke port forwarding from the compute node to the login node.
Insert following line into your jobscript or interactive shell
```
-$ ssh -TN -f -L 6000localhost6000 login1
+$ ssh -TN -f -L 6000:localhost:6000 login1
```
-In this example, we assume that port forwarding from login16000 to
-remote.host.com1234 has been established beforehand. By accessing
-localhost6000, an application running on a compute node will see
-response of remote.host.com1234
+In this example, we assume that port forwarding from login1:6000 to
+remote.host.com:1234 has been established beforehand. By accessing
+localhost:6000, an application running on a compute node will see
+response of remote.host.com:1234
### Using proxy servers
Port forwarding is static, each single port is mapped to a particular
port on remote host. Connection to other remote host, requires new
@@ -64,44 +65,18 @@ remote hosts, via single proxy server.
To establish local proxy server on your workstation, install and run
SOCKS proxy server software. On Linux, sshd demon provides the
functionality. To establish SOCKS proxy server listening on port 1080
-run
+run:
```
local $ ssh -D 1080 localhost
```
On Windows, install and run the free, open source [Sock
-Puppet](http//sockspuppet.com/) server.
+Puppet](http://sockspuppet.com/) server.
Once the proxy server is running, establish ssh port forwarding from
Salomon to the proxy server, port 1080, exactly as [described
above](#port-forwarding-from-login-nodes).
```
-local $ ssh -R 6000localhost1080 salomon.it4i.cz
+local $ ssh -R 6000:localhost:1080 salomon.it4i.cz
```
-Now, configure the applications proxy settings to **localhost6000**.
+Now, configure the applications proxy settings to **localhost:6000**.
Use port forwarding to access the [proxy server from compute
nodes](#port-forwarding-from-compute-nodes) as well .
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](shell-and-data-access.html)
-
- - [Shell access and data
- transfer](shell-and-data-access.html)
-
- - [Graphical User
- Interface](../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html)
diff --git a/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html b/docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html
old mode 100755
new mode 100644
similarity index 71%
rename from salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html
rename to docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html
index 195957b3d51f0fc56bccd112c24d7d374a907f04..4a6bb512ba11fd49bdfd19c8efbedfaa96ff51ec
--- a/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html
+++ b/docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:03 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Shell access and data transfer — IT4I Docs</title>
- <link rel="canonical" href="../shell-and-data-access.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="shell-and-data-access.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="shell-and-data-access.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../shell-and-data-access.html">Accessing the Cluster</a>
+ <a href="https://docs.it4i.cz/salomon/accessing-the-cluster">Accessing the Cluster</a>
<span class="breadcrumbSeparator">
/
@@ -278,7 +275,7 @@
</tr>
</tbody>
</table>
-<p>The authentication is by the <a target="_self" title="" class="internal-link" href="../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html">private key</a></p>
+<p>The authentication is by the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">private key</a></p>
<p class="callout">Please verify SSH fingerprints during the first logon. They are identical on all login nodes:<span class="monospace"><br />f6:28:98:e4:f9:b2:a6:8f:f2:f4:2d:0a:09:67:69:80 (DSA)<br />70:01:c9:9a:5d:88:91:c7:1b:c0:84:d1:fa:4e:83:5c (RSA)</span></p>
<p>Â </p>
<p>Private keys authentication:</p>
@@ -286,10 +283,10 @@
<pre class="prettyprint lang-sh">local $ ssh -i /path/to/id_rsa username@salomon.it4i.cz</pre>
<p>If you see warning message "UNPROTECTED PRIVATE KEY FILE!", use this command to set lower permissions to private key file.</p>
<pre class="prettyprint lang-sh">local $ chmod 600 /path/to/id_rsa</pre>
-<p>On <strong>Windows</strong>, use <a target="_self" title="" class="internal-link" href="../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html">PuTTY ssh client</a>.</p>
+<p>On <strong>Windows</strong>, use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty">PuTTY ssh client</a>.</p>
<p>After logging in, you will see the command prompt:</p>
<pre class=" ">Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â _____Â Â Â Â Â Â _Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â <br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â / ____|Â Â Â Â | |Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â <br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â | (___Â Â __ _| | ___Â _ __ ___Â Â ___Â _ __ Â <br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â \___ \ / _` | |/ _ \| '_ ` _ \ / _ \| '_ \ <br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â ____) | (_| | | (_) | | | | | | (_) | | | |<br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â |_____/ \__,_|_|\___/|_| |_| |_|\___/|_| |_|<br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â <br /><br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â http://www.it4i.cz/?lang=en<br /><br /><br />Last login: Tue Jul 9 15:57:38 2013 from your-host.example.com<br />[username@login2.salomon ~]$</pre>
-<p class="callout">The environment is <strong>not</strong> shared between login nodes, except for <a target="_self" title="" class="internal-link" href="../../storage/storage.html">shared filesystems</a>.</p>
+<p class="callout">The environment is <strong>not</strong> shared between login nodes, except for <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/storage/storage">shared filesystems</a>.</p>
<h2 class=" ">Data Transfer</h2>
<p>Data in and out of the system may be transferred by the <a class="external-link" href="http://en.wikipedia.org/wiki/Secure_copy" target="_self" title="">scp</a> and sftp protocols.</p>
<p class="hiddenForView">In case large volumes of data are transferred, use dedicated data mover nodes cedge[1-3].salomon.it4i.cz for increased performance.</p>
@@ -325,7 +322,7 @@
</tr>
</tbody>
</table>
-<p>Â The authentication is by the <a target="_self" title="" class="internal-link" href="../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html">private key</a></p>
+<p>Â The authentication is by the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys">private key</a></p>
<p class="hiddenForView">HTML commented section #2 (ssh transfer performance data need to be verified)</p>
<p>On linux or Mac, use scp or sftp client to transfer the data to Salomon:</p>
@@ -339,7 +336,7 @@
<p>Learn more on ssh, scp and sshfs by reading the manpages</p>
<pre class="prettyprint lang-sh">$ man ssh<br />$ man scp<br />$ man sshfs</pre>
<p><span>On Windows</span>, use <a class="external-link" href="http://winscp.net/eng/download.php" target="_self" title="">WinSCP client</a> to transfer the data. The <a class="external-link" href="http://code.google.com/p/win-sshfs/" target="_self" title="">win-sshfs client</a> provides a way to mount the Salomon filesystems directly as an external disc.</p>
-<p>More information about the shared file systems is available <a target="_self" title="" class="internal-link" href="../../storage/storage.html">here</a>.</p>
+<p>More information about the shared file systems is available <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/storage/storage">here</a>.</p>
</div>
@@ -416,7 +413,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -432,7 +429,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -448,7 +445,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -464,7 +461,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -480,7 +477,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -496,7 +493,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../shell-and-data-access.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -512,7 +509,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="../shell-and-data-access.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access">
<span>Shell access and data transfer</span>
</a>
@@ -528,7 +525,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface">
<span>Graphical User Interface</span>
</a>
@@ -544,7 +541,7 @@
- <a title="" class="state-published contenttype-document" href="../vpn-access.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/vpn-access">
<span>VPN Access</span>
</a>
@@ -560,7 +557,7 @@
- <a title="" class="state-published contenttype-document" href="../outgoing-connections.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections">
<span>Outgoing connections</span>
</a>
@@ -585,7 +582,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -601,7 +598,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -617,7 +614,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -633,7 +630,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -649,7 +646,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -665,7 +662,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -681,10 +678,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -700,7 +697,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -725,7 +722,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -741,7 +738,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -757,7 +754,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -773,7 +770,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -812,14 +809,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -841,12 +838,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -862,7 +859,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:03 GMT -->
</html>
diff --git a/salomon/accessing-the-cluster/shell-and-data-access.md b/docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
similarity index 60%
rename from salomon/accessing-the-cluster/shell-and-data-access.md
rename to docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
index 00210901d4822d342f57a2036bc4bc02ced40f04..db82c44a3fd9611f54757a8dde3e776d15d7e67f 100644
--- a/salomon/accessing-the-cluster/shell-and-data-access.md
+++ b/docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
@@ -1,29 +1,30 @@
-
-
+Shell access and data transfer
+==============================
+
Interactive Login
-----------------
The Salomon cluster is accessed by SSH protocol via login nodes login1,
login2, login3 and login4 at address salomon.it4i.cz. The login nodes
may be addressed specifically, by prepending the login node name to the
address.
-The alias salomon.it4i.cz is currently not available through VPN
+The alias <span>salomon.it4i.cz is currently not available through VPN
connection. Please use loginX.salomon.it4i.cz when connected to
-VPN.
+VPN.</span>
Login address Port Protocol Login node
- ------------------------ ------ ---------- -----------------------------------------
+ - ------ ---------- ------------------
salomon.it4i.cz 22 ssh round-robin DNS record for login[1-4]
login1.salomon.it4i.cz 22 ssh login1
login2.salomon.it4i.cz 22 ssh login2
login3.salomon.it4i.cz 22 ssh login3
login4.salomon.it4i.cz 22 ssh login4
The authentication is by the [private
-key](../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+key](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys)
Please verify SSH fingerprints during the first logon. They are
-identical on all login nodes
-f62898e4f9b2a68ff2f42d0a09676980Â (DSA)
-7001c99a5d8891c71bc084d1fa4e835c (RSA)
+identical on all login nodes:<span class="monospace">
+f6:28:98:e4:f9:b2:a6:8f:f2:f4:2d:0a:09:67:69:80Â (DSA)
+70:01:c9:9a:5d:88:91:c7:1b:c0:84:d1:fa:4e:83:5c (RSA)</span>
Â
-Private keys authentication
+Private keys authentication:
On **Linux** or **Mac**, use
``` {.prettyprint .lang-sh}
local $ ssh -i /path/to/id_rsa username@salomon.it4i.cz
@@ -34,8 +35,8 @@ command to set lower permissions to private key file.
local $ chmod 600 /path/to/id_rsa
```
On **Windows**, use [PuTTY ssh
-client](../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
-After logging in, you will see the command prompt
+client](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty).
+After logging in, you will see the command prompt:
                   _____      _                           Â
                  / ____|    | |                          Â
                 | (___  __ _| | ___ _ __ ___  ___ _ __ Â
@@ -43,37 +44,38 @@ After logging in, you will see the command prompt
                  ____) | (_| | | (_) | | | | | | (_) | | | |
                 |_____/ __,_|_|___/|_| |_| |_|___/|_| |_|
                Â
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â http//www.it4i.cz/?lang=en
- Last login Tue Jul 9 155738 2013 from your-host.example.com
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â http://www.it4i.cz/?lang=en
+ Last loginTue Jul 9 15:57:38 2013 from your-host.example.com
[username@login2.salomon ~]$
The environment is **not** shared between login nodes, except for
-[shared filesystems](../storage/storage.html).
+[shared
+filesystems](https://docs.it4i.cz/salomon/storage/storage).
Data Transfer
-------------
Data in and out of the system may be transferred by the
-[scp](http//en.wikipedia.org/wiki/Secure_copy) and sftp
+[scp](http://en.wikipedia.org/wiki/Secure_copy) and sftp
protocols.
In case large volumes of data are transferred, use dedicated data mover
nodes cedge[1-3].salomon.it4i.cz for increased performance.
Â
HTML commented section #1 (removed cedge servers from the table)
Address Port Protocol
- ------------------------------------------------------ ------ -----------------------------------------
+ -------- ------ ------------------
salomon.it4i.cz 22 scp, sftp
login1.salomon.it4i.cz 22 scp, sftp
login2.salomon.it4i.cz 22 scp, sftp
- login3.salomon.it4i.cz 22 scp, sftp
+ <span class="discreet"></span>login3.salomon.it4i.cz 22 <span class="discreet"></span>scp, sftp
login4.salomon.it4i.cz 22 scp, sftp
 The authentication is by the [private
-key](../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+key](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys)
HTML commented section #2 (ssh transfer performance data need to be
verified)
-On linux or Mac, use scp or sftp client to transfer the data to Salomon
+On linux or Mac, use scp or sftp client to transfer the data to Salomon:
``` {.prettyprint .lang-sh}
-local $ scp -i /path/to/id_rsa my-local-file username@salomon.it4i.czdirectory/file
+local $ scp -i /path/to/id_rsa my-local-file username@salomon.it4i.cz:directory/file
```
``` {.prettyprint .lang-sh}
-local $ scp -i /path/to/id_rsa -r my-local-dir username@salomon.it4i.czdirectory
+local $ scp -i /path/to/id_rsa -r my-local-dir username@salomon.it4i.cz:directory
```
> or
``` {.prettyprint .lang-sh}
@@ -81,9 +83,9 @@ local $ sftp -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz
```
Very convenient way to transfer files in and out of the Salomon computer
is via the fuse filesystem
-[sshfs](http//linux.die.net/man/1/sshfs)
+[sshfs](http://linux.die.net/man/1/sshfs)
``` {.prettyprint .lang-sh}
-local $ sshfs -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz. mountpoint
+local $ sshfs -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz:. mountpoint
```
Using sshfs, the users Salomon home directory will be mounted on your
local computer, just like an external disk.
@@ -93,36 +95,10 @@ $ man ssh
$ man scp
$ man sshfs
```
-On Windows, use [WinSCP
-client](http//winscp.net/eng/download.php) to transfer
+<span>On Windows</span>, use [WinSCP
+client](http://winscp.net/eng/download.php) to transfer
the data. The [win-sshfs
-client](http//code.google.com/p/win-sshfs/) provides a
+client](http://code.google.com/p/win-sshfs/) provides a
way to mount the Salomon filesystems directly as an external disc.
More information about the shared file systems is available
-[here](../storage/storage.html).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](shell-and-data-access.html)
-
- - [Shell access and data
- transfer](shell-and-data-access.html)
-
-
- - [Graphical User
+[here](https://docs.it4i.cz/salomon/storage/storage).
diff --git a/salomon/accessing-the-cluster/vpn-access.html b/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.html
old mode 100755
new mode 100644
similarity index 59%
rename from salomon/accessing-the-cluster/vpn-access.html
rename to docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.html
index 44e091584aa6afa53742eb85909df778b0a1e260..df882ec33c9c4f1b41ca498c817ba130cd4d951a
--- a/salomon/accessing-the-cluster/vpn-access.html
+++ b/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/accessing-the-cluster/vpn-access by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:10 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/accessing-the-cluster/vpn-access" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>VPN Access — IT4I Docs</title>
- <link rel="canonical" href="vpn-access.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/accessing-the-cluster/vpn-access" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="vpn-access.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/accessing-the-cluster/vpn-access#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="vpn-access.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/accessing-the-cluster/vpn-access#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="shell-and-data-access.html">Accessing the Cluster</a>
+ <a href="https://docs.it4i.cz/salomon/accessing-the-cluster">Accessing the Cluster</a>
<span class="breadcrumbSeparator">
/
@@ -253,34 +250,34 @@
<p class=" ">It is impossible to connect to VPN from other operating systems.</p>
<h2 class=" "><span>VPN client installation</span></h2>
<p class=" ">You can install VPN client from web interface after successful login with LDAP credentials on address <a class="external-link" href="https://vpn.it4i.cz/user" target="_blank" title="">https://vpn.it4i.cz/user</a></p>
-<p class=" "><a target="_blank" title="" class="internal-link" href="../vpn_web_login.png"><img title="VPN Install" class="image-inline" alt="VPN Install" src="../vpn_web_login.png/%40%40images/5eac6b9c-22e4-4abe-ab38-e4ccbe87b710.png" /></a></p>
+<p class=" "><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/vpn_web_login.png"><img alt="VPN Install" class="image-inline" title="VPN Install" src="https://docs.it4i.cz/salomon/vpn_web_login.png/@@images/5eac6b9c-22e4-4abe-ab38-e4ccbe87b710.png" /></a></p>
<p class=" ">According to the Java settings after login, the client either automatically installs, or downloads installation file for your operating system. It is necessary to allow start of installation tool for automatic installation.</p>
-<p class=" "><a target="_blank" title="" class="internal-link" href="../vpn_web_login_2.png"><img title="VPN Install" class="image-inline" alt="VPN Install" src="../vpn_web_login_2.png/%40%40images/be923364-0175-4099-a363-79229b88e252.png" /></a></p>
-<p class=" "><a target="_blank" title="" class="internal-link" href="../vpn_web_install_2.png"><img title="VPN Install" class="image-inline" alt="VPN Install" src="../vpn_web_install_2.png/%40%40images/c2baba93-824b-418d-b548-a73af8030320.png" /></a><a target="_blank" title="" class="internal-link" href="../vpn_web_install_3.png"><img title="VPN Install" class="image-inline" alt="VPN Install" src="../copy_of_vpn_web_install_3.png/%40%40images/9c34e8ad-64b1-4e1d-af3a-13c7a18fbca4.png" /></a></p>
+<p class=" "><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/vpn_web_login_2.png"><img alt="VPN Install" class="image-inline" title="VPN Install" src="https://docs.it4i.cz/salomon/vpn_web_login_2.png/@@images/be923364-0175-4099-a363-79229b88e252.png" /></a></p>
+<p class=" "><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/vpn_web_install_2.png"><img alt="VPN Install" class="image-inline" title="VPN Install" src="https://docs.it4i.cz/salomon/vpn_web_install_2.png/@@images/c2baba93-824b-418d-b548-a73af8030320.png" /></a><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/copy_of_vpn_web_install_3.png"><img alt="VPN Install" class="image-inline" title="VPN Install" src="https://docs.it4i.cz/salomon/copy_of_vpn_web_install_3.png/@@images/9c34e8ad-64b1-4e1d-af3a-13c7a18fbca4.png" /></a></p>
<p class=" ">After successful installation, VPN connection will be established and you can use available resources from IT4I network.</p>
-<p class=" "><a target="_blank" title="" class="internal-link" href="../vpn_web_install_4.png"><img title="VPN Install" class="image-inline" alt="VPN Install" src="../vpn_web_install_4.png/%40%40images/4cc26b3b-399d-413b-9a6c-82ec47899585.png" /></a></p>
+<p class=" "><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/vpn_web_install_4.png"><img alt="VPN Install" class="image-inline" title="VPN Install" src="https://docs.it4i.cz/salomon/vpn_web_install_4.png/@@images/4cc26b3b-399d-413b-9a6c-82ec47899585.png" /></a></p>
<p class=" ">If your Java setting doesn't allow automatic installation, you can download installation file and install VPN client manually.</p>
-<p class=" "><a target="_blank" title="" class="internal-link" href="../vpn_web_download.png"><img title="VPN Install" class="image-inline" alt="VPN Install" src="../vpn_web_download.png/%40%40images/06a88cce-5f51-42d3-8f0a-f615a245beef.png" /></a></p>
+<p class=" "><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/vpn_web_download.png"><img alt="VPN Install" class="image-inline" title="VPN Install" src="https://docs.it4i.cz/salomon/vpn_web_download.png/@@images/06a88cce-5f51-42d3-8f0a-f615a245beef.png" /></a></p>
<p class=" ">After you click on the link, download of installation file will start.</p>
-<p class=" "><a target="_blank" title="" class="internal-link" href="../vpn_web_download_2.png"><img title="VPN Install" class="image-inline" alt="VPN Install" src="../vpn_web_download_2.png/%40%40images/3358d2ce-fe4d-447b-9e6c-b82285f9796e.png" /></a></p>
+<p class=" "><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/vpn_web_download_2.png"><img alt="VPN Install" class="image-inline" title="VPN Install" src="https://docs.it4i.cz/salomon/vpn_web_download_2.png/@@images/3358d2ce-fe4d-447b-9e6c-b82285f9796e.png" /></a></p>
<p class=" ">After successful download of installation file, you have to execute this tool with administrator's rights and install VPN client manually.</p>
<h2 class=" ">Working with VPN client</h2>
<p class=" ">You can use graphical user interface or command line interface to run VPN client on all supported operating systems. We suggest using GUI.</p>
-<p class=" "><img title="Icon" class="image-inline" alt="Icon" src="../../anselm-cluster-documentation/icon.jpg/%40%40images/56ee3417-80b8-4988-b9d5-8cda3f894963.jpg" /></p>
+<p class=" "><img alt="Icon" class="image-inline" title="Icon" src="https://docs.it4i.cz/anselm-cluster-documentation/icon.jpg/@@images/56ee3417-80b8-4988-b9d5-8cda3f894963.jpeg" /></p>
<p>Before the first login to VPN, you have to fill URLÂ <strong>https://vpn.it4i.cz/user </strong>into the text field.</p>
-<p><a target="_blank" title="" class="internal-link" href="../vpn_contacting_https_cluster.png"><img title="VPN Contacting Cluster" class="image-inline" alt="VPN Contacting Cluster" src="../vpn_contacting_https_cluster.png/%40%40images/22b15d8c-5d5f-4c5c-8973-fbc4e9a32128.png" /></a></p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/vpn_contacting_https_cluster.png"><img alt="VPN Contacting Cluster" class="image-inline" title="VPN Contacting Cluster" src="https://docs.it4i.cz/salomon/vpn_contacting_https_cluster.png/@@images/22b15d8c-5d5f-4c5c-8973-fbc4e9a32128.png" /></a></p>
<p>After you click on the Connect button, you must fill your login credentials.</p>
-<p><a target="_blank" title="" class="internal-link" href="../vpn_contacting_https.png"><img title="VPN Contacting Cluster" class="image-inline" alt="VPN Contacting Cluster" src="../vpn_contacting_https.png/%40%40images/ff365499-d07c-4baf-abb8-ce3e15559210.png" /></a></p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/vpn_contacting_https.png"><img alt="VPN Contacting Cluster" class="image-inline" title="VPN Contacting Cluster" src="https://docs.it4i.cz/salomon/vpn_contacting_https.png/@@images/ff365499-d07c-4baf-abb8-ce3e15559210.png" /></a></p>
<p>After a successful login, the client will minimize to the system tray. If everything works, you can see a lock in the Cisco tray icon.</p>
-<p><a target="_blank" title="" class="internal-link" href="../../anselm-cluster-documentation/anyconnect%20icon.jpg"><img title="Successfull connection" class="image-inline" alt="Successfull connection" src="../../anselm-cluster-documentation/anyconnecticon.jpg/%40%40images/ebdd0e41-e839-497e-ab33-45162d00b03b.jpg" /></a></p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/anselm-cluster-documentation/anyconnecticon.jpg"><img alt="Successfull connection" class="image-inline" title="Successfull connection" src="https://docs.it4i.cz/anselm-cluster-documentation/anyconnecticon.jpg/@@images/ebdd0e41-e839-497e-ab33-45162d00b03b.jpeg" /></a></p>
<p>If you right-click on this icon, you will see a context menu in which you can control the VPN connection.</p>
-<p><a target="_blank" title="" class="internal-link" href="../../anselm-cluster-documentation/anyconnect-contextmenu.jpg"><img title="Context menu" class="image-inline" alt="Context menu" src="../../anselm-cluster-documentation/anyconnectcontextmenu.jpg/%40%40images/9655f6a6-cd7b-4462-90d6-480d43c8cc0c.jpg" /></a></p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/anselm-cluster-documentation/anyconnectcontextmenu.jpg"><img alt="Context menu" class="image-inline" title="Context menu" src="https://docs.it4i.cz/anselm-cluster-documentation/anyconnectcontextmenu.jpg/@@images/9655f6a6-cd7b-4462-90d6-480d43c8cc0c.jpeg" /></a></p>
<p>When you connect to the VPN for the first time, the client downloads the profile and creates a new item "IT4I cluster" in the connection list. For subsequent connections, it is not necessary to re-enter the URL address, but just select the corresponding item.</p>
-<p><a target="_blank" title="" class="internal-link" href="../vpn_contacting.png"><img title="VPN Contacting Cluster" class="image-inline" alt="VPN Contacting Cluster" src="../vpn_contacting.png/%40%40images/9ccabccf-581a-476a-8c24-ce9842c3e657.png" /></a></p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/vpn_contacting.png"><img alt="VPN Contacting Cluster" class="image-inline" title="VPN Contacting Cluster" src="https://docs.it4i.cz/salomon/vpn_contacting.png/@@images/9ccabccf-581a-476a-8c24-ce9842c3e657.png" /></a></p>
<p>Then AnyConnect automatically proceeds like in the case of first logon.</p>
-<p><a target="_blank" title="" class="internal-link" href="../vpn_login.png"><img title="VPN login" class="image-inline" alt="VPN login" src="../vpn_login.png/%40%40images/5102f29d-93cf-4cfd-8f55-c99c18f196ea.png" /></a></p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/vpn_login.png"><img alt="VPN login" class="image-inline" title="VPN login" src="https://docs.it4i.cz/salomon/vpn_login.png/@@images/5102f29d-93cf-4cfd-8f55-c99c18f196ea.png" /></a></p>
<p>After a successful logon, you can see a green circle with a tick mark on the lock icon.</p>
-<p><a target="_blank" title="" class="internal-link" href="../vpn_successfull_connection.png"><img title="VPN Succesfull Connection" class="image-inline" alt="VPN Succesfull Connection" src="../vpn_successfull_connection.png/%40%40images/45537053-a47f-48b2-aacd-3b519d6770e6.png" /></a></p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/vpn_successfull_connection.png"><img alt="VPN Succesfull Connection" class="image-inline" title="VPN Succesfull Connection" src="https://docs.it4i.cz/salomon/vpn_successfull_connection.png/@@images/45537053-a47f-48b2-aacd-3b519d6770e6.png" /></a></p>
<p>For disconnecting, right-click on the AnyConnect client icon in the system tray and select <strong>VPN Disconnect</strong>.</p>
</div>
@@ -357,7 +354,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -373,7 +370,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -389,7 +386,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -405,7 +402,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -421,7 +418,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -437,7 +434,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="shell-and-data-access.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -453,7 +450,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access">
<span>Shell access and data transfer</span>
</a>
@@ -469,7 +466,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface">
<span>Graphical User Interface</span>
</a>
@@ -485,7 +482,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="vpn-access.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/vpn-access">
<span>VPN Access</span>
</a>
@@ -501,7 +498,7 @@
- <a title="" class="state-published contenttype-document" href="outgoing-connections.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections">
<span>Outgoing connections</span>
</a>
@@ -526,7 +523,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -542,7 +539,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -558,7 +555,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -574,7 +571,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -590,7 +587,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -606,7 +603,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -622,10 +619,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -641,7 +638,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -666,7 +663,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -682,7 +679,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -698,7 +695,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -714,7 +711,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -782,12 +779,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -803,7 +800,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/accessing-the-cluster/vpn-access by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:17 GMT -->
</html>
diff --git a/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.md b/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.md
new file mode 100644
index 0000000000000000000000000000000000000000..5f114d10c967459e662bfc58ca6e4cb8cde9b759
--- /dev/null
+++ b/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.md
@@ -0,0 +1,79 @@
+VPN Access
+==========
+
+Accessing IT4Innovations internal resources via VPN
+-----
+For using resources and licenses which are located at IT4Innovations
+local network, it is necessary to VPN connect to this network.
+We use Cisco AnyConnect Secure Mobility Client, which is supported on
+the following operating systems:
+- <span>Windows XP</span>
+- <span>Windows Vista</span>
+- <span>Windows 7</span>
+- <span>Windows 8</span>
+- <span>Linux</span>
+- <span>MacOS</span>
+It is impossible to connect to VPN from other operating systems.
+<span>VPN client installation</span>
+-------------
+You can install VPN client from web interface after successful login
+with LDAP credentials on address <https://vpn.it4i.cz/user>
+[](https://docs.it4i.cz/salomon/vpn_web_login.png)
+According to the Java settings after login, the client either
+automatically installs, or downloads installation file for your
+operating system. It is necessary to allow start of installation tool
+for automatic installation.
+[](https://docs.it4i.cz/salomon/vpn_web_login_2.png)
+[](https://docs.it4i.cz/salomon/vpn_web_install_2.png)[](https://docs.it4i.cz/salomon/copy_of_vpn_web_install_3.png)
+After successful installation, VPN connection will be established and
+you can use available resources from IT4I network.
+[](https://docs.it4i.cz/salomon/vpn_web_install_4.png)
+If your Java setting doesn't allow automatic installation, you can
+download installation file and install VPN client manually.
+[](https://docs.it4i.cz/salomon/vpn_web_download.png)
+After you click on the link, download of installation file will start.
+[](https://docs.it4i.cz/salomon/vpn_web_download_2.png)
+After successful download of installation file, you have to execute this
+tool with administrator's rights and install VPN client manually.
+Working with VPN client
+You can use graphical user interface or command line interface to run
+VPN client on all supported operating systems. We suggest using GUI.
+
+Before the first login to VPN, you have to fill
+URLÂ **https://vpn.it4i.cz/user** into the text field.
+[](https://docs.it4i.cz/salomon/vpn_contacting_https_cluster.png)
+After you click on the Connect button, you must fill your login
+credentials.
+[](https://docs.it4i.cz/salomon/vpn_contacting_https.png)
+After a successful login, the client will minimize to the system tray.
+If everything works, you can see a lock in the Cisco tray icon.
+[](https://docs.it4i.cz/anselm-cluster-documentation/anyconnecticon.jpg)
+If you right-click on this icon, you will see a context menu in which
+you can control the VPN connection.
+[](https://docs.it4i.cz/anselm-cluster-documentation/anyconnectcontextmenu.jpg)
+When you connect to the VPN for the first time, the client downloads the
+profile and creates a new item "IT4I cluster" in the connection list.
+For subsequent connections, it is not necessary to re-enter the URL
+address, but just select the corresponding item.
+[](https://docs.it4i.cz/salomon/vpn_contacting.png)
+Then AnyConnect automatically proceeds like in the case of first logon.
+[](https://docs.it4i.cz/salomon/vpn_login.png)
+After a successful logon, you can see a green circle with a tick mark on
+the lock icon.
+[](https://docs.it4i.cz/salomon/vpn_successfull_connection.png)
+For disconnecting, right-click on the AnyConnect client icon in the
+system tray and select **VPN Disconnect**.
diff --git a/salomon/cn_m_cell.jpg b/docs.it4i.cz/salomon/cn_m_cell
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/cn_m_cell.jpg
rename to docs.it4i.cz/salomon/cn_m_cell
diff --git a/salomon/cn_mic_2.jpg b/docs.it4i.cz/salomon/cn_mic
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/cn_mic_2.jpg
rename to docs.it4i.cz/salomon/cn_mic
diff --git a/salomon/cn_mic_1.jpg b/docs.it4i.cz/salomon/cn_mic-1
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/cn_mic_1.jpg
rename to docs.it4i.cz/salomon/cn_mic-1
diff --git a/salomon/compute-nodes.html b/docs.it4i.cz/salomon/compute-nodes.html
old mode 100755
new mode 100644
similarity index 73%
rename from salomon/compute-nodes.html
rename to docs.it4i.cz/salomon/compute-nodes.html
index c37fbd2abc149551cc962f8f68bf56793670602a..47e89280e98b16b3eaaa4f6798d81595c0aed40b
--- a/salomon/compute-nodes.html
+++ b/docs.it4i.cz/salomon/compute-nodes.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/compute-nodes by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:43 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/compute-nodes" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/IEFixes-cachekey-ec9b60024fd235ff2c883b4b54db91cb.css" />
<![endif]-->
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- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
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- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Compute Nodes — IT4I Docs</title>
- <link rel="canonical" href="compute-nodes.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/compute-nodes" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="compute-nodes.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/compute-nodes#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="compute-nodes.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/compute-nodes#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../index.html">
- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -232,7 +229,7 @@
<div id="parent-fieldname-text-3028a7e1f7024efda22efc53bd8237f0" class="">
<h2 class=" ">Nodes Configuration</h2>
<p>Salomon is cluster of x86-64 Intel based nodes. The cluster contains two types of compute nodes of the same processor type and memory size. Compute nodes with MIC accelerator<strong></strong> contains two Intel Xeon Phi 7120P accelerators.</p>
-<p><a target="_self" title="" class="internal-link" href="network-1/ib-single-plane-topology.html">More about schematic representation of the Salomon cluster compute nodes IB topology</a>.</p>
+<p><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology">More about schematic representation of the Salomon cluster compute nodes IB topology</a>.</p>
<h3 class=" "><strong>Compute Nodes Without Accelerator</strong></h3>
<div class="itemizedlist">
<ul class="itemizedlist" style="list-style-type: disc; ">
@@ -248,7 +245,7 @@
<div class="itemizedlist">128 GB of physical memory per node</div>
</li>
</ul>
-<p style="padding-left: 30px; "><a target="_blank" title="" class="internal-link" href="cn_m_cell.jpg"><img title="cn_m_cell" class="image-inline" alt="cn_m_cell" src="cn_m_cell/%40%40images/ced0a5ef-b233-4f4f-9391-092abeb378d3.jpg" /></a></p>
+<p style="padding-left: 30px; "><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/cn_m_cell"><img alt="cn_m_cell" class="image-inline" title="cn_m_cell" src="https://docs.it4i.cz/salomon/cn_m_cell/@@images/8294d5d2-3fec-47d2-a467-10f66d048891.jpeg" /></a></p>
<h3 class=" "><strong>Compute Nodes With MIC Accelerator</strong></h3>
<div class="itemizedlist">
<ul>
@@ -271,8 +268,8 @@
</li>
</ul>
</div>
-<p style="padding-left: 30px; "><a target="_blank" title="" class="internal-link" href="cn_mic_1.jpg"><img title="cn_mic" class="image-inline" alt="cn_mic" src="cn_mic-1/%40%40images/b4318449-6c9a-4acf-b53c-3c7ad0998655.jpg" /></a></p>
-<p style="padding-left: 30px; "><a class="external-link" href="https://www.sgi.com/products/servers/rackable/1u_intel.html#v3" target="_self" title="(source Silicon Graphics International Corp.)"><img title="SGI-C1104-GP1" class="image-inline" alt="(source Silicon Graphics International Corp.)" src="sgi-c1104-gp1/%40%40images/c1109cbb-9bf4-4f0a-8b0f-a1e464fed0c4.jpg" /> </a><a target="_blank" title="" class="internal-link" href="cn_mic_2.jpg"><img width="87" height="122" alt="cn_mic" class="image-inline" title="cn_mic" src="cn_mic/%40%40images/08b13efa-248a-4ece-949b-f66c165cecad.jpg" /></a></p>
+<p style="padding-left: 30px; "><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/cn_mic-1"><img alt="cn_mic" class="image-inline" title="cn_mic" src="https://docs.it4i.cz/salomon/cn_mic-1/@@images/44cb01e0-2d67-4ea1-883c-d06919fbf351.jpeg" /></a></p>
+<p style="padding-left: 30px; "><a class="external-link" href="https://www.sgi.com/products/servers/rackable/1u_intel.html#v3" target="_self" title="(source Silicon Graphics International Corp.)"><img alt="(source Silicon Graphics International Corp.)" class="image-inline" title="SGI-C1104-GP1" src="https://docs.it4i.cz/salomon/sgi-c1104-gp1/@@images/c1109cbb-9bf4-4f0a-8b0f-a1e464fed0c4.jpeg" /> </a><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/cn_mic"><img class="image-inline" src="https://docs.it4i.cz/salomon/cn_mic/@@images/46081fb2-10d0-43b3-b32f-9650bedf107a.jpeg" alt="cn_mic" width="87" title="cn_mic" height="122" /></a></p>
<div class="figure">
<h3 class=" ">UV 2000</h3>
<div class="itemizedlist">
@@ -295,7 +292,7 @@
<div class="itemizedlist">1x NVIDIA GM200 (GeForce GTX TITAN X), 12GB RAM</div>
</li>
</ul>
-<img title="UV 2000" class="image-inline" alt="UV 2000" src="uv-2000/%40%40images/04ce7514-8d27-4cdb-bf0f-45d875c75df0.jpg" /><br />
+<img alt="UV 2000" class="image-inline" title="UV 2000" src="https://docs.it4i.cz/salomon/uv-2000/@@images/04ce7514-8d27-4cdb-bf0f-45d875c75df0.jpeg" /><br />
<h3 class=" ">Compute Nodes Summary<strong><strong></strong></strong></h3>
<table class="listing">
<tbody>
@@ -531,7 +528,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -547,7 +544,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -563,7 +560,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -579,7 +576,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -595,7 +592,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -611,7 +608,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -627,7 +624,7 @@
- <a title="" class="state-published contenttype-document" href="environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -643,7 +640,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -659,7 +656,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -675,7 +672,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="compute-nodes.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -691,7 +688,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -707,7 +704,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -723,10 +720,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -742,7 +739,7 @@
- <a title="" class="state-published contenttype-document" href="prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -767,7 +764,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -783,7 +780,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -799,7 +796,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -815,7 +812,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -854,14 +851,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -883,12 +880,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -904,7 +901,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/compute-nodes by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:45 GMT -->
</html>
diff --git a/docs.it4i.cz/salomon/compute-nodes.md b/docs.it4i.cz/salomon/compute-nodes.md
new file mode 100644
index 0000000000000000000000000000000000000000..0ba4cc01e03adb5117df3b66423a48939d89cd32
--- /dev/null
+++ b/docs.it4i.cz/salomon/compute-nodes.md
@@ -0,0 +1,169 @@
+Compute Nodes
+=============
+
+Nodes Configuration
+-------------------
+Salomon is cluster of x86-64 Intel based nodes. The cluster contains two
+types of compute nodes of the same processor type and memory size.
+Compute nodes with MIC accelerator**** contains two Intel Xeon Phi 7120P
+accelerators.
+[More about schematic representation of the Salomon cluster compute
+nodes IB
+topology](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology).
+### **Compute Nodes Without Accelerator**
+- <span>codename "grafton"</span>
+- <span>576Â nodes</span>
+- <div class="itemizedlist">
+ 13Â 824 cores in total
+
+- <div class="itemizedlist">
+ two Intel Xeon E5-2680v3, 12-core, 2.5GHz processors per node
+
+- <div class="itemizedlist">
+ 128 GB of physical memory per node
+
+[](https://docs.it4i.cz/salomon/cn_m_cell)
+### **Compute Nodes With MIC Accelerator**
+- codename "perrin"
+- <span>432Â nodes</span>
+- <div class="itemizedlist">
+ <span>10Â 368Â cores in total</span>
+
+- <div class="itemizedlist">
+ two Intel Xeon E5-2680v3, 12-core, 2.5GHz processors per node
+
+- <div class="itemizedlist">
+ 128 GB of physical memory per node
+
+- <div class="itemizedlist">
+ MIC accelerator 2x Intel Xeon Phi 7120P per node, 61-cores, 16GB per
+ accelerator
+
+[](https://docs.it4i.cz/salomon/cn_mic-1)
+[](https://www.sgi.com/products/servers/rackable/1u_intel.html#v3 "(source Silicon Graphics International Corp.)")[{.image-inline
+width="87"
+height="122"}](https://docs.it4i.cz/salomon/cn_mic)
+### UV 2000
+- codename "UV2000"
+- <span>1 node</span>
+- <div class="itemizedlist">
+ <span>112 cores in total</span>
+
+- <div class="itemizedlist">
+ 14x Intel Xeon E5-4627v2, 8-core, 3.3GHz processors, in 14 NUMA
+ nodes
+
+- <div class="itemizedlist">
+ 3328 GB of physical memory per node
+
+- <div class="itemizedlist">
+ 1x NVIDIA GM200 (GeForce GTX TITAN X), 12GB RAM
+
+
+### Compute Nodes Summary********
+<table>
+<colgroup>
+<col width="25%" />
+<col width="25%" />
+<col width="25%" />
+<col width="25%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Node type</th>
+<th align="left">Count</th>
+<th align="left">Memory</th>
+<th align="left">Cores</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left">Nodes without accelerator</td>
+<td align="left">576</td>
+<td align="left">128GB</td>
+<td align="left">24 @ 2.5Ghz</td>
+</tr>
+<tr class="even">
+<td align="left">Nodes with MIC accelerator</td>
+<td align="left">432</td>
+<td align="left"><p>128GB</p>
+<p>32GB</p></td>
+<td align="left"><p>24 @ 2.5Ghz</p>
+<p>61 @ <span style="text-alignstart; floatnone; ">1.238GHz</span></p></td>
+</tr>
+<tr class="odd">
+<td align="left">UV2000 SMP node</td>
+<td align="left">1</td>
+<td align="left"><p>3328GB</p></td>
+<td align="left"><p>112 @ 3.3GHz</p></td>
+</tr>
+</tbody>
+</table>
+Processor Architecture
+----------------------
+Salomon is equipped with Intel Xeon processors Intel Xeon E5-2680v3.
+Processors support Advanced Vector Extensions 2.0 (AVX2) 256-bit
+instruction set.
+### Intel Xeon E5-2680v3 Processor
+- 12-core
+- speed2.5 GHz, up to <span
+ style="text-alignstart; floatnone; ">3.3</span> GHz using Turbo
+ Boost Technology
+- peak performance<span class="emphasis">19.2 Gflop/s</span> per
+ core
+- caches:
+ <div class="itemizedlist">
+ - <span style="text-alignstart; floatnone; ">Intel® Smart
+ Cache</span>:Â <span style="text-alignstart; floatnone; ">30
+ MB</span>
+
+- memory bandwidth at the level of the processor<span
+ style="text-alignstart; floatnone; ">68 GB/s</span>
+### MIC Accelerator Intel Xeon Phi 7120PÂ Processor
+- 61-core
+- speed:Â <span style="text-alignstart; floatnone; ">1.238</span>
+ GHz, up to <span
+ style="text-alignstart; floatnone; ">1.333</span> GHz using
+ Turbo Boost Technology
+- peak performance<span class="emphasis">18.4 Gflop/s</span> per
+ core
+- caches:
+ <div class="itemizedlist">
+ - L2<span style="text-alignstart; floatnone; ">30.5
+ MB</span>
+
+- memory bandwidth at the level of the processor<span
+ style="text-alignstart; floatnone; ">352 GB/s</span>
+Â
+Memory Architecture
+-------------------
+Memory is equally distributed across all CPUs and cores for optimal
+performance. Memory is composed of memory modules of the same size and
+evenly distributed across all memory controllers and memory channels.
+### Compute Node Without Accelerator
+- 2 sockets
+- Memory Controllers are integrated into processors.
+ <div class="itemizedlist">
+ - 8Â DDR4 DIMMS per node
+ - 4Â DDR4 DIMMS per CPU
+ - <span>1Â DDR4 DIMMS per channel</span>
+
+- Populated memory8x 16GB DDR4 DIMM <span>2133MHz</span>
+### Compute Node With MIC Accelerator
+2 sockets
+Memory Controllers are integrated into processors.
+- 8Â DDR4 DIMMS per node
+- 4Â DDR4 DIMMS per CPU
+- <span>1Â DDR4 DIMMS per channel</span>
+<span>Populated memory8x 16GB DDR4 DIMM 2133MHz</span>
+MIC Accelerator Intel Xeon Phi 7120P Processor
+- 2 sockets
+- <span><span>Memory Controllers are are connected via an
+ Interprocessor Network (IPN) ring.</span></span>
+ <div class="itemizedlist">
+ - 16 GDDR5 DIMMS per node
+ - 8Â GDDR5 DIMMS per CPU
+ - 2Â GDDR5 DIMMS per channel
+
diff --git a/salomon/vpn_web_install_3.png b/docs.it4i.cz/salomon/copy_of_vpn_web_install_3.png
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/vpn_web_install_3.png
rename to docs.it4i.cz/salomon/copy_of_vpn_web_install_3.png
diff --git a/salomon/environment-and-modules.html b/docs.it4i.cz/salomon/environment-and-modules.html
old mode 100755
new mode 100644
similarity index 76%
rename from salomon/environment-and-modules.html
rename to docs.it4i.cz/salomon/environment-and-modules.html
index 84e6b8016fa630ebd07e7f310e9059c22b848df0..4fa64df6415f5368a01fe7356eb3ab406436643f
--- a/salomon/environment-and-modules.html
+++ b/docs.it4i.cz/salomon/environment-and-modules.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/environment-and-modules by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:42 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/environment-and-modules" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/IEFixes-cachekey-ec9b60024fd235ff2c883b4b54db91cb.css" />
<![endif]-->
- <style type="text/css" media="screen">@import url(../portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Environment and Modules — IT4I Docs</title>
- <link rel="canonical" href="environment-and-modules.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/environment-and-modules" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="environment-and-modules.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/environment-and-modules#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="environment-and-modules.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/environment-and-modules#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../index.html">
- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -373,7 +370,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -389,7 +386,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -405,7 +402,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -421,7 +418,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -437,7 +434,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -453,7 +450,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -469,7 +466,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="environment-and-modules.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -485,7 +482,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -501,7 +498,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -517,7 +514,7 @@
- <a title="" class="state-published contenttype-document" href="compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -533,7 +530,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -549,7 +546,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -565,10 +562,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -584,7 +581,7 @@
- <a title="" class="state-published contenttype-document" href="prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -609,7 +606,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -625,7 +622,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -641,7 +638,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -657,7 +654,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
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+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -725,12 +722,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -746,7 +743,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/environment-and-modules by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:42 GMT -->
</html>
diff --git a/salomon/environment-and-modules.md b/docs.it4i.cz/salomon/environment-and-modules.md
similarity index 68%
rename from salomon/environment-and-modules.md
rename to docs.it4i.cz/salomon/environment-and-modules.md
index e000daae8068e3656e56008764fe399ac520c1f4..6df4d9bb6ad575fa3f2d975da1b7a90f949847c5 100644
--- a/salomon/environment-and-modules.md
+++ b/docs.it4i.cz/salomon/environment-and-modules.md
@@ -1,3 +1,7 @@
+Environment and Modules
+=======================
+
+### Environment Customization
After logging in, you may want to configure the environment. Write your
preferred path definitions, aliases, functions and module loads in the
.bashrc file
@@ -19,37 +23,37 @@ fi
Do not run commands outputing to standard output (echo, module list,
etc) in .bashrc for non-interactive SSH sessions. It breaks fundamental
functionality (scp, PBS) of your account! Take care for SSH session
-interactivity for such commands as id="result_box"
-class="short_text">stated
-class="hps">in the previous example.
+interactivity for such commands as <span id="result_box"
+class="short_text"><span class="hps alt-edited">stated</span> <span
+class="hps">in the previous example.</span></span>
### Application Modules
In order to configure your shell for running particular application on
Salomon we use Module package interface.
Application modules on Salomon cluster are built using
-[EasyBuild](http//hpcugent.github.io/easybuild/ "EasyBuild"). The
-modules are divided into the following structure
+[EasyBuild](http://hpcugent.github.io/easybuild/ "EasyBuild"). The
+modules are divided into the following structure:
``` {.prettyprint}
- base Default module class
- bio Bioinformatics, biology and biomedical
- cae Computer Aided Engineering (incl. CFD)
- chem Chemistry, Computational Chemistry and Quantum Chemistry
- compiler Compilers
- data Data management & processing tools
- debugger Debuggers
- devel Development tools
- geo Earth Sciences
- ide Integrated Development Environments (e.g. editors)
- lang Languages and programming aids
- lib General purpose libraries
- math High-level mathematical software
- mpi MPI stacks
- numlib Numerical Libraries
- perf Performance tools
- phys Physics and physical systems simulations
- system System utilities (e.g. highly depending on system OS and hardware)
- toolchain EasyBuild toolchains
- tools General purpose tools
- vis Visualization, plotting, documentation and typesetting
+ baseDefault module class
+ bioBioinformatics, biology and biomedical
+ caeComputer Aided Engineering (incl. CFD)
+ chemChemistry, Computational Chemistry and Quantum Chemistry
+ compilerCompilers
+ dataData management & processing tools
+ debuggerDebuggers
+ develDevelopment tools
+ geoEarth Sciences
+ ideIntegrated Development Environments (e.g. editors)
+ langLanguages and programming aids
+ libGeneral purpose libraries
+ mathHigh-level mathematical software
+ mpiMPI stacks
+ numlibNumerical Libraries
+ perfPerformance tools
+ physPhysics and physical systems simulations
+ systemSystem utilities (e.g. highly depending on system OS and hardware)
+ toolchainEasyBuild toolchains
+ toolsGeneral purpose tools
+ visVisualization, plotting, documentation and typesetting
```
The modules set up the application paths, library paths and environment
variables for running particular application.
@@ -102,33 +106,19 @@ environment variables; that is, unless they need to be aware of, for
example, the particular compiler being used to determine the build
configuration options.
Recent releases of EasyBuild include out-of-the-box toolchain support
-for
+for:
- various compilers, including GCC, Intel, Clang, CUDA
- common MPI libraries, such as Intel MPI, MPICH, MVAPICH2, OpenMPI
- various numerical libraries, including ATLAS, Intel MKL, OpenBLAS,
ScalaPACK, FFTW
Â
-On Salomon, we have currently following toolchains installed
+On Salomon, we have currently following toolchains installed:
Toolchain Module(s)
- -------------------- ------------------------------------------------
+ -------------------- --
GCC GCC
ictce icc, ifort, imkl, impi
intel GCC, icc, ifort, imkl, impi
gompi GCC, OpenMPI
goolf BLACS, FFTW, GCC, OpenBLAS, OpenMPI, ScaLAPACK
- iompi OpenMPI, icc, ifort
+ <span>iompi</span> OpenMPI, icc, ifort
iccifort icc, ifort
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
diff --git a/salomon/salomon-gdm.png b/docs.it4i.cz/salomon/gnome_screen.jpg.1
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/salomon-gdm.png
rename to docs.it4i.cz/salomon/gnome_screen.jpg.1
diff --git a/salomon/gnome_screen.jpg/@@images/7758b792-24eb-48dc-bf72-618cda100fda.png b/docs.it4i.cz/salomon/gnome_screen.jpg/@@images/7758b792-24eb-48dc-bf72-618cda100fda.png
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/gnome_screen.jpg/@@images/7758b792-24eb-48dc-bf72-618cda100fda.png
rename to docs.it4i.cz/salomon/gnome_screen.jpg/@@images/7758b792-24eb-48dc-bf72-618cda100fda.png
diff --git a/salomon/hardware-overview-1/hardware-overview.html b/docs.it4i.cz/salomon/hardware-overview-1.1.html
old mode 100755
new mode 100644
similarity index 70%
rename from salomon/hardware-overview-1/hardware-overview.html
rename to docs.it4i.cz/salomon/hardware-overview-1.1.html
index ca94e47a11ef4e5b02d4c2a0ab5f1fc13d639725..c3020d67679f7c7e858f1645802cfeb5df416a90
--- a/salomon/hardware-overview-1/hardware-overview.html
+++ b/docs.it4i.cz/salomon/hardware-overview-1.1.html
@@ -10,45 +10,42 @@
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-<!-- Mirrored from docs.it4i.cz/salomon/hardware-overview-1/hardware-overview by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:41 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/hardware-overview-1/hardware-overview" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Hardware Overview — IT4I Docs</title>
- <link rel="canonical" href="../hardware-overview-1.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/hardware-overview-1" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="hardware-overview.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/hardware-overview-1#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="hardware-overview.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/hardware-overview-1#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -232,8 +229,8 @@
<div id="parent-fieldname-text-e3d9b88c840a474ea3bbc24a1dc19bed" class="">
<h2 class=" ">Introduction</h2>
<p>The Salomon cluster consists of 1008 computational nodes of which 576 are regular compute nodes and 432 accelerated nodes. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 24 cores (two twelve-core Intel Xeon processors) and 128GB RAM. The nodes are interlinked by high speed InfiniBand and Ethernet networks. All nodes share 0.5PB /home NFS disk storage to store the user files. Users may use a DDN Lustre shared storage with capacity of 1.69 PB which is available for the scratch project data. The user access to the Salomon cluster is provided by four login nodes.</p>
-<p><a target="_self" title="" class="internal-link" href="../network-1/ib-single-plane-topology.html">More about schematic representation of the Salomon cluster compute nodes IB topology</a>.<span class="internal-link"></span></p>
-<p style="padding-left: 30px; "><a target="_self" title="" class="internal-link" href="../salomon_2.jpg"><img title="Salomon" class="image-inline" alt="Salomon" src="../salomon-2/%40%40images/25c7db03-5c44-4981-9e19-07c1c23fcf1e.jpg" /></a></p>
+<p><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology">More about schematic representation of the Salomon cluster compute nodes IB topology</a>.<span class="internal-link"></span></p>
+<p style="padding-left: 30px; "><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/salomon-2"><img alt="Salomon" class="image-inline" title="Salomon" src="https://docs.it4i.cz/salomon/salomon-2/@@images/25c7db03-5c44-4981-9e19-07c1c23fcf1e.jpeg" /></a></p>
<p>The parameters are summarized in the following tables:</p>
<h2 class=" ">General information</h2>
<table class="listing">
@@ -251,7 +248,7 @@
<td>Operating system</td>
<td>CentOS 6.7 Linux</td>
</tr>
-<tr><th colspan="2"><a target="_self" title="" class="internal-link" href="../compute-nodes.html"><strong>Compute nodes</strong></a></th></tr>
+<tr><th colspan="2"><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/compute-nodes"><strong>Compute nodes</strong></a></th></tr>
<tr class="even">
<td>Totally</td>
<td>1008</td>
@@ -313,7 +310,7 @@
</tr>
</tbody>
</table>
-<p class="internal-link" title="">For more details please refer to the <a target="_self" title="" class="internal-link" href="../compute-nodes.html">Compute nodes</a>.</p>
+<p class="internal-link" title="">For more details please refer to the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/compute-nodes">Compute nodes</a>.</p>
<h2 class=" ">Remote visualization nodes</h2>
<p class="internal-link" title="">For remote visualization two nodes with NICE DCV software are available each configured:</p>
<table class="listing">
@@ -346,7 +343,7 @@
</tr>
</tbody>
</table>
-<p style="padding-left: 30px; "><img title="UV 2000" class="image-inline" alt="UV 2000" src="../uv-2000/%40%40images/04ce7514-8d27-4cdb-bf0f-45d875c75df0.jpg" /></p>
+<p style="padding-left: 30px; "><img alt="UV 2000" class="image-inline" title="UV 2000" src="https://docs.it4i.cz/salomon/uv-2000/@@images/04ce7514-8d27-4cdb-bf0f-45d875c75df0.jpeg" /></p>
</div>
@@ -422,7 +419,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -438,7 +435,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -454,7 +451,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -470,7 +467,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -486,7 +483,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="../hardware-overview-1.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -502,7 +499,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -518,7 +515,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -534,7 +531,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -550,7 +547,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -566,7 +563,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -582,7 +579,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -598,7 +595,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -614,10 +611,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -633,7 +630,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -658,7 +655,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -674,7 +671,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -690,7 +687,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -706,7 +703,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
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+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -774,12 +771,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -795,7 +792,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/hardware-overview-1/hardware-overview by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:41 GMT -->
</html>
diff --git a/salomon/hardware-overview-1.md b/docs.it4i.cz/salomon/hardware-overview-1.1.md
similarity index 54%
rename from salomon/hardware-overview-1.md
rename to docs.it4i.cz/salomon/hardware-overview-1.1.md
index dfb3cdf4032e0a7cc936813827231f842df35838..298cb25728bbd82d988d06f51b4e0056ea4a4d5b 100644
--- a/salomon/hardware-overview-1.md
+++ b/docs.it4i.cz/salomon/hardware-overview-1.1.md
@@ -1,7 +1,11 @@
+Hardware Overview
+=================
+
+Introduction
------------
The Salomon cluster consists of 1008 computational nodes of which 576
are regular compute nodes and 432 accelerated nodes. Each node is a
-powerful x86-64 computer, equipped
+<span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped
with 24 cores (two twelve-core Intel Xeon processors) and 128GB RAM. The
nodes are interlinked by high speed InfiniBand and Ethernet networks.
All nodes share 0.5PB /home NFS disk storage to store the user files.
@@ -10,10 +14,10 @@ is available for the scratch project data. The user access to the
Salomon cluster is provided by four login nodes.
[More about schematic representation of the Salomon cluster compute
nodes IB
-topology](network-1/ib-single-plane-topology.html).
-class="internal-link">
-[](salomon_2.jpg)
-The parameters are summarized in the following tables
+topology](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology).<span
+class="internal-link"></span>
+[](https://docs.it4i.cz/salomon/salomon-2)
+The parameters are summarized in the following tables:
General information
-------------------
**In general**
@@ -23,7 +27,8 @@ Architecture of compute nodes
x86-64
Operating system
CentOS 6.7 Linux
-[**Compute nodes**](compute-nodes.html)
+[**Compute
+nodes**](https://docs.it4i.cz/salomon/compute-nodes)
Totally
1008
Processor
@@ -42,54 +47,58 @@ MIC accelerated
Total theoretical peak performance (Rpeak)
2011 Tflop/s
Total amount of RAM
-129.024 TB
+<span>129.024 TB</span>
Compute nodes
-------------
Node Count Processor Cores Memory Accelerator
- ----------------- ------- ---------------------------------- ------- -------- --------------------------------------------
+ ----------------- ------- ----------- ------- -------- ---------------------
w/o accelerator 576 2x Intel Xeon E5-2680v3, 2.5GHz 24 128GB -
MIC accelerated 432 2x Intel Xeon E5-2680v3, 2.5GHz 24 128GB 2x Intel Xeon Phi 7120P, 61cores, 16GB RAM
For more details please refer to the [Compute
-nodes](compute-nodes.html).
+nodes](https://docs.it4i.cz/salomon/compute-nodes).
Remote visualization nodes
---------------------------
+---
For remote visualization two nodes with NICE DCV software are available
-each configured
+each configured:
Node Count Processor Cores Memory GPU Accelerator
- --------------- ------- --------------------------------- ------- -------- ------------------------------
+ --------------- ------- ---------- ------- -------- -------
visualization 2 2x Intel Xeon E5-2695v3, 2.3GHz 28 512GB NVIDIA QUADRO K5000, 4GB RAM
SGI UV 2000
-----------
For large memory computations a special SMP/NUMA SGI UV 2000 server is
-available
-Node
-Count
-Processor
-Cores
-Memory
-Extra HW
-UV2000
-1
-14x Intel Xeon E5-4627v2, 3.3GHz, 8cores
-112
-3328GB DDR3@1866MHz
-2x 400GB local SSD
-1x NVIDIA GM200
-(GeForce GTX TITAN X),
-12GB RAM
+available:
+<table style="width:100%;">
+<colgroup>
+<col width="16%" />
+<col width="16%" />
+<col width="16%" />
+<col width="16%" />
+<col width="16%" />
+<col width="16%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Node</th>
+<th align="left">Count</th>
+<th align="left">Processor</th>
+<th align="left">Cores</th>
+<th align="left">Memory</th>
+<th align="left">Extra HW</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left">UV2000</td>
+<td align="left">1</td>
+<td align="left">14x Intel Xeon E5-4627v2, 3.3GHz, 8cores</td>
+<td align="left">112</td>
+<td align="left">3328GB DDR3@1866MHz</td>
+<td align="left"><p>2x 400GB local SSD<br />
+1x NVIDIA GM200<br />
+(GeForce GTX TITAN X),<br />
+12GB RAM</p></td>
+</tr>
+</tbody>
+</table>
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
+2000](https://docs.it4i.cz/salomon/uv-2000/@@images/04ce7514-8d27-4cdb-bf0f-45d875c75df0.jpeg "UV 2000")
diff --git a/salomon/hardware-overview-1.html b/docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.html
old mode 100755
new mode 100644
similarity index 70%
rename from salomon/hardware-overview-1.html
rename to docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.html
index 1ea06b0b34cccf39d9208f36a435ca482c64eed5..cb273ff0c823cf2bea37c49ecfce5df4319b53e5
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/hardware-overview-1/hardware-overview" /><!--[if lt IE 7]></base><![endif]-->
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- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Hardware Overview — IT4I Docs</title>
- <link rel="canonical" href="hardware-overview-1.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/hardware-overview-1" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="hardware-overview-1.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/hardware-overview-1/hardware-overview#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="hardware-overview-1.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/hardware-overview-1/hardware-overview#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../index.html">
- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -232,8 +229,8 @@
<div id="parent-fieldname-text-e3d9b88c840a474ea3bbc24a1dc19bed" class="">
<h2 class=" ">Introduction</h2>
<p>The Salomon cluster consists of 1008 computational nodes of which 576 are regular compute nodes and 432 accelerated nodes. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 24 cores (two twelve-core Intel Xeon processors) and 128GB RAM. The nodes are interlinked by high speed InfiniBand and Ethernet networks. All nodes share 0.5PB /home NFS disk storage to store the user files. Users may use a DDN Lustre shared storage with capacity of 1.69 PB which is available for the scratch project data. The user access to the Salomon cluster is provided by four login nodes.</p>
-<p><a target="_self" title="" class="internal-link" href="network-1/ib-single-plane-topology.html">More about schematic representation of the Salomon cluster compute nodes IB topology</a>.<span class="internal-link"></span></p>
-<p style="padding-left: 30px; "><a target="_self" title="" class="internal-link" href="salomon_2.jpg"><img title="Salomon" class="image-inline" alt="Salomon" src="salomon-2/%40%40images/25c7db03-5c44-4981-9e19-07c1c23fcf1e.jpg" /></a></p>
+<p><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology">More about schematic representation of the Salomon cluster compute nodes IB topology</a>.<span class="internal-link"></span></p>
+<p style="padding-left: 30px; "><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/salomon-2"><img alt="Salomon" class="image-inline" title="Salomon" src="https://docs.it4i.cz/salomon/salomon-2/@@images/25c7db03-5c44-4981-9e19-07c1c23fcf1e.jpeg" /></a></p>
<p>The parameters are summarized in the following tables:</p>
<h2 class=" ">General information</h2>
<table class="listing">
@@ -251,7 +248,7 @@
<td>Operating system</td>
<td>CentOS 6.7 Linux</td>
</tr>
-<tr><th colspan="2"><a target="_self" title="" class="internal-link" href="compute-nodes.html"><strong>Compute nodes</strong></a></th></tr>
+<tr><th colspan="2"><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/compute-nodes"><strong>Compute nodes</strong></a></th></tr>
<tr class="even">
<td>Totally</td>
<td>1008</td>
@@ -313,7 +310,7 @@
</tr>
</tbody>
</table>
-<p class="internal-link" title="">For more details please refer to the <a target="_self" title="" class="internal-link" href="compute-nodes.html">Compute nodes</a>.</p>
+<p class="internal-link" title="">For more details please refer to the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/compute-nodes">Compute nodes</a>.</p>
<h2 class=" ">Remote visualization nodes</h2>
<p class="internal-link" title="">For remote visualization two nodes with NICE DCV software are available each configured:</p>
<table class="listing">
@@ -346,7 +343,7 @@
</tr>
</tbody>
</table>
-<p style="padding-left: 30px; "><img title="UV 2000" class="image-inline" alt="UV 2000" src="uv-2000/%40%40images/04ce7514-8d27-4cdb-bf0f-45d875c75df0.jpg" /></p>
+<p style="padding-left: 30px; "><img alt="UV 2000" class="image-inline" title="UV 2000" src="https://docs.it4i.cz/salomon/uv-2000/@@images/04ce7514-8d27-4cdb-bf0f-45d875c75df0.jpeg" /></p>
</div>
@@ -422,7 +419,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -438,7 +435,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -454,7 +451,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -470,7 +467,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -486,7 +483,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="hardware-overview-1.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -502,7 +499,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -518,7 +515,7 @@
- <a title="" class="state-published contenttype-document" href="environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -534,7 +531,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -550,7 +547,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -566,7 +563,7 @@
- <a title="" class="state-published contenttype-document" href="compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -582,7 +579,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -598,7 +595,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -614,10 +611,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -633,7 +630,7 @@
- <a title="" class="state-published contenttype-document" href="prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -658,7 +655,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -674,7 +671,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -690,7 +687,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -706,7 +703,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -745,14 +742,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
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@@ -774,12 +771,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -795,7 +792,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/hardware-overview-1 by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:41 GMT -->
</html>
diff --git a/salomon/hardware-overview-1/hardware-overview.md b/docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.md
similarity index 54%
rename from salomon/hardware-overview-1/hardware-overview.md
rename to docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.md
index 4d3be01a3ba862cf0b3b1e4707d9ec86a28b6710..298cb25728bbd82d988d06f51b4e0056ea4a4d5b 100644
--- a/salomon/hardware-overview-1/hardware-overview.md
+++ b/docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.md
@@ -1,7 +1,11 @@
+Hardware Overview
+=================
+
+Introduction
------------
The Salomon cluster consists of 1008 computational nodes of which 576
are regular compute nodes and 432 accelerated nodes. Each node is a
-powerful x86-64 computer, equipped
+<span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped
with 24 cores (two twelve-core Intel Xeon processors) and 128GB RAM. The
nodes are interlinked by high speed InfiniBand and Ethernet networks.
All nodes share 0.5PB /home NFS disk storage to store the user files.
@@ -10,10 +14,10 @@ is available for the scratch project data. The user access to the
Salomon cluster is provided by four login nodes.
[More about schematic representation of the Salomon cluster compute
nodes IB
-topology](../network-1/ib-single-plane-topology.html).
-class="internal-link">
-[](../salomon_2.jpg)
-The parameters are summarized in the following tables
+topology](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology).<span
+class="internal-link"></span>
+[](https://docs.it4i.cz/salomon/salomon-2)
+The parameters are summarized in the following tables:
General information
-------------------
**In general**
@@ -23,7 +27,8 @@ Architecture of compute nodes
x86-64
Operating system
CentOS 6.7 Linux
-[**Compute nodes**](../compute-nodes.html)
+[**Compute
+nodes**](https://docs.it4i.cz/salomon/compute-nodes)
Totally
1008
Processor
@@ -42,54 +47,58 @@ MIC accelerated
Total theoretical peak performance (Rpeak)
2011 Tflop/s
Total amount of RAM
-129.024 TB
+<span>129.024 TB</span>
Compute nodes
-------------
Node Count Processor Cores Memory Accelerator
- ----------------- ------- ---------------------------------- ------- -------- --------------------------------------------
+ ----------------- ------- ----------- ------- -------- ---------------------
w/o accelerator 576 2x Intel Xeon E5-2680v3, 2.5GHz 24 128GB -
MIC accelerated 432 2x Intel Xeon E5-2680v3, 2.5GHz 24 128GB 2x Intel Xeon Phi 7120P, 61cores, 16GB RAM
For more details please refer to the [Compute
-nodes](../compute-nodes.html).
+nodes](https://docs.it4i.cz/salomon/compute-nodes).
Remote visualization nodes
---------------------------
+---
For remote visualization two nodes with NICE DCV software are available
-each configured
+each configured:
Node Count Processor Cores Memory GPU Accelerator
- --------------- ------- --------------------------------- ------- -------- ------------------------------
+ --------------- ------- ---------- ------- -------- -------
visualization 2 2x Intel Xeon E5-2695v3, 2.3GHz 28 512GB NVIDIA QUADRO K5000, 4GB RAM
SGI UV 2000
-----------
For large memory computations a special SMP/NUMA SGI UV 2000 server is
-available
-Node
-Count
-Processor
-Cores
-Memory
-Extra HW
-UV2000
-1
-14x Intel Xeon E5-4627v2, 3.3GHz, 8cores
-112
-3328GB DDR3@1866MHz
-2x 400GB local SSD
-1x NVIDIA GM200
-(GeForce GTX TITAN X),
-12GB RAM
+available:
+<table style="width:100%;">
+<colgroup>
+<col width="16%" />
+<col width="16%" />
+<col width="16%" />
+<col width="16%" />
+<col width="16%" />
+<col width="16%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Node</th>
+<th align="left">Count</th>
+<th align="left">Processor</th>
+<th align="left">Cores</th>
+<th align="left">Memory</th>
+<th align="left">Extra HW</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left">UV2000</td>
+<td align="left">1</td>
+<td align="left">14x Intel Xeon E5-4627v2, 3.3GHz, 8cores</td>
+<td align="left">112</td>
+<td align="left">3328GB DDR3@1866MHz</td>
+<td align="left"><p>2x 400GB local SSD<br />
+1x NVIDIA GM200<br />
+(GeForce GTX TITAN X),<br />
+12GB RAM</p></td>
+</tr>
+</tbody>
+</table>
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
+2000](https://docs.it4i.cz/salomon/uv-2000/@@images/04ce7514-8d27-4cdb-bf0f-45d875c75df0.jpeg "UV 2000")
diff --git a/salomon/index.html b/docs.it4i.cz/salomon/index.html
old mode 100755
new mode 100644
similarity index 67%
rename from salomon/index.html
rename to docs.it4i.cz/salomon/index.html
index 9bd2b37dadcc05fb095ac00cf84769435ec27527..e4c94e68873b773e790e64147905b969b68be05c
--- a/salomon/index.html
+++ b/docs.it4i.cz/salomon/index.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/introduction" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<![endif]-->
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- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Introduction — IT4I Docs</title>
- <link rel="canonical" href="../salomon.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="index.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="index.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../index.html">
- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -216,14 +213,14 @@
<div id="parent-fieldname-text-fd059ba857eb4bd39efbd852b0776d08" class="">
- <p>Welcome to Salomon supercomputer cluster. The Salomon cluster consists of 1008 compute nodes, totaling 24192 compute cores with 129TB RAM and giving over 2 Pflop/s theoretical peak performance. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 24 cores, at least 128GB RAM. Nodes are interconnected by 7D Enhanced hypercube Infiniband network and equipped with Intel Xeon E5-2680v3 processors. The Salomon cluster consists of 576 nodes without accelerators and 432 nodes equipped with Intel Xeon Phi MIC accelerators. Read more in <a target="_self" title="" class="internal-link" href="hardware-overview-1/hardware-overview.html">Hardware Overview</a>.</p>
+ <p>Welcome to Salomon supercomputer cluster. The Salomon cluster consists of 1008 compute nodes, totaling 24192 compute cores with 129TB RAM and giving over 2 Pflop/s theoretical peak performance. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 24 cores, at least 128GB RAM. Nodes are interconnected by 7D Enhanced hypercube Infiniband network and equipped with Intel Xeon E5-2680v3 processors. The Salomon cluster consists of 576 nodes without accelerators and 432 nodes equipped with Intel Xeon Phi MIC accelerators. Read more in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/hardware-overview-1/hardware-overview">Hardware Overview</a>.</p>
<p>The cluster runs CentOS Linux <a class="external-link" href="http://www.bull.com/bullx-logiciels/systeme-exploitation.html" target="_self" title=""><span class="WYSIWYG_LINK"></span></a><span class="internal-link">operating system</span>, which is compatible with the <span class="WYSIWYG_LINK">RedHat</span> <a class="external-link" href="http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg" target="_self" title=""><span class="WYSIWYG_LINK">Linux family.</span></a></p>
<p style="padding-left: 30px; "><strong>Water-cooled Compute Nodes With MIC Accelerator</strong></p>
-<p style="padding-left: 30px; "><a target="_self" title="" class="internal-link" href="salomon_1.jpg"><img title="Salomon" class="image-inline" alt="Salomon" src="salomon/%40%40images/8fe6c2ad-25f3-48cf-abbb-6f8ba653b93e.jpg" /></a></p>
-<p style="padding-left: 30px; "><img title="Salomon" class="image-inline" alt="Salomon" src="salomon-1/%40%40images/ba2c321e-1554-4826-b6ec-3c68d370cd9f.jpg" /></p>
+<p style="padding-left: 30px; "><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/salomon"><img alt="Salomon" class="image-inline" title="Salomon" src="https://docs.it4i.cz/salomon/salomon/@@images/8fe6c2ad-25f3-48cf-abbb-6f8ba653b93e.jpeg" /></a></p>
+<p style="padding-left: 30px; "><img alt="Salomon" class="image-inline" title="Salomon" src="https://docs.it4i.cz/salomon/salomon-1/@@images/ba2c321e-1554-4826-b6ec-3c68d370cd9f.jpeg" /></p>
<p style="padding-left: 30px; "><strong>Tape Library T950B</strong></p>
-<p style="padding-left: 30px; "><img title="Salomon" class="image-inline" alt="Salomon" src="salomon-3/%40%40images/d2a6de55-62fc-454f-adda-a6a25e3f44dd.jpg" /></p>
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+<p style="padding-left: 30px; "><img alt="Salomon" class="image-inline" title="Salomon" src="https://docs.it4i.cz/salomon/salomon-3/@@images/d2a6de55-62fc-454f-adda-a6a25e3f44dd.jpeg" /></p>
+<p style="padding-left: 30px; "><img alt="Salomon" class="image-inline" title="Salomon" src="https://docs.it4i.cz/salomon/salomon-4/@@images/82997462-cd88-49eb-aad5-71d77903d903.jpeg" /></p>
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<span>What's New</span>
</a>
@@ -331,7 +328,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -347,7 +344,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -363,7 +360,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -379,7 +376,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -395,7 +392,7 @@
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<span>Environment and Modules</span>
</a>
@@ -411,7 +408,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -427,7 +424,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -443,7 +440,7 @@
- <a title="" class="state-published contenttype-document" href="compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -459,7 +456,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -475,7 +472,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -491,10 +488,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -510,7 +507,7 @@
- <a title="" class="state-published contenttype-document" href="prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -535,7 +532,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -551,7 +548,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -567,7 +564,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -583,7 +580,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -651,12 +648,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</div>
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</html>
diff --git a/docs.it4i.cz/salomon/index.md b/docs.it4i.cz/salomon/index.md
new file mode 100644
index 0000000000000000000000000000000000000000..ffd19820cf1814a49ec480289d02d1f3836e4f39
--- /dev/null
+++ b/docs.it4i.cz/salomon/index.md
@@ -0,0 +1,24 @@
+Introduction
+============
+Welcome to Salomon supercomputer cluster. The Salomon cluster consists
+of 1008 compute nodes, totaling 24192 compute cores with 129TB RAM and
+giving over 2 Pflop/s theoretical peak performance. Each node is a <span
+class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 24
+cores, at least 128GB RAM. Nodes are interconnected by 7D Enhanced
+hypercube Infiniband network and equipped with Intel Xeon E5-2680v3
+processors. The Salomon cluster consists of 576 nodes without
+accelerators and 432 nodes equipped with Intel Xeon Phi MIC
+accelerators. Read more in [Hardware
+Overview](https://docs.it4i.cz/salomon/hardware-overview-1/hardware-overview).
+The cluster runs CentOS Linux [<span
+class="WYSIWYG_LINK"></span>](http://www.bull.com/bullx-logiciels/systeme-exploitation.html)<span
+class="internal-link">operating system</span>, which is compatible with
+the <span class="WYSIWYG_LINK">RedHat</span> [<span
+class="WYSIWYG_LINK">Linux
+family.</span>](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
+**Water-cooled Compute Nodes With MIC Accelerator**
+[](https://docs.it4i.cz/salomon/salomon)
+
+**Tape Library T950B**
+
+
diff --git a/salomon/introduction.html b/docs.it4i.cz/salomon/introduction.html
old mode 100755
new mode 100644
similarity index 67%
rename from salomon/introduction.html
rename to docs.it4i.cz/salomon/introduction.html
index 9815a05f65ecd2e3383d966e1650ecff68692fd8..add408845159e18b7d27b0cd6ecd13c28e5535e9
--- a/salomon/introduction.html
+++ b/docs.it4i.cz/salomon/introduction.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/introduction" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
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<title>Introduction — IT4I Docs</title>
- <link rel="canonical" href="../salomon.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="introduction.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/introduction#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="introduction.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/introduction#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../index.html">
- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -216,14 +213,14 @@
<div id="parent-fieldname-text-fd059ba857eb4bd39efbd852b0776d08" class="">
- <p>Welcome to Salomon supercomputer cluster. The Salomon cluster consists of 1008 compute nodes, totaling 24192 compute cores with 129TB RAM and giving over 2 Pflop/s theoretical peak performance. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 24 cores, at least 128GB RAM. Nodes are interconnected by 7D Enhanced hypercube Infiniband network and equipped with Intel Xeon E5-2680v3 processors. The Salomon cluster consists of 576 nodes without accelerators and 432 nodes equipped with Intel Xeon Phi MIC accelerators. Read more in <a target="_self" title="" class="internal-link" href="hardware-overview-1/hardware-overview.html">Hardware Overview</a>.</p>
+ <p>Welcome to Salomon supercomputer cluster. The Salomon cluster consists of 1008 compute nodes, totaling 24192 compute cores with 129TB RAM and giving over 2 Pflop/s theoretical peak performance. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 24 cores, at least 128GB RAM. Nodes are interconnected by 7D Enhanced hypercube Infiniband network and equipped with Intel Xeon E5-2680v3 processors. The Salomon cluster consists of 576 nodes without accelerators and 432 nodes equipped with Intel Xeon Phi MIC accelerators. Read more in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/hardware-overview-1/hardware-overview">Hardware Overview</a>.</p>
<p>The cluster runs CentOS Linux <a class="external-link" href="http://www.bull.com/bullx-logiciels/systeme-exploitation.html" target="_self" title=""><span class="WYSIWYG_LINK"></span></a><span class="internal-link">operating system</span>, which is compatible with the <span class="WYSIWYG_LINK">RedHat</span> <a class="external-link" href="http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg" target="_self" title=""><span class="WYSIWYG_LINK">Linux family.</span></a></p>
<p style="padding-left: 30px; "><strong>Water-cooled Compute Nodes With MIC Accelerator</strong></p>
-<p style="padding-left: 30px; "><a target="_self" title="" class="internal-link" href="salomon_1.jpg"><img title="Salomon" class="image-inline" alt="Salomon" src="salomon/%40%40images/8fe6c2ad-25f3-48cf-abbb-6f8ba653b93e.jpg" /></a></p>
-<p style="padding-left: 30px; "><img title="Salomon" class="image-inline" alt="Salomon" src="salomon-1/%40%40images/ba2c321e-1554-4826-b6ec-3c68d370cd9f.jpg" /></p>
+<p style="padding-left: 30px; "><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/salomon"><img alt="Salomon" class="image-inline" title="Salomon" src="https://docs.it4i.cz/salomon/salomon/@@images/8fe6c2ad-25f3-48cf-abbb-6f8ba653b93e.jpeg" /></a></p>
+<p style="padding-left: 30px; "><img alt="Salomon" class="image-inline" title="Salomon" src="https://docs.it4i.cz/salomon/salomon-1/@@images/ba2c321e-1554-4826-b6ec-3c68d370cd9f.jpeg" /></p>
<p style="padding-left: 30px; "><strong>Tape Library T950B</strong></p>
-<p style="padding-left: 30px; "><img title="Salomon" class="image-inline" alt="Salomon" src="salomon-3/%40%40images/d2a6de55-62fc-454f-adda-a6a25e3f44dd.jpg" /></p>
-<p style="padding-left: 30px; "><img title="Salomon" class="image-inline" alt="Salomon" src="salomon-4/%40%40images/82997462-cd88-49eb-aad5-71d77903d903.jpg" /></p>
+<p style="padding-left: 30px; "><img alt="Salomon" class="image-inline" title="Salomon" src="https://docs.it4i.cz/salomon/salomon-3/@@images/d2a6de55-62fc-454f-adda-a6a25e3f44dd.jpeg" /></p>
+<p style="padding-left: 30px; "><img alt="Salomon" class="image-inline" title="Salomon" src="https://docs.it4i.cz/salomon/salomon-4/@@images/82997462-cd88-49eb-aad5-71d77903d903.jpeg" /></p>
</div>
@@ -299,7 +296,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -315,7 +312,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -331,7 +328,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -347,7 +344,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -363,7 +360,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -379,7 +376,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -395,7 +392,7 @@
- <a title="" class="state-published contenttype-document" href="environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -411,7 +408,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -427,7 +424,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -443,7 +440,7 @@
- <a title="" class="state-published contenttype-document" href="compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -459,7 +456,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -475,7 +472,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -491,10 +488,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -510,7 +507,7 @@
- <a title="" class="state-published contenttype-document" href="prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -535,7 +532,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -551,7 +548,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -567,7 +564,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -583,7 +580,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -651,12 +648,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -672,7 +669,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
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</html>
diff --git a/docs.it4i.cz/salomon/introduction.md b/docs.it4i.cz/salomon/introduction.md
new file mode 100644
index 0000000000000000000000000000000000000000..ffd19820cf1814a49ec480289d02d1f3836e4f39
--- /dev/null
+++ b/docs.it4i.cz/salomon/introduction.md
@@ -0,0 +1,24 @@
+Introduction
+============
+Welcome to Salomon supercomputer cluster. The Salomon cluster consists
+of 1008 compute nodes, totaling 24192 compute cores with 129TB RAM and
+giving over 2 Pflop/s theoretical peak performance. Each node is a <span
+class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 24
+cores, at least 128GB RAM. Nodes are interconnected by 7D Enhanced
+hypercube Infiniband network and equipped with Intel Xeon E5-2680v3
+processors. The Salomon cluster consists of 576 nodes without
+accelerators and 432 nodes equipped with Intel Xeon Phi MIC
+accelerators. Read more in [Hardware
+Overview](https://docs.it4i.cz/salomon/hardware-overview-1/hardware-overview).
+The cluster runs CentOS Linux [<span
+class="WYSIWYG_LINK"></span>](http://www.bull.com/bullx-logiciels/systeme-exploitation.html)<span
+class="internal-link">operating system</span>, which is compatible with
+the <span class="WYSIWYG_LINK">RedHat</span> [<span
+class="WYSIWYG_LINK">Linux
+family.</span>](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
+**Water-cooled Compute Nodes With MIC Accelerator**
+[](https://docs.it4i.cz/salomon/salomon)
+
+**Tape Library T950B**
+
+
diff --git a/salomon/list_of_modules.html b/docs.it4i.cz/salomon/list_of_modules.html
old mode 100755
new mode 100644
similarity index 94%
rename from salomon/list_of_modules.html
rename to docs.it4i.cz/salomon/list_of_modules.html
index d103aa8a22ef7cab4aee6c6ded2b480c7e8be23c..6fac0383e91fe137147356b1e954cf9475c4f5f9
--- a/salomon/list_of_modules.html
+++ b/docs.it4i.cz/salomon/list_of_modules.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/list_of_modules by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:42 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/list_of_modules" /><!--[if lt IE 7]></base><![endif]-->
<meta content="List of Available Modules on Salomon Cluster" name="description" />
- <link rel="stylesheet" type="text/css" media="screen" href="../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>List of Available Modules — IT4I Docs</title>
- <link rel="canonical" href="list_of_modules.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/list_of_modules" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="list_of_modules.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/list_of_modules#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="list_of_modules.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/list_of_modules#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../index.html">
- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -227,7 +224,7 @@
- <div id="parent-fieldname-text-07f9a79724204a24adc155a93c34b79c" class="">
+ <div id="parent-fieldname-text-12f4645a6b084b17bca6411df10a8022" class="">
<div>
<h2 id="categories">Categories</h2>
@@ -351,7 +348,7 @@ repeatable and robust way.</td>
<tr>
<td>
<b>Amber</b><br />
- <a href="http://ambermd.org/">http://ambermd.org</a>
+ <a href="http://ambermd.org">http://ambermd.org</a>
</td>
<td>A set of molecular mechanical force fields for the simulation of biomolecules</td>
<td>
@@ -421,7 +418,7 @@ repeatable and robust way.</td>
<tr>
<td>
<b>GROMACS</b><br />
- <a href="http://www.gromacs.org/">http://www.gromacs.org</a>
+ <a href="http://www.gromacs.org">http://www.gromacs.org</a>
</td>
<td>GROMACS is a versatile package to perform molecular dynamics,
i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.</td>
@@ -451,7 +448,7 @@ repeatable and robust way.</td>
<tr>
<td>
<b>PLUMED</b><br />
- <a href="http://www.plumed-code.org/">http://www.plumed-code.org</a>
+ <a href="http://www.plumed-code.org">http://www.plumed-code.org</a>
</td>
<td>PLUMED is an open source library for free energy calculations
in molecular systems which works together with some of the most popular molecular
@@ -569,7 +566,7 @@ repeatable and robust way.</td>
<tr>
<td>
<b>ANSYS</b><br />
- <a href="index.html"></a>
+ <a href="https://docs.it4i.cz/salomon/"></a>
</td>
<td></td>
<td>
@@ -582,7 +579,7 @@ repeatable and robust way.</td>
<tr>
<td>
<b>Adams</b><br />
- <a href="index.html"></a>
+ <a href="https://docs.it4i.cz/salomon/"></a>
</td>
<td></td>
<td>
@@ -594,7 +591,7 @@ repeatable and robust way.</td>
<tr>
<td>
<b>COMSOL</b><br />
- <a href="index.html"></a>
+ <a href="https://docs.it4i.cz/salomon/"></a>
</td>
<td></td>
<td>
@@ -607,7 +604,7 @@ repeatable and robust way.</td>
<tr>
<td>
<b>Digimat</b><br />
- <a href="index.html"></a>
+ <a href="https://docs.it4i.cz/salomon/"></a>
</td>
<td></td>
<td>
@@ -620,7 +617,7 @@ repeatable and robust way.</td>
<tr>
<td>
<b>FreeFem++</b><br />
- <a href="http://www.freefem.org/">http://www.freefem.org</a>
+ <a href="http://www.freefem.org">http://www.freefem.org</a>
</td>
<td>FreeFem++ is a partial differential equation solver. It has its own language. freefem scripts can solve multiphysics non linear systems in 2D and 3D.
Problems involving PDE (2d, 3d) from several branches of physics such as fluid-structure interactions require interpolations of data on several meshes and their manipulation within one program. FreeFem++ includes a fast 2^d-tree-based interpolation algorithm and a language for the manipulation of data on multiple meshes (as a follow up of bamg (now a part of FreeFem++ ).
@@ -635,7 +632,7 @@ FreeFem++ is written in C++ and the FreeFem++ language is a C++ idiom. It runs o
<tr>
<td>
<b>HyperWorks</b><br />
- <a href="index.html"></a>
+ <a href="https://docs.it4i.cz/salomon/"></a>
</td>
<td></td>
<td>
@@ -647,7 +644,7 @@ FreeFem++ is written in C++ and the FreeFem++ language is a C++ idiom. It runs o
<tr>
<td>
<b>Marc</b><br />
- <a href="index.html"></a>
+ <a href="https://docs.it4i.cz/salomon/"></a>
</td>
<td></td>
<td>
@@ -719,7 +716,7 @@ FreeFem++ is written in C++ and the FreeFem++ language is a C++ idiom. It runs o
<tr>
<td>
<b>LAMMPS</b><br />
- <a href="http://lammps.sandia.gov/">http://lammps.sandia.gov</a>
+ <a href="http://lammps.sandia.gov">http://lammps.sandia.gov</a>
</td>
<td>LAMMPS is a classical molecular dynamics code,
and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
@@ -752,7 +749,7 @@ matrix elements (integrals) over Cartesian Gaussian functions used in modern ato
<tr>
<td>
<b>Molpro</b><br />
- <a href="index.html"></a>
+ <a href="https://docs.it4i.cz/salomon/"></a>
</td>
<td></td>
<td>
@@ -776,7 +773,7 @@ matrix elements (integrals) over Cartesian Gaussian functions used in modern ato
<tr>
<td>
<b>NWChem</b><br />
- <a href="http://www.nwchem-sw.org/">http://www.nwchem-sw.org</a>
+ <a href="http://www.nwchem-sw.org">http://www.nwchem-sw.org</a>
</td>
<td>NWChem aims to provide its users with computational chemistry tools that are scalable both in
their ability to treat large scientific computational chemistry problems efficiently, and in their use of available
@@ -849,7 +846,7 @@ force field-driven conformational sampling and geometry optimization heuristics
<tr>
<td>
<b>BerkeleyUPC</b><br />
- <a href="http://upc.lbl.gov/">http://upc.lbl.gov</a>
+ <a href="http://upc.lbl.gov">http://upc.lbl.gov</a>
</td>
<td>The goal of the Berkeley UPC compiler group is to develop a portable,
high performance implementation of UPC for large-scale multiprocessors, PC clusters,
@@ -948,7 +945,7 @@ and clusters of shared memory multiprocessors.
<tr>
<td>
<b>PGI</b><br />
- <a href="index.html"></a>
+ <a href="https://docs.it4i.cz/salomon/"></a>
</td>
<td></td>
<td>
@@ -1117,7 +1114,7 @@ and clusters of shared memory multiprocessors.
<tr>
<td>
<b>DDT</b><br />
- <a href="index.html"></a>
+ <a href="https://docs.it4i.cz/salomon/"></a>
</td>
<td></td>
<td>
@@ -1169,7 +1166,7 @@ One single-page HTML report elegantly answers a range of vital questions for any
<tr>
<td>
<b>TotalView</b><br />
- <a href="index.html"></a>
+ <a href="https://docs.it4i.cz/salomon/"></a>
</td>
<td></td>
<td>
@@ -1194,7 +1191,7 @@ One single-page HTML report elegantly answers a range of vital questions for any
<tr>
<td>
<b>aislinn</b><br />
- <a href="index.html"></a>
+ <a href="https://docs.it4i.cz/salomon/"></a>
</td>
<td></td>
<td>
@@ -1260,7 +1257,7 @@ One single-page HTML report elegantly answers a range of vital questions for any
<tr>
<td>
<b>Autotools</b><br />
- <a href="http://autotools.io/">http://autotools.io</a>
+ <a href="http://autotools.io">http://autotools.io</a>
</td>
<td>This bundle collect the standard GNU build tools: Autoconf, Automake and libtool</td>
<td>
@@ -1297,7 +1294,7 @@ One single-page HTML report elegantly answers a range of vital questions for any
<tr>
<td>
<b>CMake</b><br />
- <a href="http://www.cmake.org/">http://www.cmake.org</a>
+ <a href="http://www.cmake.org">http://www.cmake.org</a>
</td>
<td>CMake, the cross-platform, open-source build system.
CMake is a family of tools designed to build, test and package software.</td>
@@ -1325,7 +1322,7 @@ One single-page HTML report elegantly answers a range of vital questions for any
<tr>
<td>
<b>Doxygen</b><br />
- <a href="http://www.doxygen.org/">http://www.doxygen.org</a>
+ <a href="http://www.doxygen.org">http://www.doxygen.org</a>
</td>
<td>Doxygen is a documentation system for C++, C, Java, Objective-C, Python,
IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.</td>
@@ -1483,7 +1480,7 @@ central piece of information.
<tr>
<td>
<b>Spark</b><br />
- <a href="http://spark.apache.org/">http://spark.apache.org</a>
+ <a href="http://spark.apache.org">http://spark.apache.org</a>
</td>
<td>Spark is Hadoop MapReduce done in memory</td>
<td>
@@ -1695,6 +1692,7 @@ latency hiding, direct access to the protocol, improved threading support, and e
<td>
<ul>
<li style="white-space: nowrap;">1.10-Python-2.7.8</li>
+ <li style="white-space: nowrap;">1.11-Python-2.7.9</li>
<li style="white-space: nowrap;">1.11-foss-2015g-Python-2.7.9</li>
<li style="white-space: nowrap;">1.11-intel-2015b-Python-2.7.9</li>
</ul>
@@ -1814,7 +1812,7 @@ latency hiding, direct access to the protocol, improved threading support, and e
<tr>
<td>
<b>PROJ_4</b><br />
- <a href="http://proj.osgeo.org/">http://proj.osgeo.org</a>
+ <a href="http://proj.osgeo.org">http://proj.osgeo.org</a>
</td>
<td>PROJ.4 - Cartographic Projections Library originally written by Gerald Evenden then of the USGS.
</td>
@@ -1885,7 +1883,7 @@ latency hiding, direct access to the protocol, improved threading support, and e
<tr>
<td>
<b>Mono</b><br />
- <a href="http://www.mono-project.com/">http://www.mono-project.com</a>
+ <a href="http://www.mono-project.com">http://www.mono-project.com</a>
</td>
<td>Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards
for C# and the Common Language Runtime.</td>
@@ -1976,6 +1974,7 @@ in numerous market categories from gaming and entertainment to scientific and me
<li style="white-space: nowrap;">2.7.11-intel-2015b</li>
<li style="white-space: nowrap;">2.7.8-intel-2015b</li>
<li style="white-space: nowrap;">2.7.8-intel-2016.01</li>
+ <li style="white-space: nowrap;">2.7.9</li>
<li style="white-space: nowrap;">2.7.9-GNU-5.1.0-2.25</li>
<li style="white-space: nowrap;">2.7.9-foss-2015b</li>
<li style="white-space: nowrap;">2.7.9-foss-2015g</li>
@@ -2004,7 +2003,7 @@ in numerous market categories from gaming and entertainment to scientific and me
<tr>
<td>
<b>Racket</b><br />
- <a href="http://racket-lang.org/">http://racket-lang.org</a>
+ <a href="http://racket-lang.org">http://racket-lang.org</a>
</td>
<td>Racket is a full-spectrum programming language. It goes
beyond Lisp and Scheme with dialects that support objects, types,
@@ -2018,7 +2017,7 @@ laziness, and more.</td>
<tr>
<td>
<b>Ruby</b><br />
- <a href="https://www.ruby-lang.org/">https://www.ruby-lang.org</a>
+ <a href="https://www.ruby-lang.org">https://www.ruby-lang.org</a>
</td>
<td>Ruby is a dynamic, open source programming language with
a focus on simplicity and productivity. It has an elegant syntax that is
@@ -2045,7 +2044,7 @@ laziness, and more.</td>
<tr>
<td>
<b>SnuCL</b><br />
- <a href="http://snucl.snu.ac.kr/">http://snucl.snu.ac.kr</a>
+ <a href="http://snucl.snu.ac.kr">http://snucl.snu.ac.kr</a>
</td>
<td>An OpenCL Framework for Heterogeneous Clusters</td>
<td>
@@ -2155,7 +2154,7 @@ suitable for a very wide range of uses, including web and desktop applications,
<tr>
<td>
<b>FOX</b><br />
- <a href="http://fox-toolkit.org/">http://fox-toolkit.org</a>
+ <a href="http://fox-toolkit.org">http://fox-toolkit.org</a>
</td>
<td>FOX is a C++ based Toolkit for developing Graphical User Interfaces easily and effectively.
It offers a wide, and growing, collection of Controls, and provides state of the art facilities such as
@@ -2181,7 +2180,7 @@ drag and drop, selection, as well as OpenGL widgets for 3D graphical manipulatio
<tr>
<td>
<b>OpenCoarrays</b><br />
- <a href="http://www.opencoarrays.org/">http://www.opencoarrays.org</a>
+ <a href="http://www.opencoarrays.org">http://www.opencoarrays.org</a>
</td>
<td>OpenCoarrays is an open-source software project for developing,
porting and tuning transport layers that support coarray Fortran
@@ -2223,7 +2222,7 @@ using plugins known as Providers</td>
<tr>
<td>
<b>QGIS</b><br />
- <a href="http://www.qgis.org/">http://www.qgis.org</a>
+ <a href="http://www.qgis.org">http://www.qgis.org</a>
</td>
<td>A Free and Open Source Geographic Information System</td>
<td>
@@ -2279,7 +2278,7 @@ fully fledged Spatial SQL capabilities.
<tr>
<td>
<b>libdrm</b><br />
- <a href="http://dri.freedesktop.org/">http://dri.freedesktop.org</a>
+ <a href="http://dri.freedesktop.org">http://dri.freedesktop.org</a>
</td>
<td>Direct Rendering Manager runtime library.</td>
<td>
@@ -2462,6 +2461,7 @@ latency hiding, direct access to the protocol, improved threading support, and e
<td>
<ul>
<li style="white-space: nowrap;">1.10-Python-2.7.8</li>
+ <li style="white-space: nowrap;">1.11-Python-2.7.9</li>
<li style="white-space: nowrap;">1.11-foss-2015g-Python-2.7.9</li>
<li style="white-space: nowrap;">1.11-intel-2015b-Python-2.7.9</li>
</ul>
@@ -2734,7 +2734,7 @@ static mapping, and sparse matrix block ordering, and sequential mesh and hyperg
<tr>
<td>
<b>numpy</b><br />
- <a href="http://www.numpy.org/">http://www.numpy.org</a>
+ <a href="http://www.numpy.org">http://www.numpy.org</a>
</td>
<td>NumPy is the fundamental package for scientific computing with Python. It contains among other things:
a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran
@@ -2869,7 +2869,7 @@ for Microsoft's .NET environment</td>
<tr>
<td>
<b>mpt</b><br />
- <a href="index.html"></a>
+ <a href="https://docs.it4i.cz/salomon/"></a>
</td>
<td></td>
<td>
@@ -2895,7 +2895,7 @@ for Microsoft's .NET environment</td>
<tr>
<td>
<b>FFTW</b><br />
- <a href="http://www.fftw.org/">http://www.fftw.org</a>
+ <a href="http://www.fftw.org">http://www.fftw.org</a>
</td>
<td>FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)
in one or more dimensions, of arbitrary input size, and of both real and complex data.</td>
@@ -3085,7 +3085,7 @@ for Microsoft's .NET environment</td>
<tr>
<td>
<b>MAP</b><br />
- <a href="index.html"></a>
+ <a href="https://docs.it4i.cz/salomon/"></a>
</td>
<td></td>
<td>
@@ -3098,7 +3098,7 @@ for Microsoft's .NET environment</td>
<tr>
<td>
<b>OPARI2</b><br />
- <a href="http://www.score-p.org/">http://www.score-p.org</a>
+ <a href="http://www.score-p.org">http://www.score-p.org</a>
</td>
<td>OPARI2, the successor of Forschungszentrum Juelich's OPARI,
is a source-to-source instrumentation tool for OpenMP and hybrid codes.
@@ -3113,7 +3113,7 @@ for Microsoft's .NET environment</td>
<tr>
<td>
<b>OTF2</b><br />
- <a href="http://www.score-p.org/">http://www.score-p.org</a>
+ <a href="http://www.score-p.org">http://www.score-p.org</a>
</td>
<td>The Open Trace Format 2 is a highly scalable, memory efficient event
trace data format plus support library. It will become the new standard trace format
@@ -3143,7 +3143,7 @@ for Microsoft's .NET environment</td>
<tr>
<td>
<b>PerfReports</b><br />
- <a href="index.html"></a>
+ <a href="https://docs.it4i.cz/salomon/"></a>
</td>
<td></td>
<td>
@@ -3155,7 +3155,7 @@ for Microsoft's .NET environment</td>
<tr>
<td>
<b>Vampir</b><br />
- <a href="http://www.vampir.eu/">http://www.vampir.eu</a>
+ <a href="http://www.vampir.eu">http://www.vampir.eu</a>
</td>
<td>The Vampir software tool provides an easy-to-use framework that enables
developers to quickly display and analyze arbitrary program behavior at any level of detail.
@@ -3185,7 +3185,7 @@ for Microsoft's .NET environment</td>
<tr>
<td>
<b>perfboost</b><br />
- <a href="index.html"></a>
+ <a href="https://docs.it4i.cz/salomon/"></a>
</td>
<td></td>
<td>
@@ -3197,7 +3197,7 @@ for Microsoft's .NET environment</td>
<tr>
<td>
<b>perfcatcher</b><br />
- <a href="index.html"></a>
+ <a href="https://docs.it4i.cz/salomon/"></a>
</td>
<td></td>
<td>
@@ -3209,7 +3209,7 @@ for Microsoft's .NET environment</td>
<tr>
<td>
<b>perfsuite</b><br />
- <a href="index.html"></a>
+ <a href="https://docs.it4i.cz/salomon/"></a>
</td>
<td></td>
<td>
@@ -3350,7 +3350,7 @@ for Microsoft's .NET environment</td>
<tr>
<td>
<b>foss</b><br />
- <a href="(none).html">(none)</a>
+ <a href="https://docs.it4i.cz/salomon/(none)">(none)</a>
</td>
<td>GNU Compiler Collection (GCC) based compiler toolchain, including
OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.</td>
@@ -3366,7 +3366,7 @@ for Microsoft's .NET environment</td>
<tr>
<td>
<b>gompi</b><br />
- <a href="(none).html">(none)</a>
+ <a href="https://docs.it4i.cz/salomon/(none)">(none)</a>
</td>
<td>GNU Compiler Collection (GCC) based compiler toolchain,
including OpenMPI for MPI support.</td>
@@ -3587,7 +3587,7 @@ repeatable and robust way.</td>
<tr>
<td>
<b>JOE</b><br />
- <a href="http://joe-editor.sourceforge.net/">http://joe-editor.sourceforge.net</a>
+ <a href="http://joe-editor.sourceforge.net">http://joe-editor.sourceforge.net</a>
</td>
<td>JOE is a full featured terminal-based screen editor which
is distributed under the GNU General Public License (GPL)</td>
@@ -3600,20 +3600,22 @@ is distributed under the GNU General Public License (GPL)</td>
<tr>
<td>
<b>MATLAB</b><br />
- <a href="index.html"></a>
+ <a href="https://docs.it4i.cz/salomon/"></a>
</td>
<td></td>
<td>
<ul>
<li style="white-space: nowrap;">2015a-COM</li>
<li style="white-space: nowrap;">2015a-EDU</li>
+ <li style="white-space: nowrap;">2015b-COM</li>
+ <li style="white-space: nowrap;">2015b-EDU</li>
</ul>
</td>
</tr>
<tr>
<td>
<b>MIKE</b><br />
- <a href="http://www.mikepoweredbydhi.com/">http://www.mikepoweredbydhi.com</a>
+ <a href="http://www.mikepoweredbydhi.com">http://www.mikepoweredbydhi.com</a>
</td>
<td>
MIKE Powered by DHI is a part of DHI, the global organisation dedicated to
@@ -3702,6 +3704,7 @@ virtualizer.</td>
<td>Szip compression software, providing lossless compression of scientific data</td>
<td>
<ul>
+ <li style="white-space: nowrap;">2.1</li>
<li style="white-space: nowrap;">2.1-foss-2015b</li>
<li style="white-space: nowrap;">2.1-foss-2015g</li>
<li style="white-space: nowrap;">2.1-ictce-7.3.5</li>
@@ -3713,7 +3716,7 @@ virtualizer.</td>
<tr>
<td>
<b>VDE2</b><br />
- <a href="http://vde.sourceforge.net/">http://vde.sourceforge.net</a>
+ <a href="http://vde.sourceforge.net">http://vde.sourceforge.net</a>
</td>
<td>VDE is an ethernet compliant virtual network that
can be spawned over a set of physical computer over the Internet.
@@ -3739,7 +3742,7 @@ VDE is part of virtualsquare project.</td>
<tr>
<td>
<b>VirtualGL</b><br />
- <a href="http://www.virtualgl.org/">http://www.virtualgl.org</a>
+ <a href="http://www.virtualgl.org">http://www.virtualgl.org</a>
</td>
<td>VirtualGL is an open source toolkit that gives any Unix or Linux remote display software the
ability to run OpenGL applications with full 3D hardware acceleration.</td>
@@ -3752,7 +3755,7 @@ ability to run OpenGL applications with full 3D hardware acceleration.</td>
<tr>
<td>
<b>Wine</b><br />
- <a href="https://www.winehq.org/">https://www.winehq.org</a>
+ <a href="https://www.winehq.org">https://www.winehq.org</a>
</td>
<td>Wine (originally an acronym for "Wine Is Not an Emulator")
is a compatibility layer capable of running Windows applications on several
@@ -3822,7 +3825,7 @@ compressors), whilst being around twice as fast at compression and six times fas
<tr>
<td>
<b>cURL</b><br />
- <a href="http://curl.haxx.se/">http://curl.haxx.se</a>
+ <a href="http://curl.haxx.se">http://curl.haxx.se</a>
</td>
<td>libcurl is a free and easy-to-use client-side URL transfer library,
supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS,
@@ -3910,6 +3913,7 @@ to handle everything from small to very large projects with speed and efficiency
<li style="white-space: nowrap;">2.0.10-GNU-4.9.3-2.25</li>
<li style="white-space: nowrap;">2.0.10-GNU-5.1.0-2.25</li>
<li style="white-space: nowrap;">2.0.10-iccifort-2015.3.187-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">2.0.11</li>
<li style="white-space: nowrap;">2.0.11-GCC-4.9.3-2.25</li>
<li style="white-space: nowrap;">2.0.11-GCC-5.3.0-2.26</li>
<li style="white-space: nowrap;">2.0.9-GCC-4.4.7-system</li>
@@ -3931,7 +3935,7 @@ to handle everything from small to very large projects with speed and efficiency
<tr>
<td>
<b>tcsh</b><br />
- <a href="http://www.tcsh.org/">http://www.tcsh.org</a>
+ <a href="http://www.tcsh.org">http://www.tcsh.org</a>
</td>
<td>Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh).
It is a command language interpreter usable both as an interactive login shell and a shell script command
@@ -3940,13 +3944,14 @@ to handle everything from small to very large projects with speed and efficiency
<td>
<ul>
<li style="white-space: nowrap;">6.18.01-intel-2015b</li>
+ <li style="white-space: nowrap;">6.19.00</li>
</ul>
</td>
</tr>
<tr>
<td>
<b>turbovnc</b><br />
- <a href="http://www.turbovnc.org/">http://www.turbovnc.org</a>
+ <a href="http://www.turbovnc.org">http://www.turbovnc.org</a>
</td>
<td>
TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to
@@ -3987,7 +3992,7 @@ provide peak performance for 3D and video workloads.</td>
<tr>
<td>
<b>FLTK</b><br />
- <a href="http://www.fltk.org/">http://www.fltk.org</a>
+ <a href="http://www.fltk.org">http://www.fltk.org</a>
</td>
<td>FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows,
and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL
@@ -4056,7 +4061,7 @@ asynchronous and fault tolerant parallel applications.
<tr>
<td>
<b>OSPRay</b><br />
- <a href="http://www.ospray.org/">http://www.ospray.org</a>
+ <a href="http://www.ospray.org">http://www.ospray.org</a>
</td>
<td>
A Ray Tracing Based Rendering Engine for High-Fidelity Visualization</td>
@@ -4085,7 +4090,7 @@ asynchronous and fault tolerant parallel applications.
<tr>
<td>
<b>OpenDX</b><br />
- <a href="http://www.opendx.org/">http://www.opendx.org</a>
+ <a href="http://www.opendx.org">http://www.opendx.org</a>
</td>
<td>Open source visualization software package based on IBM's Visualization Data Explorer.</td>
<td>
@@ -4097,7 +4102,7 @@ asynchronous and fault tolerant parallel applications.
<tr>
<td>
<b>ParaView</b><br />
- <a href="http://www.paraview.org/">http://www.paraview.org</a>
+ <a href="http://www.paraview.org">http://www.paraview.org</a>
</td>
<td>ParaView is a scientific parallel visualizer.</td>
<td>
@@ -4170,7 +4175,7 @@ microscopic and continuous road traffic simulation package designed to handle la
<tr>
<td>
<b>cairo</b><br />
- <a href="http://cairographics.org/">http://cairographics.org</a>
+ <a href="http://cairographics.org">http://cairographics.org</a>
</td>
<td>Cairo is a 2D graphics library with support for multiple output devices.
Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers,
@@ -4223,7 +4228,7 @@ application access.</td>
<tr>
<td>
<b>freetype</b><br />
- <a href="http://freetype.org/">http://freetype.org</a>
+ <a href="http://freetype.org">http://freetype.org</a>
</td>
<td>FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and
portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display
@@ -4333,6 +4338,7 @@ and documentation</td>
<td>
<ul>
<li style="white-space: nowrap;">1.6.2-Python-2.7.8</li>
+ <li style="white-space: nowrap;">1.6.2-Python-2.7.9</li>
<li style="white-space: nowrap;">1.6.2-foss-2015g-Python-2.7.9</li>
<li style="white-space: nowrap;">1.6.2-intel-2015b-Python-2.7.9</li>
</ul>
@@ -4390,6 +4396,7 @@ useful for allowing clients to interact with the X Display Manager.
<td>
<ul>
<li style="white-space: nowrap;">1.3.2-Python-2.7.8</li>
+ <li style="white-space: nowrap;">1.3.3</li>
<li style="white-space: nowrap;">1.3.3-foss-2015g</li>
<li style="white-space: nowrap;">1.3.3-foss-2015g-Python-2.7.9</li>
<li style="white-space: nowrap;">1.3.3-intel-2015b</li>
@@ -4467,6 +4474,7 @@ useful for allowing clients to interact with the X Display Manager.
<ul>
<li style="white-space: nowrap;">1.1.4-foss-2015g-libX11-1.6.2</li>
<li style="white-space: nowrap;">1.1.4-intel-2015b-libX11-1.6.2</li>
+ <li style="white-space: nowrap;">1.1.4-libX11-1.6.2</li>
<li style="white-space: nowrap;">1.1.5-foss-2015g</li>
</ul>
</td>
@@ -4489,7 +4497,7 @@ useful for allowing clients to interact with the X Display Manager.
<tr>
<td>
<b>p4vasp</b><br />
- <a href="http://www.p4vasp.at/">http://www.p4vasp.at</a>
+ <a href="http://www.p4vasp.at">http://www.p4vasp.at</a>
</td>
<td>p4vasp is a visualization suite for the Vienna Ab-initio Simulation Package
(VASP). It contains an extensible GUI framework, that can be used to view
@@ -4578,7 +4586,7 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -4594,7 +4602,7 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -4610,7 +4618,7 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -4626,7 +4634,7 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -4642,7 +4650,7 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -4658,7 +4666,7 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -4674,7 +4682,7 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
- <a title="" class="state-published contenttype-document" href="environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -4690,7 +4698,7 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
- <a title="List of Available Modules on Salomon Cluster" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="list_of_modules.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -4706,7 +4714,7 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -4722,7 +4730,7 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
- <a title="" class="state-published contenttype-document" href="compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -4738,7 +4746,7 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -4754,7 +4762,7 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -4770,10 +4778,10 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -4789,7 +4797,7 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
- <a title="" class="state-published contenttype-document" href="prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -4814,7 +4822,7 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -4830,7 +4838,7 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -4846,7 +4854,7 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -4862,7 +4870,7 @@ compositing and trapezoid rasterization. Important users of pixman are the cairo
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</html>
diff --git a/docs.it4i.cz/salomon/list_of_modules.md b/docs.it4i.cz/salomon/list_of_modules.md
new file mode 100644
index 0000000000000000000000000000000000000000..121d2a3a3533e55cb0b06d79814cd06cdaed0679
--- /dev/null
+++ b/docs.it4i.cz/salomon/list_of_modules.md
@@ -0,0 +1,2979 @@
+List of Available Modules
+=========================
+List of Available Modules on Salomon Cluster
+Categories
+----------
+- [base](#base)
+- [bio](#bio)
+- [cae](#cae)
+- [chem](#chem)
+- [compiler](#compiler)
+- [data](#data)
+- [debugger](#debugger)
+- [devel](#devel)
+- [geo](#geo)
+- [lang](#lang)
+- [lib](#lib)
+- [math](#math)
+- [mpi](#mpi)
+- [numlib](#numlib)
+- [perf](#perf)
+- [phys](#phys)
+- [system](#system)
+- [toolchain](#toolchain)
+- [tools](#tools)
+- [vis](#vis)
+[base](#categories "Go to list of categories..."){.tooltip}
+-------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>EasyBuild</strong><br />
+<a href="http://hpcugent.github.com/easybuild/" class="uri">http://hpcugent.github.com/easybuild/</a></td>
+<td align="left">EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.</td>
+<td align="left"><ul>
+<li>2.1.1</li>
+<li>2.2.0</li>
+<li>2.3.0</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>Python</strong><br />
+<a href="http://python.org/" class="uri">http://python.org/</a></td>
+<td align="left">Python is a programming language that lets you work more quickly and integrate your systems more effectively.</td>
+<td align="left"><ul>
+<li>3.4.3-intel-2015b</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+[bio](#categories "Go to list of categories..."){.tooltip}
+------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>Amber</strong><br />
+<a href="http://ambermd.org" class="uri">http://ambermd.org</a></td>
+<td align="left">A set of molecular mechanical force fields for the simulation of biomolecules</td>
+<td align="left"><ul>
+<li>14</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>BCFtools</strong><br />
+<a href="http://www.htslib.org/" class="uri">http://www.htslib.org/</a></td>
+<td align="left">Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants</td>
+<td align="left"><ul>
+<li>1.3-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>BWA</strong><br />
+<a href="http://bio-bwa.sourceforge.net/" class="uri">http://bio-bwa.sourceforge.net/</a></td>
+<td align="left">Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.</td>
+<td align="left"><ul>
+<li>0.7.5a-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>FastQC</strong><br />
+<a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" class="uri">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/</a></td>
+<td align="left">FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.</td>
+<td align="left"><ul>
+<li>0.11.3</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>GATK</strong><br />
+<a href="http://www.broadinstitute.org/gatk/" class="uri">http://www.broadinstitute.org/gatk/</a></td>
+<td align="left">The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.</td>
+<td align="left"><ul>
+<li>2.6-5-Java-1.7.0_79</li>
+<li>3.5-Java-1.7.0_79</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>GROMACS</strong><br />
+<a href="http://www.gromacs.org" class="uri">http://www.gromacs.org</a></td>
+<td align="left">GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.</td>
+<td align="left"><ul>
+<li>4.6.7-foss-2015g-hybrid-single-PLUMED</li>
+<li>5.0.4-foss-2015e-hybrid-single-PLUMED</li>
+<li>5.0.4-foss-2015g-hybrid-single</li>
+<li>5.0.4-foss-2015g-hybrid-single-PLUMED</li>
+<li>5.0.4-ictce-7.3.5-hybrid-single</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>HTSlib</strong><br />
+<a href="http://www.htslib.org/" class="uri">http://www.htslib.org/</a></td>
+<td align="left">A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix</td>
+<td align="left"><ul>
+<li>1.3-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>PLUMED</strong><br />
+<a href="http://www.plumed-code.org" class="uri">http://www.plumed-code.org</a></td>
+<td align="left">PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.</td>
+<td align="left"><ul>
+<li>2.1.3-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>RELION</strong><br />
+<a href="http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page" class="uri">http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page</a></td>
+<td align="left">RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).</td>
+<td align="left"><ul>
+<li>1.3-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>SAMtools</strong><br />
+<a href="http://www.htslib.org/" class="uri">http://www.htslib.org/</a></td>
+<td align="left">SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.</td>
+<td align="left"><ul>
+<li>1.3-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>SnpEff</strong><br />
+<a href="http://snpeff.sourceforge.net/" class="uri">http://snpeff.sourceforge.net/</a></td>
+<td align="left">Genetic variant annotation and effect prediction toolbox.</td>
+<td align="left"><ul>
+<li>4.1_G</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>Trimmomatic</strong><br />
+<a href="http://www.usadellab.org/cms/?page=trimmomatic" class="uri">http://www.usadellab.org/cms/?page=trimmomatic</a></td>
+<td align="left">Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.</td>
+<td align="left"><ul>
+<li>0.35-Java-1.7.0_79</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>almost</strong><br />
+<a href="http://www-almost.ch.cam.ac.uk/site" class="uri">http://www-almost.ch.cam.ac.uk/site</a></td>
+<td align="left">all atom molecular simulation toolkit - is a fast and flexible molecular modeling environment that provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations.</td>
+<td align="left"><ul>
+<li>2.1.0-foss-2015b</li>
+<li>2.1.0-foss-2015g</li>
+<li>2.1.0-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>picard</strong><br />
+<a href="http://sourceforge.net/projects/picard" class="uri">http://sourceforge.net/projects/picard</a></td>
+<td align="left">A set of tools (in Java) for working with next generation sequencing data in the BAM format.</td>
+<td align="left"><ul>
+<li>1.119</li>
+<li>2.1.0</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+[cae](#categories "Go to list of categories..."){.tooltip}
+------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>ANSYS</strong><br />
+<a href="https://docs.it4i.cz/salomon/"></a></td>
+<td align="left"></td>
+<td align="left"><ul>
+<li>16.1</li>
+<li>17.0</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>Adams</strong><br />
+<a href="https://docs.it4i.cz/salomon/"></a></td>
+<td align="left"></td>
+<td align="left"><ul>
+<li>2013.2</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>COMSOL</strong><br />
+<a href="https://docs.it4i.cz/salomon/"></a></td>
+<td align="left"></td>
+<td align="left"><ul>
+<li>51-COM</li>
+<li>51-EDU</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>Digimat</strong><br />
+<a href="https://docs.it4i.cz/salomon/"></a></td>
+<td align="left"></td>
+<td align="left"><ul>
+<li>5.0.1-COM</li>
+<li>5.0.1-EDU</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>FreeFem++</strong><br />
+<a href="http://www.freefem.org" class="uri">http://www.freefem.org</a></td>
+<td align="left">FreeFem++ is a partial differential equation solver. It has its own language. freefem scripts can solve multiphysics non linear systems in 2D and 3D. Problems involving PDE (2d, 3d) from several branches of physics such as fluid-structure interactions require interpolations of data on several meshes and their manipulation within one program. FreeFem++ includes a fast 2^d-tree-based interpolation algorithm and a language for the manipulation of data on multiple meshes (as a follow up of bamg (now a part of FreeFem++ ). FreeFem++ is written in C++ and the FreeFem++ language is a C++ idiom. It runs on Macs, Windows, Unix machines. FreeFem++ replaces the older freefem and freefem+.</td>
+<td align="left"><ul>
+<li>3.45-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>HyperWorks</strong><br />
+<a href="https://docs.it4i.cz/salomon/"></a></td>
+<td align="left"></td>
+<td align="left"><ul>
+<li>13.0</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>Marc</strong><br />
+<a href="https://docs.it4i.cz/salomon/"></a></td>
+<td align="left"></td>
+<td align="left"><ul>
+<li>2013.1.0</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>OpenFOAM</strong><br />
+<a href="http://www.openfoam.com/" class="uri">http://www.openfoam.com/</a></td>
+<td align="left">OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.</td>
+<td align="left"><ul>
+<li>2.2.2-intel-2015b</li>
+<li>2.3.0-intel-2015b</li>
+<li>3.0.0-intel-2016.01</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+[chem](#categories "Go to list of categories..."){.tooltip}
+-------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>ABINIT</strong><br />
+<a href="http://www.abinit.org/" class="uri">http://www.abinit.org/</a></td>
+<td align="left">Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.</td>
+<td align="left"><ul>
+<li>7.10.1-foss-2015b</li>
+<li>7.10.1-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>CP2K</strong><br />
+<a href="http://www.cp2k.org/" class="uri">http://www.cp2k.org/</a></td>
+<td align="left">CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.</td>
+<td align="left"><ul>
+<li>2.6.0-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>LAMMPS</strong><br />
+<a href="http://lammps.sandia.gov" class="uri">http://lammps.sandia.gov</a></td>
+<td align="left">LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. Has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.</td>
+<td align="left"><ul>
+<li>28Jun14-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>Libint</strong><br />
+<a href="https://sourceforge.net/p/libint/" class="uri">https://sourceforge.net/p/libint/</a></td>
+<td align="left">Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.</td>
+<td align="left"><ul>
+<li>1.1.4-foss-2015b</li>
+<li>1.1.4-gompi-2015b</li>
+<li>1.1.4-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>Molpro</strong><br />
+<a href="https://docs.it4i.cz/salomon/"></a></td>
+<td align="left"></td>
+<td align="left"><ul>
+<li>2010.1-patch-57-intel2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>NAMD</strong><br />
+<a href="http://www.ks.uiuc.edu/Research/namd/" class="uri">http://www.ks.uiuc.edu/Research/namd/</a></td>
+<td align="left">NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.</td>
+<td align="left"><ul>
+<li>2.9-mpi</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>NWChem</strong><br />
+<a href="http://www.nwchem-sw.org" class="uri">http://www.nwchem-sw.org</a></td>
+<td align="left">NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handlebiomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity.</td>
+<td align="left"><ul>
+<li>6.3.revision2-2013-10-17-Python-2.7.8</li>
+<li>6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.8</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>S4MPLE</strong><br />
+<a href="http://infochim.u-strasbg.fr/spip.php?rubrique152" class="uri">http://infochim.u-strasbg.fr/spip.php?rubrique152</a></td>
+<td align="left">S4MPLE (Sampler For Multiple Protein-Ligand Entities) is a flexible molecular modeling tool, supporting empirical force field-driven conformational sampling and geometry optimization heuristics using a hybrid genetic algorithm (GA).</td>
+<td align="left"><ul>
+<li>1.0.0</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>libctl</strong><br />
+<a href="http://ab-initio.mit.edu/libctl" class="uri">http://ab-initio.mit.edu/libctl</a></td>
+<td align="left">libctl is a free Guile-based library implementing flexible control files for scientific simulations.</td>
+<td align="left"><ul>
+<li>3.2.2-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>libxc</strong><br />
+<a href="http://www.tddft.org/programs/octopus/wiki/index.php/Libxc" class="uri">http://www.tddft.org/programs/octopus/wiki/index.php/Libxc</a></td>
+<td align="left">Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.</td>
+<td align="left"><ul>
+<li>2.2.0-foss-2015b</li>
+<li>2.2.0-gompi-2015b</li>
+<li>2.2.1-intel-2015b</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+[compiler](#categories "Go to list of categories..."){.tooltip}
+-----------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>BerkeleyUPC</strong><br />
+<a href="http://upc.lbl.gov" class="uri">http://upc.lbl.gov</a></td>
+<td align="left">The goal of the Berkeley UPC compiler group is to develop a portable, high performance implementation of UPC for large-scale multiprocessors, PC clusters, and clusters of shared memory multiprocessors.</td>
+<td align="left"><ul>
+<li>2.16.2-gompi-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>Clang</strong><br />
+<a href="http://clang.llvm.org/" class="uri">http://clang.llvm.org/</a></td>
+<td align="left">C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.</td>
+<td align="left"><ul>
+<li>3.7.0-GNU-5.1.0-2.25</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>GCC</strong><br />
+<a href="http://gcc.gnu.org/" class="uri">http://gcc.gnu.org/</a></td>
+<td align="left">The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).</td>
+<td align="left"><ul>
+<li>4.4.7-system</li>
+<li>4.7.4</li>
+<li>4.8.3</li>
+<li>4.9.2-binutils-2.25</li>
+<li>4.9.3</li>
+<li>4.9.3-2.25</li>
+<li>4.9.3-binutils-2.25</li>
+<li>5.1.0-binutils-2.25</li>
+<li>5.2.0</li>
+<li>5.3.0-2.25</li>
+<li>5.3.0-2.26</li>
+<li>5.3.0-binutils-2.25</li>
+<li>5.3.1-snapshot-20160419-2.25</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>GCCcore</strong><br />
+<a href="http://gcc.gnu.org/" class="uri">http://gcc.gnu.org/</a></td>
+<td align="left">The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).</td>
+<td align="left"><ul>
+<li>4.9.3</li>
+<li>5.3.0</li>
+<li>5.3.1-snapshot-20160419</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>LLVM</strong><br />
+<a href="http://llvm.org/" class="uri">http://llvm.org/</a></td>
+<td align="left">The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator.</td>
+<td align="left"><ul>
+<li>3.7.1-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>OpenCoarrays</strong><br />
+<a href="http://www.opencoarrays.org/" class="uri">http://www.opencoarrays.org/</a></td>
+<td align="left">A transport layer for coarray Fortran compilers.</td>
+<td align="left"><ul>
+<li>1.4.0-GCC-5.3.0-2.25</li>
+<li>1.4.0-GCC-5.3.1-snapshot-20160419-2.25</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>PGI</strong><br />
+<a href="https://docs.it4i.cz/salomon/"></a></td>
+<td align="left"></td>
+<td align="left"><ul>
+<li>15.7</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>icc</strong><br />
+<a href="http://software.intel.com/en-us/intel-compilers/" class="uri">http://software.intel.com/en-us/intel-compilers/</a></td>
+<td align="left">C and C++ compiler from Intel</td>
+<td align="left"><ul>
+<li>2013.5.192</li>
+<li>2013.5.192-GCC-4.8.3</li>
+<li>2015.3.187</li>
+<li>2015.3.187-GNU-4.9.3-2.25</li>
+<li>2015.3.187-GNU-5.1.0-2.25</li>
+<li>2016.0.109-GCC-4.9.3</li>
+<li>2016.1.150</li>
+<li>2016.1.150-GCC-4.9.3</li>
+<li>2016.1.150-GCC-4.9.3-2.25</li>
+<li>2016.3.210-GCC-5.3.0-2.26</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>ifort</strong><br />
+<a href="http://software.intel.com/en-us/intel-compilers/" class="uri">http://software.intel.com/en-us/intel-compilers/</a></td>
+<td align="left">Fortran compiler from Intel</td>
+<td align="left"><ul>
+<li>2013.5.192</li>
+<li>2013.5.192-GCC-4.8.3</li>
+<li>2015.3.187</li>
+<li>2015.3.187-GNU-4.9.3-2.25</li>
+<li>2015.3.187-GNU-5.1.0-2.25</li>
+<li>2016.0.109-GCC-4.9.3</li>
+<li>2016.1.150</li>
+<li>2016.1.150-GCC-4.9.3</li>
+<li>2016.1.150-GCC-4.9.3-2.25</li>
+<li>2016.3.210-GCC-5.3.0-2.26</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+[data](#categories "Go to list of categories..."){.tooltip}
+-------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>GDAL</strong><br />
+<a href="http://www.gdal.org/" class="uri">http://www.gdal.org/</a></td>
+<td align="left">GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.</td>
+<td align="left"><ul>
+<li>1.9.2-foss-2015g</li>
+<li>2.0.1-foss-2015b</li>
+<li>2.1.0-GNU-5.1.0-2.25</li>
+<li>2.1.0-GNU-5.1.0-2.25-intel-2015b</li>
+<li>2.1.0-foss-2015g</li>
+<li>2.1.0-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>HDF5</strong><br />
+<a href="http://www.hdfgroup.org/HDF5/" class="uri">http://www.hdfgroup.org/HDF5/</a></td>
+<td align="left">HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.</td>
+<td align="left"><ul>
+<li>1.10.0-patch1-intel-2016.01-mic</li>
+<li>1.8.13-foss-2015g</li>
+<li>1.8.13-intel-2015b</li>
+<li>1.8.13-intel-2015b-no-mpi</li>
+<li>1.8.13-intel-2016.01</li>
+<li>1.8.14-ictce-7.3.5-serial</li>
+<li>1.8.15-patch1-foss-2015b</li>
+<li>1.8.16-foss-2015g</li>
+<li>1.8.16-intel-2015b</li>
+<li>1.8.16-intel-2015b-threadsafe</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>h5py</strong><br />
+<a href="http://www.h5py.org/" class="uri">http://www.h5py.org/</a></td>
+<td align="left">HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.</td>
+<td align="left"><ul>
+<li>2.4.0-ictce-7.3.5-Python-2.7.9-serial</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>netCDF</strong><br />
+<a href="http://www.unidata.ucar.edu/software/netcdf/" class="uri">http://www.unidata.ucar.edu/software/netcdf/</a></td>
+<td align="left">NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.</td>
+<td align="left"><ul>
+<li>4.3.2-foss-2015g</li>
+<li>4.3.2-intel-2015b</li>
+<li>4.3.2-intel-2016.01</li>
+<li>4.3.3.1-foss-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>netCDF-Fortran</strong><br />
+<a href="http://www.unidata.ucar.edu/software/netcdf/" class="uri">http://www.unidata.ucar.edu/software/netcdf/</a></td>
+<td align="left">NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.</td>
+<td align="left"><ul>
+<li>4.4.0-intel-2016.01</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+[debugger](#categories "Go to list of categories..."){.tooltip}
+-----------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>DDT</strong><br />
+<a href="https://docs.it4i.cz/salomon/"></a></td>
+<td align="left"></td>
+<td align="left"><ul>
+<li>4.2</li>
+<li>5.0.1</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>Forge</strong><br />
+<a href="http://www.allinea.com/products/develop-allinea-forge" class="uri">http://www.allinea.com/products/develop-allinea-forge</a></td>
+<td align="left">Allinea Forge is the complete toolsuite for software development - with everything needed to debug, profile, optimize, edit and build C, C++ and FORTRAN applications on Linux for high performance - from single threads through to complex parallel HPC codes with MPI, OpenMP, threads or CUDA.</td>
+<td align="left"><ul>
+<li>5.1-43967</li>
+<li>6.0.5</li>
+<li>6.0.6</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>PerformanceReports</strong><br />
+<a href="http://www.allinea.com/products/allinea-performance-reports" class="uri">http://www.allinea.com/products/allinea-performance-reports</a></td>
+<td align="left">Allinea Performance Reports are the most effective way to characterize and understand the performance of HPC application runs. One single-page HTML report elegantly answers a range of vital questions for any HPC site. - Is this application well-optimized for the system and the processors it is running on? - Does it benefit from running at this scale? - Are there I/O, networking or threading bottlenecks affecting performance? - Which hardware, software or configuration changes can we make to improve performance further. - How much energy did this application use?</td>
+<td align="left"><ul>
+<li>5.1-43967</li>
+<li>6.0.6</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>TotalView</strong><br />
+<a href="https://docs.it4i.cz/salomon/"></a></td>
+<td align="left"></td>
+<td align="left"><ul>
+<li>8.15.4-6-linux-x86-64</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>Valgrind</strong><br />
+<a href="http://valgrind.org/downloads/" class="uri">http://valgrind.org/downloads/</a></td>
+<td align="left">ValgrindDebugging and profiling tools</td>
+<td align="left"><ul>
+<li>3.11.0-foss-2015b</li>
+<li>3.11.0-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>aislinn</strong><br />
+<a href="https://docs.it4i.cz/salomon/"></a></td>
+<td align="left"></td>
+<td align="left"><ul>
+<li>20160105-Python-2.7.9-gompi-2015e</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+[devel](#categories "Go to list of categories..."){.tooltip}
+--------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>Autoconf</strong><br />
+<a href="http://www.gnu.org/software/autoconf/" class="uri">http://www.gnu.org/software/autoconf/</a></td>
+<td align="left">Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.</td>
+<td align="left"><ul>
+<li>2.69</li>
+<li>2.69-GCC-4.9.3-2.25</li>
+<li>2.69-GNU-4.9.3-2.25</li>
+<li>2.69-GNU-5.1.0-2.25</li>
+<li>2.69-foss-2015g</li>
+<li>2.69-intel-2015b</li>
+<li>2.69-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>Automake</strong><br />
+<a href="http://www.gnu.org/software/automake/automake.html" class="uri">http://www.gnu.org/software/automake/automake.html</a></td>
+<td align="left">AutomakeGNU Standards-compliant Makefile generator</td>
+<td align="left"><ul>
+<li>1.15</li>
+<li>1.15-GCC-4.9.3-2.25</li>
+<li>1.15-GNU-4.9.3-2.25</li>
+<li>1.15-GNU-5.1.0-2.25</li>
+<li>1.15-foss-2015g</li>
+<li>1.15-intel-2015b</li>
+<li>1.15-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>Autotools</strong><br />
+<a href="http://autotools.io" class="uri">http://autotools.io</a></td>
+<td align="left">This bundle collect the standard GNU build toolsAutoconf, Automake and libtool</td>
+<td align="left"><ul>
+<li>20150215</li>
+<li>20150215-GCC-4.9.3-2.25</li>
+<li>20150215-GNU-4.9.3-2.25</li>
+<li>20150215-GNU-5.1.0-2.25</li>
+<li>20150215-intel-2015b</li>
+<li>20150215-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>Boost</strong><br />
+<a href="http://www.boost.org/" class="uri">http://www.boost.org/</a></td>
+<td align="left">Boost provides free peer-reviewed portable C++ source libraries.</td>
+<td align="left"><ul>
+<li>1.58.0-Python-2.7.9</li>
+<li>1.58.0-foss-2015g-Python-2.7.9</li>
+<li>1.58.0-gompi-2015e-Python-2.7.9</li>
+<li>1.58.0-ictce-7.3.5-Python-2.7.9</li>
+<li>1.58.0-intel-2015b-Python-2.7.9</li>
+<li>1.58.0-intel-2016.01-Python-2.7.9</li>
+<li>1.59.0-intel-2015b-Python-2.7.11</li>
+<li>1.59.0-intel-2016.01</li>
+<li>1.60.0-foss-2015g-Python-2.7.9</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>CMake</strong><br />
+<a href="http://www.cmake.org" class="uri">http://www.cmake.org</a></td>
+<td align="left">CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.</td>
+<td align="left"><ul>
+<li>3.0.0-foss-2015g</li>
+<li>3.0.0-ictce-7.3.5</li>
+<li>3.0.0-intel-2015b</li>
+<li>3.0.0-intel-2016.01</li>
+<li>3.3.1-GCC-5.3.0-2.25</li>
+<li>3.3.1-GCC-5.3.1-snapshot-20160419-2.25</li>
+<li>3.3.1-GNU-4.9.3-2.25</li>
+<li>3.3.1-GNU-5.1.0-2.25</li>
+<li>3.3.1-foss-2015g</li>
+<li>3.3.1-intel-2016.01</li>
+<li>3.3.2-GNU-4.9.3-2.25</li>
+<li>3.3.2-intel-2016.01</li>
+<li>3.4.1-GCCcore-4.9.3</li>
+<li>3.4.1-foss-2015b</li>
+<li>3.4.1-intel-2015b</li>
+<li>3.5.2</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>Doxygen</strong><br />
+<a href="http://www.doxygen.org" class="uri">http://www.doxygen.org</a></td>
+<td align="left">Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.</td>
+<td align="left"><ul>
+<li>1.8.10-foss-2015b</li>
+<li>1.8.11</li>
+<li>1.8.7-foss-2015g</li>
+<li>1.8.7-intel-2015b</li>
+<li>1.8.7-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>JUnit</strong><br />
+<a href="http://sourceforge.net/projects/junit" class="uri">http://sourceforge.net/projects/junit</a></td>
+<td align="left">A programmer-oriented testing framework for Java.</td>
+<td align="left"><ul>
+<li>4.11-Java-1.7.0_79</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>M4</strong><br />
+<a href="http://www.gnu.org/software/m4/m4.html" class="uri">http://www.gnu.org/software/m4/m4.html</a></td>
+<td align="left">GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.</td>
+<td align="left"><ul>
+<li>1.4.16-foss-2015g</li>
+<li>1.4.16-intel-2015b</li>
+<li>1.4.17</li>
+<li>1.4.17-GCC-4.9.3-2.25</li>
+<li>1.4.17-GCC-4.9.3-binutils-2.25</li>
+<li>1.4.17-GCC-5.1.0-binutils-2.25</li>
+<li>1.4.17-GCCcore-4.9.3</li>
+<li>1.4.17-GCCcore-5.3.0</li>
+<li>1.4.17-GCCcore-5.3.1-snapshot-20160419</li>
+<li>1.4.17-GNU-4.9.3-2.25</li>
+<li>1.4.17-GNU-5.1.0-2.25</li>
+<li>1.4.17-foss-2015b</li>
+<li>1.4.17-foss-2015g</li>
+<li>1.4.17-intel-2015b</li>
+<li>1.4.17-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>Maven</strong><br />
+<a href="http://maven.apache.org/index.html" class="uri">http://maven.apache.org/index.html</a></td>
+<td align="left">Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information.</td>
+<td align="left"><ul>
+<li>3.3.9</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>PCRE</strong><br />
+<a href="http://www.pcre.org/" class="uri">http://www.pcre.org/</a></td>
+<td align="left">The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.</td>
+<td align="left"><ul>
+<li>8.36-foss-2015g</li>
+<li>8.36-intel-2015b</li>
+<li>8.36-intel-2016.01</li>
+<li>8.37</li>
+<li>8.37-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>Qt</strong><br />
+<a href="http://qt-project.org/" class="uri">http://qt-project.org/</a></td>
+<td align="left">Qt is a comprehensive cross-platform C++ application framework.</td>
+<td align="left"><ul>
+<li>4.8.6-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>SCons</strong><br />
+<a href="http://www.scons.org/" class="uri">http://www.scons.org/</a></td>
+<td align="left">SCons is a software construction tool.</td>
+<td align="left"><ul>
+<li>2.3.6-Python-2.7.9</li>
+<li>2.3.6-foss-2015g-Python-2.7.9</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>SQLite</strong><br />
+<a href="http://www.sqlite.org/" class="uri">http://www.sqlite.org/</a></td>
+<td align="left">SQLiteSQL Database Engine in a C Library</td>
+<td align="left"><ul>
+<li>3.10.1-foss-2015g</li>
+<li>3.8.10.2-GCC-4.9.3-2.25</li>
+<li>3.8.10.2-GNU-4.9.3-2.25</li>
+<li>3.8.8.1</li>
+<li>3.8.8.1-GNU-5.1.0-2.25</li>
+<li>3.8.8.1-foss-2015b</li>
+<li>3.8.8.1-foss-2015g</li>
+<li>3.8.8.1-gompi-2015e</li>
+<li>3.8.8.1-ictce-7.3.5</li>
+<li>3.8.8.1-intel-2015b</li>
+<li>3.8.8.1-intel-2016.01</li>
+<li>3.9.2-foss-2015g</li>
+<li>3.9.2-intel-2015b</li>
+<li>3.9.2-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>SWIG</strong><br />
+<a href="http://www.swig.org/" class="uri">http://www.swig.org/</a></td>
+<td align="left">SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.</td>
+<td align="left"><ul>
+<li>2.0.12-Python-2.7.9</li>
+<li>2.0.12-intel-2015b-Python-2.7.9</li>
+<li>3.0.7-Python-2.7.9</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>Spark</strong><br />
+<a href="http://spark.apache.org" class="uri">http://spark.apache.org</a></td>
+<td align="left">Spark is Hadoop MapReduce done in memory</td>
+<td align="left"><ul>
+<li>1.5.2</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>ant</strong><br />
+<a href="http://ant.apache.org/" class="uri">http://ant.apache.org/</a></td>
+<td align="left">Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.</td>
+<td align="left"><ul>
+<li>1.9.3-Java-1.7.0_79</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>fontsproto</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">X11 font extension wire protocol</td>
+<td align="left"><ul>
+<li>2.1.3-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>glproto</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">X protocol and ancillary headers</td>
+<td align="left"><ul>
+<li>1.4.16-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>gperf</strong><br />
+<a href="http://www.gnu.org/software/gperf/" class="uri">http://www.gnu.org/software/gperf/</a></td>
+<td align="left">GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.</td>
+<td align="left"><ul>
+<li>3.0.4-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>guile</strong><br />
+<a href="http://www.gnu.org/software/guile" class="uri">http://www.gnu.org/software/guile</a></td>
+<td align="left">Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system.</td>
+<td align="left"><ul>
+<li>1.8.8-foss-2015b</li>
+<li>1.8.8-foss-2015g</li>
+<li>1.8.8-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>libSM</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">X11 Session Management library, which allows for applications to both manage sessions, and make use of session managers to save and restore their state for later use.</td>
+<td align="left"><ul>
+<li>1.2.2</li>
+<li>1.2.2-foss-2015g</li>
+<li>1.2.2-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>make</strong><br />
+<a href="http://www.gnu.org/software/make/make.html" class="uri">http://www.gnu.org/software/make/make.html</a></td>
+<td align="left">make-3.82GNU version of make utility</td>
+<td align="left"><ul>
+<li>3.82</li>
+<li>3.82-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>makedepend</strong><br />
+<a href="http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" class="uri">http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html</a></td>
+<td align="left">The makedepend package contains a C-preprocessor like utility to determine build-time dependencies.</td>
+<td align="left"><ul>
+<li>1.0.4-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>ncurses</strong><br />
+<a href="http://www.gnu.org/software/ncurses/" class="uri">http://www.gnu.org/software/ncurses/</a></td>
+<td align="left">The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.</td>
+<td align="left"><ul>
+<li>5.9</li>
+<li>5.9-GCC-5.3.0-2.25</li>
+<li>5.9-GCC-5.3.1-snapshot-20160419-2.25</li>
+<li>5.9-GNU-4.9.3-2.25</li>
+<li>5.9-GNU-5.1.0-2.25</li>
+<li>5.9-foss-2015b</li>
+<li>5.9-foss-2015g</li>
+<li>5.9-gompi-2015e</li>
+<li>5.9-ictce-5.5.0</li>
+<li>5.9-ictce-7.3.5</li>
+<li>5.9-intel-2015b</li>
+<li>5.9-intel-2016.01</li>
+<li>6.0</li>
+<li>6.0-GCCcore-4.9.3</li>
+<li>6.0-foss-2015b</li>
+<li>6.0-foss-2015g</li>
+<li>6.0-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>pkg-config</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/pkg-config/" class="uri">http://www.freedesktop.org/wiki/Software/pkg-config/</a></td>
+<td align="left">pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries).</td>
+<td align="left"><ul>
+<li>0.27.1</li>
+<li>0.27.1-foss-2015b</li>
+<li>0.27.1-foss-2015g</li>
+<li>0.27.1-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>python-meep</strong><br />
+<a href="https://code.launchpad.net/python-meep" class="uri">https://code.launchpad.net/python-meep</a></td>
+<td align="left">Python wrapper for the Meep FDTD solver.</td>
+<td align="left"><ul>
+<li>1.4.2-intel-2015b-Python-2.7.9-Meep-1.3</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>renderproto</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">Xrender protocol and ancillary headers</td>
+<td align="left"><ul>
+<li>0.11-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>xbitmaps</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">provides bitmaps for x</td>
+<td align="left"><ul>
+<li>1.1.1</li>
+<li>1.1.1-foss-2015g</li>
+<li>1.1.1-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>xcb-proto</strong><br />
+<a href="http://xcb.freedesktop.org/" class="uri">http://xcb.freedesktop.org/</a></td>
+<td align="left">The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.</td>
+<td align="left"><ul>
+<li>1.10-Python-2.7.8</li>
+<li>1.11-Python-2.7.9</li>
+<li>1.11-foss-2015g-Python-2.7.9</li>
+<li>1.11-intel-2015b-Python-2.7.9</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>xextproto</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">XExtProto protocol headers.</td>
+<td align="left"><ul>
+<li>7.3.0</li>
+<li>7.3.0-foss-2015g</li>
+<li>7.3.0-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>xineramaproto</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">X protocol and ancillary headers for xinerama</td>
+<td align="left"><ul>
+<li>1.2.1-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>xorg-macros</strong><br />
+<a href="http://cgit.freedesktop.org/xorg/util/macros" class="uri">http://cgit.freedesktop.org/xorg/util/macros</a></td>
+<td align="left">X.org macros utilities.</td>
+<td align="left"><ul>
+<li>1.17-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>xproto</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">X protocol and ancillary headers</td>
+<td align="left"><ul>
+<li>7.0.26</li>
+<li>7.0.26-foss-2015g</li>
+<li>7.0.26-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>xtrans</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">xtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet.</td>
+<td align="left"><ul>
+<li>1.3.4-intel-2015b</li>
+<li>1.3.5</li>
+<li>1.3.5-foss-2015g</li>
+<li>1.3.5-intel-2015b</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+[geo](#categories "Go to list of categories..."){.tooltip}
+------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>DCW</strong><br />
+<a href="http://gmt.soest.hawaii.edu/projects/gmt" class="uri">http://gmt.soest.hawaii.edu/projects/gmt</a></td>
+<td align="left">country polygons for GMT</td>
+<td align="left"><ul>
+<li>1.1.2</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>GMT</strong><br />
+<a href="http://gmt.soest.hawaii.edu/" class="uri">http://gmt.soest.hawaii.edu/</a></td>
+<td align="left">GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools.</td>
+<td align="left"><ul>
+<li>5.2.1-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>PROJ_4</strong><br />
+<a href="http://proj.osgeo.org" class="uri">http://proj.osgeo.org</a></td>
+<td align="left">PROJ.4 - Cartographic Projections Library originally written by Gerald Evenden then of the USGS.</td>
+<td align="left"><ul>
+<li>4.9.2-foss-2015g</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+[lang](#categories "Go to list of categories..."){.tooltip}
+-------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>Bison</strong><br />
+<a href="http://www.gnu.org/software/bison" class="uri">http://www.gnu.org/software/bison</a></td>
+<td align="left">Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.</td>
+<td align="left"><ul>
+<li>2.5-intel-2015b</li>
+<li>2.7-GNU-5.1.0-2.25</li>
+<li>2.7-foss-2015b</li>
+<li>2.7-foss-2015g</li>
+<li>2.7-intel-2015b</li>
+<li>3.0.2</li>
+<li>3.0.2-foss-2015g</li>
+<li>3.0.2-intel-2015b</li>
+<li>3.0.2-intel-2016.01</li>
+<li>3.0.4</li>
+<li>3.0.4-GCC-4.9.3-binutils-2.25</li>
+<li>3.0.4-GCC-5.1.0-binutils-2.25</li>
+<li>3.0.4-GCCcore-4.9.3</li>
+<li>3.0.4-GCCcore-5.3.0</li>
+<li>3.0.4-GCCcore-5.3.1-snapshot-20160419</li>
+<li>3.0.4-foss-2015b</li>
+<li>3.0.4-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>Java</strong><br />
+<a href="http://java.com/" class="uri">http://java.com/</a></td>
+<td align="left">Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.</td>
+<td align="left"><ul>
+<li>1.7.0_79</li>
+<li>1.8.0_51</li>
+<li>1.8.0_72</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>Mono</strong><br />
+<a href="http://www.mono-project.com" class="uri">http://www.mono-project.com</a></td>
+<td align="left">Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.</td>
+<td align="left"><ul>
+<li>3.12.1</li>
+<li>3.12.1-GCC-4.4.7-system</li>
+<li>4.0.3.20-GNU-5.1.0-2.25</li>
+<li>4.2.2.10-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>NASM</strong><br />
+<a href="http://www.nasm.us/" class="uri">http://www.nasm.us/</a></td>
+<td align="left">NASMGeneral-purpose x86 assembler</td>
+<td align="left"><ul>
+<li>2.11.05</li>
+<li>2.11.05-foss-2015b</li>
+<li>2.11.05-foss-2015g</li>
+<li>2.11.05-intel-2015b</li>
+<li>2.11.06-intel-2015b</li>
+<li>2.11.08-foss-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>OpenCL-builder</strong><br />
+<a href="https://software.intel.com/en-us/intel-opencl" class="uri">https://software.intel.com/en-us/intel-opencl</a></td>
+<td align="left">OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software. This is builder (formerly runtime) package.</td>
+<td align="left"><ul>
+<li>2015</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>OpenCL-runtime</strong><br />
+<a href="https://software.intel.com/en-us/intel-opencl" class="uri">https://software.intel.com/en-us/intel-opencl</a></td>
+<td align="left">OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software.</td>
+<td align="left"><ul>
+<li>15.1</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>Perl</strong><br />
+<a href="http://www.perl.org/" class="uri">http://www.perl.org/</a></td>
+<td align="left">Larry Wall's Practical Extraction and Report Language</td>
+<td align="left"><ul>
+<li>5.16.3-intel-2015b</li>
+<li>5.20.2-GNU-4.9.3-2.25-bare</li>
+<li>5.20.2-bare</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>Python</strong><br />
+<a href="http://python.org/" class="uri">http://python.org/</a></td>
+<td align="left">Python is a programming language that lets you work more quickly and integrate your systems more effectively.</td>
+<td align="left"><ul>
+<li>2.7.10-GCC-4.9.3-2.25-bare</li>
+<li>2.7.10-GNU-4.9.3-2.25-bare</li>
+<li>2.7.11-intel-2015b</li>
+<li>2.7.8-intel-2015b</li>
+<li>2.7.8-intel-2016.01</li>
+<li>2.7.9</li>
+<li>2.7.9-GNU-5.1.0-2.25</li>
+<li>2.7.9-foss-2015b</li>
+<li>2.7.9-foss-2015g</li>
+<li>2.7.9-gompi-2015e</li>
+<li>2.7.9-ictce-7.3.5</li>
+<li>2.7.9-intel-2015b</li>
+<li>2.7.9-intel-2016.01</li>
+<li>3.5.1-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>R</strong><br />
+<a href="http://www.r-project.org/" class="uri">http://www.r-project.org/</a></td>
+<td align="left">R is a free software environment for statistical computing and graphics.</td>
+<td align="left"><ul>
+<li>3.1.1-intel-2015b</li>
+<li>3.2.3-foss-2015b</li>
+<li>3.2.3-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>Racket</strong><br />
+<a href="http://racket-lang.org" class="uri">http://racket-lang.org</a></td>
+<td align="left">Racket is a full-spectrum programming language. It goes beyond Lisp and Scheme with dialects that support objects, types, laziness, and more.</td>
+<td align="left"><ul>
+<li>6.1.1-GNU-5.1.0-2.25</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>Ruby</strong><br />
+<a href="https://www.ruby-lang.org" class="uri">https://www.ruby-lang.org</a></td>
+<td align="left">Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.</td>
+<td align="left"><ul>
+<li>2.1.5-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>SIP</strong><br />
+<a href="http://www.riverbankcomputing.com/software/sip/" class="uri">http://www.riverbankcomputing.com/software/sip/</a></td>
+<td align="left">SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.</td>
+<td align="left"><ul>
+<li>4.16.4-foss-2015g-Python-2.7.9</li>
+<li>4.17-foss-2015g-Python-2.7.9</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>SnuCL</strong><br />
+<a href="http://snucl.snu.ac.kr" class="uri">http://snucl.snu.ac.kr</a></td>
+<td align="left">An OpenCL Framework for Heterogeneous Clusters</td>
+<td align="left"><ul>
+<li>1.3.3-gompi-2015e</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>Tcl</strong><br />
+<a href="http://www.tcl.tk/" class="uri">http://www.tcl.tk/</a></td>
+<td align="left">Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.</td>
+<td align="left"><ul>
+<li>8.5.12-intel-2015b</li>
+<li>8.6.3</li>
+<li>8.6.3-GNU-5.1.0-2.25</li>
+<li>8.6.3-foss-2015b</li>
+<li>8.6.3-foss-2015g</li>
+<li>8.6.3-gompi-2015e</li>
+<li>8.6.3-ictce-7.3.5</li>
+<li>8.6.3-intel-2015b</li>
+<li>8.6.3-intel-2016.01</li>
+<li>8.6.4</li>
+<li>8.6.4-GCC-4.9.3-2.25</li>
+<li>8.6.4-GNU-4.9.3-2.25</li>
+<li>8.6.4-foss-2015b</li>
+<li>8.6.4-foss-2015g</li>
+<li>8.6.4-intel-2015b</li>
+<li>8.6.4-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>byacc</strong><br />
+<a href="http://invisible-island.net/byacc/byacc.html" class="uri">http://invisible-island.net/byacc/byacc.html</a></td>
+<td align="left">Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular compiler.</td>
+<td align="left"><ul>
+<li>20120526-foss-2015b</li>
+<li>20120526-foss-2015g</li>
+<li>20120526-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>flex</strong><br />
+<a href="http://flex.sourceforge.net/" class="uri">http://flex.sourceforge.net/</a></td>
+<td align="left">Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.</td>
+<td align="left"><ul>
+<li>2.5.35-intel-2015b</li>
+<li>2.5.37-intel-2015b</li>
+<li>2.5.38-GCC-4.8.3</li>
+<li>2.5.39</li>
+<li>2.5.39-GCC-4.9.3-binutils-2.25</li>
+<li>2.5.39-GCC-5.1.0-binutils-2.25</li>
+<li>2.5.39-GCCcore-4.9.3</li>
+<li>2.5.39-GCCcore-5.3.0</li>
+<li>2.5.39-GCCcore-5.3.1-snapshot-20160419</li>
+<li>2.5.39-foss-2015b</li>
+<li>2.5.39-foss-2015g</li>
+<li>2.5.39-intel-2015b</li>
+<li>2.5.39-intel-2016.01</li>
+<li>2.6.0</li>
+<li>2.6.0-GCCcore-5.3.0</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>libgdiplus</strong><br />
+<a href="https://github.com/mono/libgdiplus" class="uri">https://github.com/mono/libgdiplus</a></td>
+<td align="left">An Open Source implementation of the GDI+ API.</td>
+<td align="left"><ul>
+<li>3.12-GCC-4.4.7-system</li>
+<li>3.12-GNU-5.1.0-2.25</li>
+<li>3.12-intel-2016.01</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+[lib](#categories "Go to list of categories..."){.tooltip}
+------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>FOX</strong><br />
+<a href="http://fox-toolkit.org" class="uri">http://fox-toolkit.org</a></td>
+<td align="left">FOX is a C++ based Toolkit for developing Graphical User Interfaces easily and effectively. It offers a wide, and growing, collection of Controls, and provides state of the art facilities such as drag and drop, selection, as well as OpenGL widgets for 3D graphical manipulation.</td>
+<td align="left"><ul>
+<li>1.6.51-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>LibTIFF</strong><br />
+<a href="http://www.remotesensing.org/libtiff/" class="uri">http://www.remotesensing.org/libtiff/</a></td>
+<td align="left">tiffLibrary and tools for reading and writing TIFF data files</td>
+<td align="left"><ul>
+<li>4.0.3-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>OpenCoarrays</strong><br />
+<a href="http://www.opencoarrays.org" class="uri">http://www.opencoarrays.org</a></td>
+<td align="left">OpenCoarrays is an open-source software project for developing, porting and tuning transport layers that support coarray Fortran compilers.</td>
+<td align="left"><ul>
+<li>1.0.0-GNU-5.1.0-2.25</li>
+<li>1.0.1-GNU-5.1.0-2.25</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>PROJ</strong><br />
+<a href="http://trac.osgeo.org/proj/" class="uri">http://trac.osgeo.org/proj/</a></td>
+<td align="left">Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates</td>
+<td align="left"><ul>
+<li>4.8.0-foss-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>QCA</strong><br />
+<a href="http://delta.affinix.com/qca/" class="uri">http://delta.affinix.com/qca/</a></td>
+<td align="left">QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers</td>
+<td align="left"><ul>
+<li>2.1.0-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>QGIS</strong><br />
+<a href="http://www.qgis.org" class="uri">http://www.qgis.org</a></td>
+<td align="left">A Free and Open Source Geographic Information System</td>
+<td align="left"><ul>
+<li>2.12.3-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>Qwt</strong><br />
+<a href="http://qwt.sourceforge.net/index.html" class="uri">http://qwt.sourceforge.net/index.html</a></td>
+<td align="left">The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Beside a framework for 2D plots it provides scales, sliders, dials, compasses, thermometers, wheels and knobs to control or display values, arrays, or ranges of type double.</td>
+<td align="left"><ul>
+<li>6.1.2-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>SpatiaLite</strong><br />
+<a href="https://www.gaia-gis.it/fossil/libspatialite/index" class="uri">https://www.gaia-gis.it/fossil/libspatialite/index</a></td>
+<td align="left">SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities.</td>
+<td align="left"><ul>
+<li>4.3.0a-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>libMesh</strong><br />
+<a href="http://libmesh.github.io/" class="uri">http://libmesh.github.io/</a></td>
+<td align="left">The libMesh library provides a framework for the numerical simulation of partial differential equations using arbitrary unstructured discretizations on serial and parallel platforms. A major goal of the library is to provide support for adaptive mesh refinement (AMR) computations in parallel while allowing a research scientist to focus on the physics they are modeling.</td>
+<td align="left"><ul>
+<li>0.9.5-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>libdrm</strong><br />
+<a href="http://dri.freedesktop.org" class="uri">http://dri.freedesktop.org</a></td>
+<td align="left">Direct Rendering Manager runtime library.</td>
+<td align="left"><ul>
+<li>2.4.27-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>libffi</strong><br />
+<a href="http://sourceware.org/libffi/" class="uri">http://sourceware.org/libffi/</a></td>
+<td align="left">The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.</td>
+<td align="left"><ul>
+<li>3.0.13-foss-2015b</li>
+<li>3.0.13-foss-2015g</li>
+<li>3.0.13-intel-2015b</li>
+<li>3.1-GNU-5.1.0-2.25</li>
+<li>3.1-foss-2015b</li>
+<li>3.1-intel-2015b</li>
+<li>3.1-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>libfontenc</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs/" class="uri">http://www.freedesktop.org/wiki/Software/xlibs/</a></td>
+<td align="left">X11 font encoding library</td>
+<td align="left"><ul>
+<li>1.1.3-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>libjpeg-turbo</strong><br />
+<a href="http://sourceforge.net/libjpeg-turbo/" class="uri">http://sourceforge.net/libjpeg-turbo/</a></td>
+<td align="left">libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.</td>
+<td align="left"><ul>
+<li>1.3.1-foss-2015b</li>
+<li>1.3.1-intel-2015b</li>
+<li>1.4.0</li>
+<li>1.4.0-foss-2015g</li>
+<li>1.4.0-intel-2015b</li>
+<li>1.4.1-foss-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>libmatheval</strong><br />
+<a href="http://www.gnu.org/software/libmatheval/" class="uri">http://www.gnu.org/software/libmatheval/</a></td>
+<td align="left">GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.</td>
+<td align="left"><ul>
+<li>1.1.8-foss-2015b</li>
+<li>1.1.8-foss-2015g</li>
+<li>1.1.8-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>libpng</strong><br />
+<a href="http://www.libpng.org/pub/png/libpng.html" class="uri">http://www.libpng.org/pub/png/libpng.html</a></td>
+<td align="left">libpng is the official PNG reference library</td>
+<td align="left"><ul>
+<li>1.6.12</li>
+<li>1.6.12-foss-2015b</li>
+<li>1.6.12-foss-2015g</li>
+<li>1.6.12-intel-2015b</li>
+<li>1.6.12-intel-2016.01</li>
+<li>1.6.17-foss-2015b</li>
+<li>1.6.21-foss-2015b</li>
+<li>1.6.21-foss-2015g</li>
+<li>1.6.9-ictce-5.5.0</li>
+<li>1.6.9-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>libpthread-stubs</strong><br />
+<a href="http://xcb.freedesktop.org/" class="uri">http://xcb.freedesktop.org/</a></td>
+<td align="left">The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.</td>
+<td align="left"><ul>
+<li>0.3</li>
+<li>0.3-foss-2015g</li>
+<li>0.3-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>libreadline</strong><br />
+<a href="http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html" class="uri">http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html</a></td>
+<td align="left">The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.</td>
+<td align="left"><ul>
+<li>6.2-ictce-5.5.0</li>
+<li>6.2-intel-2015b</li>
+<li>6.3</li>
+<li>6.3-GCCcore-4.9.3</li>
+<li>6.3-GNU-4.9.3-2.25</li>
+<li>6.3-GNU-5.1.0-2.25</li>
+<li>6.3-foss-2015b</li>
+<li>6.3-foss-2015g</li>
+<li>6.3-gompi-2015e</li>
+<li>6.3-ictce-7.3.5</li>
+<li>6.3-intel-2015b</li>
+<li>6.3-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>libtool</strong><br />
+<a href="http://www.gnu.org/software/libtool" class="uri">http://www.gnu.org/software/libtool</a></td>
+<td align="left">GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.</td>
+<td align="left"><ul>
+<li>2.4.2-foss-2015b</li>
+<li>2.4.2-foss-2015g</li>
+<li>2.4.2-intel-2015b</li>
+<li>2.4.6</li>
+<li>2.4.6-GCC-4.9.3-2.25</li>
+<li>2.4.6-GNU-4.9.3-2.25</li>
+<li>2.4.6-GNU-5.1.0-2.25</li>
+<li>2.4.6-foss-2015g</li>
+<li>2.4.6-intel-2015b</li>
+<li>2.4.6-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>libunistring</strong><br />
+<a href="http://www.gnu.org/software/libunistring/" class="uri">http://www.gnu.org/software/libunistring/</a></td>
+<td align="left">This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.</td>
+<td align="left"><ul>
+<li>0.9.3-foss-2015b</li>
+<li>0.9.3-foss-2015g</li>
+<li>0.9.3-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>libxcb</strong><br />
+<a href="http://xcb.freedesktop.org/" class="uri">http://xcb.freedesktop.org/</a></td>
+<td align="left">The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.</td>
+<td align="left"><ul>
+<li>1.10-Python-2.7.8</li>
+<li>1.11-Python-2.7.9</li>
+<li>1.11-foss-2015g-Python-2.7.9</li>
+<li>1.11-intel-2015b-Python-2.7.9</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>libxml2</strong><br />
+<a href="http://xmlsoft.org/" class="uri">http://xmlsoft.org/</a></td>
+<td align="left">Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).</td>
+<td align="left"><ul>
+<li>2.9.2-GCC-4.9.3-2.25</li>
+<li>2.9.2-GNU-4.9.3-2.25</li>
+<li>2.9.2-GNU-5.1.0-2.25</li>
+<li>2.9.2-foss-2015b</li>
+<li>2.9.2-foss-2015g</li>
+<li>2.9.2-foss-2015g-Python-2.7.9</li>
+<li>2.9.2-gompi-2015e</li>
+<li>2.9.2-ictce-7.3.5</li>
+<li>2.9.2-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>spatialindex</strong><br />
+<a href="https://libspatialindex.github.io/index.html" class="uri">https://libspatialindex.github.io/index.html</a></td>
+<td align="left">The purpose of this library is to provide* An extensible framework that will support robust spatial indexing methods. * Support for sophisticated spatial queries. Range, point location, nearest neighbor and k-nearest neighbor as well as parametric queries (defined by spatial constraints) should be easy to deploy and run. * Easy to use interfaces for inserting, deleting and updating information.</td>
+<td align="left"><ul>
+<li>1.8.5-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>tbb</strong><br />
+<a href="http://software.intel.com/en-us/articles/intel-tbb/" class="uri">http://software.intel.com/en-us/articles/intel-tbb/</a></td>
+<td align="left">Intel Threading Building Blocks 4.0 (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms.</td>
+<td align="left"><ul>
+<li>4.3.5.187</li>
+<li>4.4.2.152</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>zlib</strong><br />
+<a href="http://www.zlib.net/" class="uri">http://www.zlib.net/</a></td>
+<td align="left">zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.</td>
+<td align="left"><ul>
+<li>1.2.7-foss-2015b</li>
+<li>1.2.7-ictce-5.5.0</li>
+<li>1.2.7-intel-2015b</li>
+<li>1.2.8</li>
+<li>1.2.8-GCC-4.9.3-2.25</li>
+<li>1.2.8-GCC-4.9.3-binutils-2.25</li>
+<li>1.2.8-GCC-5.1.0-binutils-2.25</li>
+<li>1.2.8-GCCcore-4.9.3</li>
+<li>1.2.8-GCCcore-5.3.0</li>
+<li>1.2.8-GCCcore-5.3.1-snapshot-20160419</li>
+<li>1.2.8-GNU-4.9.3-2.25</li>
+<li>1.2.8-GNU-5.1.0-2.25</li>
+<li>1.2.8-GNU-5.1.0-2.25-intel-2015b</li>
+<li>1.2.8-foss-2015b</li>
+<li>1.2.8-foss-2015g</li>
+<li>1.2.8-gompi-2015e</li>
+<li>1.2.8-ictce-7.3.5</li>
+<li>1.2.8-intel-2015b</li>
+<li>1.2.8-intel-2016.01</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+[math](#categories "Go to list of categories..."){.tooltip}
+-------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>FIAT</strong><br />
+<a href="https://bitbucket.org/fenics-project/fiat" class="uri">https://bitbucket.org/fenics-project/fiat</a></td>
+<td align="left">The FInite element Automatic Tabulator FIAT supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.</td>
+<td align="left"><ul>
+<li>1.6.0-intel-2015b-Python-2.7.11</li>
+<li>1.6.0-intel-2015b-Python-2.7.9</li>
+<li>1.6.0-intel-2016.01-Python-2.7.9</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>GEOS</strong><br />
+<a href="http://trac.osgeo.org/geos" class="uri">http://trac.osgeo.org/geos</a></td>
+<td align="left">GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)</td>
+<td align="left"><ul>
+<li>3.5.0-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>GMP</strong><br />
+<a href="http://gmplib.org/" class="uri">http://gmplib.org/</a></td>
+<td align="left">GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.</td>
+<td align="left"><ul>
+<li>5.0.5-foss-2015b</li>
+<li>5.0.5-foss-2015g</li>
+<li>5.0.5-intel-2015b</li>
+<li>6.0.0a-GNU-4.9.3-2.25</li>
+<li>6.0.0a-GNU-5.1.0-2.25</li>
+<li>6.0.0a-foss-2015b</li>
+<li>6.1.0-GCC-4.9.3-2.25</li>
+<li>6.1.0-intel-2015b</li>
+<li>6.1.0-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>Harminv</strong><br />
+<a href="http://ab-initio.mit.edu/wiki/index.php/Harminv" class="uri">http://ab-initio.mit.edu/wiki/index.php/Harminv</a></td>
+<td align="left">Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.</td>
+<td align="left"><ul>
+<li>1.4-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>ISL</strong><br />
+<a href="http://isl.gforge.inria.fr/" class="uri">http://isl.gforge.inria.fr/</a></td>
+<td align="left">isl is a library for manipulating sets and relations of integer points bounded by linear constraints.</td>
+<td align="left"><ul>
+<li>0.14-GNU-5.1.0-2.25</li>
+<li>0.15-GCC-4.9.3-2.25</li>
+<li>0.15-GNU-4.9.3-2.25</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>METIS</strong><br />
+<a href="http://glaros.dtc.umn.edu/gkhome/metis/metis/overview" class="uri">http://glaros.dtc.umn.edu/gkhome/metis/metis/overview</a></td>
+<td align="left">METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.</td>
+<td align="left"><ul>
+<li>5.1.0-intel-2015b</li>
+<li>5.1.0-intel-2016.01</li>
+<li>5.1.0-intel-2016.01-32bitIDX</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>Octave</strong><br />
+<a href="http://www.gnu.org/software/octave/" class="uri">http://www.gnu.org/software/octave/</a></td>
+<td align="left">GNU Octave is a high-level interpreted language, primarily intended for numerical computations.</td>
+<td align="left"><ul>
+<li>3.8.2-foss-2015g</li>
+<li>3.8.2-intel-2015b</li>
+<li>4.0.0-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>ParMETIS</strong><br />
+<a href="http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview" class="uri">http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview</a></td>
+<td align="left">ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.</td>
+<td align="left"><ul>
+<li>4.0.3-intel-2015b</li>
+<li>4.0.3-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>SCOTCH</strong><br />
+<a href="http://gforge.inria.fr/projects/scotch/" class="uri">http://gforge.inria.fr/projects/scotch/</a></td>
+<td align="left">Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.</td>
+<td align="left"><ul>
+<li>5.1.12b_esmumps-foss-2015b</li>
+<li>6.0.0_esmumps-intel-2015b</li>
+<li>6.0.3-intel-2015b</li>
+<li>6.0.3-intel-2016.01</li>
+<li>6.0.4-intel-2015b</li>
+<li>6.0.4-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>ScientificPython</strong><br />
+<a href="https://sourcesup.cru.fr/projects/scientific-py/" class="uri">https://sourcesup.cru.fr/projects/scientific-py/</a></td>
+<td align="left">ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization.</td>
+<td align="left"><ul>
+<li>2.9.4-intel-2015b-Python-2.7.11</li>
+<li>2.9.4-intel-2015b-Python-2.7.9</li>
+<li>2.9.4-intel-2016.01-Python-2.7.9</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>numpy</strong><br />
+<a href="http://www.numpy.org" class="uri">http://www.numpy.org</a></td>
+<td align="left">NumPy is the fundamental package for scientific computing with Python. It contains among other thingsa powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.</td>
+<td align="left"><ul>
+<li>1.8.2-intel-2015b-Python-2.7.11</li>
+<li>1.8.2-intel-2015b-Python-2.7.9</li>
+<li>1.8.2-intel-2016.01-Python-2.7.9</li>
+<li>1.9.1-intel-2015b-Python-2.7.9</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>sympy</strong><br />
+<a href="http://sympy.org/" class="uri">http://sympy.org/</a></td>
+<td align="left">SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries.</td>
+<td align="left"><ul>
+<li>0.7.6-intel-2015b-Python-2.7.9</li>
+<li>0.7.6-intel-2016.01-Python-2.7.9</li>
+<li>0.7.6.1-intel-2015b-Python-2.7.11</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+[mpi](#categories "Go to list of categories..."){.tooltip}
+------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>MPICH</strong><br />
+<a href="http://www.mpich.org/" class="uri">http://www.mpich.org/</a></td>
+<td align="left">MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).</td>
+<td align="left"><ul>
+<li>3.2-GCC-5.3.0-2.25</li>
+<li>3.2-GCC-5.3.1-snapshot-20160419-2.25</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>MPI_NET</strong><br />
+<a href="http://www.osl.iu.edu/research/mpi.net/" class="uri">http://www.osl.iu.edu/research/mpi.net/</a></td>
+<td align="left">MPI.NET is a high-performance, easy-to-use implementation of the Message Passing Interface (MPI) for Microsoft's .NET environment</td>
+<td align="left"><ul>
+<li>1.2.0-gompi-2015e</li>
+<li>1.2.0-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>MVAPICH2</strong><br />
+<a href="http://mvapich.cse.ohio-state.edu/overview/mvapich2/" class="uri">http://mvapich.cse.ohio-state.edu/overview/mvapich2/</a></td>
+<td align="left">This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH.</td>
+<td align="left"><ul>
+<li>2.1-GCC-4.4.7-system</li>
+<li>2.1-GNU-5.1.0-2.25</li>
+<li>2.1-iccifort-2015.3.187-GNU-5.1.0-2.25</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>OpenMPI</strong><br />
+<a href="http://www.open-mpi.org/" class="uri">http://www.open-mpi.org/</a></td>
+<td align="left">The Open MPI Project is an open source MPI-2 implementation.</td>
+<td align="left"><ul>
+<li>1.10.1-GNU-4.9.3-2.25</li>
+<li>1.10.2-GCC-5.3.0-2.26</li>
+<li>1.8.6-GCC-4.4.7-system</li>
+<li>1.8.6-GNU-5.1.0-2.25</li>
+<li>1.8.6-iccifort-2015.3.187-GNU-5.1.0-2.25</li>
+<li>1.8.8-GNU-4.9.3-2.25</li>
+<li>1.8.8-GNU-5.1.0-2.25</li>
+<li>1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>impi</strong><br />
+<a href="http://software.intel.com/en-us/intel-mpi-library/" class="uri">http://software.intel.com/en-us/intel-mpi-library/</a></td>
+<td align="left">The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.</td>
+<td align="left"><ul>
+<li>2017-BETA.ENG</li>
+<li>4.1.1.036-iccifort-2013.5.192</li>
+<li>4.1.1.036-iccifort-2013.5.192-GCC-4.8.3</li>
+<li>5.0.3.048</li>
+<li>5.0.3.048-iccifort-2015.3.187</li>
+<li>5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25</li>
+<li>5.1.1.109-iccifort-2016.0.109-GCC-4.9.3</li>
+<li>5.1.2.150-iccifort-2016.1.150</li>
+<li>5.1.2.150-iccifort-2016.1.150-GCC-4.9.3</li>
+<li>5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25</li>
+<li>5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>mpt</strong><br />
+<a href="https://docs.it4i.cz/salomon/"></a></td>
+<td align="left"></td>
+<td align="left"><ul>
+<li>2.12</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+[numlib](#categories "Go to list of categories..."){.tooltip}
+---------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>FFTW</strong><br />
+<a href="http://www.fftw.org" class="uri">http://www.fftw.org</a></td>
+<td align="left">FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.</td>
+<td align="left"><ul>
+<li>2.1.5-gompi-2015b</li>
+<li>2.1.5-iimpi-7.3.5-GNU-5.1.0-2.25</li>
+<li>3.3.4-gompi-2015b</li>
+<li>3.3.4-gompi-2015e</li>
+<li>3.3.4-gompi-2015g</li>
+<li>3.3.4-gompi-2016.04</li>
+<li>3.3.4-intel-2015b</li>
+<li>3.3.4-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>GSL</strong><br />
+<a href="http://www.gnu.org/software/gsl/" class="uri">http://www.gnu.org/software/gsl/</a></td>
+<td align="left">The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.</td>
+<td align="left"><ul>
+<li>1.16-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>Hypre</strong><br />
+<a href="https://computation.llnl.gov/casc/linear_solvers/sls_hypre.html" class="uri">https://computation.llnl.gov/casc/linear_solvers/sls_hypre.html</a></td>
+<td align="left">Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.</td>
+<td align="left"><ul>
+<li>2.10.0b-intel-2015b</li>
+<li>2.10.0b-intel-2016.01</li>
+<li>2.10.1-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>LAPACKE</strong><br />
+<a href="http://www.netlib.org/lapack/lapacke.html" class="uri">http://www.netlib.org/lapack/lapacke.html</a></td>
+<td align="left">LAPACKE C Interface to LAPACK header files and library</td>
+<td align="left"><ul>
+<li>3.5.0-LAPACK-3.5.0</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>OpenBLAS</strong><br />
+<a href="http://xianyi.github.com/OpenBLAS/" class="uri">http://xianyi.github.com/OpenBLAS/</a></td>
+<td align="left">OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.</td>
+<td align="left"><ul>
+<li>0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0</li>
+<li>0.2.14-GNU-5.1.0-2.25-LAPACK-3.5.0</li>
+<li>0.2.14-LAPACK-3.5.0</li>
+<li>0.2.14-gompi-2015e-LAPACK-3.5.0</li>
+<li>0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>PETSc</strong><br />
+<a href="http://www.mcs.anl.gov/petsc" class="uri">http://www.mcs.anl.gov/petsc</a></td>
+<td align="left">PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.</td>
+<td align="left"><ul>
+<li>3.6.1-intel-2015b-Python-2.7.9</li>
+<li>3.6.1-intel-2016.01-Python-2.7.9</li>
+<li>3.6.3-intel-2015b-Python-2.7.11</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>ScaLAPACK</strong><br />
+<a href="http://www.netlib.org/scalapack/" class="uri">http://www.netlib.org/scalapack/</a></td>
+<td align="left">The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.</td>
+<td align="left"><ul>
+<li>2.0.2-OpenBLAS-0.2.14-LAPACK-3.5.0</li>
+<li>2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0</li>
+<li>2.0.2-gompi-2015e-OpenBLAS-0.2.14-LAPACK-3.5.0</li>
+<li>2.0.2-gompi-2015g-OpenBLAS-0.2.14-LAPACK-3.5.0</li>
+<li>2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>SuiteSparse</strong><br />
+<a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/" class="uri">http://www.cise.ufl.edu/research/sparse/SuiteSparse/</a></td>
+<td align="left">SuiteSparse is a collection of libraries manipulate sparse matrices.</td>
+<td align="left"><ul>
+<li>4.4.3-intel-2015b-ParMETIS-4.0.3</li>
+<li>4.4.3-intel-2016.01-ParMETIS-4.0.3</li>
+<li>4.4.6-intel-2015b-ParMETIS-4.0.3</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>arpack-ng</strong><br />
+<a href="http://forge.scilab.org/index.php/p/arpack-ng/" class="uri">http://forge.scilab.org/index.php/p/arpack-ng/</a></td>
+<td align="left">ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.</td>
+<td align="left"><ul>
+<li>3.3.0-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>imkl</strong><br />
+<a href="http://software.intel.com/en-us/intel-mkl/" class="uri">http://software.intel.com/en-us/intel-mkl/</a></td>
+<td align="left">Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.</td>
+<td align="left"><ul>
+<li>11.0.5.192-iimpi-5.5.0</li>
+<li>11.0.5.192-iimpi-5.5.0-GCC-4.8.3</li>
+<li>11.2.3.187</li>
+<li>11.2.3.187-iimpi-7.3.5</li>
+<li>11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25</li>
+<li>11.2.3.187-iompi-2015.03</li>
+<li>11.3.0.109-iimpi-2016.00-GCC-4.9.3</li>
+<li>11.3.1.150-iimpi-2016.00-GCC-4.9.3</li>
+<li>11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25</li>
+<li>11.3.1.150-iimpi-8.3.5</li>
+<li>11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+[perf](#categories "Go to list of categories..."){.tooltip}
+-------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>Advisor</strong><br />
+<a href="https://software.intel.com/intel-advisor-xe" class="uri">https://software.intel.com/intel-advisor-xe</a></td>
+<td align="left">Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance “dies” - Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain</td>
+<td align="left"><ul>
+<li>2016_update2</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>MAP</strong><br />
+<a href="https://docs.it4i.cz/salomon/"></a></td>
+<td align="left"></td>
+<td align="left"><ul>
+<li>4.2</li>
+<li>5.0.1</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>OPARI2</strong><br />
+<a href="http://www.score-p.org" class="uri">http://www.score-p.org</a></td>
+<td align="left">OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface.</td>
+<td align="left"><ul>
+<li>1.1.4-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>OTF2</strong><br />
+<a href="http://www.score-p.org" class="uri">http://www.score-p.org</a></td>
+<td align="left">The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library. It will become the new standard trace format for Scalasca, Vampir, and Tau and is open for other tools.</td>
+<td align="left"><ul>
+<li>1.4-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>PAPI</strong><br />
+<a href="http://icl.cs.utk.edu/projects/papi/" class="uri">http://icl.cs.utk.edu/projects/papi/</a></td>
+<td align="left">PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack.</td>
+<td align="left"><ul>
+<li>5.4.0-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>PerfReports</strong><br />
+<a href="https://docs.it4i.cz/salomon/"></a></td>
+<td align="left"></td>
+<td align="left"><ul>
+<li>5.0.1</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>Vampir</strong><br />
+<a href="http://www.vampir.eu" class="uri">http://www.vampir.eu</a></td>
+<td align="left">The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.</td>
+<td align="left"><ul>
+<li>8.5.0</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>ipp</strong><br />
+<a href="http://software.intel.com/en-us/articles/intel-ipp/" class="uri">http://software.intel.com/en-us/articles/intel-ipp/</a></td>
+<td align="left">Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms.</td>
+<td align="left"><ul>
+<li>9.0.1.150</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>perfboost</strong><br />
+<a href="https://docs.it4i.cz/salomon/"></a></td>
+<td align="left"></td>
+<td align="left"><ul>
+<li>1.0</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>perfcatcher</strong><br />
+<a href="https://docs.it4i.cz/salomon/"></a></td>
+<td align="left"></td>
+<td align="left"><ul>
+<li>1.0</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>perfsuite</strong><br />
+<a href="https://docs.it4i.cz/salomon/"></a></td>
+<td align="left"></td>
+<td align="left"><ul>
+<li>1a5.3</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+[phys](#categories "Go to list of categories..."){.tooltip}
+-------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>Meep</strong><br />
+<a href="http://ab-initio.mit.edu/wiki/index.php/Meep" class="uri">http://ab-initio.mit.edu/wiki/index.php/Meep</a></td>
+<td align="left">Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems.</td>
+<td align="left"><ul>
+<li>1.3-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>phono3py</strong><br />
+<a href="http://phonopy.sourceforge.net/phono3py/index.html" class="uri">http://phonopy.sourceforge.net/phono3py/index.html</a></td>
+<td align="left">This software calculates phonon-phonon interaction related properties</td>
+<td align="left"><ul>
+<li>0.9.14-ictce-7.3.5-Python-2.7.9</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+[system](#categories "Go to list of categories..."){.tooltip}
+---------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>hwloc</strong><br />
+<a href="http://www.open-mpi.org/projects/hwloc/" class="uri">http://www.open-mpi.org/projects/hwloc/</a></td>
+<td align="left">The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.</td>
+<td align="left"><ul>
+<li>1.11.0-GNU-4.9.3-2.25</li>
+<li>1.11.0-GNU-5.1.0-2.25</li>
+<li>1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25</li>
+<li>1.11.2-GCC-4.9.3-2.25</li>
+<li>1.11.3-GCC-5.3.0-2.26</li>
+<li>1.5-GCC-4.4.7-system</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>libpciaccess</strong><br />
+<a href="http://cgit.freedesktop.org/xorg/lib/libpciaccess/" class="uri">http://cgit.freedesktop.org/xorg/lib/libpciaccess/</a></td>
+<td align="left">Generic PCI access library.</td>
+<td align="left"><ul>
+<li>0.13.1-foss-2015g</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+[toolchain](#categories "Go to list of categories..."){.tooltip}
+------------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>GNU</strong><br />
+<a href="http://www.gnu.org/software/" class="uri">http://www.gnu.org/software/</a></td>
+<td align="left">Compiler-only toolchain with GCC and binutils.</td>
+<td align="left"><ul>
+<li>4.9.3-2.25</li>
+<li>5.1.0-2.25</li>
+<li>5.1.0-2.25-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>PRACE</strong><br />
+<a href="http://www.prace-ri.eu/PRACE-Common-Production" class="uri">http://www.prace-ri.eu/PRACE-Common-Production</a></td>
+<td align="left">The PRACE Common Production Environment (PCPE) is a set of software tools and libraries that are planned to be available on all PRACE execution sites. The PCPE also defines a set of environment variables that try to make compilation on all sites as homogeneous and simple as possible.</td>
+<td align="left"><ul>
+<li>20150630-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>foss</strong><br />
+<a href="https://docs.it4i.cz/salomon/(none)">(none)</a></td>
+<td align="left">GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.</td>
+<td align="left"><ul>
+<li>2015b</li>
+<li>2015e</li>
+<li>2015g</li>
+<li>2016.04</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>gompi</strong><br />
+<a href="https://docs.it4i.cz/salomon/(none)">(none)</a></td>
+<td align="left">GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.</td>
+<td align="left"><ul>
+<li>2015b</li>
+<li>2015e</li>
+<li>2015g</li>
+<li>2016.04</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>iccifort</strong><br />
+<a href="http://software.intel.com/en-us/intel-cluster-toolkit-compiler/" class="uri">http://software.intel.com/en-us/intel-cluster-toolkit-compiler/</a></td>
+<td align="left">Intel C, C++ and Fortran compilers</td>
+<td align="left"><ul>
+<li>2013.5.192</li>
+<li>2013.5.192-GCC-4.8.3</li>
+<li>2015.3.187</li>
+<li>2015.3.187-GNU-4.9.3-2.25</li>
+<li>2015.3.187-GNU-5.1.0-2.25</li>
+<li>2016.0.109-GCC-4.9.3</li>
+<li>2016.1.150</li>
+<li>2016.1.150-GCC-4.9.3</li>
+<li>2016.1.150-GCC-4.9.3-2.25</li>
+<li>2016.3.210-GCC-5.3.0-2.26</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>ictce</strong><br />
+<a href="http://software.intel.com/en-us/intel-cluster-toolkit-compiler/" class="uri">http://software.intel.com/en-us/intel-cluster-toolkit-compiler/</a></td>
+<td align="left">Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.</td>
+<td align="left"><ul>
+<li>5.5.0</li>
+<li>7.3.5</li>
+<li>8.3.5</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>iimpi</strong><br />
+<a href="http://software.intel.com/en-us/intel-cluster-toolkit-compiler/" class="uri">http://software.intel.com/en-us/intel-cluster-toolkit-compiler/</a></td>
+<td align="left">Intel C/C++ and Fortran compilers, alongside Intel MPI.</td>
+<td align="left"><ul>
+<li>2016.00-GCC-4.9.3</li>
+<li>2016.01-GCC-4.9.3</li>
+<li>2016.01-GCC-4.9.3-2.25</li>
+<li>2016.03-GCC-5.3.0-2.26</li>
+<li>5.5.0</li>
+<li>5.5.0-GCC-4.8.3</li>
+<li>7.3.5</li>
+<li>7.3.5-GNU-5.1.0-2.25</li>
+<li>8.3.5</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>intel</strong><br />
+<a href="http://software.intel.com/en-us/intel-cluster-toolkit-compiler/" class="uri">http://software.intel.com/en-us/intel-cluster-toolkit-compiler/</a></td>
+<td align="left">Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.</td>
+<td align="left"><ul>
+<li>2014.06</li>
+<li>2015b</li>
+<li>2015b-intel-2015b</li>
+<li>2016.00</li>
+<li>2016.01</li>
+<li>2016.03-GCC-5.3</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>prace</strong><br />
+<a href="http://www.prace-ri.eu/PRACE-Common-Production" class="uri">http://www.prace-ri.eu/PRACE-Common-Production</a></td>
+<td align="left">**** PRACE Common Production Environment (PCPE) **** Initialisation of the PRACE common production environment. This allows you to assume that the following tools/libraries are available by default in your PATH/environment. * Fortran, C, C++ Compilers * MPI * BLAS, LAPACK, BLACS, ScaLAPACK * FFTW * HDF5, NetCDF The compiler commands on are* mpif90 - Fortran compiler * mpicc - C compiler * mpicxx - C++ compiler For more information on the PCPE please see the documentation athttp://www.prace-ri.eu/PRACE-Common-Production For help using this system, please see Local User Guide available athttp://prace-ri.eu/Best-Practice-Guide-Anselm-HTML</td>
+<td align="left"><ul>
+<li>20160107-intel-2016.01</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+[tools](#categories "Go to list of categories..."){.tooltip}
+--------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>APR</strong><br />
+<a href="http://apr.apache.org/" class="uri">http://apr.apache.org/</a></td>
+<td align="left">Apache Portable Runtime (APR) libraries.</td>
+<td align="left"><ul>
+<li>1.5.2-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>APR-util</strong><br />
+<a href="http://apr.apache.org/" class="uri">http://apr.apache.org/</a></td>
+<td align="left">Apache Portable Runtime (APR) util libraries.</td>
+<td align="left"><ul>
+<li>1.5.4-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>Bash</strong><br />
+<a href="http://www.gnu.org/software/bash" class="uri">http://www.gnu.org/software/bash</a></td>
+<td align="left">Bash is an sh-compatible command language interpreter that executes commands read from the standard input or from a file. Bash also incorporates useful features from the Korn and C shells (ksh and csh).</td>
+<td align="left"><ul>
+<li>4.2-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>EasyBuild</strong><br />
+<a href="http://hpcugent.github.com/easybuild/" class="uri">http://hpcugent.github.com/easybuild/</a></td>
+<td align="left">EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.</td>
+<td align="left"><ul>
+<li>2.4.0</li>
+<li>2.5.0</li>
+<li>2.7.0</li>
+<li>2.8.0</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>HPL</strong><br />
+<a href="http://www.netlib.org/benchmark/hpl/" class="uri">http://www.netlib.org/benchmark/hpl/</a></td>
+<td align="left">HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.</td>
+<td align="left"><ul>
+<li>2.1-foss-2015b</li>
+<li>2.1-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>Inspector</strong><br />
+<a href="http://software.intel.com/en-us/intel-inspector-xe" class="uri">http://software.intel.com/en-us/intel-inspector-xe</a></td>
+<td align="left">Intel Inspector XE 2013 is an easy to use memory error checker and thread checker for serial and parallel applications</td>
+<td align="left"><ul>
+<li>2016_update1</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>JOE</strong><br />
+<a href="http://joe-editor.sourceforge.net" class="uri">http://joe-editor.sourceforge.net</a></td>
+<td align="left">JOE is a full featured terminal-based screen editor which is distributed under the GNU General Public License (GPL)</td>
+<td align="left"><ul>
+<li>4.2</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>MATLAB</strong><br />
+<a href="https://docs.it4i.cz/salomon/"></a></td>
+<td align="left"></td>
+<td align="left"><ul>
+<li>2015a-COM</li>
+<li>2015a-EDU</li>
+<li>2015b-COM</li>
+<li>2015b-EDU</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>MIKE</strong><br />
+<a href="http://www.mikepoweredbydhi.com" class="uri">http://www.mikepoweredbydhi.com</a></td>
+<td align="left">MIKE Powered by DHI is a part of DHI, the global organisation dedicated to solving challenges in water environments worldwide.</td>
+<td align="left"><ul>
+<li>2014</li>
+<li>2016</li>
+<li>2016-SP2</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>Mercurial</strong><br />
+<a href="http://mercurial.selenic.com/" class="uri">http://mercurial.selenic.com/</a></td>
+<td align="left">Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface.</td>
+<td align="left"><ul>
+<li>3.5-Python-2.7.9</li>
+<li>3.7.3-foss-2015g-Python-2.7.9</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>QEMU</strong><br />
+<a href="http://wiki.qemu.org/Main_Page" class="uri">http://wiki.qemu.org/Main_Page</a></td>
+<td align="left">QEMU is a generic and open source machine emulator and virtualizer.</td>
+<td align="left"><ul>
+<li>2.1.2-GCC-4.4.7-system</li>
+<li>2.1.2-GCC-4.4.7-system-VDE2</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>SDE</strong><br />
+<a href="https://software.intel.com/en-us/articles/intel-software-development-emulator" class="uri">https://software.intel.com/en-us/articles/intel-software-development-emulator</a></td>
+<td align="left">Intel Software Development Emulator is a pintool that enables the development of applications using instruction set extensions that are not currently implemented in hardware.</td>
+<td align="left"><ul>
+<li>7.41.0</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>Serf</strong><br />
+<a href="http://serf.apache.org/" class="uri">http://serf.apache.org/</a></td>
+<td align="left">The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library</td>
+<td align="left"><ul>
+<li>1.3.8-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>Subversion</strong><br />
+<a href="http://subversion.apache.org/" class="uri">http://subversion.apache.org/</a></td>
+<td align="left">Subversion is an open source version control system.</td>
+<td align="left"><ul>
+<li>1.8.16-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>Szip</strong><br />
+<a href="http://www.hdfgroup.org/doc_resource/SZIP/" class="uri">http://www.hdfgroup.org/doc_resource/SZIP/</a></td>
+<td align="left">Szip compression software, providing lossless compression of scientific data</td>
+<td align="left"><ul>
+<li>2.1</li>
+<li>2.1-foss-2015b</li>
+<li>2.1-foss-2015g</li>
+<li>2.1-ictce-7.3.5</li>
+<li>2.1-intel-2015b</li>
+<li>2.1-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>VDE2</strong><br />
+<a href="http://vde.sourceforge.net" class="uri">http://vde.sourceforge.net</a></td>
+<td align="left">VDE is an ethernet compliant virtual network that can be spawned over a set of physical computer over the Internet. VDE is part of virtualsquare project.</td>
+<td align="left"><ul>
+<li>2.3.2-GCC-4.4.7-system</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>VTune</strong><br />
+<a href="http://software.intel.com/en-us/intel-vtune-amplifier-xe" class="uri">http://software.intel.com/en-us/intel-vtune-amplifier-xe</a></td>
+<td align="left">Intel VTune Amplifier XE 2016 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.</td>
+<td align="left"><ul>
+<li>2016_update1</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>VirtualGL</strong><br />
+<a href="http://www.virtualgl.org" class="uri">http://www.virtualgl.org</a></td>
+<td align="left">VirtualGL is an open source toolkit that gives any Unix or Linux remote display software the ability to run OpenGL applications with full 3D hardware acceleration.</td>
+<td align="left"><ul>
+<li>2.4.1</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>Wine</strong><br />
+<a href="https://www.winehq.org" class="uri">https://www.winehq.org</a></td>
+<td align="left">Wine (originally an acronym for "Wine Is Not an Emulator") is a compatibility layer capable of running Windows applications on several POSIX-compliant operating systems, such as Linux, Mac OSX, & BSD.</td>
+<td align="left"><ul>
+<li>1.7.29-GCC-4.4.7-system</li>
+<li>1.7.29-GNU-5.1.0-2.25</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>XZ</strong><br />
+<a href="http://tukaani.org/xz/" class="uri">http://tukaani.org/xz/</a></td>
+<td align="left">xzXZ utilities</td>
+<td align="left"><ul>
+<li>5.2.2-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>binutils</strong><br />
+<a href="http://directory.fsf.org/project/binutils/" class="uri">http://directory.fsf.org/project/binutils/</a></td>
+<td align="left">binutilsGNU binary utilities</td>
+<td align="left"><ul>
+<li>2.25</li>
+<li>2.25-GCC-4.9.3-binutils-2.25</li>
+<li>2.25-GCC-5.1.0-binutils-2.25</li>
+<li>2.25-GCCcore-4.9.3</li>
+<li>2.25-GCCcore-5.3.0</li>
+<li>2.25-GCCcore-5.3.1-snapshot-20160419</li>
+<li>2.25-foss-2015b</li>
+<li>2.26</li>
+<li>2.26-GCCcore-5.3.0</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>bzip2</strong><br />
+<a href="http://www.bzip.org/" class="uri">http://www.bzip.org/</a></td>
+<td align="left">bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.</td>
+<td align="left"><ul>
+<li>1.0.6</li>
+<li>1.0.6-GCC-4.9.3-2.25</li>
+<li>1.0.6-GNU-4.9.3-2.25</li>
+<li>1.0.6-GNU-5.1.0-2.25</li>
+<li>1.0.6-foss-2015b</li>
+<li>1.0.6-foss-2015g</li>
+<li>1.0.6-gompi-2015e</li>
+<li>1.0.6-ictce-7.3.5</li>
+<li>1.0.6-intel-2015b</li>
+<li>1.0.6-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>cURL</strong><br />
+<a href="http://curl.haxx.se" class="uri">http://curl.haxx.se</a></td>
+<td align="left">libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.</td>
+<td align="left"><ul>
+<li>7.37.1</li>
+<li>7.37.1-foss-2015g</li>
+<li>7.37.1-intel-2015b</li>
+<li>7.37.1-intel-2016.01</li>
+<li>7.45.0-foss-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>expat</strong><br />
+<a href="http://expat.sourceforge.net/" class="uri">http://expat.sourceforge.net/</a></td>
+<td align="left">Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags)</td>
+<td align="left"><ul>
+<li>2.1.0</li>
+<li>2.1.0-foss-2015b</li>
+<li>2.1.0-foss-2015g</li>
+<li>2.1.0-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>git</strong><br />
+<a href="http://git-scm.com/" class="uri">http://git-scm.com/</a></td>
+<td align="left">Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.</td>
+<td align="left"><ul>
+<li>2.8.0</li>
+<li>2.8.0-GNU-4.9.3-2.25</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>gzip</strong><br />
+<a href="http://www.gnu.org/software/gzip/" class="uri">http://www.gnu.org/software/gzip/</a></td>
+<td align="left">gzip (GNU zip) is a popular data compression program as a replacement for compress</td>
+<td align="left"><ul>
+<li>1.6-foss-2015g</li>
+<li>1.6-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>itac</strong><br />
+<a href="http://software.intel.com/en-us/intel-trace-analyzer/" class="uri">http://software.intel.com/en-us/intel-trace-analyzer/</a></td>
+<td align="left">The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays.</td>
+<td align="left"><ul>
+<li>9.1.2.024</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>numactl</strong><br />
+<a href="http://oss.sgi.com/projects/libnuma/" class="uri">http://oss.sgi.com/projects/libnuma/</a></td>
+<td align="left">The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.</td>
+<td align="left"><ul>
+<li>2.0.10-GNU-4.9.3-2.25</li>
+<li>2.0.10-GNU-5.1.0-2.25</li>
+<li>2.0.10-iccifort-2015.3.187-GNU-4.9.3-2.25</li>
+<li>2.0.11</li>
+<li>2.0.11-GCC-4.9.3-2.25</li>
+<li>2.0.11-GCC-5.3.0-2.26</li>
+<li>2.0.9-GCC-4.4.7-system</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>parallel</strong><br />
+<a href="http://savannah.gnu.org/projects/parallel/" class="uri">http://savannah.gnu.org/projects/parallel/</a></td>
+<td align="left">parallelBuild and execute shell commands in parallel</td>
+<td align="left"><ul>
+<li>20150322-GNU-5.1.0-2.25</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>tcsh</strong><br />
+<a href="http://www.tcsh.org" class="uri">http://www.tcsh.org</a></td>
+<td align="left">Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax.</td>
+<td align="left"><ul>
+<li>6.18.01-intel-2015b</li>
+<li>6.19.00</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>turbovnc</strong><br />
+<a href="http://www.turbovnc.org" class="uri">http://www.turbovnc.org</a></td>
+<td align="left">TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide peak performance for 3D and video workloads.</td>
+<td align="left"><ul>
+<li>1.2.3</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>util-linux</strong><br />
+<a href="http://www.kernel.org/pub/linux/utils/util-linux" class="uri">http://www.kernel.org/pub/linux/utils/util-linux</a></td>
+<td align="left">Set of Linux utilities</td>
+<td align="left"><ul>
+<li>2.26.1</li>
+<li>2.26.1-foss-2015g</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
+[vis](#categories "Go to list of categories..."){.tooltip}
+------------
+<table>
+<colgroup>
+<col width="33%" />
+<col width="33%" />
+<col width="33%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Module</th>
+<th align="left">Description</th>
+<th align="left">Available versions</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>FLTK</strong><br />
+<a href="http://www.fltk.org" class="uri">http://www.fltk.org</a></td>
+<td align="left">FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.</td>
+<td align="left"><ul>
+<li>1.3.2-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>GLib</strong><br />
+<a href="http://www.gtk.org/" class="uri">http://www.gtk.org/</a></td>
+<td align="left">GLib is one of the base libraries of the GTK+ project</td>
+<td align="left"><ul>
+<li>2.40.0-foss-2015g</li>
+<li>2.40.0-intel-2015b</li>
+<li>2.40.0-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>GPI-2</strong><br />
+<a href="http://www.gpi-site.com/gpi2/" class="uri">http://www.gpi-site.com/gpi2/</a></td>
+<td align="left">GPI-2 is an API for the development of scalable, asynchronous and fault tolerant parallel applications.</td>
+<td align="left"><ul>
+<li>1.1.1-gompi-2015e</li>
+<li>1.1.1-gompi-2015e-MPI</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>JasPer</strong><br />
+<a href="http://www.ece.uvic.ca/~frodo/jasper/" class="uri">http://www.ece.uvic.ca/~frodo/jasper/</a></td>
+<td align="left">The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.</td>
+<td align="left"><ul>
+<li>1.900.1-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>Mesa</strong><br />
+<a href="http://www.mesa3d.org/" class="uri">http://www.mesa3d.org/</a></td>
+<td align="left">Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.</td>
+<td align="left"><ul>
+<li>11.0.8-foss-2015g-Python-2.7.9</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>OSPRay</strong><br />
+<a href="http://www.ospray.org" class="uri">http://www.ospray.org</a></td>
+<td align="left">A Ray Tracing Based Rendering Engine for High-Fidelity Visualization</td>
+<td align="left"><ul>
+<li>0.9.1</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>OpenCV</strong><br />
+<a href="http://opencv.org/" class="uri">http://opencv.org/</a></td>
+<td align="left">OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products.</td>
+<td align="left"><ul>
+<li>2.4.9-intel-2015b</li>
+<li>3.0.0-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>OpenDX</strong><br />
+<a href="http://www.opendx.org" class="uri">http://www.opendx.org</a></td>
+<td align="left">Open source visualization software package based on IBM's Visualization Data Explorer.</td>
+<td align="left"><ul>
+<li>4.4.4-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>ParaView</strong><br />
+<a href="http://www.paraview.org" class="uri">http://www.paraview.org</a></td>
+<td align="left">ParaView is a scientific parallel visualizer.</td>
+<td align="left"><ul>
+<li>4.3-OSPRay</li>
+<li>5.0.0-binary</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>PyQt</strong><br />
+<a href="http://www.riverbankcomputing.co.uk/software/pyqt" class="uri">http://www.riverbankcomputing.co.uk/software/pyqt</a></td>
+<td align="left">PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.</td>
+<td align="left"><ul>
+<li>4.11.3-foss-2015g-Python-2.7.9</li>
+<li>4.11.4-foss-2015g-Python-2.7.9</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>SUMO</strong><br />
+<a href="http://www.sumo.dlr.de/wiki/Main_Page" class="uri">http://www.sumo.dlr.de/wiki/Main_Page</a></td>
+<td align="left">Simulation of Urban MObility (SUMO) is an open source, highly portable, microscopic and continuous road traffic simulation package designed to handle large road networks.</td>
+<td align="left"><ul>
+<li>0.25.0-foss-2015g</li>
+<li>0.26.0-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>Tk</strong><br />
+<a href="http://www.tcl.tk/" class="uri">http://www.tcl.tk/</a></td>
+<td align="left">Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.</td>
+<td align="left"><ul>
+<li>8.5.12-intel-2015b</li>
+<li>8.6.4-GCC-4.9.3-2.25-no-X11</li>
+<li>8.6.4-GNU-4.9.3-2.25-no-X11</li>
+<li>8.6.4-foss-2015b-no-X11</li>
+<li>8.6.4-foss-2015g-no-X11</li>
+<li>8.6.4-intel-2015b-no-X11</li>
+<li>8.6.4-intel-2016.01-no-X11</li>
+<li>8.6.4-no-X11</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>VisIt</strong><br />
+<a href="https://wci.llnl.gov/simulation/computer-codes/visit" class="uri">https://wci.llnl.gov/simulation/computer-codes/visit</a></td>
+<td align="left">VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool</td>
+<td align="left"><ul>
+<li>2.10.0</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>cairo</strong><br />
+<a href="http://cairographics.org" class="uri">http://cairographics.org</a></td>
+<td align="left">Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB</td>
+<td align="left"><ul>
+<li>1.12.18-foss-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>ffmpeg</strong><br />
+<a href="https://www.ffmpeg.org/" class="uri">https://www.ffmpeg.org/</a></td>
+<td align="left">A complete, cross-platform solution to record, convert and stream audio and video.</td>
+<td align="left"><ul>
+<li>2.4-foss-2015g</li>
+<li>2.4-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>fixesproto</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">X.org FixesProto protocol headers.</td>
+<td align="left"><ul>
+<li>5.0-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>fontconfig</strong><br />
+<a href="http://www.freedesktop.org/software/fontconfig" class="uri">http://www.freedesktop.org/software/fontconfig</a></td>
+<td align="left">Fontconfig is a library designed to provide system-wide font configuration, customization and application access.</td>
+<td align="left"><ul>
+<li>2.11.1-foss-2015b</li>
+<li>2.11.1-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>freetype</strong><br />
+<a href="http://freetype.org" class="uri">http://freetype.org</a></td>
+<td align="left">FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.</td>
+<td align="left"><ul>
+<li>2.5.3</li>
+<li>2.5.3-foss-2015b</li>
+<li>2.5.3-foss-2015g</li>
+<li>2.5.3-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>gettext</strong><br />
+<a href="http://www.gnu.org/software/gettext/" class="uri">http://www.gnu.org/software/gettext/</a></td>
+<td align="left">GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation</td>
+<td align="left"><ul>
+<li>0.19.2</li>
+<li>0.19.2-GNU-5.1.0-2.25</li>
+<li>0.19.2-foss-2015b</li>
+<li>0.19.2-foss-2015g</li>
+<li>0.19.2-intel-2015b</li>
+<li>0.19.2-intel-2016.01</li>
+<li>0.19.6-foss-2015g</li>
+<li>0.19.6-intel-2016.01</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>grace</strong><br />
+<a href="http://freecode.com/projects/grace" class="uri">http://freecode.com/projects/grace</a></td>
+<td align="left">Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.</td>
+<td align="left"><ul>
+<li>5.1.25-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>inputproto</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">X.org InputProto protocol headers.</td>
+<td align="left"><ul>
+<li>2.3</li>
+<li>2.3-foss-2015g</li>
+<li>2.3-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>kbproto</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">X.org KBProto protocol headers.</td>
+<td align="left"><ul>
+<li>1.0.6</li>
+<li>1.0.6-foss-2015g</li>
+<li>1.0.6-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>libGLU</strong><br />
+<a href="ftp://ftp.freedesktop.org/pub/mesa/glu/" class="uri">ftp://ftp.freedesktop.org/pub/mesa/glu/</a></td>
+<td align="left">The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.</td>
+<td align="left"><ul>
+<li>9.0.0-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>libICE</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">X Inter-Client Exchange library for freedesktop.org</td>
+<td align="left"><ul>
+<li>1.0.9</li>
+<li>1.0.9-foss-2015g</li>
+<li>1.0.9-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>libX11</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">X11 client-side library</td>
+<td align="left"><ul>
+<li>1.6.2-Python-2.7.8</li>
+<li>1.6.2-Python-2.7.9</li>
+<li>1.6.2-foss-2015g-Python-2.7.9</li>
+<li>1.6.2-intel-2015b-Python-2.7.9</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>libXau</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display.</td>
+<td align="left"><ul>
+<li>1.0.8</li>
+<li>1.0.8-foss-2015g</li>
+<li>1.0.8-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>libXdamage</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">X Damage extension library</td>
+<td align="left"><ul>
+<li>1.1.4-foss-2015g-Python-2.7.9</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>libXdmcp</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is useful for allowing clients to interact with the X Display Manager.</td>
+<td align="left"><ul>
+<li>1.1.2</li>
+<li>1.1.2-foss-2015g</li>
+<li>1.1.2-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>libXext</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">Common X Extensions library</td>
+<td align="left"><ul>
+<li>1.3.2-Python-2.7.8</li>
+<li>1.3.3</li>
+<li>1.3.3-foss-2015g</li>
+<li>1.3.3-foss-2015g-Python-2.7.9</li>
+<li>1.3.3-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>libXfixes</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">X Fixes extension library</td>
+<td align="left"><ul>
+<li>5.0.1-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>libXfont</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">X font libary</td>
+<td align="left"><ul>
+<li>1.5.1-foss-2015g-Python-2.7.9</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>libXft</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">X11 client-side library</td>
+<td align="left"><ul>
+<li>2.3.2-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>libXinerama</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">Xinerama multiple monitor library</td>
+<td align="left"><ul>
+<li>1.1.3-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>libXrender</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">X11 client-side library</td>
+<td align="left"><ul>
+<li>0.9.8-intel-2015b</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>libXt</strong><br />
+<a href="http://www.freedesktop.org/wiki/Software/xlibs" class="uri">http://www.freedesktop.org/wiki/Software/xlibs</a></td>
+<td align="left">libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).</td>
+<td align="left"><ul>
+<li>1.1.4-foss-2015g-libX11-1.6.2</li>
+<li>1.1.4-intel-2015b-libX11-1.6.2</li>
+<li>1.1.4-libX11-1.6.2</li>
+<li>1.1.5-foss-2015g</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>motif</strong><br />
+<a href="http://motif.ics.com/" class="uri">http://motif.ics.com/</a></td>
+<td align="left">Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix.</td>
+<td align="left"><ul>
+<li>2.3.4-foss-2015g-libX11-1.6.2</li>
+<li>2.3.4-intel-2015b-libX11-1.6.2</li>
+</ul></td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>p4vasp</strong><br />
+<a href="http://www.p4vasp.at" class="uri">http://www.p4vasp.at</a></td>
+<td align="left">p4vasp is a visualization suite for the Vienna Ab-initio Simulation Package (VASP). It contains an extensible GUI framework, that can be used to view material structure, density of states, band-structure and more.</td>
+<td align="left"><ul>
+<li>0.3.29-GNU-4.9.3-2.25</li>
+</ul></td>
+</tr>
+<tr class="even">
+<td align="left"><strong>pixman</strong><br />
+<a href="http://www.pixman.org/" class="uri">http://www.pixman.org/</a></td>
+<td align="left">Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.</td>
+<td align="left"><ul>
+<li>0.32.6-foss-2015b</li>
+<li>0.32.6-intel-2015b</li>
+</ul></td>
+</tr>
+</tbody>
+</table>
diff --git a/salomon/network-1.html b/docs.it4i.cz/salomon/network-1.html
old mode 100755
new mode 100644
similarity index 69%
rename from salomon/network-1.html
rename to docs.it4i.cz/salomon/network-1.html
index 9d6d56f773d172cea3e254f6b7e9c0a974f29d28..51e687c0584617f047d51b83295ea4b70642878e
--- a/salomon/network-1.html
+++ b/docs.it4i.cz/salomon/network-1.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/network-1 by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:45 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/network-1/network" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Network — IT4I Docs</title>
- <link rel="canonical" href="network-1.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/network-1" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="network-1.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/network-1#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="network-1.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/network-1#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../index.html">
- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -232,8 +229,8 @@
<div id="parent-fieldname-text-40fbce9e3def4e3882ed5a3627aeb8a1" class="">
<p>All compute and login nodes of Salomon are interconnected by 7D Enhanced hypercube <a class="external-link" href="http://en.wikipedia.org/wiki/InfiniBand" target="_self" title="">Infiniband</a> network and by Gigabit <a class="external-link" href="http://en.wikipedia.org/wiki/Ethernet" target="_self" title="">Ethernet</a> network. Only <a class="external-link" href="http://en.wikipedia.org/wiki/InfiniBand" target="_self" title="">Infiniband</a> network may be used to transfer user data.</p>
<h2 class=" ">Infiniband Network</h2>
-<p>All compute and login nodes of Salomon are interconnected by 7D Enhanced hypercube <a class="external-link" href="http://en.wikipedia.org/wiki/InfiniBand" target="_self" title="">Infiniband</a> network (56 Gbps). The network topology is a <a target="_self" title="" class="internal-link" href="network-1/7d-enhanced-hypercube.html">7D Enhanced hypercube</a>.</p>
-<p>Read more about schematic representation of the Salomon cluster <a target="_self" title="" class="internal-link" href="network-1/ib-single-plane-topology.html">IB single-plain topology</a> (<a target="_self" title="" class="internal-link" href="network-1/7d-enhanced-hypercube.html">hypercube dimension</a> 0).<a title="" class="state-missing-value contenttype-file" href="network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf/view.html"><span></span></a> </p>
+<p>All compute and login nodes of Salomon are interconnected by 7D Enhanced hypercube <a class="external-link" href="http://en.wikipedia.org/wiki/InfiniBand" target="_self" title="">Infiniband</a> network (56 Gbps). The network topology is a <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube">7D Enhanced hypercube</a>.</p>
+<p>Read more about schematic representation of the Salomon cluster <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology">IB single-plain topology</a> (<a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube">hypercube dimension</a> 0).<a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/network-1/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf/view"><span></span></a> </p>
<ul class="navTree navTreeLevel2">
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@@ -322,7 +319,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -338,7 +335,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -354,7 +351,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -370,7 +367,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -386,7 +383,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -402,7 +399,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -418,7 +415,7 @@
- <a title="" class="state-published contenttype-document" href="environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -434,7 +431,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -450,7 +447,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -466,7 +463,7 @@
- <a title="" class="state-published contenttype-document" href="compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -482,7 +479,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -498,7 +495,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="network-1.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -514,7 +511,7 @@
- <a title="" class="state-published contenttype-document" href="network-1/7d-enhanced-hypercube.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube">
<span>7D Enhanced Hypercube</span>
</a>
@@ -530,7 +527,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="network-1/ib-single-plane-topology.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology">
<span>IB single-plane topology</span>
</a>
@@ -555,10 +552,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -574,7 +571,7 @@
- <a title="" class="state-published contenttype-document" href="prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -599,7 +596,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -615,7 +612,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -631,7 +628,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -647,7 +644,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -686,14 +683,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -715,12 +712,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -736,7 +733,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/network-1 by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:46 GMT -->
</html>
diff --git a/docs.it4i.cz/salomon/network-1.md b/docs.it4i.cz/salomon/network-1.md
new file mode 100644
index 0000000000000000000000000000000000000000..51e23f72489530d4d3eb5683323a9138453c3b05
--- /dev/null
+++ b/docs.it4i.cz/salomon/network-1.md
@@ -0,0 +1,61 @@
+Network
+=======
+
+All compute and login nodes of Salomon are interconnected by 7D Enhanced
+hypercube
+[Infiniband](http://en.wikipedia.org/wiki/InfiniBand)
+network and by Gigabit
+[Ethernet](http://en.wikipedia.org/wiki/Ethernet)
+network. Only
+[Infiniband](http://en.wikipedia.org/wiki/InfiniBand)
+network may be used to transfer user data.
+Infiniband Network
+------------------
+All compute and login nodes of Salomon are interconnected by 7D Enhanced
+hypercube
+[Infiniband](http://en.wikipedia.org/wiki/InfiniBand)
+network (56 Gbps). The network topology is a [7D Enhanced
+hypercube](https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube).
+Read more about schematic representation of the Salomon cluster [IB
+single-plain
+topology](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology)
+([hypercube
+dimension](https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube)
+0).[<span></span>](https://docs.it4i.cz/salomon/network-1/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf/view){.state-missing-value
+.contenttype-file}
+- -
+The compute nodes may be accessed via the Infiniband network using ib0
+network interface, in address range 10.17.0.0 (mask 255.255.224.0). The
+MPI may be used to establish native Infiniband connection among the
+nodes.
+The network provides **2170MB/s** transfer rates via the TCP connection
+(single stream) and up to **3600MB/s** via native Infiniband protocol.
+Â
+Example
+-------
+``` {.prettyprint .lang-sh}
+$ qsub -q qexp -l select=4:ncpus=16 -N Name0 ./myjob
+$ qstat -n -u username
+ Req'd Req'd Elap
+Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
+--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
+15209.isrv5 username qexp Name0 5530 4 96 -- 01:00 R 00:00
+ r4i1n0/0*24+r4i1n1/0*24+r4i1n2/0*24+r4i1n3/0*24
+```
+In this example, we access the node r4i1n0 by Infiniband network via the
+ib0 interface.
+``` {.prettyprint .lang-sh}
+$ ssh 10.17.35.19
+```
+In this example, we <span style="text-alignstart; floatnone; ">get
+information of the Infiniband network.</span>
+``` {.prettyprint .lang-sh}
+$ ifconfig
+....
+inet addr:10.17.35.19....
+....
+$ ip addr show ib0
+....
+inet 10.17.35.19....
+....
+```
diff --git a/salomon/network-1/7D_Enhanced_hypercube.png.txt b/docs.it4i.cz/salomon/network-1/7D_Enhanced_hypercube.png
old mode 100755
new mode 100644
similarity index 100%
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diff --git a/salomon/network-1/7d-enhanced-hypercube.html b/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.html
old mode 100755
new mode 100644
similarity index 65%
rename from salomon/network-1/7d-enhanced-hypercube.html
rename to docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.html
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<title>7D Enhanced Hypercube — IT4I Docs</title>
- <link rel="canonical" href="7d-enhanced-hypercube.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
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<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="7d-enhanced-hypercube.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="7d-enhanced-hypercube.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
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</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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</div>
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- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
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@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
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@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../network-1.html">Network</a>
+ <a href="https://docs.it4i.cz/salomon/network-1">Network</a>
<span class="breadcrumbSeparator">
/
@@ -236,7 +233,7 @@
<div id="parent-fieldname-text-40990c6e5349434683ef01f4a0dccbd1" class="">
- <p class=" "><a target="_self" title="" class="internal-link" href="../resource-allocation-and-job-execution/job-submission-and-execution.html">More about Job submission - Placement by IB switch / Hypercube dimension.</a></p>
+ <p class=" "><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">More about Job submission - Placement by IB switch / Hypercube dimension.</a></p>
<p>Nodes may be selected via the PBS resource attribute ehc_[1-7]d .</p>
<table class="listing">
<tbody>
@@ -271,9 +268,9 @@
</tr>
</tbody>
</table>
-<p><a target="_self" title="" class="internal-link" href="ib-single-plane-topology.html">Schematic representation of the Salomon cluster IB single-plain topology represents <span class="internal-link">hypercube dimension</span> 0</a>.</p>
+<p><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology">Schematic representation of the Salomon cluster IB single-plain topology represents <span class="internal-link">hypercube dimension</span> 0</a>.</p>
<h3 class=" ">7D Enhanced Hypercube</h3>
-<p><a target="_blank" title="" class="internal-link" href="7D_Enhanced_hypercube.png"><img title="7D_Enhanced_hypercube.png" class="image-inline" alt="7D_Enhanced_hypercube.png" src="7D_Enhanced_hypercube.png/%40%40images/03693a91-beec-4d04-bf11-7d89c20420a6.png" /></a></p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/network-1/7D_Enhanced_hypercube.png"><img alt="7D_Enhanced_hypercube.png" class="image-inline" title="7D_Enhanced_hypercube.png" src="https://docs.it4i.cz/salomon/network-1/7D_Enhanced_hypercube.png/@@images/03693a91-beec-4d04-bf11-7d89c20420a6.png" /></a></p>
<p>Â </p>
<table class="plain">
<tbody>
@@ -295,7 +292,7 @@
</tbody>
</table>
<h3 class=" ">Â IB Topology</h3>
-<p>Â <a target="_blank" title="" class="internal-link" href="Salomon_IB_topology.png"><img title=" Salomon IB topology" class="image-inline" alt=" Salomon IB topology" src="Salomon_IB_topology.png/%40%40images/93b8536b-60de-438d-ac4d-a33a843c4eb2.png" /></a></p>
+<p>Â <a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/network-1/Salomon_IB_topology.png"><img alt=" Salomon IB topology" class="image-inline" title=" Salomon IB topology" src="https://docs.it4i.cz/salomon/network-1/Salomon_IB_topology.png/@@images/93b8536b-60de-438d-ac4d-a33a843c4eb2.png" /></a></p>
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<dt class="portletHeader hiddenStructure">
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<span>Get Started with IT4Innovations</span>
</a>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../salomon.html">
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<span>Salomon Cluster Documentation</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -467,7 +464,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
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- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -499,7 +496,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -515,7 +512,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -531,7 +528,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -547,7 +544,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../network-1.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -563,7 +560,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="7d-enhanced-hypercube.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube">
<span>7D Enhanced Hypercube</span>
</a>
@@ -579,7 +576,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="ib-single-plane-topology.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology">
<span>IB single-plane topology</span>
</a>
@@ -604,10 +601,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -623,7 +620,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -664,7 +661,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -680,7 +677,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -696,7 +693,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
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})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -764,12 +761,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -785,7 +782,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
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</html>
diff --git a/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.md b/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.md
new file mode 100644
index 0000000000000000000000000000000000000000..bdd229b2043d711e9af22ca5a8b34b004806d60b
--- /dev/null
+++ b/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.md
@@ -0,0 +1,28 @@
+7D Enhanced Hypercube
+=====================
+[More about Job submission - Placement by IB switch / Hypercube
+dimension.](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution)
+Nodes may be selected via the PBS resource attribute ehc_[1-7]d .
+ Hypercube dimension <span class="pun">node_group_key</span>
+ --------------------- --------------------
+ 1D ehc_1d
+ 2D ehc_2d
+ 3D ehc_3d
+ 4D ehc_4d
+ 5D ehc_5d
+ 6D ehc_6d
+ 7D ehc_7d
+[Schematic representation of the Salomon cluster IB single-plain
+topology represents <span class="internal-link">hypercube
+dimension</span>
+0](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology).
+### 7D Enhanced Hypercube {#d-enhanced-hypercube}
+[](https://docs.it4i.cz/salomon/network-1/7D_Enhanced_hypercube.png)
+Â
+ Node type Count Short name Long name Rack
+ --------------- ------- ------------------ --- -------
+ M-Cell compute nodes w/o accelerator 576 cns1 -cns576 r1i0n0 - r4i7n17 1-4
+ compute nodes MIC accelerated 432 cns577 - cns1008 r21u01n577 - r37u31n1008 21-38
+### Â IB Topology
+Â [](https://docs.it4i.cz/salomon/network-1/Salomon_IB_topology.png)
diff --git a/salomon/network-1/ib-single-plane-topology/IB single-plane topology - Accelerated nodes.pdf/view.html b/docs.it4i.cz/salomon/network-1/IB single-plane topology - Accelerated nodes.pdf/view.html
old mode 100755
new mode 100644
similarity index 64%
rename from salomon/network-1/ib-single-plane-topology/IB single-plane topology - Accelerated nodes.pdf/view.html
rename to docs.it4i.cz/salomon/network-1/IB single-plane topology - Accelerated nodes.pdf/view.html
index caaa0140648bd2408ba6c2516dfa3e91fe3c6764..3d333e4609724070dfbbbfac38408476f4228f9f
--- a/salomon/network-1/ib-single-plane-topology/IB single-plane topology - Accelerated nodes.pdf/view.html
+++ b/docs.it4i.cz/salomon/network-1/IB single-plane topology - Accelerated nodes.pdf/view.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
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</ul>
<h3><strong>IB single-plane topology - ICEX Mcell</strong></h3>
<p>Each colour in each physical IRU represents one dual-switch ASIC switch.</p>
-<p><a target="_self" title="" class="internal-link" href="ib-single-plane-topology/IB%20single-plane%20topology%20-%20ICEX%20Mcell.pdf"><img title="Mcell" class="image-inline" alt="Mcell" src="ib-single-plane-topology/IB%20single-plane%20topology%20-%20ICEX%20Mcell-small.png" /></a></p>
+<p><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20ICEX%20Mcell.pdf"><img alt="Mcell" class="image-inline" title="Mcell" src="https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IBsingleplanetopologyICEXMcellsmall.png" /></a></p>
<p>Â </p>
<h3>IB single-plane topology - Accelerated nodes</h3>
-<p>Each of the 3 inter-connected D racks are equivalent to one half of Mcell rack. 18x D rack with MIC accelerated nodes [r21-r38] are equivalent to 3 Mcell racks as shown in a diagram <a target="_self" title="" class="internal-link" href="7d-enhanced-hypercube.html">7D Enhanced Hypercube</a>.</p>
-<p>As shown in a diagram <a target="_self" title="" class="internal-link" href="Salomon_IB_topology.png">IB Topology</a>:</p>
+<p>Each of the 3 inter-connected D racks are equivalent to one half of Mcell rack. 18x D rack with MIC accelerated nodes [r21-r38] are equivalent to 3 Mcell racks as shown in a diagram <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube">7D Enhanced Hypercube</a>.</p>
+<p>As shown in a diagram <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1/Salomon_IB_topology.png">IB Topology</a>:</p>
<ul>
<li>Racks 21, 22, 23, 24, 25, 26 are equivalent to one Mcell rack.</li>
<li>Racks 27, 28, 29, 30, 31, 32 are equivalent to one Mcell rack.</li>
<li>Racks 33, 34, 35, 36, 37, 38 are equivalent to one Mcell rack.</li>
</ul>
-<p><a target="_self" title="" class="internal-link" href="ib-single-plane-topology/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf"><img title="Accelerated nodes" class="image-inline" alt="Accelerated nodes" src="ib-single-plane-topology/IB%20single-plane%20topology%20-%20Accelerated%20nodes-small.png" /></a></p>
+<p><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf"><img alt="Accelerated nodes" class="image-inline" title="Accelerated nodes" src="https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IBsingleplanetopologyAcceleratednodessmall.png" /></a></p>
<p>Â </p>
</div>
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<span>Salomon Cluster Documentation</span>
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<span>Hardware Overview</span>
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<span>Accessing the Cluster</span>
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<span>Environment and Modules</span>
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- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
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<span>List of Available Modules</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage.html">
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<span>Storage</span>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../network-1.html">
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<span>Network</span>
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<span>7D Enhanced Hypercube</span>
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<span>IB single-plane topology</span>
</a>
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- <img width="16" height="16" src="../../pdf.png" alt="Soubor PDF document" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20ICEX%20Mcell.pdf/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/pdf.png" alt="Soubor PDF document" />
<span>IB single-plane topology - ICEX Mcell.pdf</span>
</a>
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+ <img width="16" height="16" src="https://docs.it4i.cz/pdf.png" alt="Soubor PDF document" />
<span>IB single-plane topology - Accelerated nodes.pdf</span>
</a>
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- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
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<span>Software</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
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<span>Anselm Cluster Documentation</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
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- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
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- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
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+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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</html>
diff --git a/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.md b/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.md
new file mode 100644
index 0000000000000000000000000000000000000000..dcd472760ef118f528d79f5ad668e2905bcb4e92
--- /dev/null
+++ b/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.md
@@ -0,0 +1,32 @@
+IB single-plane topology
+========================
+
+A complete M-Cell assembly consists of four compute racks. Each rack
+contains 4x physical IRUs - Independent rack units. Using one dual
+socket node per one blade slot leads to 8 logical IRUs. Each rack
+contains 4x2 SGI ICE X IB Premium Blades.
+The SGI ICE X IB Premium Blade provides the first level of
+interconnection via dual 36-port Mellanox FDR InfiniBand ASIC switch
+with connections as follows:
+- 9 ports from each switch chip connect to the unified backplane, to
+ connect the 18 compute node slots
+- 3 ports on each chip provide connectivity between the chips
+- 24 ports from each switch chip connect to the external bulkhead, for
+ a total of 48
+### **IB single-plane topology - ICEX Mcell**
+Each colour in each physical IRU represents one dual-switch ASIC switch.
+[](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20ICEX%20Mcell.pdf)
+Â
+### IB single-plane topology - Accelerated nodes
+Each of the 3 inter-connected D racks are equivalent to one half of
+Mcell rack. 18x D rack with MIC accelerated nodes [r21-r38] are
+equivalent to 3 Mcell racks as shown in a diagram [7D Enhanced
+Hypercube](https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube).
+As shown in a diagram [IB
+Topology](https://docs.it4i.cz/salomon/network-1/Salomon_IB_topology.png):
+- Racks 21, 22, 23, 24, 25, 26 are equivalent to one Mcell rack.
+- Racks 27, 28, 29, 30, 31, 32 are equivalent to one Mcell rack.
+- Racks 33, 34, 35, 36, 37, 38 are equivalent to one Mcell rack.
+[](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf)
+Â
diff --git a/salomon/network-1/ib-single-plane-topology/IB single-plane topology - Accelerated nodes.pdf/at_download/IB single-plane topology - Accelerated nodes.pdf b/docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB single-plane topology - Accelerated nodes.pdf
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+ <p>A complete M-Cell assembly consists of four compute racks. Each rack contains 4x physical IRUs - Independent rack units. Using one dual socket node per one blade slot leads to 8 logical IRUs. Each rack contains 4x2 SGI ICE X IB Premium Blades.</p>
+<p>The SGI ICE X IB Premium Blade provides the first level of interconnection via dual 36-port Mellanox FDR InfiniBand ASIC switch with connections as follows:</p>
+<ul>
+<li>9 ports from each switch chip connect to the unified backplane, to connect the 18 compute node slots</li>
+<li>3 ports on each chip provide connectivity between the chips</li>
+<li>24 ports from each switch chip connect to the external bulkhead, for a total of 48</li>
+</ul>
+<h3><strong>IB single-plane topology - ICEX Mcell</strong></h3>
+<p>Each colour in each physical IRU represents one dual-switch ASIC switch.</p>
+<p><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20ICEX%20Mcell.pdf"><img alt="Mcell" class="image-inline" title="Mcell" src="https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IBsingleplanetopologyICEXMcellsmall.png" /></a></p>
+<p>Â </p>
+<h3>IB single-plane topology - Accelerated nodes</h3>
+<p>Each of the 3 inter-connected D racks are equivalent to one half of Mcell rack. 18x D rack with MIC accelerated nodes [r21-r38] are equivalent to 3 Mcell racks as shown in a diagram <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube">7D Enhanced Hypercube</a>.</p>
+<p>As shown in a diagram <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1/Salomon_IB_topology.png">IB Topology</a>:</p>
+<ul>
+<li>Racks 21, 22, 23, 24, 25, 26 are equivalent to one Mcell rack.</li>
+<li>Racks 27, 28, 29, 30, 31, 32 are equivalent to one Mcell rack.</li>
+<li>Racks 33, 34, 35, 36, 37, 38 are equivalent to one Mcell rack.</li>
+</ul>
+<p><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf"><img alt="Accelerated nodes" class="image-inline" title="Accelerated nodes" src="https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IBsingleplanetopologyAcceleratednodessmall.png" /></a></p>
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diff --git a/docs.it4i.cz/salomon/network-1/ib-single-plane-topology/schematic-representation-of-the-salomon-cluster-ib-single-plain-topology-hypercube-dimension-0.md b/docs.it4i.cz/salomon/network-1/ib-single-plane-topology/schematic-representation-of-the-salomon-cluster-ib-single-plain-topology-hypercube-dimension-0.md
new file mode 100644
index 0000000000000000000000000000000000000000..dcd472760ef118f528d79f5ad668e2905bcb4e92
--- /dev/null
+++ b/docs.it4i.cz/salomon/network-1/ib-single-plane-topology/schematic-representation-of-the-salomon-cluster-ib-single-plain-topology-hypercube-dimension-0.md
@@ -0,0 +1,32 @@
+IB single-plane topology
+========================
+
+A complete M-Cell assembly consists of four compute racks. Each rack
+contains 4x physical IRUs - Independent rack units. Using one dual
+socket node per one blade slot leads to 8 logical IRUs. Each rack
+contains 4x2 SGI ICE X IB Premium Blades.
+The SGI ICE X IB Premium Blade provides the first level of
+interconnection via dual 36-port Mellanox FDR InfiniBand ASIC switch
+with connections as follows:
+- 9 ports from each switch chip connect to the unified backplane, to
+ connect the 18 compute node slots
+- 3 ports on each chip provide connectivity between the chips
+- 24 ports from each switch chip connect to the external bulkhead, for
+ a total of 48
+### **IB single-plane topology - ICEX Mcell**
+Each colour in each physical IRU represents one dual-switch ASIC switch.
+[](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20ICEX%20Mcell.pdf)
+Â
+### IB single-plane topology - Accelerated nodes
+Each of the 3 inter-connected D racks are equivalent to one half of
+Mcell rack. 18x D rack with MIC accelerated nodes [r21-r38] are
+equivalent to 3 Mcell racks as shown in a diagram [7D Enhanced
+Hypercube](https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube).
+As shown in a diagram [IB
+Topology](https://docs.it4i.cz/salomon/network-1/Salomon_IB_topology.png):
+- Racks 21, 22, 23, 24, 25, 26 are equivalent to one Mcell rack.
+- Racks 27, 28, 29, 30, 31, 32 are equivalent to one Mcell rack.
+- Racks 33, 34, 35, 36, 37, 38 are equivalent to one Mcell rack.
+[](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf)
+Â
diff --git a/docs.it4i.cz/salomon/network-1/network.html b/docs.it4i.cz/salomon/network-1/network.html
new file mode 100644
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+ <p>All compute and login nodes of Salomon are interconnected by 7D Enhanced hypercube <a class="external-link" href="http://en.wikipedia.org/wiki/InfiniBand" target="_self" title="">Infiniband</a> network and by Gigabit <a class="external-link" href="http://en.wikipedia.org/wiki/Ethernet" target="_self" title="">Ethernet</a> network. Only <a class="external-link" href="http://en.wikipedia.org/wiki/InfiniBand" target="_self" title="">Infiniband</a> network may be used to transfer user data.</p>
+<h2 class=" ">Infiniband Network</h2>
+<p>All compute and login nodes of Salomon are interconnected by 7D Enhanced hypercube <a class="external-link" href="http://en.wikipedia.org/wiki/InfiniBand" target="_self" title="">Infiniband</a> network (56 Gbps). The network topology is a <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube">7D Enhanced hypercube</a>.</p>
+<p>Read more about schematic representation of the Salomon cluster <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology">IB single-plain topology</a> (<a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube">hypercube dimension</a> 0).<a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/network-1/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf/view"><span></span></a> </p>
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+<p>The compute nodes may be accessed via the Infiniband network using ib0 network interface, in address range 10.17.0.0 (mask 255.255.224.0). The MPI may be used to establish native Infiniband connection among the nodes.</p>
+<p class="hiddenForView">The network provides <strong>2170MB/s</strong> transfer rates via the TCP connection (single stream) and up to <strong>3600MB/s</strong> via native Infiniband protocol.</p>
+<p>Â </p>
+<h2 class=" ">Example</h2>
+<pre class="prettyprint lang-sh">$ qsub -q qexp -l select=4:ncpus=16 -N Name0 ./myjob<br />$ qstat -n -u username<br /> Req'd Req'd Elap<br />Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time<br />--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----<br />15209.isrv5 username qexp Name0 5530 4 96 -- 01:00 R 00:00<br /> r4i1n0/0*24+r4i1n1/0*24+r4i1n2/0*24+r4i1n3/0*24</pre>
+<p class=" ">In this example, we access the node r4i1n0 by Infiniband network via the ib0 interface.</p>
+<pre class="prettyprint lang-sh">$ ssh 10.17.35.19</pre>
+<p class=" ">In this example, we <span style="text-align: start; float: none; ">get information of the Infiniband network.</span></p>
+<pre class="prettyprint lang-sh">$ ifconfig<br />....<br />inet addr:10.17.35.19....<br />....<br /><br />$ ip addr show ib0<br /><br />....<br />inet 10.17.35.19....<br />....</pre>
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+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
+ <a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
+ <a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
+ </p>
+ <!-- nagios_check_http_expect_string -->
+</div>
+
+ </div>
+ </div>
+
+ <!-- TODO -->
+ <!-- nagios_check_http_expect_string -->
+ <!-- TODO -->
+
+</div>
+</body>
+</html>
+
diff --git a/docs.it4i.cz/salomon/network-1/network.md b/docs.it4i.cz/salomon/network-1/network.md
new file mode 100644
index 0000000000000000000000000000000000000000..51e23f72489530d4d3eb5683323a9138453c3b05
--- /dev/null
+++ b/docs.it4i.cz/salomon/network-1/network.md
@@ -0,0 +1,61 @@
+Network
+=======
+
+All compute and login nodes of Salomon are interconnected by 7D Enhanced
+hypercube
+[Infiniband](http://en.wikipedia.org/wiki/InfiniBand)
+network and by Gigabit
+[Ethernet](http://en.wikipedia.org/wiki/Ethernet)
+network. Only
+[Infiniband](http://en.wikipedia.org/wiki/InfiniBand)
+network may be used to transfer user data.
+Infiniband Network
+------------------
+All compute and login nodes of Salomon are interconnected by 7D Enhanced
+hypercube
+[Infiniband](http://en.wikipedia.org/wiki/InfiniBand)
+network (56 Gbps). The network topology is a [7D Enhanced
+hypercube](https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube).
+Read more about schematic representation of the Salomon cluster [IB
+single-plain
+topology](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology)
+([hypercube
+dimension](https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube)
+0).[<span></span>](https://docs.it4i.cz/salomon/network-1/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf/view){.state-missing-value
+.contenttype-file}
+- -
+The compute nodes may be accessed via the Infiniband network using ib0
+network interface, in address range 10.17.0.0 (mask 255.255.224.0). The
+MPI may be used to establish native Infiniband connection among the
+nodes.
+The network provides **2170MB/s** transfer rates via the TCP connection
+(single stream) and up to **3600MB/s** via native Infiniband protocol.
+Â
+Example
+-------
+``` {.prettyprint .lang-sh}
+$ qsub -q qexp -l select=4:ncpus=16 -N Name0 ./myjob
+$ qstat -n -u username
+ Req'd Req'd Elap
+Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
+--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
+15209.isrv5 username qexp Name0 5530 4 96 -- 01:00 R 00:00
+ r4i1n0/0*24+r4i1n1/0*24+r4i1n2/0*24+r4i1n3/0*24
+```
+In this example, we access the node r4i1n0 by Infiniband network via the
+ib0 interface.
+``` {.prettyprint .lang-sh}
+$ ssh 10.17.35.19
+```
+In this example, we <span style="text-alignstart; floatnone; ">get
+information of the Infiniband network.</span>
+``` {.prettyprint .lang-sh}
+$ ifconfig
+....
+inet addr:10.17.35.19....
+....
+$ ip addr show ib0
+....
+inet 10.17.35.19....
+....
+```
diff --git a/salomon/prace.html b/docs.it4i.cz/salomon/prace.html
old mode 100755
new mode 100644
similarity index 77%
rename from salomon/prace.html
rename to docs.it4i.cz/salomon/prace.html
index e226224aff557982c894406127f6c80b4df907b5..dc86dbd117216088ec2c6c938c12fc26583171ff
--- a/salomon/prace.html
+++ b/docs.it4i.cz/salomon/prace.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/prace by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:46 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/prace" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
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- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>PRACE User Support — IT4I Docs</title>
- <link rel="canonical" href="prace.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/prace" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="prace.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/prace#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="prace.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/prace#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../index.html">
- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -231,14 +228,14 @@
<div id="parent-fieldname-text-d1fb69d45afe43cea052f14182ce60a6" class="">
<h2 class=" ">Intro</h2>
-<p>PRACE users coming to Salomon as to TIER-1 system offered through the DECI calls are in general treated as standard users and so most of the general documentation applies to them as well. This section shows the main differences for quicker orientation, but often uses references to the original documentation. PRACE users who don't undergo the full procedure (including signing the IT4I AuP on top of the PRACE AuP) will not have a password and thus access to some services intended for regular users. This can lower their comfort, but otherwise they should be able to use the TIER-1 system as intended. Please see the <a target="_self" title="" class="internal-link" href="../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html">Obtaining Login Credentials section</a>, if the same level of access is required.</p>
+<p>PRACE users coming to Salomon as to TIER-1 system offered through the DECI calls are in general treated as standard users and so most of the general documentation applies to them as well. This section shows the main differences for quicker orientation, but often uses references to the original documentation. PRACE users who don't undergo the full procedure (including signing the IT4I AuP on top of the PRACE AuP) will not have a password and thus access to some services intended for regular users. This can lower their comfort, but otherwise they should be able to use the TIER-1 system as intended. Please see the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials">Obtaining Login Credentials section</a>, if the same level of access is required.</p>
<p>All general <a class="external-link" href="http://www.prace-ri.eu/user-documentation/" target="_self" title="">PRACE User Documentation</a> should be read before continuing reading the local documentation here.</p>
<h2 class=" "><a name="help-and-support"></a><a name="PRACE_support"></a>Help and Support</h2>
<p>If you have any troubles, need information, request support or want to install additional software, please use <a class="external-link" href="http://www.prace-ri.eu/helpdesk-guide264/" target="_self" title="">PRACE Helpdesk</a>.</p>
-<p>Information about the local services are provided in the <a target="_self" title="" class="internal-link" href="introduction.html">introduction of general user documentation</a>. Please keep in mind, that standard PRACE accounts don't have a password to access the web interface of the local (IT4Innovations) request tracker and thus a new ticket should be created by sending an e-mail to support[at]it4i.cz.</p>
+<p>Information about the local services are provided in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/introduction">introduction of general user documentation</a>. Please keep in mind, that standard PRACE accounts don't have a password to access the web interface of the local (IT4Innovations) request tracker and thus a new ticket should be created by sending an e-mail to support[at]it4i.cz.</p>
<h2 class=" ">Obtaining Login Credentials</h2>
<p>In general PRACE users already have a PRACE account setup through their HOMESITE (institution from their country) as a result of rewarded PRACE project proposal. This includes signed PRACE AuP, generated and registered certificates, etc.</p>
-<p>If there's a special need a PRACE user can get a standard (local) account at IT4Innovations. To get an account on the Salomon cluster, the user needs to obtain the login credentials. The procedure is the same as for general users of the cluster, so please see the corresponding <a target="_self" title="" class="internal-link" href="../get-started-with-it4innovations/obtaining-login-credentials.html">section of the general documentation here</a>.</p>
+<p>If there's a special need a PRACE user can get a standard (local) account at IT4Innovations. To get an account on the Salomon cluster, the user needs to obtain the login credentials. The procedure is the same as for general users of the cluster, so please see the corresponding <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials">section of the general documentation here</a>.</p>
<h2 class=" ">Accessing the cluster</h2>
<h3 class=" ">Access with GSI-SSH</h3>
<p>For all PRACE users the method for interactive access (login) and data transfer based on grid services from Globus Toolkit (GSI SSH and GridFTP) is supported.</p>
@@ -347,13 +344,13 @@
<pre>$ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ salomon-prace.it4i.cz:_SALOMON_PATH_TO_YOUR_FILE_</pre>
<pre>$ gsiscp -P 2222 salomon-prace.it4i.cz:_SALOMON_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_ </pre>
<h3 class=" ">Access to X11 applications (VNC)</h3>
-<p>If the user needs to run X11 based graphical application and does not have a X11 server, the applications can be run using VNC service. If the user is using regular SSH based access, please see the <a target="_self" title="" class="internal-link" href="../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html">section in general documentation</a>.</p>
-<p>If the user uses GSI SSH based access, then the procedure is similar to the SSH based access (<a target="_self" title="" class="internal-link" href="../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html">look here</a>), only the port forwarding must be done using GSI SSH:</p>
+<p>If the user needs to run X11 based graphical application and does not have a X11 server, the applications can be run using VNC service. If the user is using regular SSH based access, please see the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">section in general documentation</a>.</p>
+<p>If the user uses GSI SSH based access, then the procedure is similar to the SSH based access (<a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">look here</a>), only the port forwarding must be done using GSI SSH:</p>
<pre class=" ">$ gsissh -p 2222 salomon.it4i.cz -L 5961:localhost:5961</pre>
<h3 class=" ">Access with SSH</h3>
-<p class=" ">After successful obtainment of login credentials for the local IT4Innovations account, the PRACE users can access the cluster as regular users using SSH. For more information please see the <a target="_self" title="" class="internal-link" href="accessing-the-cluster/shell-and-data-access/shell-and-data-access.html">section in general documentation</a>.</p>
+<p class=" ">After successful obtainment of login credentials for the local IT4Innovations account, the PRACE users can access the cluster as regular users using SSH. For more information please see the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access">section in general documentation</a>.</p>
<h2 class=" "><a name="file-transfers"></a>File transfers</h2>
-<p>PRACE users can use the same transfer mechanisms as regular users (if they've undergone the full registration procedure). For information about this, please see <a target="_self" title="" class="internal-link" href="accessing-the-cluster/shell-and-data-access/shell-and-data-access.html">the section in the general documentation</a>.</p>
+<p>PRACE users can use the same transfer mechanisms as regular users (if they've undergone the full registration procedure). For information about this, please see <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access">the section in the general documentation</a>.</p>
<p>Apart from the standard mechanisms, for PRACE users to transfer data to/from Salomon cluster, a GridFTP server running Globus Toolkit GridFTP service is available. The service is available from public Internet as well as from the internal PRACE network (accessible only from other PRACE partners).</p>
<p>There's one control server and three backend servers for striping and/or backup in case one of them would fail.</p>
<p><strong>Access from PRACE network:</strong></p>
@@ -442,7 +439,7 @@
</tr>
</tbody>
</table>
-<p class=" ">More information about the shared file systems is available <a target="_self" title="" class="internal-link" href="storage.html">here</a>.</p>
+<p class=" ">More information about the shared file systems is available <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/storage">here</a>.</p>
<p class=" ">Please note, that for PRACE users a "prace" directory is used also on the SCRATCH file system.</p>
<table class="listing" summary="PRACE SCRATCH space">
<tbody>
@@ -459,14 +456,14 @@
</table>
<h2 class=" ">Usage of the cluster</h2>
<p>There are some limitations for PRACE user when using the cluster. By default PRACE users aren't allowed to access special queues in the PBS Pro to have high priority or exclusive access to some special equipment like accelerated nodes and high memory (fat) nodes. There may be also restrictions obtaining a working license for the commercial software installed on the cluster, mostly because of the license agreement or because of insufficient amount of licenses.</p>
-<p>For production runs always use scratch file systems. The available file systems are described <a target="_self" title="" class="internal-link" href="storage/storage.html">here</a>.</p>
+<p>For production runs always use scratch file systems. The available file systems are described <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/storage/storage">here</a>.</p>
<h3 class=" ">Software, Modules and PRACE Common Production Environment</h3>
-<p>All system wide installed software on the cluster is made available to the users via the modules. The information about the environment and modules usage is in this <a target="_self" title="" class="internal-link" href="environment-and-modules.html">section of general documentation</a>.</p>
+<p>All system wide installed software on the cluster is made available to the users via the modules. The information about the environment and modules usage is in this <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/environment-and-modules">section of general documentation</a>.</p>
<p>PRACE users can use the "prace" module to use the <a class="external-link" href="http://www.prace-ri.eu/PRACE-common-production" target="_self" title="">PRACE Common Production Environment</a>.</p>
<pre class=" ">$ module load prace</pre>
<p>Â </p>
<h3 class=" ">Resource Allocation and Job Execution</h3>
-<p>General information about the resource allocation, job queuing and job execution is in this <a target="_self" title="" class="internal-link" href="resource-allocation-and-job-execution/introduction.html">section of general documentation</a>.</p>
+<p>General information about the resource allocation, job queuing and job execution is in this <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction">section of general documentation</a>.</p>
<p>For PRACE users, the default production run queue is "qprace". PRACE users can also use two other queues "qexp" and "qfree".</p>
<table class="listing">
<tbody>
@@ -502,7 +499,7 @@
</table>
<p class=" "><strong>qprace</strong>, the PRACE Production queue<strong></strong>: This queue is intended for normal production runs. It is required that active project with nonzero remaining resources is specified to enter the qprace. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qprace is 48 hours. If the job needs longer time, it must use checkpoint/restart functionality.</p>
<h3 class=" ">Accounting & Quota</h3>
-<p>The resources that are currently subject to accounting are the core hours. The core hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. See <a target="_self" title="" class="internal-link" href="resource-allocation-and-job-execution/resources-allocation-policy.html">example in the general documentation</a>.</p>
+<p>The resources that are currently subject to accounting are the core hours. The core hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. See <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy">example in the general documentation</a>.</p>
<p>PRACE users should check their project accounting using the <a class="external-link" href="http://www.prace-ri.eu/accounting-report-tool/" target="_self" title="">PRACE Accounting Tool (DART)</a>.</p>
<p>Users who have undergone the full local registration procedure (including signing the IT4Innovations Acceptable Use Policy) and who have received local password may check at any time, how many core-hours have been consumed by themselves and their projects using the command "it4ifree". Please note that you need to know your user password to use the command and that the displayed core hours are "system core hours" which differ from PRACE "standardized core hours".</p>
<p class="callout">The <strong>it4ifree</strong> command is a part of it4i.portal.clients package, located here:<br /><a class="external-link" href="https://pypi.python.org/pypi/it4i.portal.clients" target="_self" title="">https://pypi.python.org/pypi/it4i.portal.clients</a></p>
@@ -588,7 +585,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -604,7 +601,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -620,7 +617,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -636,7 +633,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -652,7 +649,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -668,7 +665,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -684,7 +681,7 @@
- <a title="" class="state-published contenttype-document" href="environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -700,7 +697,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -716,7 +713,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -732,7 +729,7 @@
- <a title="" class="state-published contenttype-document" href="compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -748,7 +745,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -764,7 +761,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -780,10 +777,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -799,7 +796,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="prace.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -824,7 +821,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -840,7 +837,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -856,7 +853,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -872,7 +869,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -911,14 +908,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -940,12 +937,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -961,7 +958,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/prace by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:48 GMT -->
</html>
diff --git a/salomon/prace.md b/docs.it4i.cz/salomon/prace.md
similarity index 65%
rename from salomon/prace.md
rename to docs.it4i.cz/salomon/prace.md
index d595d24e2a2870208e13fcc19f1f68eb303cd668..f02965f8a44160a665567d0735818a719bba2b33 100644
--- a/salomon/prace.md
+++ b/docs.it4i.cz/salomon/prace.md
@@ -1,3 +1,7 @@
+PRACE User Support
+==================
+
+Intro
-----
PRACE users coming to Salomon as to TIER-1 system offered through the
DECI calls are in general treated as standard users and so most of the
@@ -9,24 +13,25 @@ not have a password and thus access to some services intended for
regular users. This can lower their comfort, but otherwise they should
be able to use the TIER-1 system as intended. Please see the [Obtaining
Login Credentials
-section](../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html),
+section](https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials),
if the same level of access is required.
All general [PRACE User
-Documentation](http//www.prace-ri.eu/user-documentation/)
+Documentation](http://www.prace-ri.eu/user-documentation/)
should be read before continuing reading the local documentation here.
[]()[]()Help and Support
-------------------------
+-
If you have any troubles, need information, request support or want to
install additional software, please use [PRACE
-Helpdesk](http//www.prace-ri.eu/helpdesk-guide264/).
+Helpdesk](http://www.prace-ri.eu/helpdesk-guide264/).
Information about the local services are provided in the [introduction
-of general user documentation](introduction.html).
+of general user
+documentation](https://docs.it4i.cz/salomon/introduction).
Please keep in mind, that standard PRACE accounts don't have a password
to access the web interface of the local (IT4Innovations) request
tracker and thus a new ticket should be created by sending an e-mail to
support[at]it4i.cz.
Obtaining Login Credentials
----------------------------
+----
In general PRACE users already have a PRACE account setup through their
HOMESITE (institution from their country) as a result of rewarded PRACE
project proposal. This includes signed PRACE AuP, generated and
@@ -36,7 +41,7 @@ account at IT4Innovations. To get an account on the Salomon cluster, the
user needs to obtain the login credentials. The procedure is the same as
for general users of the cluster, so please see the corresponding
[section of the general documentation
-here](../get-started-with-it4innovations/obtaining-login-credentials.html).
+here](https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials).
Accessing the cluster
---------------------
### Access with GSI-SSH
@@ -47,35 +52,35 @@ The user will need a valid certificate and to be present in the PRACE
LDAP (please contact your HOME SITE or the primary investigator of your
project for LDAP account creation).
Most of the information needed by PRACE users accessing the Salomon
-TIER-1 system can be found here
+TIER-1 system can be found here:
- [General user's
- FAQ](http//www.prace-ri.eu/Users-General-FAQs)
+ FAQ](http://www.prace-ri.eu/Users-General-FAQs)
- [Certificates
- FAQ](http//www.prace-ri.eu/Certificates-FAQ)
+ FAQ](http://www.prace-ri.eu/Certificates-FAQ)
- [Interactive access using
- GSISSH](http//www.prace-ri.eu/Interactive-Access-Using-gsissh)
+ GSISSH](http://www.prace-ri.eu/Interactive-Access-Using-gsissh)
- [Data transfer with
- GridFTP](http//www.prace-ri.eu/Data-Transfer-with-GridFTP-Details)
+ GridFTP](http://www.prace-ri.eu/Data-Transfer-with-GridFTP-Details)
- [Data transfer with
- gtransfer](http//www.prace-ri.eu/Data-Transfer-with-gtransfer)
+ gtransfer](http://www.prace-ri.eu/Data-Transfer-with-gtransfer)
Â
Before you start to use any of the services don't forget to create a
-proxy certificate from your certificate
+proxy certificate from your certificate:
$ grid-proxy-init
To check whether your proxy certificate is still valid (by default it's
-valid 12 hours), use
+valid 12 hours), use:
$ grid-proxy-info
Â
To access Salomon cluster, two login nodes running GSI SSH service are
available. The service is available from public Internet as well as from
the internal PRACE network (accessible only from other PRACE partners).
-**Access from PRACE network**
-It is recommended to use the single DNS name
-class="monospace">salomon-prace.it4i.cz which is distributed
+**Access from PRACE network:**
+It is recommended to use the single DNS name <span
+class="monospace">salomon-prace.it4i.cz</span> which is distributed
between the two login nodes. If needed, user can login directly to one
-of the login nodes. The addresses are
+of the login nodes. The addresses are:
Login address Port Protocol Login node
- ------------------------------ ------ ---------- ----------------------------------
+ ------- ------ ---------- -----------
salomon-prace.it4i.cz 2222 gsissh login1, login2, login3 or login4
login1-prace.salomon.it4i.cz 2222 gsissh login1
login2-prace.salomon.it4i.cz 2222 gsissh login2
@@ -84,57 +89,57 @@ of the login nodes. The addresses are
Â
$ gsissh -p 2222 salomon-prace.it4i.cz
When logging from other PRACE system, the prace_service script can be
-used
+used:
$ gsissh `prace_service -i -s salomon`
Â
-**Access from public Internet**
-It is recommended to use the single DNS name
-class="monospace">salomon.it4i.cz which is distributed between
+**Access from public Internet:**
+It is recommended to use the single DNS name <span
+class="monospace">salomon.it4i.cz</span> which is distributed between
the two login nodes. If needed, user can login directly to one of the
-login nodes. The addresses are
+login nodes. The addresses are:
Login address Port Protocol Login node
- ------------------------ ------ ---------- ----------------------------------
+ - ------ ---------- -----------
salomon.it4i.cz 2222 gsissh login1, login2, login3 or login4
login1.salomon.it4i.cz 2222 gsissh login1
login2.salomon.it4i.cz 2222 gsissh login2
login3.salomon.it4i.cz 2222 gsissh login3
login4.salomon.it4i.cz 2222 gsissh login4
$ gsissh -p 2222 salomon.it4i.cz
-When logging from other PRACE system, the
-class="monospace">prace_service script can be used
+When logging from other PRACE system, the <span
+class="monospace">prace_service</span> script can be used:
$ gsissh `prace_service -e -s salomon`
Â
Although the preferred and recommended file transfer mechanism is [using
GridFTP](#file-transfers), the GSI SSH implementation on
Salomon supports also SCP, so for small files transfer gsiscp can be
-used
- $ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ salomon.it4i.cz_SALOMON_PATH_TO_YOUR_FILE_
- $ gsiscp -P 2222 salomon.it4i.cz_SALOMON_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_
- $ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ salomon-prace.it4i.cz_SALOMON_PATH_TO_YOUR_FILE_
- $ gsiscp -P 2222 salomon-prace.it4i.cz_SALOMON_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_
+used:
+ $ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ salomon.it4i.cz:_SALOMON_PATH_TO_YOUR_FILE_
+ $ gsiscp -P 2222 salomon.it4i.cz:_SALOMON_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_
+ $ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ salomon-prace.it4i.cz:_SALOMON_PATH_TO_YOUR_FILE_
+ $ gsiscp -P 2222 salomon-prace.it4i.cz:_SALOMON_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_
### Access to X11 applications (VNC)
If the user needs to run X11 based graphical application and does not
have a X11 server, the applications can be run using VNC service. If the
user is using regular SSH based access, please see the [section in
general
-documentation](../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+documentation](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc).
If the user uses GSI SSH based access, then the procedure is similar to
the SSH based access ([look
-here](../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)),
-only the port forwarding must be done using GSI SSH
- $ gsissh -p 2222 salomon.it4i.cz -L 5961localhost5961
+here](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc)),
+only the port forwarding must be done using GSI SSH:
+ $ gsissh -p 2222 salomon.it4i.cz -L 5961:localhost:5961
### Access with SSH
After successful obtainment of login credentials for the local
IT4Innovations account, the PRACE users can access the cluster as
regular users using SSH. For more information please see the [section in
general
-documentation](accessing-the-cluster/shell-and-data-access/shell-and-data-access.html).
+documentation](https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access).
[]()File transfers
------------------
PRACE users can use the same transfer mechanisms as regular users (if
they've undergone the full registration procedure). For information
about this, please see [the section in the general
-documentation](accessing-the-cluster/shell-and-data-access/shell-and-data-access.html).
+documentation](https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access).
Apart from the standard mechanisms, for PRACE users to transfer data
to/from Salomon cluster, a GridFTP server running Globus Toolkit GridFTP
service is available. The service is available from public Internet as
@@ -142,51 +147,51 @@ well as from the internal PRACE network (accessible only from other
PRACE partners).
There's one control server and three backend servers for striping and/or
backup in case one of them would fail.
-**Access from PRACE network**
+**Access from PRACE network:**
Login address Port Node role
- ------------------------------- ------ -----------------------------
+ -------- ------ ------
gridftp-prace.salomon.it4i.cz 2812 Front end /control server
lgw1-prace.salomon.it4i.cz 2813 Backend / data mover server
lgw2-prace.salomon.it4i.cz 2813 Backend / data mover server
lgw3-prace.salomon.it4i.cz 2813 Backend / data mover server
Copy files **to** Salomon by running the following commands on your
-local machine
- $ globus-url-copy file//_LOCAL_PATH_TO_YOUR_FILE_ gsiftp//gridftp-prace.salomon.it4i.cz2812/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_
-Or by using prace_service script
- $ globus-url-copy file//_LOCAL_PATH_TO_YOUR_FILE_ gsiftp//`prace_service -i -f salomon`/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_
-Copy files **from** Salomon
- $ globus-url-copy gsiftp//gridftp-prace.salomon.it4i.cz2812/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_ file//_LOCAL_PATH_TO_YOUR_FILE_
-Or by using prace_service script
- $ globus-url-copy gsiftp//`prace_service -i -f salomon`/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_ file//_LOCAL_PATH_TO_YOUR_FILE_
+local machine:
+ $ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://gridftp-prace.salomon.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_
+Or by using <span class="monospace">prace_service</span> script:
+ $ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://`prace_service -i -f salomon`/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_
+Copy files **from** Salomon:
+ $ globus-url-copy gsiftp://gridftp-prace.salomon.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
+Or by using <span class="monospace">prace_service</span> script:
+ $ globus-url-copy gsiftp://`prace_service -i -f salomon`/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
Â
-**Access from public Internet**
+**Access from public Internet:**
Login address Port Node role
- ------------------------- ------ -----------------------------
+ -- ------ ------
gridftp.salomon.it4i.cz 2812 Front end /control server
lgw1.salomon.it4i.cz 2813 Backend / data mover server
lgw2.salomon.it4i.cz 2813 Backend / data mover server
lgw3.salomon.it4i.cz 2813 Backend / data mover server
Copy files **to** Salomon by running the following commands on your
-local machine
- $ globus-url-copy file//_LOCAL_PATH_TO_YOUR_FILE_ gsiftp//gridftp.salomon.it4i.cz2812/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_
-Or by using prace_service script
- $ globus-url-copy file//_LOCAL_PATH_TO_YOUR_FILE_ gsiftp//`prace_service -e -f salomon`/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_
-Copy files **from** Salomon
- $ globus-url-copy gsiftp//gridftp.salomon.it4i.cz2812/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_ file//_LOCAL_PATH_TO_YOUR_FILE_
-Or by using prace_service script
- $ globus-url-copy gsiftp//`prace_service -e -f salomon`/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_ file//_LOCAL_PATH_TO_YOUR_FILE_
+local machine:
+ $ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://gridftp.salomon.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_
+Or by using <span class="monospace">prace_service</span> script:
+ $ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://`prace_service -e -f salomon`/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_
+Copy files **from** Salomon:
+ $ globus-url-copy gsiftp://gridftp.salomon.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
+Or by using <span class="monospace">prace_service</span> script:
+ $ globus-url-copy gsiftp://`prace_service -e -f salomon`/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
Â
-Generally both shared file systems are available through GridFTP
+Generally both shared file systems are available through GridFTP:
File system mount point Filesystem Comment
- ------------------------- ------------ ----------------------------------------------------------------
+ -- ------------ ------------------
/home Lustre Default HOME directories of users in format /home/prace/login/
/scratch Lustre Shared SCRATCH mounted on the whole cluster
More information about the shared file systems is available
-[here](storage.html).
+[here](https://docs.it4i.cz/salomon/storage).
Please note, that for PRACE users a "prace" directory is used also on
the SCRATCH file system.
Data type Default path
- ------------------------------ ---------------------------------
+ ------- ----------
large project files /scratch/work/user/prace/login/
large scratch/temporary data /scratch/temp/
Usage of the cluster
@@ -199,36 +204,37 @@ restrictions obtaining a working license for the commercial software
installed on the cluster, mostly because of the license agreement or
because of insufficient amount of licenses.
For production runs always use scratch file systems. The available file
-systems are described [here](storage/storage.html).
+systems are described
+[here](https://docs.it4i.cz/salomon/storage/storage).
### Software, Modules and PRACE Common Production Environment
All system wide installed software on the cluster is made available to
the users via the modules. The information about the environment and
modules usage is in this [section of general
-documentation](environment-and-modules.html).
+documentation](https://docs.it4i.cz/salomon/environment-and-modules).
PRACE users can use the "prace" module to use the [PRACE Common
Production
-Environment](http//www.prace-ri.eu/PRACE-common-production).
+Environment](http://www.prace-ri.eu/PRACE-common-production).
$ module load prace
Â
### Resource Allocation and Job Execution
General information about the resource allocation, job queuing and job
execution is in this [section of general
-documentation](resource-allocation-and-job-execution/introduction.html).
+documentation](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction).
For PRACE users, the default production run queue is "qprace". PRACE
users can also use two other queues "qexp" and "qfree".
- ---------------------------------------------------------------------------------------------------------------------------------------------
+ ---
queue Active project Project resources Nodes priority authorization walltime
default/max
- --------------------- ---------------- ------------------- ----------------------------------------- ---------- --------------- -------------
+ --------------------- ---------------- ------------------- ------------------ ---------- --------------- -------------
**qexp** no none required 32 nodes, max 8 per user 150 no 1 / 1h
Express queue
- **qprace** yes > 0 1006 nodes, max 86 per job 0 no 24 / 48h
+ **qprace** yes > 0 <span>1006 nodes, max 86 per job</span> 0 no 24 / 48h
Production queue
**qfree** yes none required 752 nodes, max 86 per job -1024 no 12 / 12h
Free resource queue
- ---------------------------------------------------------------------------------------------------------------------------------------------
-**qprace**, the PRACE Production queue**** This queue is intended for
+ ---
+**qprace**, the PRACE Production queue****This queue is intended for
normal production runs. It is required that active project with nonzero
remaining resources is specified to enter the qprace. The queue runs
with medium priority and no special authorization is required to use it.
@@ -241,10 +247,10 @@ accounting runs whenever the computational cores are allocated or
blocked via the PBS Pro workload manager (the qsub command), regardless
of whether the cores are actually used for any calculation. See [example
in the general
-documentation](resource-allocation-and-job-execution/resources-allocation-policy.html).
+documentation](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy).
PRACE users should check their project accounting using the [PRACE
Accounting Tool
-(DART)](http//www.prace-ri.eu/accounting-report-tool/).
+(DART)](http://www.prace-ri.eu/accounting-report-tool/).
Users who have undergone the full local registration procedure
(including signing the IT4Innovations Acceptable Use Policy) and who
have received local password may check at any time, how many core-hours
@@ -253,9 +259,10 @@ have been consumed by themselves and their projects using the command
the command and that the displayed core hours are "system core hours"
which differ from PRACE "standardized core hours".
The **it4ifree** command is a part of it4i.portal.clients package,
-located here
+located here:
+<https://pypi.python.org/pypi/it4i.portal.clients>
$ it4ifree
- Password
+ Password:
    PID  Total Used ...by me Free
  -------- ------- ------ -------- -------
  OPEN-0-0 1500000 400644  225265 1099356
@@ -269,17 +276,3 @@ If the quota is insufficient, please contact the
[support](#help-and-support) and request an increase.
Â
Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
diff --git a/salomon/resource-allocation-and-job-execution.html b/docs.it4i.cz/salomon/resource-allocation-and-job-execution.html
old mode 100755
new mode 100644
similarity index 64%
rename from salomon/resource-allocation-and-job-execution.html
rename to docs.it4i.cz/salomon/resource-allocation-and-job-execution.html
index a22e3903dbcc14397315d7e01e52b9396593cca4..666983d1fc48fc7eb4f2dbb24e343ccc01200b79
--- a/salomon/resource-allocation-and-job-execution.html
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/resource-allocation-and-job-execution by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:42 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/IEFixes-cachekey-ec9b60024fd235ff2c883b4b54db91cb.css" />
<![endif]-->
- <style type="text/css" media="screen">@import url(../portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Resource Allocation and Job Execution — IT4I Docs</title>
- <link rel="canonical" href="resource-allocation-and-job-execution.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="resource-allocation-and-job-execution.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="resource-allocation-and-job-execution.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../index.html">
- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -230,9 +227,9 @@
<div id="parent-fieldname-text-5df9e884138d4c5899d0e186ed6fa426" class="">
- <p>To run a <a target="_self" title="" class="internal-link" href="resource-allocation-and-job-execution/job-submission-and-execution.html">job</a>, <a target="_self" title="" class="internal-link" href="resource-allocation-and-job-execution/resources-allocation-policy.html">computational resources</a> for this particular job must be allocated. This is done via the PBS Pro job workload manager software, which efficiently distributes workloads across the supercomputer. Extensive informations about PBS Pro can be found in the <a target="_self" title="" class="internal-link" href="../pbspro-documentation.html">official documentation here</a>, especially in the <a target="_self" title="" class="internal-link" href="../pbspro-documentation/PBSProUserGuide12.pdf">PBS Pro User's Guide</a>.</p>
+ <p>To run a <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">job</a>, <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy">computational resources</a> for this particular job must be allocated. This is done via the PBS Pro job workload manager software, which efficiently distributes workloads across the supercomputer. Extensive informations about PBS Pro can be found in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/pbspro-documentation">official documentation here</a>, especially in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/pbspro-documentation/pbspro-users-guide">PBS Pro User's Guide</a>.</p>
<h2 class=" ">Resources Allocation Policy</h2>
-<p>The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. <a target="_self" title="" class="internal-link" href="resource-allocation-and-job-execution/job-priority.html">The Fairshare</a> at Salomon ensures that individual users may consume approximately equal amount of resources per week. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following queues are available to Anselm users:</p>
+<p>The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority">The Fairshare</a> at Salomon ensures that individual users may consume approximately equal amount of resources per week. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following queues are available to Anselm users:</p>
<ul>
<li><strong>qexp</strong>, the Express queue</li>
<li><strong>qprod</strong>, the Production queue<strong></strong></li>
@@ -242,11 +239,11 @@
<li><strong>qfree, </strong>the Free resource utilization queue</li>
</ul>
<p class="callout">Check the queue status at <a class="external-link" href="https://extranet.it4i.cz/rsweb/salomon/" target="_self" title="">https://extranet.it4i.cz/rsweb/salomon/</a></p>
-<p>Read more on the <a target="_self" title="" class="internal-link" href="resource-allocation-and-job-execution/resources-allocation-policy.html">Resource Allocation Policy</a> page.</p>
+<p>Read more on the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy">Resource Allocation Policy</a> page.</p>
<h2 class=" ">Job submission and execution</h2>
<p class="callout">Use the <strong>qsub</strong> command to submit your jobs.</p>
<p class=" ">The qsub submits the job into the queue. The qsub command creates a request to the PBS Job manager for allocation of specified resources. The <strong>smallest allocation unit is entire node, 24 cores</strong>, with exception of the qexp queue. The resources will be allocated when available, subject to allocation policies and constraints. <strong>After the resources are allocated the jobscript or interactive shell is executed on first of the allocated nodes.</strong></p>
-<p class=" ">Read more on the <a target="_self" title="" class="internal-link" href="resource-allocation-and-job-execution/job-submission-and-execution.html">Job submission and execution</a> page.</p>
+<p class=" ">Read more on the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">Job submission and execution</a> page.</p>
<p class="hiddenForView">HTML commented section #1 (removed Capacity computing section, this will be optimized for Salomon)</p>
@@ -324,7 +321,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -340,7 +337,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -356,7 +353,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -372,7 +369,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -388,7 +385,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -404,7 +401,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -420,7 +417,7 @@
- <a title="" class="state-published contenttype-document" href="environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -436,7 +433,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -452,7 +449,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -468,7 +465,7 @@
- <a title="" class="state-published contenttype-document" href="resource-allocation-and-job-execution/resources-allocation-policy.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy">
<span>Resources Allocation Policy</span>
</a>
@@ -484,7 +481,7 @@
- <a title="" class="state-published contenttype-document" href="resource-allocation-and-job-execution/job-submission-and-execution.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">
<span>Job submission and execution</span>
</a>
@@ -500,7 +497,7 @@
- <a title="" class="state-published contenttype-document" href="resource-allocation-and-job-execution/job-priority.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority">
<span>Job scheduling</span>
</a>
@@ -516,7 +513,7 @@
- <a title="" class="state-published contenttype-document" href="resource-allocation-and-job-execution/capacity-computing.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing">
<span>Capacity computing</span>
</a>
@@ -541,7 +538,7 @@
- <a title="" class="state-published contenttype-document" href="compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -557,7 +554,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -573,7 +570,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -589,10 +586,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -608,7 +605,7 @@
- <a title="" class="state-published contenttype-document" href="prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -633,7 +630,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -649,7 +646,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -665,7 +662,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -681,7 +678,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -720,14 +717,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
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+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -749,12 +746,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -770,7 +767,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
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-<!-- Mirrored from docs.it4i.cz/salomon/resource-allocation-and-job-execution by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:43 GMT -->
</html>
diff --git a/salomon/resource-allocation-and-job-execution.md b/docs.it4i.cz/salomon/resource-allocation-and-job-execution.md
similarity index 50%
rename from salomon/resource-allocation-and-job-execution.md
rename to docs.it4i.cz/salomon/resource-allocation-and-job-execution.md
index 9d5a2b47405bb310ac9974c92596732eb228321c..ca4160e21fe25241cca4ca2ec5d350132d9a665d 100644
--- a/salomon/resource-allocation-and-job-execution.md
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution.md
@@ -1,38 +1,40 @@
-
+Resource Allocation and Job Execution
+=====================================
+
To run a
-[job](resource-allocation-and-job-execution/job-submission-and-execution.html),
+[job](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution),
[computational
-resources](resource-allocation-and-job-execution/resources-allocation-policy.html)
+resources](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy)
for this particular job must be allocated. This is done via the PBS Pro
job workload manager software, which efficiently distributes workloads
across the supercomputer. Extensive informations about PBS Pro can be
found in the [official documentation
-here](../pbspro-documentation.html), especially in the
-[PBS Pro User's
-Guide](../pbspro-documentation/PBSProUserGuide12.pdf).
+here](https://docs.it4i.cz/pbspro-documentation),
+especially in the [PBS Pro User's
+Guide](https://docs.it4i.cz/pbspro-documentation/pbspro-users-guide).
Resources Allocation Policy
----------------------------
+----
The resources are allocated to the job in a fairshare fashion, subject
to constraints set by the queue and resources available to the Project.
[The
-Fairshare](resource-allocation-and-job-execution/job-priority.html)
+Fairshare](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority)
at Salomon ensures that individual users may consume approximately equal
amount of resources per week. The resources are accessible via several
queues for queueing the jobs. The queues provide prioritized and
exclusive access to the computational resources. Following queues are
-available to Anselm users
+available to Anselm users:
- **qexp**, the Express queue
- **qprod**, the Production queue****
- **qlong**, the Long queue
- **qmpp**, the Massively parallel queue
- **qfat**, the queue to access SMP UV2000 machine
- **qfree,** the Free resource utilization queue
-Check the queue status at
+Check the queue status at <https://extranet.it4i.cz/rsweb/salomon/>
Read more on the [Resource Allocation
-Policy](resource-allocation-and-job-execution/resources-allocation-policy.html)
+Policy](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy)
page.
Job submission and execution
-----------------------------
+-----
Use the **qsub** command to submit your jobs.
The qsub submits the job into the queue. The qsub command creates a
request to the PBS Job manager for allocation of specified resources.Â
@@ -42,33 +44,7 @@ available, subject to allocation policies and constraints. **After the
resources are allocated the jobscript or interactive shell is executed
on first of the allocated nodes.**
Read more on the [Job submission and
-execution](resource-allocation-and-job-execution/job-submission-and-execution.html)
+execution](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution)
page.
HTML commented section #1 (removed Capacity computing section, this
will be optimized for Salomon)
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
-
- - [Hardware
- Overview](hardware-overview-1.html)
-
- - [Accessing the
- Cluster](accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](environment-and-modules.html)
-
- - [List of Available
- Modules](list_of_modules.html "List of Available Modules on Salomon Cluster")
diff --git a/salomon/resource-allocation-and-job-execution/capacity-computing.html b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.html
old mode 100755
new mode 100644
similarity index 80%
rename from salomon/resource-allocation-and-job-execution/capacity-computing.html
rename to docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.html
index c154e6d66c95473bf11c20f8fd968916b1bdb4a8..3f0f4f1671077d679c9ea9985234b045fb6166c5
--- a/salomon/resource-allocation-and-job-execution/capacity-computing.html
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:18 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<![endif]-->
- <style type="text/css" media="screen">@import url(../../portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Capacity computing — IT4I Docs</title>
- <link rel="canonical" href="capacity-computing.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="capacity-computing.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="capacity-computing.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../resource-allocation-and-job-execution.html">Resource Allocation and Job Execution</a>
+ <a href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">Resource Allocation and Job Execution</a>
<span class="breadcrumbSeparator">
/
@@ -293,7 +290,7 @@
<pre class="prettyprint lang-sh">$ qstat -u $USER -t</pre>
<p>Display status information for all user's subjobs.</p>
<pre class="prettyprint lang-sh">$ qstat -u $USER -tJ</pre>
-<p>Read more on job arrays in the <a target="_self" title="" class="internal-link" href="../../pbspro-documentation.html">PBSPro Users guide</a>.</p>
+<p>Read more on job arrays in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/pbspro-documentation">PBSPro Users guide</a>.</p>
<h2 class=" "><a name="gnu-parallel"></a>GNU parallel</h2>
<p class="callout">Use GNU parallel to run many single core tasks on one node.</p>
<p class=" ">GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input. GNU parallel is most useful in running single core jobs via the queue system on Anselm.</p>
@@ -341,7 +338,7 @@
<p>In this example, we submit a job array of 31 subjobs. Note the -J 1-992:<strong>48</strong>, this must be the same as the number sent to numtasks file. Each subjob will run on full node and process 24 input files in parallel, 48 in total per subjob. Every subjob is assumed to complete in less than 2 hours.</p>
<p>Please note the #PBS directives in the beginning of the jobscript file, dont' forget to set your valid PROJECT_ID and desired queue.</p>
<h2 class=" ">Examples</h2>
-<p>Download the examples in <a target="_self" title="" class="internal-link" href="capacity.zip">capacity.zip</a>, illustrating the above listed ways to run huge number of jobs. We recommend to try out the examples, before using this for running production jobs.</p>
+<p>Download the examples in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing-example">capacity.zip</a>, illustrating the above listed ways to run huge number of jobs. We recommend to try out the examples, before using this for running production jobs.</p>
<p>Unzip the archive in an empty directory on Anselm and follow the instructions in the README file</p>
<pre class="prettyprint lang-sh">$ unzip capacity.zip<br />$ cd capacity<br />$ cat README</pre>
<p>Â </p>
@@ -420,7 +417,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -436,7 +433,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -452,7 +449,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -468,7 +465,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -484,7 +481,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -500,7 +497,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -516,7 +513,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -532,7 +529,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -548,7 +545,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -564,7 +561,7 @@
- <a title="" class="state-published contenttype-document" href="resources-allocation-policy.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy">
<span>Resources Allocation Policy</span>
</a>
@@ -580,7 +577,7 @@
- <a title="" class="state-published contenttype-document" href="job-submission-and-execution.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">
<span>Job submission and execution</span>
</a>
@@ -596,7 +593,7 @@
- <a title="" class="state-published contenttype-document" href="job-priority.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority">
<span>Job scheduling</span>
</a>
@@ -612,7 +609,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="capacity-computing.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing">
<span>Capacity computing</span>
</a>
@@ -637,7 +634,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -653,7 +650,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -669,7 +666,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -685,10 +682,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -704,7 +701,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -729,7 +726,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -745,7 +742,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -761,7 +758,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -777,7 +774,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
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+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -845,12 +842,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -866,7 +863,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:18 GMT -->
</html>
diff --git a/salomon/resource-allocation-and-job-execution/capacity-computing.md b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.md
similarity index 85%
rename from salomon/resource-allocation-and-job-execution/capacity-computing.md
rename to docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.md
index bcfb5c2ca409de2479eeb2b2655c1afefd50da74..8bd8c2272a5756bee74cdfbfdec47e0928992583 100644
--- a/salomon/resource-allocation-and-job-execution/capacity-computing.md
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.md
@@ -1,8 +1,9 @@
-
-
+Capacity computing
+==================
+
Introduction
------------
-In many cases, it is useful to submit huge (100+) number of
+In many cases, it is useful to submit huge (<span>100+</span>) number of
computational jobs into the PBS queue system. Huge number of (small)
jobs is one of the most effective ways to execute embarrassingly
parallel calculations, achieving best runtime, throughput and computer
@@ -13,7 +14,7 @@ scheduling and overall degradation of performance and user experience,
for all users. For this reason, the number of jobs is **limited to 100
per user, 1500 per job array**
Please follow one of the procedures below, in case you wish to schedule
-more than 100 jobs at a time.
+more than <span>100</span> jobs at a time.
- Use [Job arrays](#job-arrays) when running huge number
of [multithread](#shared-jobscript-on-one-node) (bound
to one node only) or multinode (multithread across several nodes)
@@ -33,7 +34,7 @@ Policy
Huge number of jobs may be easily submitted and managed as a job array.
A job array is a compact representation of many jobs, called subjobs.
The subjobs share the same job script, and have the same values for all
-attributes and resources, with the following exceptions
+attributes and resources, with the following exceptions:
- each subjob has a unique index, $PBS_ARRAY_INDEX
- job Identifiers of subjobs only differ by their indices
- the state of subjobs can differ (R,Q,...etc.)
@@ -45,21 +46,21 @@ managed by qdel, qalter, qhold, qrls and qsig commands as a single job.
All subjobs in job array use the very same, single jobscript. Each
subjob runs its own instance of the jobscript. The instances execute
different work controlled by $PBS_ARRAY_INDEX variable.
-[]()Example
+[]()Example:
Assume we have 900 input files with name beginning with "file" (e. g.
file001, ..., file900). Assume we would like to use each of these input
files with program executable myprog.x, each as a separate job.
First, we create a tasklist file (or subjobs list), listing all tasks
-(subjobs) - all input files in our example
+(subjobs) - all input files in our example:
``` {.prettyprint .lang-sh}
$ find . -name 'file*' > tasklist
```
-Then we create jobscript
+Then we create jobscript:
``` {.prettyprint .lang-sh}
#!/bin/bash
#PBS -A PROJECT_ID
#PBS -q qprod
-#PBS -l select=1ncpus=24,walltime=020000
+#PBS -l select=1:ncpus=24,walltime=02:00:00
# change to local scratch directory
SCR=/scratch/work/user/$USER/$PBS_JOBID
mkdir -p $SCR ; cd $SCR || exit
@@ -68,7 +69,7 @@ TASK=$(sed -n "${PBS_ARRAY_INDEX}p" $PBS_O_WORKDIR/tasklist)
# copy input file and executable to scratch
cp $PBS_O_WORKDIR/$TASK input ; cp $PBS_O_WORKDIR/myprog.x .
# execute the calculation
-./myprog.x output
+./myprog.x < input > output
# copy output file to submit directory
cp output $PBS_O_WORKDIR/$TASK.out
```
@@ -76,8 +77,8 @@ In this example, the submit directory holds the 900 input files,
executable myprog.x and the jobscript file. As input for each run, we
take the filename of input file from created tasklist file. We copy the
input file to scratch /scratch/work/user/$USER/$PBS_JOBID, execute
-the myprog.x and copy the output file back to the submit
-directory, under the $TASK.out name. The myprog.x runs on one
+the myprog.x and copy the output file back to <span>the submit
+directory</span>, under the $TASK.out name. The myprog.x runs on one
node only and must use threads to run in parallel. Be aware, that if the
myprog.x **is not multithreaded**, then all the **jobs are run as single
thread programs in sequential** manner. Due to allocation of the whole
@@ -92,7 +93,7 @@ run has to be used properly.
### Submit the job array
To submit the job array, use the qsub -J command. The 900 jobs of the
[example above](#array_example) may be submitted like
-this
+this:
``` {.prettyprint .lang-sh}
$ qsub -N JOBNAME -J 1-900 jobscript
506493[].isrv5
@@ -102,9 +103,9 @@ run on full node and is assumed to take less than 2 hours (please note
the #PBS directives in the beginning of the jobscript file, dont'
forget to set your valid PROJECT_ID and desired queue).
Sometimes for testing purposes, you may need to submit only one-element
-array. This is not allowed by PBSPro, but there's a workaround
+array. This is not allowed by PBSPro, but there's a workaround:
``` {.prettyprint .lang-sh}
-$ qsub -N JOBNAME -J 9-102 jobscript
+$ qsub -N JOBNAME -J 9-10:2 jobscript
```
This will only choose the lower index (9 in this example) for
submitting/running your job.
@@ -112,27 +113,27 @@ submitting/running your job.
Check status of the job array by the qstat command.
``` {.prettyprint .lang-sh}
$ qstat -a 506493[].isrv5
-isrv5
+isrv5:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
-12345[].dm2 user2 qprod xx 13516 1 24 -- 0050 B 0002
+12345[].dm2 user2 qprod xx 13516 1 24 -- 00:50 B 00:02
```
The status B means that some subjobs are already running.
Check status of the first 100 subjobs by the qstat command.
``` {.prettyprint .lang-sh}
$ qstat -a 12345[1-100].isrv5
-isrv5
+isrv5:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
-12345[1].isrv5 user2 qprod xx 13516 1 24 -- 0050 R 0002
-12345[2].isrv5 user2 qprod xx 13516 1 24 -- 0050 R 0002
-12345[3].isrv5 user2 qprod xx 13516 1 24 -- 0050 R 0001
-12345[4].isrv5 user2 qprod xx 13516 1 24 -- 0050 Q --
+12345[1].isrv5 user2 qprod xx 13516 1 24 -- 00:50 R 00:02
+12345[2].isrv5 user2 qprod xx 13516 1 24 -- 00:50 R 00:02
+12345[3].isrv5 user2 qprod xx 13516 1 24 -- 00:50 R 00:01
+12345[4].isrv5 user2 qprod xx 13516 1 24 -- 00:50 Q --
. . . . . . . . . . .
, . . . . . . . . . .
-12345[100].isrv5 user2 qprod xx 13516 1 24 -- 0050 Q --
+12345[100].isrv5 user2 qprod xx 13516 1 24 -- 00:50 Q --
```
Delete the entire job array. Running subjobs will be killed, queueing
subjobs will be deleted.
@@ -149,7 +150,7 @@ Display status information for all user's subjobs.
$ qstat -u $USER -tJ
```
Read more on job arrays in the [PBSPro Users
-guide](../../pbspro-documentation.html).
+guide](https://docs.it4i.cz/pbspro-documentation).
[]()GNU parallel
----------------
Use GNU parallel to run many single core tasks on one node.
@@ -157,7 +158,7 @@ GNU parallel is a shell tool for executing jobs in parallel using one or
more computers. A job can be a single command or a small script that has
to be run for each of the lines in the input. GNU parallel is most
useful in running single core jobs via the queue system on Anselm.
-For more information and examples see the parallel man page
+For more information and examples see the parallel man page:
``` {.prettyprint .lang-sh}
$ module add parallel
$ man parallel
@@ -166,22 +167,22 @@ $ man parallel
The GNU parallel shell executes multiple instances of the jobscript
using all cores on the node. The instances execute different work,
controlled by the $PARALLEL_SEQ variable.
-[]()Example
+[]()Example:
Assume we have 101 input files with name beginning with "file" (e. g.
file001, ..., file101). Assume we would like to use each of these input
files with program executable myprog.x, each as a separate single core
job. We call these single core jobs tasks.
First, we create a tasklist file, listing all tasks - all input files in
-our example
+our example:
``` {.prettyprint .lang-sh}
$ find . -name 'file*' > tasklist
```
-Then we create jobscript
+Then we create jobscript:
``` {.prettyprint .lang-sh}
#!/bin/bash
#PBS -A PROJECT_ID
#PBS -q qprod
-#PBS -l select=1ncpus=24,walltime=020000
+#PBS -l select=1:ncpus=24,walltime=02:00:00
[ -z "$PARALLEL_SEQ" ] &&
{ module add parallel ; exec parallel -a $PBS_O_WORKDIR/tasklist $0 ; }
# change to local scratch directory
@@ -207,7 +208,7 @@ and copy the output file back to the submit directory, under the
$TASK.out name.Â
### Submit the job
To submit the job, use the qsub command. The 101 tasks' job of the
-[example above](#gp_example) may be submitted like this
+[example above](#gp_example) may be submitted like this:
``` {.prettyprint .lang-sh}
$ qsub -N JOBNAME jobscript
12345.dm2
@@ -218,7 +219,7 @@ complete in less than 2 hours.
Please note the #PBS directives in the beginning of the jobscript file,
dont' forget to set your valid PROJECT_ID and desired queue.
[]()Job arrays and GNU parallel
--------------------------------
+--------
Combine the Job arrays and GNU parallel for best throughput of single
core jobs
While job arrays are able to utilize all available computational nodes,
@@ -233,13 +234,13 @@ is submitted to the queuing system. The subjobs run GNU parallel. The
GNU parallel shell executes multiple instances of the jobscript using
all cores on the node. The instances execute different work, controlled
by the $PBS_JOB_ARRAY and $PARALLEL_SEQ variables.
-[]()Example
+[]()Example:
Assume we have 992 input files with name beginning with "file" (e. g.
file001, ..., file992). Assume we would like to use each of these input
files with program executable myprog.x, each as a separate single core
job. We call these single core jobs tasks.
First, we create a tasklist file, listing all tasks - all input files in
-our example
+our example:
``` {.prettyprint .lang-sh}
$ find . -name 'file*' > tasklist
```
@@ -248,12 +249,12 @@ one subjob
``` {.prettyprint .lang-sh}
$ seq 32 > numtasks
```
-Then we create jobscript
+Then we create jobscript:
``` {.prettyprint .lang-sh}
#!/bin/bash
#PBS -A PROJECT_ID
#PBS -q qprod
-#PBS -l select=1ncpus=24,walltime=020000
+#PBS -l select=1:ncpus=24,walltime=02:00:00
[ -z "$PARALLEL_SEQ" ] &&
{ module add parallel ; exec parallel -a $PBS_O_WORKDIR/numtasks $0 ; }
# change to local scratch directory
@@ -278,7 +279,7 @@ submit directory, under the $TASK.out name. The numtasks file controls
how many tasks will be run per subjob. Once an task is finished, new
task starts, until the number of tasks in numtasks file is reached.
Select subjob walltime and number of tasks per subjob carefully
-Â When deciding this values, think about following guiding rules
+Â When deciding this values, think about following guiding rules :
1. Let n=N/24. Inequality (n+1) * T < W should hold. The N is
number of tasks per subjob, T is expected single task walltime and W
is subjob walltime. Short subjob walltime improves scheduling and
@@ -289,13 +290,13 @@ Select subjob walltime and number of tasks per subjob carefully
### Submit the job array
To submit the job array, use the qsub -J command. The 992 tasks' job of
the [example above](#combined_example) may be submitted
-like this
+like this:
``` {.prettyprint .lang-sh}
-$ qsub -N JOBNAME -J 1-99232 jobscript
+$ qsub -N JOBNAME -J 1-992:32 jobscript
12345[].dm2
```
In this example, we submit a job array of 31 subjobs. Note the -J
-1-992**48**, this must be the same as the number sent to numtasks file.
+1-992:**48**, this must be the same as the number sent to numtasks file.
Each subjob will run on full node and process 24 input files in
parallel, 48 in total per subjob. Every subjob is assumed to complete
in less than 2 hours.
@@ -303,7 +304,8 @@ Please note the #PBS directives in the beginning of the jobscript file,
dont' forget to set your valid PROJECT_ID and desired queue.
Examples
--------
-Download the examples in [capacity.zip](capacity.zip),Â
+Download the examples in
+[capacity.zip](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing-example),Â
illustrating the above listed ways to run huge number of jobs. We
recommend to try out the examples, before using this for running
production jobs.
@@ -315,29 +317,3 @@ $ cd capacity
$ cat README
```
Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [List of Available
- Modules](../list_of_modules.html "List of Available Modules on Salomon Cluster")
diff --git a/salomon/resource-allocation-and-job-execution/introduction.html b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.html
old mode 100755
new mode 100644
similarity index 64%
rename from salomon/resource-allocation-and-job-execution/introduction.html
rename to docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.html
index d84bf5a64bb700ae70c1d174ea9f440e7c1dbe2a..f9dffe42808b6ad050efc1bff66b7b5597f81d2c
--- a/salomon/resource-allocation-and-job-execution/introduction.html
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.html
@@ -10,45 +10,42 @@
-
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Resource Allocation and Job Execution — IT4I Docs</title>
- <link rel="canonical" href="../resource-allocation-and-job-execution.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="introduction.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="introduction.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -230,9 +227,9 @@
<div id="parent-fieldname-text-5df9e884138d4c5899d0e186ed6fa426" class="">
- <p>To run a <a target="_self" title="" class="internal-link" href="job-submission-and-execution.html">job</a>, <a target="_self" title="" class="internal-link" href="resources-allocation-policy.html">computational resources</a> for this particular job must be allocated. This is done via the PBS Pro job workload manager software, which efficiently distributes workloads across the supercomputer. Extensive informations about PBS Pro can be found in the <a target="_self" title="" class="internal-link" href="../../pbspro-documentation.html">official documentation here</a>, especially in the <a target="_self" title="" class="internal-link" href="../../pbspro-documentation/PBSProUserGuide12.pdf">PBS Pro User's Guide</a>.</p>
+ <p>To run a <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">job</a>, <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy">computational resources</a> for this particular job must be allocated. This is done via the PBS Pro job workload manager software, which efficiently distributes workloads across the supercomputer. Extensive informations about PBS Pro can be found in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/pbspro-documentation">official documentation here</a>, especially in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/pbspro-documentation/pbspro-users-guide">PBS Pro User's Guide</a>.</p>
<h2 class=" ">Resources Allocation Policy</h2>
-<p>The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. <a target="_self" title="" class="internal-link" href="job-priority.html">The Fairshare</a> at Salomon ensures that individual users may consume approximately equal amount of resources per week. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following queues are available to Anselm users:</p>
+<p>The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority">The Fairshare</a> at Salomon ensures that individual users may consume approximately equal amount of resources per week. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following queues are available to Anselm users:</p>
<ul>
<li><strong>qexp</strong>, the Express queue</li>
<li><strong>qprod</strong>, the Production queue<strong></strong></li>
@@ -242,11 +239,11 @@
<li><strong>qfree, </strong>the Free resource utilization queue</li>
</ul>
<p class="callout">Check the queue status at <a class="external-link" href="https://extranet.it4i.cz/rsweb/salomon/" target="_self" title="">https://extranet.it4i.cz/rsweb/salomon/</a></p>
-<p>Read more on the <a target="_self" title="" class="internal-link" href="resources-allocation-policy.html">Resource Allocation Policy</a> page.</p>
+<p>Read more on the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy">Resource Allocation Policy</a> page.</p>
<h2 class=" ">Job submission and execution</h2>
<p class="callout">Use the <strong>qsub</strong> command to submit your jobs.</p>
<p class=" ">The qsub submits the job into the queue. The qsub command creates a request to the PBS Job manager for allocation of specified resources. The <strong>smallest allocation unit is entire node, 24 cores</strong>, with exception of the qexp queue. The resources will be allocated when available, subject to allocation policies and constraints. <strong>After the resources are allocated the jobscript or interactive shell is executed on first of the allocated nodes.</strong></p>
-<p class=" ">Read more on the <a target="_self" title="" class="internal-link" href="job-submission-and-execution.html">Job submission and execution</a> page.</p>
+<p class=" ">Read more on the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">Job submission and execution</a> page.</p>
<p class="hiddenForView">HTML commented section #1 (removed Capacity computing section, this will be optimized for Salomon)</p>
@@ -324,7 +321,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -340,7 +337,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -356,7 +353,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -372,7 +369,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -388,7 +385,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -404,7 +401,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -420,7 +417,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -436,7 +433,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -452,7 +449,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -468,7 +465,7 @@
- <a title="" class="state-published contenttype-document" href="resources-allocation-policy.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy">
<span>Resources Allocation Policy</span>
</a>
@@ -484,7 +481,7 @@
- <a title="" class="state-published contenttype-document" href="job-submission-and-execution.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">
<span>Job submission and execution</span>
</a>
@@ -500,7 +497,7 @@
- <a title="" class="state-published contenttype-document" href="job-priority.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority">
<span>Job scheduling</span>
</a>
@@ -516,7 +513,7 @@
- <a title="" class="state-published contenttype-document" href="capacity-computing.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing">
<span>Capacity computing</span>
</a>
@@ -541,7 +538,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -557,7 +554,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -573,7 +570,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -589,10 +586,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -608,7 +605,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -633,7 +630,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -649,7 +646,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -665,7 +662,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -681,7 +678,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
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+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -749,12 +746,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -770,7 +767,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.md b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.md
new file mode 100644
index 0000000000000000000000000000000000000000..ca4160e21fe25241cca4ca2ec5d350132d9a665d
--- /dev/null
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.md
@@ -0,0 +1,50 @@
+Resource Allocation and Job Execution
+=====================================
+
+To run a
+[job](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution),
+[computational
+resources](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy)
+for this particular job must be allocated. This is done via the PBS Pro
+job workload manager software, which efficiently distributes workloads
+across the supercomputer. Extensive informations about PBS Pro can be
+found in the [official documentation
+here](https://docs.it4i.cz/pbspro-documentation),
+especially in the [PBS Pro User's
+Guide](https://docs.it4i.cz/pbspro-documentation/pbspro-users-guide).
+Resources Allocation Policy
+----
+The resources are allocated to the job in a fairshare fashion, subject
+to constraints set by the queue and resources available to the Project.
+[The
+Fairshare](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority)
+at Salomon ensures that individual users may consume approximately equal
+amount of resources per week. The resources are accessible via several
+queues for queueing the jobs. The queues provide prioritized and
+exclusive access to the computational resources. Following queues are
+available to Anselm users:
+- **qexp**, the Express queue
+- **qprod**, the Production queue****
+- **qlong**, the Long queue
+- **qmpp**, the Massively parallel queue
+- **qfat**, the queue to access SMP UV2000 machine
+- **qfree,** the Free resource utilization queue
+Check the queue status at <https://extranet.it4i.cz/rsweb/salomon/>
+Read more on the [Resource Allocation
+Policy](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy)
+page.
+Job submission and execution
+-----
+Use the **qsub** command to submit your jobs.
+The qsub submits the job into the queue. The qsub command creates a
+request to the PBS Job manager for allocation of specified resources.Â
+The **smallest allocation unit is entire node, 24 cores**, with
+exception of the qexp queue. The resources will be allocated when
+available, subject to allocation policies and constraints. **After the
+resources are allocated the jobscript or interactive shell is executed
+on first of the allocated nodes.**
+Read more on the [Job submission and
+execution](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution)
+page.
+HTML commented section #1 (removed Capacity computing section, this
+will be optimized for Salomon)
diff --git a/salomon/resource-allocation-and-job-execution/job-priority.html b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.html
old mode 100755
new mode 100644
similarity index 71%
rename from salomon/resource-allocation-and-job-execution/job-priority.html
rename to docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.html
index a270b8f5d86fbfb3ea5f77b2cc52423498bdde7a..46d34693ed043c18b36c56aef1689bdf0b341349
--- a/salomon/resource-allocation-and-job-execution/job-priority.html
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.html
@@ -10,45 +10,42 @@
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Job scheduling — IT4I Docs</title>
- <link rel="canonical" href="job-priority.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="job-priority.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="job-priority.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../resource-allocation-and-job-execution.html">Resource Allocation and Job Execution</a>
+ <a href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">Resource Allocation and Job Execution</a>
<span class="breadcrumbSeparator">
/
@@ -252,7 +249,7 @@
<p>Fairshare priority is priority calculated on recent usage of resources. Fairshare priority is calculated per project, all members of project share same fairshare priority. Projects with higher recent usage have lower fairshare priority than projects with lower or none recent usage.</p>
<p>Fairshare priority is used for ranking jobs with equal queue priority.</p>
<p>Fairshare priority is calculated as</p>
-<p class=" "><img title="" class="image-inline" alt="" src="../../anselm-cluster-documentation/resource-allocation-and-job-execution/fairshare_formula.png" /></p>
+<p class=" "><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/fairshare_formula.png" /></p>
<p class=" ">where MAX_FAIRSHARE has value 1E6,<br />usage<sub>Project</sub> is cumulated usage by all members of selected project,<br /> usage<sub>Total</sub> is total usage by all users, by all projects.</p>
<p class=" ">Usage counts allocated corehours (ncpus*walltime). Usage is decayed, or cut in half periodically, at the interval 168 hours (one week).<br />Jobs queued in queue qexp are not calculated to project's usage.</p>
<p class="callout"><span>Calculated usage and fairshare priority can be seen at <a class="external-link" href="https://extranet.it4i.cz/rsweb/salomon/projects" target="_self" title="">https://extranet.it4i.cz/rsweb/salomon/projects</a>.</span></p>
@@ -263,7 +260,7 @@
<p><span><span>Eligible time can be seen as eligible_time attribute of job.</span></span></p>
<h3 class=" ">Formula</h3>
<p class=" ">Job execution priority (job sort formula) is calculated as:</p>
-<p class=" "><img title="" class="image-inline" alt="" src="../../anselm-cluster-documentation/resource-allocation-and-job-execution/job_sort_formula.png" /></p>
+<p class=" "><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job_sort_formula.png" /></p>
<h3 class=" ">Job backfilling</h3>
<p><span>The scheduler uses job backfilling.</span></p>
<p>Backfilling means fitting smaller jobs around the higher-priority jobs that the scheduler is going to run next, in such a way that the higher-priority jobs are not delayed. Backfilling allows us to keep resources from becoming idle when the top job (job with the highest execution priority) cannot run.</p>
@@ -272,7 +269,7 @@
<p class="exclamation">It is <strong>very beneficial to specify the walltime</strong> when submitting jobs.</p>
<p class=" ">Specifying more accurate walltime enables better schedulling, better execution times and better resource usage. Jobs with suitable (small) walltime could be backfilled - and overtake job(s) with higher priority.</p>
<h3 class=" ">Job placement</h3>
-<p>Job <a target="_self" title="" class="internal-link" href="job-submission-and-execution.html#job_placement">placement can be controlled by flags during submission</a>.</p>
+<p>Job <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution#job_placement">placement can be controlled by flags during submission</a>.</p>
</div>
@@ -348,7 +345,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -364,7 +361,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -380,7 +377,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -396,7 +393,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -412,7 +409,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -428,7 +425,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -444,7 +441,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -460,7 +457,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -476,7 +473,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -492,7 +489,7 @@
- <a title="" class="state-published contenttype-document" href="resources-allocation-policy.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy">
<span>Resources Allocation Policy</span>
</a>
@@ -508,7 +505,7 @@
- <a title="" class="state-published contenttype-document" href="job-submission-and-execution.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">
<span>Job submission and execution</span>
</a>
@@ -524,7 +521,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="job-priority.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority">
<span>Job scheduling</span>
</a>
@@ -540,7 +537,7 @@
- <a title="" class="state-published contenttype-document" href="capacity-computing.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing">
<span>Capacity computing</span>
</a>
@@ -565,7 +562,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -581,7 +578,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -597,7 +594,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -613,10 +610,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -632,7 +629,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -657,7 +654,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -673,7 +670,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -689,7 +686,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -705,7 +702,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -744,14 +741,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -773,12 +770,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -794,7 +791,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:18 GMT -->
</html>
diff --git a/salomon/resource-allocation-and-job-execution/job-priority.md b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.md
similarity index 63%
rename from salomon/resource-allocation-and-job-execution/job-priority.md
rename to docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.md
index e9ed5b0ae9d995087fd47150e385214581c1c0e7..55556b92119cdef6799da57b0d3507b7a9c70832 100644
--- a/salomon/resource-allocation-and-job-execution/job-priority.md
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.md
@@ -1,9 +1,11 @@
+Job scheduling
+==============
Job execution priority
----------------------
Scheduler gives each job an execution priority and then uses this job
execution priority to select which job(s) to run.
Job execution priority is determined by these job properties (in order
-of importance)
+of importance):
1. queue priority
2. fairshare priority
3. eligible time
@@ -16,6 +18,7 @@ than execution priority of jobs in lower priority queues. Other
properties of job used for determining job execution priority (fairshare
priority, eligible time) cannot compete with queue priority.
Queue priorities can be seen at
+<https://extranet.it4i.cz/rsweb/salomon/queues>
### Fairshare priority
Fairshare priority is priority calculated on recent usage of resources.
Fairshare priority is calculated per project, all members of project
@@ -23,33 +26,34 @@ share same fairshare priority. Projects with higher recent usage have
lower fairshare priority than projects with lower or none recent usage.
Fairshare priority is used for ranking jobs with equal queue priority.
Fairshare priority is calculated as
-
+
where MAX_FAIRSHARE has value 1E6,
usage~Project~ is cumulated usage by all members of selected project,
usage~Total~ is total usage by all users, by all projects.
Usage counts allocated corehours (ncpus*walltime). Usage is decayed, or
cut in half periodically, at the interval 168 hours (one week).
Jobs queued in queue qexp are not calculated to project's usage.
-Calculated usage and fairshare priority can be seen at
-.
-
-Calculated fairshare priority can be also seen as
-Resource_List.fairshare attribute of a job.
-### Eligible time
+<span>Calculated usage and fairshare priority can be seen at
+<https://extranet.it4i.cz/rsweb/salomon/projects>.</span>
+<span>
+<span>Calculated fairshare priority can be also seen as
+Resource_List.fairshare attribute of a job.</span>
+</span>
+### <span>Eligible time</span>
Eligible time is amount (in seconds) of eligible time job accrued while
waiting to run. Jobs with higher eligible time gains higher
-priority.
+pri<span><span></span></span>ority.
Eligible time has the least impact on execution priority. Eligible time
is used for sorting jobs with equal queue priority and fairshare
-priority. It is very, very difficult for eligible time to
+priority. It is very, very difficult for <span>eligible time</span> to
compete with fairshare priority.
-Eligible time can be seen as eligible_time attribute of
-job.
+<span><span>Eligible time can be seen as eligible_time attribute of
+job.</span></span>
### Formula
-Job execution priority (job sort formula) is calculated as
-
+Job execution priority (job sort formula) is calculated as:
+
### Job backfilling
-The scheduler uses job backfilling.
+<span>The scheduler uses job backfilling.</span>
Backfilling means fitting smaller jobs around the higher-priority jobs
that the scheduler is going to run next, in such a way that the
higher-priority jobs are not delayed. Backfilling allows us to keep
@@ -70,30 +74,4 @@ execution times and better resource usage. Jobs with suitable (small)
walltime could be backfilled - and overtake job(s) with higher priority.
### Job placement
Job [placement can be controlled by flags during
-submission](job-submission-and-execution.html#job_placement).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [List of Available
- Modules](../list_of_modules.html "List of Available Modules on Salomon Cluster")
+submission](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution#job_placement).
diff --git a/salomon/resource-allocation-and-job-execution/job-submission-and-execution.html b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.html
old mode 100755
new mode 100644
similarity index 81%
rename from salomon/resource-allocation-and-job-execution/job-submission-and-execution.html
rename to docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.html
index 1cb0e96086341dba8243344e4672801bbc64172b..630a3320ff9694a058a3274013d20654f64d216f
--- a/salomon/resource-allocation-and-job-execution/job-submission-and-execution.html
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:18 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
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- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Job submission and execution — IT4I Docs</title>
- <link rel="canonical" href="job-submission-and-execution.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="job-submission-and-execution.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="job-submission-and-execution.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../resource-allocation-and-job-execution.html">Resource Allocation and Job Execution</a>
+ <a href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">Resource Allocation and Job Execution</a>
<span class="breadcrumbSeparator">
/
@@ -276,7 +273,7 @@
<p class=" ">In this example, we allocate 4 nodes, with 24 cores per node (totalling 96 cores), with 2 Xeon Phi 7120p cards per node (totalling 8 Phi cards), running interactive job for 56 hours. The accelerator model name was omitted.</p>
<h3 class=" ">UV2000 SMP</h3>
<p class="callout">14 NUMA nodes available on UV2000<br /> Per NUMA node allocation.<br />Jobs are isolated by cpusets.</p>
-<p class=" ">The UV2000 (node uv1) offers 3328GB of RAM and 112 cores, distributed in 14 NUMA nodes. A NUMA node packs 8 cores and approx. 236GB RAM. In the PBS the UV2000 provides 14 chunks, a chunk per NUMA node (see <a target="_self" title="" class="internal-link" href="resources-allocation-policy.html">Resource allocation policy</a>). The jobs on UV2000 are isolated from each other by cpusets, so that a job by one user may not utilize CPU or memory allocated to a job by other user. Always, full chunks are allocated, a job may only use resources of the NUMA nodes allocated to itself.</p>
+<p class=" ">The UV2000 (node uv1) offers 3328GB of RAM and 112 cores, distributed in 14 NUMA nodes. A NUMA node packs 8 cores and approx. 236GB RAM. In the PBS the UV2000 provides 14 chunks, a chunk per NUMA node (see <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy">Resource allocation policy</a>). The jobs on UV2000 are isolated from each other by cpusets, so that a job by one user may not utilize CPU or memory allocated to a job by other user. Always, full chunks are allocated, a job may only use resources of the NUMA nodes allocated to itself.</p>
<pre class="prettyprint lang-sh">Â $ qsub -A OPEN-0-0 -q qfat -l select=14 ./myjob</pre>
<p class=" ">In this example, we allocate all 14 NUMA nodes (corresponds to 14 chunks), 112 cores of the SGI UV2000 node for 72 hours. Jobscript myjob will be executed on the node uv1.</p>
<pre class="prettyprint lang-sh">$ qsub -A OPEN-0-0 -q qfat -l select=1:mem=2000GB ./myjob</pre>
@@ -331,9 +328,9 @@
</table>
<p>Â </p>
<pre class="prettyprint lang-sh prettyprinted"><span class="pln">$ qsub </span><span class="pun">-</span><span class="pln">A OPEN</span><span class="pun">-</span><span class="lit">0</span><span class="pun">-</span><span class="lit">0</span><span class="pln"> </span><span class="pun">-</span><span class="pln">q qprod </span><span class="pun">-</span><span class="pln">l select</span><span class="pun">=</span><span class="lit">4</span><span class="pun">:</span><span class="pln">ncpus</span><span class="pun">=24 </span><span class="pln">-l place=group=ehc_1d <span class="pln"></span><span class="pun">-</span><span class="pln">I</span></span></pre>
-<div>In this example, we allocate 4 nodes, 24 cores, selecting only the nodes with <a target="_self" title="" class="internal-link" href="../network-1/7d-enhanced-hypercube.html">hypercube dimension</a> 1.</div>
+<div>In this example, we allocate 4 nodes, 24 cores, selecting only the nodes with <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube">hypercube dimension</a> 1.</div>
<h3 class=" ">Placement by IB switch</h3>
-<div class="internal-link">Groups of computational nodes are connected to chassis integrated Infiniband switches. These switches form the leaf switch layer of the <a target="_self" title="" class="internal-link" href="../network-1.html">Infiniband network</a> . Nodes sharing the leaf switch can communicate most efficiently. Sharing the same switch prevents hops in the network and provides for unbiased, most efficient network communication.</div>
+<div class="internal-link">Groups of computational nodes are connected to chassis integrated Infiniband switches. These switches form the leaf switch layer of the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/network-1">Infiniband network</a> . Nodes sharing the leaf switch can communicate most efficiently. Sharing the same switch prevents hops in the network and provides for unbiased, most efficient network communication.</div>
<div class="internal-link"></div>
<div class="internal-link">There are at most 9 nodes sharing the same Infiniband switch.<br /><br /></div>
<div class="internal-link">Infiniband switch list:</div>
@@ -394,7 +391,7 @@
<p>The recommended way to run production jobs is to change to /scratch directory early in the jobscript, copy all inputs to /scratch, execute the calculations and copy outputs to home directory.</p>
<pre class="prettyprint lang-sh">#!/bin/bash<br /><br /># change to scratch directory, exit on failure<br />SCRDIR=/scratch/<span class="pln">work</span><span class="pun">/</span><span class="pln"></span>user/$USER/myjob<br />mkdir -p $SCRDIR<br />cd $SCRDIR || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/input .<br />cp $PBS_O_WORKDIR/mympiprog.x .<br /><br /># load the mpi module<br />module load OpenMPI<br /><br /># execute the calculation<br />mpiexec -pernode ./mympiprog.x<br /><br /># copy output file to home<br />cp output $PBS_O_WORKDIR/.<br /><br />#exit<br />exit</pre>
<p class=" ">In this example, some directory on the /home holds the input file input and executable mympiprog.x . We create a directory myjob on the /scratch filesystem, copy input and executable files from the /home directory where the qsub was invoked ($PBS_O_WORKDIR) to /scratch, execute the MPI programm mympiprog.x and copy the output file back to the /home directory. The mympiprog.x is executed as one process per node, on all allocated nodes.</p>
-<p class="callout">Consider preloading inputs and executables onto <a target="_self" title="" class="internal-link" href="../storage.html">shared scratch</a> before the calculation starts.</p>
+<p class="callout">Consider preloading inputs and executables onto <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/storage">shared scratch</a> before the calculation starts.</p>
<p>In some cases, it may be impractical to copy the inputs to scratch and outputs to home. This is especially true when very large input and output files are expected, or when the files should be reused by a subsequent calculation. In such a case, it is users responsibility to preload the input files on shared /scratch before the job submission and retrieve the outputs manually, after all calculations are finished.</p>
<p class="callout"><a name="PBSsaved"></a>Store the qsub options within the jobscript. <br />Use <strong>mpiprocs</strong> and <strong>ompthreads</strong> qsub options to control the MPI job execution.</p>
<p>Example jobscript for an MPI job with preloaded inputs and executables, options for qsub are stored within the script :</p>
@@ -404,7 +401,7 @@
<h3 class=" ">Example Jobscript for Single Node Calculation<a name="JobscriptLocal"></a></h3>
<p class="callout">Local scratch directory is often useful for single node jobs. Local scratch will be deleted immediately after the job ends.<br />Be very careful, use of RAM disk filesystem is at the expense of operational memory.</p>
-<p>Example jobscript for single node calculation, using <a target="_self" title="" class="internal-link" href="../storage.html">local scratch</a> on the node:</p>
+<p>Example jobscript for single node calculation, using <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/storage">local scratch</a> on the node:</p>
<pre class="prettyprint lang-sh">#!/bin/bash<br /><br /># change to local scratch directory<br />cd /lscratch/$PBS_JOBID || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/input .<br />cp $PBS_O_WORKDIR/myprog.x .<br /><br /># execute the calculation<br />./myprog.x<br /><br /># copy output file to home<br />cp output $PBS_O_WORKDIR/.<br /><br />#exit<br />exit</pre>
<p class=" ">In this example, some directory on the home holds the input file input and executable myprog.x . We copy input and executable files from the home directory where the qsub was invoked ($PBS_O_WORKDIR) to local scratch /lscratch/$PBS_JOBID, execute the myprog.x and copy the output file back to the /home directory. The myprog.x runs on one node only and may use threads.</p>
<p class="hiddenForView">HTML commented section #3 (Capacity computing need to be reworked)</p>
@@ -484,7 +481,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -500,7 +497,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -516,7 +513,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -532,7 +529,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -548,7 +545,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -564,7 +561,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -580,7 +577,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -596,7 +593,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -612,7 +609,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -628,7 +625,7 @@
- <a title="" class="state-published contenttype-document" href="resources-allocation-policy.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy">
<span>Resources Allocation Policy</span>
</a>
@@ -644,7 +641,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="job-submission-and-execution.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">
<span>Job submission and execution</span>
</a>
@@ -660,7 +657,7 @@
- <a title="" class="state-published contenttype-document" href="job-priority.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority">
<span>Job scheduling</span>
</a>
@@ -676,7 +673,7 @@
- <a title="" class="state-published contenttype-document" href="capacity-computing.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing">
<span>Capacity computing</span>
</a>
@@ -701,7 +698,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -717,7 +714,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -733,7 +730,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -749,10 +746,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -768,7 +765,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -793,7 +790,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -809,7 +806,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -825,7 +822,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -841,7 +838,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -880,14 +877,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -909,12 +906,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -930,7 +927,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:18 GMT -->
</html>
diff --git a/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
similarity index 80%
rename from salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
rename to docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
index 1fd806f2e98f5e057e37d4c4f244e0ca589277fb..ca28db65094cf965efd6d3b0881e5eae154eef41 100644
--- a/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
@@ -1,6 +1,6 @@
+Job submission and execution
============================
-
-
+
Job Submission
--------------
When allocating computational resources for the job, please specify
@@ -13,9 +13,9 @@ When allocating computational resources for the job, please specify
6. Jobscript or interactive switch
Use the **qsub** command to submit your job to a queue for allocation of
the computational resources.
-Submit the job using the qsub command
+Submit the job using the qsub command:
``` {.prettyprint .lang-sh}
-$ qsub -A Project_ID -q queue -l select=xncpus=y,walltime=[[hh]mm]ss[.ms] jobscript
+$ qsub -A Project_ID -q queue -l select=x:ncpus=y,walltime=[[hh:]mm:]ss[.ms] jobscript
```
The qsub submits the job into the queue, in another words the qsub
command creates a request to the PBS Job manager for allocation of
@@ -28,7 +28,7 @@ cluster.**
**
### Job Submission Examples
``` {.prettyprint .lang-sh}
-$ qsub -A OPEN-0-0 -q qprod -l select=64ncpus=24,walltime=030000 ./myjob
+$ qsub -A OPEN-0-0 -q qprod -l select=64:ncpus=24,walltime=03:00:00 ./myjob
```
In this example, we allocate 64 nodes, 24 cores per node, for 3 hours.
We allocate these resources via the qprod queue, consumed resources will
@@ -36,21 +36,21 @@ be accounted to the Project identified by Project ID OPEN-0-0. Jobscript
myjob will be executed on the first node in the allocation.
Â
``` {.prettyprint .lang-sh}
-$ qsub -q qexp -l select=4ncpus=24 -I
+$ qsub -q qexp -l select=4:ncpus=24 -I
```
In this example, we allocate 4 nodes, 24 cores per node, for 1 hour. We
allocate these resources via the qexp queue. The resources will be
available interactively
Â
``` {.prettyprint .lang-sh}
-$ qsub -A OPEN-0-0 -q qlong -l select=10ncpus=24 ./myjob
+$ qsub -A OPEN-0-0 -q qlong -l select=10:ncpus=24 ./myjob
```
In this example, we allocate 10 nodes, 24 cores per node, for 72 hours.
We allocate these resources via the qlong queue. Jobscript myjob will be
executed on the first node in the allocation.
Â
``` {.prettyprint .lang-sh}
-$ qsub -A OPEN-0-0 -q qfree -l select=10ncpus=24 ./myjob
+$ qsub -A OPEN-0-0 -q qfree -l select=10:ncpus=24 ./myjob
```
In this example, we allocate 10Â nodes, 24 cores per node, for 12 hours.
We allocate these resources via the qfree queue. It is not required that
@@ -71,13 +71,13 @@ resources have been spent, etc. The Phi cards are thus also available to
PRACE users. There's no need to ask for permission to utilize the Phi
cards in project proposals.
``` {.prettyprint .lang-sh}
-$ qsub -A OPEN-0-0 -I -q qprod -l select=1ncpus=24accelerator=Truenaccelerators=2accelerator_model=phi7120 ./myjob
+$ qsub -A OPEN-0-0 -I -q qprod -l select=1:ncpus=24:accelerator=True:naccelerators=2:accelerator_model=phi7120 ./myjob
```
In this example, we allocate 1 node, with 24 cores, with 2 Xeon Phi
7120p cards, running batch job ./myjob. The default time for qprod is
used, e. g. 24 hours.
``` {.prettyprint .lang-sh}
-$ qsub -A OPEN-0-0 -I -q qlong -l select=4ncpus=24accelerator=Truenaccelerators=2 -l walltime=560000 -I
+$ qsub -A OPEN-0-0 -I -q qlong -l select=4:ncpus=24:accelerator=True:naccelerators=2 -l walltime=56:00:00 -I
```
In this example, we allocate 4 nodes, with 24 cores per node (totalling
96 cores), with 2 Xeon Phi 7120p cards per node (totalling 8 Phi cards),
@@ -91,11 +91,11 @@ The UV2000 (node uv1) offers 3328GB of RAM and 112 cores, distributed in
14 NUMA nodes. A NUMA node packs 8 cores and approx. 236GB RAM. In the
PBSÂ the UV2000 provides 14 chunks, a chunk per NUMA node (seeÂ
[Resource allocation
-policy](resources-allocation-policy.html)). The jobs on
-UV2000 are isolated from each other by cpusets, so that a job by one
-user may not utilize CPU or memory allocated to a job by other user.
-Always, full chunks are allocated, a job may only use resources of the
-NUMA nodes allocated to itself.
+policy](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy)).
+The jobs on UV2000 are isolated from each other by cpusets, so that a
+job by one user may not utilize CPU or memory allocated to a job by
+other user. Always, full chunks are allocated, a job may only use
+resources of the NUMA nodes allocated to itself.
``` {.prettyprint .lang-sh}
 $ qsub -A OPEN-0-0 -q qfat -l select=14 ./myjob
```
@@ -103,7 +103,7 @@ In this example, we allocate all 14 NUMA nodes (corresponds to 14
chunks), 112 cores of the SGI UV2000 node for 72 hours. Jobscript myjob
will be executed on the node uv1.
``` {.prettyprint .lang-sh}
-$ qsub -A OPEN-0-0 -q qfat -l select=1mem=2000GB ./myjob
+$ qsub -A OPEN-0-0 -q qfat -l select=1:mem=2000GB ./myjob
```
In this example, we allocate 2000GB of memory on the UV2000 for 72
hours. By requesting 2000GB of memory, 10 chunks are allocated.
@@ -117,20 +117,20 @@ $ qsub ./myjob
```
Â
By default, the PBS batch system sends an e-mail only when the job is
-aborted. Disabling mail events completely can be done like this
+aborted. Disabling mail events completely can be done like this:
``` {.prettyprint .lang-sh}
$ qsub -m n
```
[]()Advanced job placement
---------------------------
+---
### Placement by name
Specific nodes may be allocated via the PBS
``` {.prettyprint .lang-sh}
-qsub -A OPEN-0-0 -q qprod -l select=1ncpus=24host=r24u35n680+1ncpus=24host=r24u36n681 -I
+qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=24:host=r24u35n680+1:ncpus=24:host=r24u36n681 -I
```
Or using short names
``` {.prettyprint .lang-sh}
-qsub -A OPEN-0-0 -q qprod -l select=1ncpus=24host=cns680+1ncpus=24host=cns681 -I
+qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=24:host=cns680+1:ncpus=24:host=cns681 -I
```
In this example, we allocate nodes r24u35n680 and r24u36n681, all 24
cores per node, for 24 hours. Consumed resources will be accounted to
@@ -138,8 +138,8 @@ the Project identified by Project ID OPEN-0-0. The resources will be
available interactively.
### Placement by Hypercube dimension
Nodes may be selected via the PBS resource attribute ehc_[1-7]d .
- Hypercube dimension node_group_key
- --------------------- -------------------------------------------
+ Hypercube dimension <span class="pun">node_group_key</span>
+ --------------------- --------------------
1D ehc_1d
2D ehc_2d
3D ehc_3d
@@ -149,21 +149,22 @@ Nodes may be selected via the PBS resource attribute ehc_[1-7]d .
7D ehc_7d
Â
```
-$ qsub -A OPEN-0-0 -q qprod -l select=4ncpus=24 -l place=group=ehc_1d -I
+$ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=24 -l place=group=ehc_1d -I
```
In this example, we allocate 4 nodes, 24 cores, selecting only the nodes
with [hypercube
-dimension](../network-1/7d-enhanced-hypercube.html) 1.
+dimension](https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube)
+1.
### Placement by IB switch
Groups of computational nodes are connected to chassis integrated
Infiniband switches. These switches form the leaf switch layer of the
-[Infiniband network](../network-1.html) . Nodes sharing
-the leaf switch can communicate most efficiently. Sharing the same
-switch prevents hops in the network and provides for unbiased, most
+[InfinibandÂ
+network](https://docs.it4i.cz/salomon/network-1) . Nodes
+sharing the leaf switch can communicate most efficiently. Sharing the
+same switch prevents hops in the network and provides for unbiased, most
efficient network communication.
There are at most 9 nodes sharing the same Infiniband switch.
-
-Infiniband switch list
+Infiniband switch list:
``` {.prettyprint .lang-sh}
$ qmgr -c "print node @a" | grep switch
set node r4i1n11 resources_available.switch = r4i1s0sw1
@@ -171,7 +172,7 @@ set node r2i0n0 resources_available.switch = r2i0s0sw1
set node r2i0n1 resources_available.switch = r2i0s0sw1
...
```
-List of all nodes per Infiniband switch
+List of all nodes per Infiniband switch:
``` {.prettyprint .lang-sh}
$ qmgr -c "print node @a" | grep r36sw3
set node r36u31n964 resources_available.switch = r36sw3
@@ -188,14 +189,14 @@ Nodes sharing the same switch may be selected via the PBS resource
attribute switch.
We recommend allocating compute nodes of a single switch when best
possible computational network performance is required to run the job
-efficiently
+efficiently:
``` {.prettyprint .lang-sh}
-$ qsub -A OPEN-0-0 -q qprod -l select=9ncpus=24switch=r4i1s0sw1 ./myjob
+$ qsub -A OPEN-0-0 -q qprod -l select=9:ncpus=24:switch=r4i1s0sw1 ./myjob
```
In this example, we request all the 9 nodes sharing the r4i1s0sw1 switch
for 24 hours.
``` {.prettyprint .lang-sh}
-$ qsub -A OPEN-0-0 -q qprod -l select=9ncpus=24 -l place=group=switch ./myjob
+$ qsub -A OPEN-0-0 -q qprod -l select=9:ncpus=24 -l place=group=switch ./myjob
```
In this example, we request 9 nodes placed on the same switch using node
grouping placement for 24 hours.
@@ -210,16 +211,16 @@ $ qstat -a -u username
$ qstat -an -u username
$ qstat -f 12345.isrv5
```
-[]()Example
+[]()Example:
``` {.prettyprint .lang-sh}
$ qstat -a
-srv11
+srv11:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
-16287.isrv5 user1 qlong job1 6183 4 64 -- 1440 R 3825
-16468.isrv5 user1 qlong job2 8060 4 64 -- 1440 R 1744
-16547.isrv5 user2 qprod job3x 13516 2 32 -- 4800 R 0058
+16287.isrv5 user1 qlong job1 6183 4 64 -- 144:0 R 38:25
+16468.isrv5 user1 qlong job2 8060 4 64 -- 144:0 R 17:44
+16547.isrv5 user2 qprod job3x 13516 2 32 -- 48:00 R 00:58
```
In this example user1 and user2 are running jobs named job1, job2 and
job3x. The jobs job1 and job2 are using 4 nodes, 16 cores per node each.
@@ -239,14 +240,14 @@ $ check-pbs-jobs --print-job-out --print-job-err
$ check-pbs-jobs --jobid JOBID --check-all --print-all
$ check-pbs-jobs --jobid JOBID --tailf-job-out
```
-Examples
+Examples:
``` {.prettyprint .lang-sh}
$ check-pbs-jobs --check-all
JOB 35141.dm2, session_id 71995, user user2, nodes r3i6n2,r3i6n3
-Check session id OK
+Check session idOK
Check processes
-r3i6n2 OK
-r3i6n3 No process
+r3i6n2OK
+r3i6n3No process
```
In this example we see that job 35141.dm2 currently runs no process on
allocated node r3i6n2, which may indicate an execution error.
@@ -254,13 +255,13 @@ allocated node r3i6n2, which may indicate an execution error.
$ check-pbs-jobs --print-load --print-processes
JOB 35141.dm2, session_id 71995, user user2, nodes r3i6n2,r3i6n3
Print load
-r3i6n2 LOAD 16.01, 16.01, 16.00
-r3i6n3 LOAD 0.01, 0.00, 0.01
+r3i6n2LOAD16.01, 16.01, 16.00
+r3i6n3LOAD 0.01, 0.00, 0.01
Print processes
%CPU CMD
-r3i6n2 0.0 -bash
-r3i6n2 0.0 /bin/bash /var/spool/PBS/mom_priv/jobs/35141.dm2.SC
-r3i6n2 99.7 run-task
+r3i6n2 0.0 -bash
+r3i6n2 0.0 /bin/bash /var/spool/PBS/mom_priv/jobs/35141.dm2.SC
+r3i6n299.7 run-task
...
```
In this example we see that job 35141.dm2 currently runs process
@@ -269,10 +270,10 @@ empty, which may indicate an execution error.
``` {.prettyprint .lang-sh}
$ check-pbs-jobs --jobid 35141.dm2 --print-job-out
JOB 35141.dm2, session_id 71995, user user2, nodes r3i6n2,r3i6n3
-Print job standard output
+Print job standard output:
======================== Job start ==========================
-Started at   Fri Aug 30 024753 CEST 2013
-Script name  script
+Started at   Fri Aug 30 02:47:53 CEST 2013
+Script name  script
Run loop 1
Run loop 2
Run loop 3
@@ -305,13 +306,13 @@ manager.
The jobscript or interactive shell is executed on first of the allocated
nodes.
``` {.prettyprint .lang-sh}
-$ qsub -q qexp -l select=4ncpus=24 -N Name0 ./myjob
+$ qsub -q qexp -l select=4:ncpus=24 -N Name0 ./myjob
$ qstat -n -u username
-isrv5
+isrv5:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
-15209.isrv5 username qexp Name0 5530 4 96 -- 0100 R 0000
+15209.isrv5 username qexp Name0 5530 4 96 -- 01:00 R 00:00
r21u01n577/0*24+r21u02n578/0*24+r21u03n579/0*24+r21u04n580/0*24
```
 In this example, the nodes r21u01n577, r21u02n578, r21u03n579,
@@ -321,9 +322,9 @@ nodes r21u02n578, r21u03n579, r21u04n580 are available for use as well.
The jobscript or interactive shell is by default executed in home
directory
``` {.prettyprint .lang-sh}
-$ qsub -q qexp -l select=4ncpus=24 -I
-qsub waiting for job 15210.isrv5 to start
-qsub job 15210.isrv5 ready
+$ qsub -q qexp -l select=4:ncpus=24 -I
+qsubwaiting for job 15210.isrv5 to start
+qsubjob 15210.isrv5 ready
$ pwd
/home/username
```
@@ -337,9 +338,9 @@ Calculations on allocated nodes may be executed remotely via the MPI,
ssh, pdsh or clush. You may find out which nodes belong to the
allocation by reading the $PBS_NODEFILE file
``` {.prettyprint .lang-sh}
-qsub -q qexp -l select=2ncpus=24 -I
-qsub waiting for job 15210.isrv5 to start
-qsub job 15210.isrv5 ready
+qsub -q qexp -l select=2:ncpus=24 -I
+qsubwaiting for job 15210.isrv5 to start
+qsubjob 15210.isrv5 ready
$ pwd
/home/username
$ sort -u $PBS_NODEFILE
@@ -349,10 +350,10 @@ r4i7n0.ib0.smc.salomon.it4i.cz
r4i7n2.ib0.smc.salomon.it4i.cz
$ pdsh -w r2i5n6,r4i6n13,r4i7n[0,2] hostname
-r4i6n13 r4i6n13
-r2i5n6 r2i5n6
-r4i7n2 r4i7n2
-r4i7n0 r4i7n0
+r4i6n13r4i6n13
+r2i5n6r2i5n6
+r4i7n2r4i7n2
+r4i7n0r4i7n0
```
In this example, the hostname program is executed via pdsh from the
interactive shell. The execution runs on all four allocated nodes. The
@@ -389,7 +390,8 @@ MPI programm mympiprog.x and copy the output file back to the /home
directory. The mympiprog.x is executed as one process per node, on all
allocated nodes.
Consider preloading inputs and executables onto [shared
-scratch](../storage.html) before the calculation starts.
+scratch](https://docs.it4i.cz/salomon/storage) before
+the calculation starts.
In some cases, it may be impractical to copy the inputs to scratch and
outputs to home. This is especially true when very large input and
output files are expected, or when the files should be reused by a
@@ -400,12 +402,12 @@ retrieve the outputs manually, after all calculations are finished.
Use **mpiprocs** and **ompthreads** qsub options to control the MPI job
execution.
Example jobscript for an MPI job with preloaded inputs and executables,
-options for qsub are stored within the script
+options for qsub are stored within the script :
``` {.prettyprint .lang-sh}
#!/bin/bash
#PBS -q qprod
#PBS -N MYJOB
-#PBS -l select=100ncpus=24mpiprocs=1ompthreads=24
+#PBS -l select=100:ncpus=24:mpiprocs=1:ompthreads=24
#PBS -A OPEN-0-0
# change to scratch directory, exit on failure
SCRDIR=/scratch/work/user/$USER/myjob
@@ -430,7 +432,8 @@ scratch will be deleted immediately after the job ends.
Be very careful, use of RAM disk filesystem is at the expense of
operational memory.
Example jobscript for single node calculation, using [local
-scratch](../storage.html) on the node
+scratch](https://docs.it4i.cz/salomon/storage) on the
+node:
``` {.prettyprint .lang-sh}
#!/bin/bash
# change to local scratch directory
@@ -452,29 +455,3 @@ scratch /lscratch/$PBS_JOBID, execute the myprog.x and copy the output
file back to the /home directory. The myprog.x runs on one node only and
may use threads.
HTML commented section #3 (Capacity computing need to be reworked)
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
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-
- - [Salomon Cluster
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-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [List of Available
- Modules](../list_of_modules.html "List of Available Modules on Salomon Cluster")
diff --git a/salomon/resource-allocation-and-job-execution/resources-allocation-policy.html b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.html
old mode 100755
new mode 100644
similarity index 75%
rename from salomon/resource-allocation-and-job-execution/resources-allocation-policy.html
rename to docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.html
index a34e949bc413be234e8aa0035dad2d1d7c4d895b..e62517c653c054091682e8776f560b8c0507b29c
--- a/salomon/resource-allocation-and-job-execution/resources-allocation-policy.html
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.html
@@ -10,45 +10,42 @@
-
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Resources Allocation Policy — IT4I Docs</title>
- <link rel="canonical" href="resources-allocation-policy.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="resources-allocation-policy.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="resources-allocation-policy.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../resource-allocation-and-job-execution.html">Resource Allocation and Job Execution</a>
+ <a href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">Resource Allocation and Job Execution</a>
<span class="breadcrumbSeparator">
/
@@ -241,7 +238,7 @@
<div id="parent-fieldname-text-1abe7c1b150e4d758ffa0dd0be5a7d7b" class="">
<h2 class=" ">Resources Allocation Policy</h2>
-<p>The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. The Fairshare at Anselm ensures that individual users may consume approximately equal amount of resources per week. Detailed information in the <a target="_self" title="" class="internal-link" href="job-priority.html">Job scheduling</a> section. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following table provides the queue partitioning overview:</p>
+<p>The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. The Fairshare at Anselm ensures that individual users may consume approximately equal amount of resources per week. Detailed information in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority">Job scheduling</a> section. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following table provides the queue partitioning overview:</p>
<p>Â </p>
<table class="listing">
<tbody>
@@ -337,14 +334,14 @@
<li><strong>qviz</strong>, the Visualization queue<strong></strong>: Intended for pre-/post-processing using OpenGL accelerated graphics. Currently when accessing the node, each user gets 4 cores of a CPU allocated, thus approximately 73 GB of RAM and 1/7 of the GPU capacity (default "chunk"). <em>If more GPU power or RAM is required, it is recommended to allocate more chunks (with 4 cores each) up to one whole node per user, so that all 28 cores, 512 GB RAM and whole GPU is exclusive. This is currently also the maximum allowed allocation per one user. One hour of work is allocated by default, the user may ask for 2 hours maximum.</em></li>
</ul>
<p>Â </p>
-<p class="callout">To access node with Xeon Phi co-processor user needs to specify that in <a target="_self" title="" class="internal-link" href="job-submission-and-execution.html">job submission select statement</a>.</p>
+<p class="callout">To access node with Xeon Phi co-processor user needs to specify that in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">job submission select statement</a>.</p>
<h3 class=" ">Notes<strong><br /></strong></h3>
-<p>The job wall clock time defaults to<strong> half the maximum time</strong>, see table above. Longer wall time limits can be <a target="_self" title="" class="internal-link" href="job-submission-and-execution.html">set manually, see examples</a>. <br /><br />Jobs that exceed the reserved wall clock time (Req'd Time) get killed automatically. Wall clock time limit can be changed for queuing jobs (state Q) using the qalter command, however can not be changed for a running job (state R).</p>
+<p>The job wall clock time defaults to<strong> half the maximum time</strong>, see table above. Longer wall time limits can be <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">set manually, see examples</a>. <br /><br />Jobs that exceed the reserved wall clock time (Req'd Time) get killed automatically. Wall clock time limit can be changed for queuing jobs (state Q) using the qalter command, however can not be changed for a running job (state R).</p>
<p>Salomon users may check current queue configuration at <a class="external-link" href="https://extranet.it4i.cz/rsweb/salomon/queues" target="_self" title="">https://extranet.it4i.cz/rsweb/salomon/queues</a>.</p>
<h3 class=" ">Queue status</h3>
<p class="callout">Check the status of jobs, queues and compute nodes at <a class="external-link" href="https://extranet.it4i.cz/rsweb/salomon" target="_self" title="">https://extranet.it4i.cz/rsweb/salomon/</a></p>
<p>Â </p>
-<p><img title="RSWEB Salomon" class="image-inline" alt="RSWEB Salomon" src="rsweb-salomon.png" /></p>
+<p><img alt="RSWEB Salomon" class="image-inline" title="RSWEB Salomon" src="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/rswebsalomon.png" /></p>
<p>Â </p>
<p>Display the queue status on Salomon:</p>
<pre class="prettyprint lang-sh">$ qstat -q</pre>
@@ -353,7 +350,7 @@
<pre class="prettyprint lang-sh">$ rspbs<br />Usage: rspbs [options]<br /><br />Options:<br /> --version            show program's version number and exit<br /> -h, --help           show this help message and exit<br /> --get-server-details Print server<br /> --get-queues         Print queues<br /> --get-queues-details Print queues details<br /> --get-reservations   Print reservations<br /> --get-reservations-details<br />                       Print reservations details<br /> --get-nodes          Print nodes of PBS complex<br /> --get-nodeset        Print nodeset of PBS complex<br /> --get-nodes-details  Print nodes details<br /> --get-jobs           Print jobs<br /> --get-jobs-details   Print jobs details<br /> --get-jobs-check-params<br />                       Print jobid, job state, session_id, user, nodes<br /> --get-users          Print users of jobs<br /> --get-allocated-nodes<br />                       Print allocated nodes of jobs<br /> --get-allocated-nodeset<br />                       Print allocated nodeset of jobs<br /> --get-node-users     Print node users<br /> --get-node-jobs      Print node jobs<br /> --get-node-ncpus     Print number of ncpus per node<br /> --get-node-allocated-ncpus<br />                       Print number of allocated ncpus per node<br /> --get-node-qlist     Print node qlist<br /> --get-node-ibswitch  Print node ibswitch<br /> --get-user-nodes     Print user nodes<br /> --get-user-nodeset   Print user nodeset<br /> --get-user-jobs      Print user jobs<br /> --get-user-jobc      Print number of jobs per user<br /> --get-user-nodec     Print number of allocated nodes per user<br /> --get-user-ncpus     Print number of allocated ncpus per user<br /> --get-qlist-nodes    Print qlist nodes<br /> --get-qlist-nodeset  Print qlist nodeset<br /> --get-ibswitch-nodes Print ibswitch nodes<br /> --get-ibswitch-nodeset<br />                       Print ibswitch nodeset<br /> --summary            Print summary<br /> --get-node-ncpu-chart<br />                       Obsolete. Print chart of allocated ncpus per node<br /> --server=SERVER      Use given PBS server<br /> --state=STATE        Only for given job state<br /> --jobid=JOBID        Only for given job ID<br /> --user=USER          Only for given user<br /> --node=NODE          Only for given node<br /> --nodestate=NODESTATE<br />                       Only for given node state (affects only --get-node*<br />                       --get-qlist-* --get-ibswitch-* actions)<br /> --incl-finished      Include finished jobs<br /><br /></pre>
<h2 class=" "><a name="resources-accounting-policy"></a>Resources Accounting Policy</h2>
<h3 class=" ">The Core-Hour</h3>
-<p>The resources that are currently subject to accounting are the core-hours. The core-hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. 1 core-hour is defined as 1 processor core allocated for 1 hour of wall clock time. Allocating a full node (24 cores) for 1 hour accounts to 24 core-hours. See example in the <a target="_self" title="" class="internal-link" href="job-submission-and-execution.html">Job submission and execution</a> section.</p>
+<p>The resources that are currently subject to accounting are the core-hours. The core-hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. 1 core-hour is defined as 1 processor core allocated for 1 hour of wall clock time. Allocating a full node (24 cores) for 1 hour accounts to 24 core-hours. See example in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">Job submission and execution</a> section.</p>
<h3 class=" ">Check consumed resources</h3>
<p class="callout">The <strong>it4ifree</strong> command is a part of it4i.portal.clients package, located here:<br /><a class="external-link" href="https://pypi.python.org/pypi/it4i.portal.clients" target="_self" title="">https://pypi.python.org/pypi/it4i.portal.clients</a></p>
<p>User may check at any time, how many core-hours have been consumed by himself/herself and his/her projects. The command is available on clusters' login nodes.</p>
@@ -434,7 +431,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -450,7 +447,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -466,7 +463,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -482,7 +479,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -498,7 +495,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -514,7 +511,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -530,7 +527,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -546,7 +543,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -562,7 +559,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -578,7 +575,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="resources-allocation-policy.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy">
<span>Resources Allocation Policy</span>
</a>
@@ -594,7 +591,7 @@
- <a title="" class="state-published contenttype-document" href="job-submission-and-execution.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">
<span>Job submission and execution</span>
</a>
@@ -610,7 +607,7 @@
- <a title="" class="state-published contenttype-document" href="job-priority.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority">
<span>Job scheduling</span>
</a>
@@ -626,7 +623,7 @@
- <a title="" class="state-published contenttype-document" href="capacity-computing.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing">
<span>Capacity computing</span>
</a>
@@ -651,7 +648,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -667,7 +664,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -683,7 +680,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -699,10 +696,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -718,7 +715,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -743,7 +740,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -759,7 +756,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -775,7 +772,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -791,7 +788,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -830,14 +827,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -859,12 +856,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -880,7 +877,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:18 GMT -->
</html>
diff --git a/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
similarity index 63%
rename from salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
rename to docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
index 2eac48c69e1c1dc9bf672c42425879bf2a033636..75f0aa81b34b92eb1811c290ea7eb3de94aef169 100644
--- a/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
@@ -1,89 +1,125 @@
+Resources Allocation Policy
===========================
-
-
+
Resources Allocation Policy {#resources-allocation-policy}
----------------------------
+----
The resources are allocated to the job in a fairshare fashion, subject
to constraints set by the queue and resources available to the Project.
The Fairshare at Anselm ensures that individual users may consume
approximately equal amount of resources per week. Detailed information
-in the [Job scheduling](job-priority.html) section. The
-resources are accessible via several queues for queueing the jobs. The
-queues provide prioritized and exclusive access to the computational
-resources. Following table provides the queue partitioning overview
+in the [Job
+scheduling](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority)
+section. The resources are accessible via several queues for queueing
+the jobs. The queues provide prioritized and exclusive access to the
+computational resources. Following table provides the queue partitioning
+overview:
Â
-queue
-active project
-project resources
-nodes
-min ncpus*
-priority
-authorization
-walltime
-default/max
-qexp
-Express queue
-no
-none required
-32 nodes, max 8 per user
-24
-150
-no
-1 / 1h
-qprod
-Production queue
-yes
-> 0
-1006 nodes, max 86 per job
-24
-0
-no
-24 / 48h
-qlong
-Long queue
-yes
-> 0
-256 nodes, max 40 per job
-24
-0
-no
-72 / 144h
-qmpp
-Massive parallel queue
-yes
-> 0
-1006 nodes
-24
-0
-yes
-2 / 4h
-qfat
-UV2000 queue
-yes
-> 0
-1 (uv1)
-8
-0
-yes
-24 / 48h
-qfree
-Free resource queue
-yes
-none required
-752 nodes, max 86 per job
-24
--1024
-no
-12 / 12h
-qviz
-Visualization queue
-yes
-none required
-2 (with NVIDIA Quadro K5000)
-4
-150
-no
-1 / 2h
+<table>
+<colgroup>
+<col width="12%" />
+<col width="12%" />
+<col width="12%" />
+<col width="12%" />
+<col width="12%" />
+<col width="12%" />
+<col width="12%" />
+<col width="12%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">queue</th>
+<th align="left">active project</th>
+<th align="left">project resources</th>
+<th align="left">nodes</th>
+<th align="left">min ncpus*</th>
+<th align="left">priority</th>
+<th align="left">authorization</th>
+<th align="left">walltime<br />
+default/max</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left"><strong>qexp</strong><br />
+Express queue</td>
+<td align="left">no</td>
+<td align="left">none required</td>
+<td align="left">32 nodes, max 8 per user</td>
+<td align="left">24</td>
+<td align="left"><span>150</span></td>
+<td align="left">no</td>
+<td align="left">1 / 1h</td>
+</tr>
+<tr class="even">
+<td align="left"><strong>qprod</strong><br />
+Production queue</td>
+<td align="left">yes<br />
+<br />
+</td>
+<td align="left">> 0</td>
+<td align="left"><p><span>1006 nodes, max 86 per job</span></p></td>
+<td align="left">24</td>
+<td align="left">0</td>
+<td align="left">no</td>
+<td align="left">24 / 48h</td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>qlong</strong><br />
+Long queue</td>
+<td align="left">yes</td>
+<td align="left">> 0</td>
+<td align="left">256 nodes, max 40 per job</td>
+<td align="left">24</td>
+<td align="left">0</td>
+<td align="left">no</td>
+<td align="left">72 / 144h</td>
+</tr>
+<tr class="even">
+<td align="left"><strong>qmpp<br />
+</strong>Massive parallel queue</td>
+<td align="left">yes</td>
+<td align="left">> 0</td>
+<td align="left">1006 nodes</td>
+<td align="left">24</td>
+<td align="left">0</td>
+<td align="left">yes</td>
+<td align="left">2 / 4h</td>
+</tr>
+<tr class="odd">
+<td align="left"><strong>qfat<br />
+</strong>UV2000 queue</td>
+<td align="left">yes</td>
+<td align="left"><p>> 0</p></td>
+<td align="left">1 (uv1)</td>
+<td align="left">8</td>
+<td align="left">0</td>
+<td align="left">yes</td>
+<td align="left">24 / 48h</td>
+</tr>
+<tr class="even">
+<td align="left"><strong>qfree</strong><br />
+Free resource queue</td>
+<td align="left">yes</td>
+<td align="left">none required</td>
+<td align="left">752 nodes, max 86 per job</td>
+<td align="left">24</td>
+<td align="left">-1024</td>
+<td align="left">no</td>
+<td align="left">12 / 12h</td>
+</tr>
+<tr class="odd">
+<td align="left"><strong><strong>qviz</strong><br />
+</strong>Visualization queue</td>
+<td align="left">yes</td>
+<td align="left">none required</td>
+<td align="left">2 (with NVIDIA Quadro K5000)</td>
+<td align="left">4</td>
+<td align="left">150</td>
+<td align="left">no</td>
+<td align="left">1 / 2h</td>
+</tr>
+</tbody>
+</table>
Â
**The qfree queue is not free of charge**. [Normal
accounting](#resources-accounting-policy) applies.
@@ -93,47 +129,47 @@ for Directors Discreation's projects (DD projects) by default. Usage of
qfree after exhaustion of DD projects computational resources is allowed
after request for this queue.
Â
-- **qexp**, the Express queue This queue is dedicated for testing and
+- **qexp**, the Express queueThis queue is dedicated for testing and
running very small jobs. It is not required to specify a project to
- enter the qexp. *There are 2 nodes always reserved for
+ enter the qexp. <span>*<span>There are 2 nodes always reserved for
this queue (w/o accelerator), maximum 8 nodes are available via the
- qexp for a particular user. *The nodes may be
+ qexp for a particular user. </span>*</span>The nodes may be
allocated on per core basis. No special authorization is required to
use it. The maximum runtime in qexp is 1 hour.
-- **qprod**, the Production queue**** This queue is intended for
+- **qprod**, the Production queue****This queue is intended for
normal production runs. It is required that active project with
nonzero remaining resources is specified to enter the qprod. All
nodes may be accessed via the qprod queue, however only 86 per job.
** Full nodes, 24 cores per node are allocated. The queue runs with
medium priority and no special authorization is required to use it.
The maximum runtime in qprod is 48 hours.
-- **qlong**, the Long queue**** This queue is intended for long
+- **qlong**, the Long queue****This queue is intended for long
production runs. It is required that active project with nonzero
remaining resources is specified to enter the qlong. Only 336 nodes
without acceleration may be accessed via the qlong queue. Full
nodes, 24 cores per node are allocated. The queue runs with medium
- priority and no special authorization is required to use it.
+ priority and no special authorization is required to use it.<span>
*The maximum runtime in qlong is 144 hours (three times of the
- standard qprod time - 3 * 48 h)*
-- ****qmpp**, the massively parallel queue. This queue is
+ standard qprod time - 3 * 48 h)*</span>
+- <span>****qmpp**, the massively parallel queue. This queue is
intended for massively parallel runs. It is required that active
project with nonzero remaining resources is specified to enter
the qmpp. All nodes may be accessed via the qmpp queue. ** Full
nodes, 24 cores per node are allocated. The queue runs with medium
priority and no special authorization is required to use it. The
- maximum runtime in qmpp is 4 hours. An PI *needs explicitly*
- ask [support](https//support.it4i.cz/rt/)
+ maximum runtime in qmpp is 4 hours. An PI<span> *needs explicitly*
+ </span>ask [support](https://support.it4i.cz/rt/)
for authorization to enter the queue for all users associated to
her/his Project.
-
-- ****qfat**, the UV2000 queue. This queue is dedicated
+ </span>
+- <span>**</span>**qfat**, the UV2000 queue. This queue is dedicated
to access the fat SGI UV2000 SMP machine. The machine (uv1) has 112
- Intel IvyBridge cores at 3.3GHz and 3.25TB RAM. An PI *needs
- explicitly* ask
- [support](https//support.it4i.cz/rt/) for
+ Intel IvyBridge cores at 3.3GHz and 3.25TB RAM. An PI<span> *needs
+ explicitly* </span>ask
+ [support](https://support.it4i.cz/rt/) for
authorization to enter the queue for all users associated to her/his
Project.****
-- **qfree**, the Free resource queue**** The queue qfree is intended
+- **qfree**, the Free resource queue****The queue qfree is intended
for utilization of free resources, after a Project exhausted all its
allocated computational resources (Does not apply to DD projects
by default. DD projects have to request for persmission on qfree
@@ -144,7 +180,7 @@ after request for this queue.
this queue. Full nodes, 24 cores per node are allocated. The queue
runs with very low priority and no special authorization is required
to use it. The maximum runtime in qfree is 12 hours.
-- **qviz**, the Visualization queue**** Intended for
+- **qviz**, the Visualization queue****Intended for
pre-/post-processing using OpenGL accelerated graphics. Currently
when accessing the node, each user gets 4 cores of a CPU allocated,
thus approximately 73 GB of RAM and 1/7 of the GPU capacity
@@ -157,26 +193,26 @@ after request for this queue.
Â
To access node with Xeon Phi co-processor user needs to specify that in
[job submission select
-statement](job-submission-and-execution.html).
+statement](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution).
### Notes**
**
The job wall clock time defaults to **half the maximum time**, see table
above. Longer wall time limits can be [set manually, see
-examples](job-submission-and-execution.html).
-
+examples](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution).
Jobs that exceed the reserved wall clock time (Req'd Time) get killed
automatically. Wall clock time limit can be changed for queuing jobs
(state Q) using the qalter command, however can not be changed for a
running job (state R).
Salomon users may check current queue configuration at
-.
+<https://extranet.it4i.cz/rsweb/salomon/queues>.
### Queue status
Check the status of jobs, queues and compute nodes at
-[https//extranet.it4i.cz/rsweb/salomon/](https//extranet.it4i.cz/rsweb/salomon)
+[https://extranet.it4i.cz/rsweb/salomon/](https://extranet.it4i.cz/rsweb/salomon)
Â
-
+
Â
-Display the queue status on Salomon
+Display the queue status on Salomon:
``` {.prettyprint .lang-sh}
$ qstat -q
```
@@ -184,8 +220,8 @@ The PBS allocation overview may be obtained also using the rspbs
command.
``` {.prettyprint .lang-sh}
$ rspbs
-Usage rspbs [options]
-Options
+Usagerspbs [options]
+Options:
 --version            show program's version number and exit
 -h, --help           show this help message and exit
 --get-server-details Print server
@@ -238,7 +274,7 @@ Options
 --incl-finished      Include finished jobs
```
[]()Resources Accounting Policy
--------------------------------
+--------
### The Core-Hour
The resources that are currently subject to accounting are the
core-hours. The core-hours are accounted on the wall clock basis. The
@@ -248,45 +284,21 @@ of whether the cores are actually used for any calculation. 1 core-hour
is defined as 1 processor core allocated for 1 hour of wall clock time.
Allocating a full node (24 cores) for 1 hour accounts to 24 core-hours.
See example in the [Job submission and
-execution](job-submission-and-execution.html) section.
+execution](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution)
+section.
### Check consumed resources
The **it4ifree** command is a part of it4i.portal.clients package,
-located here
+located here:
+<https://pypi.python.org/pypi/it4i.portal.clients>
User may check at any time, how many core-hours have been consumed by
himself/herself and his/her projects. The command is available on
clusters' login nodes.
``` {.prettyprint .lang-sh}
$ it4ifree
-Password
+Password:
    PID  Total Used ...by me Free
  -------- ------- ------ -------- -------
  OPEN-0-0 1500000 400644  225265 1099356
  DD-13-1   10000 2606 2606 7394
```
Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [List of Available
- Modules](../list_of_modules.html "List of Available Modules on Salomon Cluster")
diff --git a/salomon/resource-allocation-and-job-execution/rsweb-salomon.png b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/rswebsalomon.png
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/resource-allocation-and-job-execution/rsweb-salomon.png
rename to docs.it4i.cz/salomon/resource-allocation-and-job-execution/rswebsalomon.png
diff --git a/salomon/salomon_1.jpg b/docs.it4i.cz/salomon/salomon
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/salomon_1.jpg
rename to docs.it4i.cz/salomon/salomon
diff --git a/salomon/salomon-1/@@images/ba2c321e-1554-4826-b6ec-3c68d370cd9f.jpg b/docs.it4i.cz/salomon/salomon-1/@@images/ba2c321e-1554-4826-b6ec-3c68d370cd9f.jpeg
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/salomon-1/@@images/ba2c321e-1554-4826-b6ec-3c68d370cd9f.jpg
rename to docs.it4i.cz/salomon/salomon-1/@@images/ba2c321e-1554-4826-b6ec-3c68d370cd9f.jpeg
diff --git a/salomon/salomon_2.jpg b/docs.it4i.cz/salomon/salomon-2
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/salomon_2.jpg
rename to docs.it4i.cz/salomon/salomon-2
diff --git a/salomon/salomon-3/@@images/d2a6de55-62fc-454f-adda-a6a25e3f44dd.jpg b/docs.it4i.cz/salomon/salomon-3/@@images/d2a6de55-62fc-454f-adda-a6a25e3f44dd.jpeg
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/salomon-3/@@images/d2a6de55-62fc-454f-adda-a6a25e3f44dd.jpg
rename to docs.it4i.cz/salomon/salomon-3/@@images/d2a6de55-62fc-454f-adda-a6a25e3f44dd.jpeg
diff --git a/salomon/salomon-4/@@images/82997462-cd88-49eb-aad5-71d77903d903.jpg b/docs.it4i.cz/salomon/salomon-4/@@images/82997462-cd88-49eb-aad5-71d77903d903.jpeg
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/salomon-4/@@images/82997462-cd88-49eb-aad5-71d77903d903.jpg
rename to docs.it4i.cz/salomon/salomon-4/@@images/82997462-cd88-49eb-aad5-71d77903d903.jpeg
diff --git a/salomon/sgi-c1104-gp1/@@images/c1109cbb-9bf4-4f0a-8b0f-a1e464fed0c4.jpg b/docs.it4i.cz/salomon/sgi-c1104-gp1/@@images/c1109cbb-9bf4-4f0a-8b0f-a1e464fed0c4.jpeg
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/sgi-c1104-gp1/@@images/c1109cbb-9bf4-4f0a-8b0f-a1e464fed0c4.jpg
rename to docs.it4i.cz/salomon/sgi-c1104-gp1/@@images/c1109cbb-9bf4-4f0a-8b0f-a1e464fed0c4.jpeg
diff --git a/salomon/software.html b/docs.it4i.cz/salomon/software.html
old mode 100755
new mode 100644
similarity index 68%
rename from salomon/software.html
rename to docs.it4i.cz/salomon/software.html
index d32a5cfdbe1de275c1f922d64a0c88bce04377d2..ef1bf015b9cc9cb03bbd8b1df27bce3a5e974077
--- a/salomon/software.html
+++ b/docs.it4i.cz/salomon/software.html
@@ -10,14 +10,11 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/software by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:46 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/" /><!--[if lt IE 7]></base><![endif]-->
@@ -27,31 +24,31 @@
" name="description" />
- <link rel="stylesheet" type="text/css" media="screen" href="../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
<!--[if lt IE 8]>
<link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/IEFixes-cachekey-ec9b60024fd235ff2c883b4b54db91cb.css" />
<![endif]-->
- <style type="text/css" media="screen">@import url(../portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Software — IT4I Docs</title>
- <link rel="canonical" href="software.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -67,7 +64,7 @@
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -90,9 +87,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="software.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="software.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -128,13 +125,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../index.html">
- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -148,7 +145,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -156,7 +153,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -245,7 +242,7 @@
<span class="summary">
- <a href="software/ansys.html" class="contenttype-folder state-published url">ANSYS</a>
+ <a href="https://docs.it4i.cz/salomon/software/ansys" class="contenttype-folder state-published url">ANSYS</a>
</span>
<span class="documentByLine">
@@ -271,7 +268,7 @@
<span class="summary">
- <a href="software/comsol.html" class="contenttype-folder state-published url">COMSOL</a>
+ <a href="https://docs.it4i.cz/salomon/software/comsol" class="contenttype-folder state-published url">COMSOL</a>
</span>
<span class="documentByLine">
@@ -297,7 +294,7 @@
<span class="summary">
- <a href="software/debuggers.html" class="contenttype-folder state-published url">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/salomon/software/debuggers" class="contenttype-folder state-published url">Debuggers and profilers</a>
</span>
<span class="documentByLine">
@@ -323,7 +320,7 @@
<span class="summary">
- <a href="software/chemistry.html" class="contenttype-folder state-published url">Chemistry, Physics and Materials science</a>
+ <a href="https://docs.it4i.cz/salomon/software/chemistry" class="contenttype-folder state-published url">Chemistry, Physics and Materials science</a>
</span>
<span class="documentByLine">
@@ -349,7 +346,7 @@
<span class="summary">
- <a href="software/intel-suite.html" class="contenttype-folder state-published url">Intel Parallel studio</a>
+ <a href="https://docs.it4i.cz/salomon/software/intel-suite" class="contenttype-folder state-published url">Intel Parallel studio</a>
</span>
<span class="documentByLine">
@@ -375,7 +372,7 @@
<span class="summary">
- <a href="software/mpi-1.html" class="contenttype-folder state-published url">MPI</a>
+ <a href="https://docs.it4i.cz/salomon/software/mpi-1" class="contenttype-folder state-published url">MPI</a>
</span>
<span class="documentByLine">
@@ -401,7 +398,7 @@
<span class="summary">
- <a href="software/numerical-languages.html" class="contenttype-folder state-published url">Numerical languages</a>
+ <a href="https://docs.it4i.cz/salomon/software/numerical-languages" class="contenttype-folder state-published url">Numerical languages</a>
</span>
<span class="documentByLine">
@@ -427,7 +424,7 @@
<span class="summary">
- <a href="software/compilers.html" class="contenttype-document state-published url">Compilers</a>
+ <a href="https://docs.it4i.cz/salomon/software/compilers" class="contenttype-document state-published url">Compilers</a>
</span>
<span class="documentByLine">
@@ -453,7 +450,7 @@
<span class="summary">
- <a href="software/intel-xeon-phi.html" class="contenttype-document state-published url">Intel Xeon Phi</a>
+ <a href="https://docs.it4i.cz/salomon/software/intel-xeon-phi" class="contenttype-document state-published url">Intel Xeon Phi</a>
</span>
<span class="documentByLine">
@@ -479,7 +476,7 @@
<span class="summary">
- <a href="software/java.html" class="contenttype-document state-published url">Java</a>
+ <a href="https://docs.it4i.cz/salomon/software/java" class="contenttype-document state-published url">Java</a>
</span>
<span class="documentByLine">
@@ -505,7 +502,7 @@
<span class="summary">
- <a href="software/operating-system.html" class="contenttype-document state-published url">Operating System</a>
+ <a href="https://docs.it4i.cz/salomon/software/operating-system" class="contenttype-document state-published url">Operating System</a>
</span>
<span class="documentByLine">
@@ -590,7 +587,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -606,7 +603,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -622,7 +619,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -638,7 +635,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -654,7 +651,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -670,7 +667,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -686,7 +683,7 @@
- <a title="" class="state-published contenttype-document" href="environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -702,7 +699,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -718,7 +715,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -734,7 +731,7 @@
- <a title="" class="state-published contenttype-document" href="compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -750,7 +747,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -766,7 +763,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -782,10 +779,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
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<span>ANSYS</span>
</a>
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<span>COMSOL</span>
</a>
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<span>Debuggers and profilers</span>
</a>
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<span>Chemistry, Physics and Materials science</span>
</a>
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<span>Intel Parallel studio</span>
</a>
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<span>MPI</span>
</a>
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<span>Numerical languages</span>
</a>
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<span>Compilers</span>
</a>
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<span>Intel Xeon Phi</span>
</a>
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+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
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+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -986,7 +983,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
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<span>Anselm Cluster Documentation</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
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+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1059,7 +1056,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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old mode 100755
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rename from salomon/software/ansys.html
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--- a/salomon/software/ansys.html
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl" /><!--[if lt IE 7]></base><![endif]-->
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<title>Overview of ANSYS Products — IT4I Docs</title>
- <link rel="canonical" href="ansys.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/ansys" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
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<script type="text/javascript">
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<div id="portal-header">
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- <a accesskey="6" href="ansys.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/ansys#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<div id="portal-advanced-search" class="hiddenStructure">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
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</span>
<span id="breadcrumbs-1" dir="ltr">
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</span>
<span id="breadcrumbs-2" dir="ltr">
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+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
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<div id="parent-fieldname-text-649fda655dce4a4f87c9076dfcfed4b1" class="">
<p><strong><a class="external-link" href="http://www.svsfem.cz/" target="_blank" title="">SVS FEM</a></strong> as <em><strong><a class="external-link" href="http://www.ansys.com/" target="_self" title="">ANSYS Channel partner</a></strong></em> for Czech Republic provided all ANSYS licenses for all clusters and supports of all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent, Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging to problem of ANSYS functionality contact please <a class="email-link" href="mailto:hotline@svsfem.cz?subject=Ostrava%20-%20ANSELM" target="_self" title="">hotline@svsfem.cz</a></p>
-<p>The clusters provides as commercial as academic variants. Academic variants are distinguished by "<strong>Academic...</strong>" word in the name of  license or by two letter preposition "<strong>aa_</strong>" in the license feature name. Change of license is realized on command line respectively directly in user's pbs file (see individual products). <a target="_self" title="" class="internal-link" href="ansys/licensing.html">More about licensing here</a></p>
+<p>The clusters provides as commercial as academic variants. Academic variants are distinguished by "<strong>Academic...</strong>" word in the name of  license or by two letter preposition "<strong>aa_</strong>" in the license feature name. Change of license is realized on command line respectively directly in user's pbs file (see individual products). <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/ansys/licensing">More about licensing here</a></p>
<p>To load the latest version of any ANSYS product (Mechanical, Fluent, CFX, MAPDL,...) load the module:</p>
<pre class=" ">$ module load ANSYS</pre>
<p>ANSYS supports interactive regime, but due to assumed solution of extremely difficult tasks it is not recommended.</p>
@@ -317,7 +314,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
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<span class="portletTopRight"></span>
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<span>Get Started with IT4Innovations</span>
</a>
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<span>Salomon Cluster Documentation</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
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<span>Accessing the Cluster</span>
</a>
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<span>Environment and Modules</span>
</a>
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+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
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<span>Resource Allocation and Job Execution</span>
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<span>Compute Nodes</span>
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<span>Storage</span>
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<span>Network</span>
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+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
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<span>ANSYS</span>
</a>
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<span>ANSYS MAPDL</span>
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<span>ANSYS CFX</span>
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<span>ANSYS Fluent</span>
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<span>ANSYS LS-DYNA</span>
</a>
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<span>Licensing and Available Versions</span>
</a>
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- <img width="16" height="16" src="../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS MAPDL PBS file</span>
</a>
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- <img width="16" height="16" src="../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS CFX PBS file</span>
</a>
@@ -656,8 +653,8 @@
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- <img width="16" height="16" src="../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS Fluent PBS file</span>
</a>
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- <img width="16" height="16" src="../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS LS-DYNA PBS file</span>
</a>
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- <img width="16" height="16" src="../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>LS-DYNA PBS file</span>
</a>
@@ -704,7 +701,7 @@
- <a title="" class="state-published contenttype-document" href="ansys/workbench.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/workbench">
<span>Workbench</span>
</a>
@@ -720,7 +717,7 @@
- <a title="" class="state-published contenttype-document" href="ansys/setting-license-preferences.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/setting-license-preferences">
<span>Setting license preferences</span>
</a>
@@ -745,7 +742,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
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- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
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<span>MPI</span>
</a>
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<span>Numerical languages</span>
</a>
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+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
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+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
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+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
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+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -914,7 +911,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -939,7 +936,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
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+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -987,7 +984,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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-
-<!-- Mirrored from docs.it4i.cz/salomon/software/ansys by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:26 GMT -->
</html>
diff --git a/docs.it4i.cz/salomon/software/ansys.md b/docs.it4i.cz/salomon/software/ansys.md
new file mode 100644
index 0000000000000000000000000000000000000000..7b9535924fdf95994646696efcf45adcb8f0bfc9
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/ansys.md
@@ -0,0 +1,25 @@
+Overview of ANSYS Products
+==========================
+**[SVS FEM](http://www.svsfem.cz/)** as ***[ANSYS
+Channel partner](http://www.ansys.com/)***Â for Czech
+Republic provided all ANSYS licenses for all clusters and supports of
+all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent,
+Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging
+to problem of ANSYS functionality contact
+please [hotline@svsfem.cz](mailto:hotline@svsfem.cz?subject=Ostrava%20-%20ANSELM){.email-link}
+The clusters provides as commercial as academic variants. Academic
+variants are distinguished by "**Academic...**" word in the name of
+Â license or by two letter preposition "**aa_**" in the license feature
+name. Change of license is realized on command line respectively
+directly in user's pbs file (see individual products). [More about
+licensing
+here](https://docs.it4i.cz/salomon/software/ansys/licensing)
+To load the latest version of any ANSYS product (Mechanical, Fluent,
+CFX, MAPDL,...) load the module:
+ $ module load ANSYS
+ANSYS supports interactive regime, but due to assumed solution of
+extremely difficult tasks it is not recommended.
+If user needs to work in interactive regime we recommend to configure
+the RSM service on the client machine which allows to forward the
+solution to the clusters directly from the client's Workbench project
+(see ANSYS RSM service).
diff --git a/salomon/software/ansys/AMsetPar1.png/@@images/a34a45cc-9385-4f05-b12e-efadf1bd93bb.png b/docs.it4i.cz/salomon/software/ansys/AMsetPar1.png/@@images/a34a45cc-9385-4f05-b12e-efadf1bd93bb.png
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old mode 100755
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old mode 100755
new mode 100644
similarity index 100%
rename from salomon/software/ansys/cfx.pbs
rename to docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/at_download/file
diff --git a/salomon/software/ansys/ansys-cfx-pbs-file/view.html b/docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/view.html
old mode 100755
new mode 100644
similarity index 61%
rename from salomon/software/ansys/ansys-cfx-pbs-file/view.html
rename to docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/view.html
index 92ac114e039728529171d8ff6c4b40b007cc7006..0487ec30a0543422962eb378492ba0f7f6a6f49d
--- a/salomon/software/ansys/ansys-cfx-pbs-file/view.html
+++ b/docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/view.html
@@ -10,45 +10,42 @@
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<title>ANSYS CFX PBS file — IT4I Docs</title>
- <link rel="canonical" href="../cfx.pbs" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="view.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/view#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="view.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/view#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
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+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../../ansys.html">ANSYS</a>
+ <a href="https://docs.it4i.cz/salomon/software/ansys">ANSYS</a>
<span class="breadcrumbSeparator">
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cfx.pbs
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<span class="discreet">
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<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
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<span>What's New</span>
</a>
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<span>Get Started with IT4Innovations</span>
</a>
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<span>Salomon Cluster Documentation</span>
</a>
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<span>Hardware Overview</span>
</a>
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<span>Accessing the Cluster</span>
</a>
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<span>Environment and Modules</span>
</a>
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<span>List of Available Modules</span>
</a>
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<span>Resource Allocation and Job Execution</span>
</a>
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<span>Compute Nodes</span>
</a>
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<span>Storage</span>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../network-1.html">
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<span>Network</span>
</a>
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-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../software.html">
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<span>Software</span>
</a>
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<span>ANSYS</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../ansys-mechanical-apdl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl">
<span>ANSYS MAPDL</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx">
<span>ANSYS CFX</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../ansys-fluent.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent">
<span>ANSYS Fluent</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna">
<span>ANSYS LS-DYNA</span>
</a>
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<span>Licensing and Available Versions</span>
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- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view">
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<span>ANSYS MAPDL PBS file</span>
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<span>ANSYS CFX PBS file</span>
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- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view">
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<span>ANSYS Fluent PBS file</span>
</a>
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- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/view">
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<span>ANSYS LS-DYNA PBS file</span>
</a>
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- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>LS-DYNA PBS file</span>
</a>
@@ -700,7 +697,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/workbench">
<span>Workbench</span>
</a>
@@ -716,7 +713,7 @@
- <a title="" class="state-published contenttype-document" href="../setting-license-preferences.html">
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<span>Setting license preferences</span>
</a>
@@ -741,7 +738,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -757,7 +754,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -773,7 +770,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -789,7 +786,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -805,7 +802,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -821,7 +818,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -837,7 +834,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -853,7 +850,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -869,7 +866,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -885,7 +882,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -910,7 +907,7 @@
- <a title="" class="state-published contenttype-document" href="../../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -935,7 +932,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -951,7 +948,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -967,7 +964,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -983,7 +980,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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diff --git a/docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/view.md b/docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/view.md
new file mode 100644
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diff --git a/salomon/software/ansys/ansys-cfx.html b/docs.it4i.cz/salomon/software/ansys/ansys-cfx.html
old mode 100755
new mode 100644
similarity index 65%
rename from salomon/software/ansys/ansys-cfx.html
rename to docs.it4i.cz/salomon/software/ansys/ansys-cfx.html
index 84f915441c5eeb53a802f2fa78914f1f4162b6e7..ee6066f9434249ed028ee5d071d8f809bb0c0d2c
--- a/salomon/software/ansys/ansys-cfx.html
+++ b/docs.it4i.cz/salomon/software/ansys/ansys-cfx.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx" /><!--[if lt IE 7]></base><![endif]-->
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<title>ANSYS CFX — IT4I Docs</title>
- <link rel="canonical" href="ansys-cfx.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
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<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="ansys-cfx.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="ansys-cfx.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../ansys.html">ANSYS</a>
+ <a href="https://docs.it4i.cz/salomon/software/ansys">ANSYS</a>
<span class="breadcrumbSeparator">
/
@@ -249,10 +246,10 @@
<p><a class="external-link" href="http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+CFX" target="_blank" title="">ANSYS CFX</a> software is a high-performance, general purpose fluid dynamics program that has been applied to solve wide-ranging fluid flow problems for over 20 years. At the heart of ANSYS CFX is its advanced solver technology, the key to achieving reliable and accurate solutions quickly and robustly. The modern, highly parallelized solver is the foundation for an abundant choice of physical models to capture virtually any type of phenomena related to fluid flow. The solver and its many physical models are wrapped in a modern, intuitive, and flexible GUI and user environment, with extensive capabilities for customization and automation using session files, scripting and a powerful expression language.</p>
<p><span>To run ANSYS CFX in batch mode you can utilize/modify the default cfx.pbs script and execute it via the qsub command.</span></p>
<pre class=" ">#!/bin/bash<br />#PBS -l nodes=2:ppn=24<br />#PBS -q qprod<br />#PBS -N $USER-CFX-Project<br />#PBS -A OPEN-0-0<br /><br />#! Mail to user when job terminate or abort<br />#PBS -m ae<br /><br />#!change the working directory (default is home directory)<br />#cd <working directory> (working directory must exists)<br />WORK_DIR="/scratch/work/user<strong>/</strong>$USER"<br />cd $WORK_DIR<br /><br />echo Running on host `hostname`<br />echo Time is `date`<br />echo Directory is `pwd`<br />echo This jobs runs on the following processors:<br />echo `cat $PBS_NODEFILE`<br /><br />module load ANSYS<br /><br />#### Set number of processors per host listing<br />procs_per_host=24<br />#### Create host list<br />hl=""<br />for host in `cat $PBS_NODEFILE`<br />do<br /> if [ "$hl" = "" ]<br /> then hl="$host:$procs_per_host"<br /> else hl="${hl}:$host:$procs_per_host"<br /> fi<br />done<br /><br />echo Machines: $hl<br /><br /># prevent ANSYS from attempting to use scif0 interface<br />export MPI_IC_ORDER="UDAPL"<br /><br />#-dev input.def includes the input of CFX analysis in DEF format<br />#-P the name of prefered license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial))<br />cfx5solve -def input.def -size 4 -size-ni 4x -part-large -start-method "Platform MPI Distributed Parallel" -par-dist $hl -P aa_r</pre>
-<p>Header of the pbs file (above) is common and description can be find <a target="_blank" title="" class="internal-link" href="../../resource-allocation-and-job-execution/job-submission-and-execution.html">this site</a>. SVS FEM recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
+<p>Header of the pbs file (above) is common and description can be find <a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">this site</a>. SVS FEM recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
<p>Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. <span>Input file has to be defined by common CFX def file which is attached to the cfx solver via parameter -def</span></p>
-<p><strong>License</strong>Â should be selected by parameter -P (Big letter <strong>P</strong>). Licensed products are the following: aa_r (ANSYSÂ <strong>Academic</strong>Â Research), ane3fl (ANSYS Multiphysics)-<strong>Commercial.</strong> <br /><span><a target="_self" title="" class="internal-link" href="licensing.html">More about licensing here</a></span></p>
-<p class="exclamation">Â We have observed that the -P settings does not always work. Please set your <a target="_self" title="" class="internal-link" href="setting-license-preferences.html">license preferences</a> instead.</p>
+<p><strong>License</strong>Â should be selected by parameter -P (Big letter <strong>P</strong>). Licensed products are the following: aa_r (ANSYSÂ <strong>Academic</strong>Â Research), ane3fl (ANSYS Multiphysics)-<strong>Commercial.</strong> <br /><span><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/ansys/licensing">More about licensing here</a></span></p>
+<p class="exclamation">Â We have observed that the -P settings does not always work. Please set your <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/ansys/setting-license-preferences">license preferences</a> instead.</p>
</div>
@@ -328,7 +325,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -344,7 +341,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -360,7 +357,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -376,7 +373,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -392,7 +389,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -408,7 +405,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -424,7 +421,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -440,7 +437,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -456,7 +453,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -472,7 +469,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -488,7 +485,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -504,7 +501,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -520,10 +517,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -539,7 +536,7 @@
- <a title="An engineering simulation software " class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -555,7 +552,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-mechanical-apdl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl">
<span>ANSYS MAPDL</span>
</a>
@@ -571,7 +568,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="ansys-cfx.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx">
<span>ANSYS CFX</span>
</a>
@@ -587,7 +584,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-fluent.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent">
<span>ANSYS Fluent</span>
</a>
@@ -603,7 +600,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-ls-dyna.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna">
<span>ANSYS LS-DYNA</span>
</a>
@@ -619,7 +616,7 @@
- <a title="" class="state-published contenttype-document" href="licensing.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/licensing">
<span>Licensing and Available Versions</span>
</a>
@@ -635,8 +632,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-mapdl-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS MAPDL PBS file</span>
</a>
@@ -651,8 +648,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-cfx-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS CFX PBS file</span>
</a>
@@ -667,8 +664,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-fluent-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS Fluent PBS file</span>
</a>
@@ -683,8 +680,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS LS-DYNA PBS file</span>
</a>
@@ -699,8 +696,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>LS-DYNA PBS file</span>
</a>
@@ -715,7 +712,7 @@
- <a title="" class="state-published contenttype-document" href="workbench.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/workbench">
<span>Workbench</span>
</a>
@@ -731,7 +728,7 @@
- <a title="" class="state-published contenttype-document" href="setting-license-preferences.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/setting-license-preferences">
<span>Setting license preferences</span>
</a>
@@ -756,7 +753,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -772,7 +769,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -788,7 +785,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -804,7 +801,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -820,7 +817,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -836,7 +833,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -852,7 +849,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -868,7 +865,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -884,7 +881,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -900,7 +897,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -925,7 +922,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -950,7 +947,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -966,7 +963,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -982,7 +979,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -998,7 +995,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1037,14 +1034,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1066,12 +1063,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1087,7 +1084,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/ansys/ansys-cfx by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:19 GMT -->
</html>
diff --git a/docs.it4i.cz/salomon/software/ansys/ansys-cfx.md b/docs.it4i.cz/salomon/software/ansys/ansys-cfx.md
new file mode 100644
index 0000000000000000000000000000000000000000..2038509e37819e5e190cffeb0b8a95faa1478b0a
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/ansys/ansys-cfx.md
@@ -0,0 +1,73 @@
+ANSYS CFX
+=========
+[ANSYS
+CFX](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+CFX)
+software is a high-performance, general purpose fluid dynamics program
+that has been applied to solve wide-ranging fluid flow problems for over
+20 years. At the heart of ANSYS CFX is its advanced solver technology,
+the key to achieving reliable and accurate solutions quickly and
+robustly. The modern, highly parallelized solver is the foundation for
+an abundant choice of physical models to capture virtually any type of
+phenomena related to fluid flow. The solver and its many physical models
+are wrapped in a modern, intuitive, and flexible GUI and user
+environment, with extensive capabilities for customization and
+automation using session files, scripting and a powerful expression
+language.
+<span>To run ANSYS CFX in batch mode you can utilize/modify the default
+cfx.pbs script and execute it via the qsub command.</span>
+ #!/bin/bash
+ #PBS -l nodes=2:ppn=24
+ #PBS -q qprod
+ #PBS -N $USER-CFX-Project
+ #PBS -A OPEN-0-0
+ #! Mail to user when job terminate or abort
+ #PBS -m ae
+ #!change the working directory (default is home directory)
+ #cd <working directory> (working directory must exists)
+ WORK_DIR="/scratch/work/user/$USER"
+ cd $WORK_DIR
+ echo Running on host `hostname`
+ echo Time is `date`
+ echo Directory is `pwd`
+ echo This jobs runs on the following processors:
+ echo `cat $PBS_NODEFILE`
+ module load ANSYS
+ #### Set number of processors per host listing
+ procs_per_host=24
+ #### Create host list
+ hl=""
+ for host in `cat $PBS_NODEFILE`
+ do
+ if [ "$hl" = "" ]
+ then hl="$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
+ fi
+ done
+ echo Machines$hl
+ # prevent ANSYS from attempting to use scif0 interface
+ export MPI_IC_ORDER="UDAPL"
+ #-dev input.def includes the input of CFX analysis in DEF format
+ #-P the name of prefered license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial))
+ cfx5solve -def input.def -size 4 -size-ni 4x -part-large -start-method "Platform MPI Distributed Parallel" -par-dist $hl -P aa_r
+Header of the pbs file (above) is common and description can be findÂ
+[this
+site](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution).
+SVS FEM recommends to utilize sources by keywordsnodes, ppn. These
+keywords allows to address directly the number of nodes (computers) and
+cores (ppn) which will be utilized in the job. Also the rest of code
+assumes such structure of allocated resources.
+Working directory has to be created before sending pbs job into the
+queue. Input file should be in working directory or full path to input
+file has to be specified. <span>Input file has to be defined by common
+CFX def file which is attached to the cfx solver via parameter
+-def</span>
+**License**Â should be selected by parameter -P (Big letter **P**).
+Licensed products are the followingaa_r
+(ANSYSÂ **Academic**Â Research), ane3fl (ANSYS
+Multiphysics)-**Commercial.**
+<span>[More about licensing
+here](https://docs.it4i.cz/salomon/software/ansys/licensing)</span>
+Â We have observed that the -P settings does not always work. Please set
+your [license
+preferences](https://docs.it4i.cz/salomon/software/ansys/setting-license-preferences)
+instead.
diff --git a/salomon/software/ansys/ansys-fluent-pbs-file/at_download/fluent.pbs b/docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file.1
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/software/ansys/ansys-fluent-pbs-file/at_download/fluent.pbs
rename to docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file.1
diff --git a/salomon/software/ansys/fluent.pbs b/docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/at_download/file
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/software/ansys/fluent.pbs
rename to docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/at_download/file
diff --git a/salomon/software/ansys/ansys-fluent-pbs-file/view.html b/docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view.html
old mode 100755
new mode 100644
similarity index 61%
rename from salomon/software/ansys/ansys-fluent-pbs-file/view.html
rename to docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view.html
index 882df75a41b371b03dad32e570c302f6c457c9d9..f02c26165f63ca7d25516a41f9af311f9ce3f4b8
--- a/salomon/software/ansys/ansys-fluent-pbs-file/view.html
+++ b/docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:20 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/IEFixes-cachekey-ec9b60024fd235ff2c883b4b54db91cb.css" />
<![endif]-->
- <style type="text/css" media="screen">@import url(../../../../portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
- <link rel="stylesheet" type="text/css" href="../../../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="../../../../portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
- <script type="text/javascript" src="../../../../portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
- <script type="text/javascript" src="../../../../portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
- <script type="text/javascript" src="../../../../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="../../../../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>ANSYS Fluent PBS file — IT4I Docs</title>
- <link rel="canonical" href="../fluent.pbs" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="view.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="view.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../../index.html">
- <img src="../../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../../ansys.html">ANSYS</a>
+ <a href="https://docs.it4i.cz/salomon/software/ansys">ANSYS</a>
<span class="breadcrumbSeparator">
/
@@ -250,8 +247,8 @@
- <a href="at_download/fluent.pbs">
- <img src="../../../../sh.png" alt="shell script icon" />
+ <a href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/at_download/file">
+ <img src="https://docs.it4i.cz/sh.png" alt="shell script icon" />
fluent.pbs
</a>
<span class="discreet">
@@ -313,7 +310,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -329,7 +326,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -345,7 +342,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -361,7 +358,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -377,7 +374,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -393,7 +390,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -409,7 +406,7 @@
- <a title="" class="state-published contenttype-document" href="../../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -425,7 +422,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -441,7 +438,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -457,7 +454,7 @@
- <a title="" class="state-published contenttype-document" href="../../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -473,7 +470,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -489,7 +486,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -505,10 +502,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -524,7 +521,7 @@
- <a title="An engineering simulation software " class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../ansys.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -540,7 +537,7 @@
- <a title="" class="state-published contenttype-document" href="../ansys-mechanical-apdl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl">
<span>ANSYS MAPDL</span>
</a>
@@ -556,7 +553,7 @@
- <a title="" class="state-published contenttype-document" href="../ansys-cfx.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx">
<span>ANSYS CFX</span>
</a>
@@ -572,7 +569,7 @@
- <a title="" class="state-published contenttype-document" href="../ansys-fluent.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent">
<span>ANSYS Fluent</span>
</a>
@@ -588,7 +585,7 @@
- <a title="" class="state-published contenttype-document" href="../ansys-ls-dyna.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna">
<span>ANSYS LS-DYNA</span>
</a>
@@ -604,7 +601,7 @@
- <a title="" class="state-published contenttype-document" href="../licensing.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/licensing">
<span>Licensing and Available Versions</span>
</a>
@@ -620,8 +617,8 @@
- <a title="" class="state-missing-value contenttype-file" href="../ansys-mapdl-pbs-file/view.html">
- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS MAPDL PBS file</span>
</a>
@@ -636,8 +633,8 @@
- <a title="" class="state-missing-value contenttype-file" href="../ansys-cfx-pbs-file/view.html">
- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS CFX PBS file</span>
</a>
@@ -652,8 +649,8 @@
- <a title="" class="state-missing-value navTreeCurrentItem navTreeCurrentNode contenttype-file" href="view.html">
- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value navTreeCurrentItem navTreeCurrentNode contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS Fluent PBS file</span>
</a>
@@ -668,8 +665,8 @@
- <a title="" class="state-missing-value contenttype-file" href="../ansys-ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS LS-DYNA PBS file</span>
</a>
@@ -684,8 +681,8 @@
- <a title="" class="state-missing-value contenttype-file" href="../ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>LS-DYNA PBS file</span>
</a>
@@ -700,7 +697,7 @@
- <a title="" class="state-published contenttype-document" href="../workbench.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/workbench">
<span>Workbench</span>
</a>
@@ -716,7 +713,7 @@
- <a title="" class="state-published contenttype-document" href="../setting-license-preferences.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/setting-license-preferences">
<span>Setting license preferences</span>
</a>
@@ -741,7 +738,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -757,7 +754,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -773,7 +770,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -789,7 +786,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -805,7 +802,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -821,7 +818,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../../numerical-languages.html">
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<span>Numerical languages</span>
</a>
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+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
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- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
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+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
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- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
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- <a title="" class="state-published contenttype-collection" href="../../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
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- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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</html>
diff --git a/docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view.md b/docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view.md
new file mode 100644
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diff --git a/salomon/software/ansys/ansys-fluent.html b/docs.it4i.cz/salomon/software/ansys/ansys-fluent.html
old mode 100755
new mode 100644
similarity index 69%
rename from salomon/software/ansys/ansys-fluent.html
rename to docs.it4i.cz/salomon/software/ansys/ansys-fluent.html
index 96a8d6e5b474f8c5c0d9e39221e4784da15752eb..1fbc8f9f835755eb74146bdbdc85708d0dead285
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<title>ANSYS Fluent — IT4I Docs</title>
- <link rel="canonical" href="ansys-fluent.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
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<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="ansys-fluent.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="ansys-fluent.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent#portal-globalnav">PĹ™ejĂt na navigaci</a>
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+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
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</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
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</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
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/
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</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../ansys.html">ANSYS</a>
+ <a href="https://docs.it4i.cz/salomon/software/ansys">ANSYS</a>
<span class="breadcrumbSeparator">
/
@@ -250,7 +247,7 @@
<h2 class=" "><span>1. Common way to run Fluent over pbs file</span></h2>
<p><span>To run ANSYS Fluent in batch mode you can utilize/modify the default fluent.pbs script and execute it via the qsub command.</span></p>
<pre class=" ">#!/bin/bash<br />#PBS -S /bin/bash<br />#PBS -l nodes=2:ppn=24<br />#PBS -q qprod<br />#PBS -N Fluent-Project<br />#PBS -A OPEN-0-0<br /><br />#! Mail to user when job terminate or abort<br />#PBS -m ae<br /><br />#!change the working directory (default is home directory)<br />#cd <working directory> (working directory must exists)<br />WORK_DIR="/scratch/work/user<strong>/</strong>$USER"<br />cd $WORK_DIR<br /><br />echo Running on host `hostname`<br />echo Time is `date`<br />echo Directory is `pwd`<br />echo This jobs runs on the following processors:<br />echo `cat $PBS_NODEFILE`<br /><br />#### Load ansys module so that we find the cfx5solve command<br />module load ANSYS<br /><br /># Use following line to specify MPI for message-passing instead<br />NCORES=`wc -l $PBS_NODEFILE |awk '{print $1}'`<br /><br />/apps/cae/ANSYS/16.1/v161/fluent/bin/fluent 3d -t$NCORES -cnf=$PBS_NODEFILE -g -i fluent.jou</pre>
-<p>Header of the pbs file (above) is common and description can be find on <a target="_blank" title="" class="internal-link" href="../../resource-allocation-and-job-execution/job-submission-and-execution.html">this site</a>. <a class="external-link" href="http://www.svsfem.cz/" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
+<p>Header of the pbs file (above) is common and description can be find on <a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">this site</a>. <a class="external-link" href="http://www.svsfem.cz" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
<p>Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common Fluent journal file which is attached to the Fluent solver via parameter -i fluent.jou</p>
<p>Journal file with definition of the input geometry and boundary conditions and defined process of solution has e.g. the following structure:</p>
<pre class=" ">/file/read-case aircraft_2m.cas.gz<br />/solve/init<br />init<br />/solve/iterate<br />10<br />/file/write-case-dat aircraft_2m-solution<br />/exit yes</pre>
@@ -327,7 +324,7 @@
</div>
<p><span>It runs the jobs out of the directory from which they are submitted (PBS_O_WORKDIR).</span></p>
<h2 class=" ">4. Running Fluent in parralel</h2>
-<p><a name="license_preferences"></a>Fluent could be run in parallel only under Academic Research license. To do so this ANSYS Academic Research license must be placed before ANSYS CFD license in user preferences. To make this change <a target="_self" title="" class="internal-link" href="setting-license-preferences.html">anslic_admin utility should be run</a>.</p>
+<p><a name="license_preferences"></a>Fluent could be run in parallel only under Academic Research license. To do so this ANSYS Academic Research license must be placed before ANSYS CFD license in user preferences. To make this change <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/ansys/setting-license-preferences">anslic_admin utility should be run</a>.</p>
<p>Â </p>
</div>
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<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
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- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -596,10 +593,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -615,7 +612,7 @@
- <a title="An engineering simulation software " class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
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- <a title="" class="state-published contenttype-document" href="ansys-mechanical-apdl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl">
<span>ANSYS MAPDL</span>
</a>
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- <a title="" class="state-published contenttype-document" href="ansys-cfx.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx">
<span>ANSYS CFX</span>
</a>
@@ -663,7 +660,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="ansys-fluent.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent">
<span>ANSYS Fluent</span>
</a>
@@ -679,7 +676,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-ls-dyna.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna">
<span>ANSYS LS-DYNA</span>
</a>
@@ -695,7 +692,7 @@
- <a title="" class="state-published contenttype-document" href="licensing.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/licensing">
<span>Licensing and Available Versions</span>
</a>
@@ -711,8 +708,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-mapdl-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS MAPDL PBS file</span>
</a>
@@ -727,8 +724,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-cfx-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS CFX PBS file</span>
</a>
@@ -743,8 +740,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-fluent-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS Fluent PBS file</span>
</a>
@@ -759,8 +756,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS LS-DYNA PBS file</span>
</a>
@@ -775,8 +772,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>LS-DYNA PBS file</span>
</a>
@@ -791,7 +788,7 @@
- <a title="" class="state-published contenttype-document" href="workbench.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/workbench">
<span>Workbench</span>
</a>
@@ -807,7 +804,7 @@
- <a title="" class="state-published contenttype-document" href="setting-license-preferences.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/setting-license-preferences">
<span>Setting license preferences</span>
</a>
@@ -832,7 +829,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -848,7 +845,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -864,7 +861,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -880,7 +877,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -896,7 +893,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -912,7 +909,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -928,7 +925,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -944,7 +941,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -960,7 +957,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -976,7 +973,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -1001,7 +998,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -1026,7 +1023,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -1042,7 +1039,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1058,7 +1055,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1074,7 +1071,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1113,14 +1110,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1142,12 +1139,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1163,7 +1160,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/ansys/ansys-fluent by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:19 GMT -->
</html>
diff --git a/docs.it4i.cz/salomon/software/ansys/ansys-fluent.md b/docs.it4i.cz/salomon/software/ansys/ansys-fluent.md
new file mode 100644
index 0000000000000000000000000000000000000000..be67f0a505a3e61547154402eaf221327c48362b
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/ansys/ansys-fluent.md
@@ -0,0 +1,169 @@
+ANSYS Fluent
+============
+[ANSYS
+Fluent](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent)
+software contains the broad physical modeling capabilities needed to
+model flow, turbulence, heat transfer, and reactions for industrial
+applications ranging from air flow over an aircraft wing to combustion
+in a furnace, from bubble columns to oil platforms, from blood flow to
+semiconductor manufacturing, and from clean room design to wastewater
+treatment plants. Special models that give the software the ability to
+model in-cylinder combustion, aeroacoustics, turbomachinery, and
+multiphase systems have served to broaden its reach.
+<span>1. Common way to run Fluent over pbs file</span>
+--------
+<span>To run ANSYS Fluent in batch mode you can utilize/modify the
+default fluent.pbs script and execute it via the qsub command.</span>
+ #!/bin/bash
+ #PBS -S /bin/bash
+ #PBS -l nodes=2:ppn=24
+ #PBS -q qprod
+ #PBS -N Fluent-Project
+ #PBS -A OPEN-0-0
+ #! Mail to user when job terminate or abort
+ #PBS -m ae
+ #!change the working directory (default is home directory)
+ #cd <working directory> (working directory must exists)
+ WORK_DIR="/scratch/work/user/$USER"
+ cd $WORK_DIR
+ echo Running on host `hostname`
+ echo Time is `date`
+ echo Directory is `pwd`
+ echo This jobs runs on the following processors:
+ echo `cat $PBS_NODEFILE`
+ #### Load ansys module so that we find the cfx5solve command
+ module load ANSYS
+ # Use following line to specify MPI for message-passing instead
+ NCORES=`wc -l $PBS_NODEFILE |awk '{print $1}'`
+ /apps/cae/ANSYS/16.1/v161/fluent/bin/fluent 3d -t$NCORES -cnf=$PBS_NODEFILE -g -i fluent.jou
+Header of the pbs file (above) is common and description can be find on
+[this
+site](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution).
+[SVS FEM](http://www.svsfem.cz) recommends to utilize
+sources by keywordsnodes, ppn. These keywords allows to address
+directly the number of nodes (computers) and cores (ppn) which will be
+utilized in the job. Also the rest of code assumes such structure of
+allocated resources.
+Working directory has to be created before sending pbs job into the
+queue. Input file should be in working directory or full path to input
+file has to be specified. Input file has to be defined by common Fluent
+journal file which is attached to the Fluent solver via parameter -i
+fluent.jou
+Journal file with definition of the input geometry and boundary
+conditions and defined process of solution has e.g. the following
+structure:
+ /file/read-case aircraft_2m.cas.gz
+ /solve/init
+ init
+ /solve/iterate
+ 10
+ /file/write-case-dat aircraft_2m-solution
+ /exit yes
+<span>The appropriate dimension of the problem has to be set by
+parameter (2d/3d). </span>
+<span>2. Fast way to run Fluent from command line</span>
+----------
+ fluent solver_version [FLUENT_options] -i journal_file -pbs
+This syntax will start the ANSYS FLUENT job under PBS Professional using
+the <span class="monospace">qsub</span>Â command in a batch manner. When
+resources are available, PBS Professional will start the job and return
+a job ID, usually in the form of <span
+class="emphasis">*job_ID.hostname*</span>. This job ID can then be used
+to query, control, or stop the job using standard PBS Professional
+commands, such as <span class="monospace">qstat</span>Â or <span
+class="monospace">qdel</span>. The job will be run out of the current
+working directory, and all output will be written to the file <span
+class="monospace">fluent.o</span><span>Â </span><span
+class="emphasis">*job_ID*</span>. Â Â Â Â
+3. Running Fluent via user's config file
+-----------------
+The sample script uses a configuration file called <span
+class="monospace">pbs_fluent.conf</span> Â if no command line arguments
+are present. This configuration file should be present in the directory
+from which the jobs are submitted (which is also the directory in which
+the jobs are executed). The following is an example of what the content
+of <span class="monospace">pbs_fluent.conf</span>Â can be:
+``` {.screen}
+ input="example_small.flin"
+ case="Small-1.65m.cas"
+ fluent_args="3d -pmyrinet"
+ outfile="fluent_test.out"
+ mpp="true"
+```
+The following is an explanation of the parameters:
+<span><span class="monospace">input</span> is the name of the input
+file.</span>
+<span class="monospace">case</span> is the name of the <span
+class="monospace">.cas</span>Â file that the input file will utilize.
+<span class="monospace">fluent_args</span> are extra ANSYS FLUENT
+arguments. As shown in the previous example, you can specify the
+interconnect by using the <span class="monospace">-p</span>Â interconnect
+command. The available interconnects include <span
+class="monospace">ethernet</span>Â (the default), <span
+class="monospace">myrinet</span>,<span class="monospace">
+infiniband</span>, <span class="monospace">vendor</span>, <span
+class="monospace">altix</span><span>,</span> and <span
+class="monospace">crayx</span>. The MPI is selected automatically, based
+on the specified interconnect.
+<span class="monospace">outfile</span> is the name of the file to which
+the standard output will be sent.
+<span class="monospace">mpp="true"</span> will tell the job script to
+execute the job across multiple processors. Â Â Â Â Â Â Â Â
+<span>To run ANSYS Fluent in batch mode with user's config file you can
+utilize/modify the following script and execute it via the qsub
+command.</span>
+``` {.screen}
+#!/bin/sh
+#PBS -l nodes=2:ppn=24
+#PBS -1 qprod
+#PBS -N Fluent-Project
+#PBS -A OPEN-0-0
+ cd $PBS_O_WORKDIR
+
+ #We assume that if they didn’t specify arguments then they should use the
+ #config file if [ "xx${input}${case}${mpp}${fluent_args}zz" = "xxzz" ]; then
+ if [ -f pbs_fluent.conf ]; then
+ . pbs_fluent.conf
+ else
+ printf "No command line arguments specified, "
+ printf "and no configuration file found. Exiting n"
+ fi
+ fi
+
+ #Augment the ANSYS FLUENT command line arguments case "$mpp" in
+ true)
+ #MPI job execution scenario
+ num_nodes=â€cat $PBS_NODEFILE | sort -u | wc -lâ€
+ cpus=â€expr $num_nodes * $NCPUSâ€
+ #Default arguments for mpp jobs, these should be changed to suit your
+ #needs.
+ fluent_args="-t${cpus} $fluent_args -cnf=$PBS_NODEFILE"
+ ;;
+ *)
+ #SMP case
+ #Default arguments for smp jobs, should be adjusted to suit your
+ #needs.
+ fluent_args="-t$NCPUS $fluent_args"
+ ;;
+ esac
+ #Default arguments for all jobs
+ fluent_args="-ssh -g -i $input $fluent_args"
+ echo "---------- Going to start a fluent job with the following settings:
+ Input$input
+ Case$case
+ Output$outfile
+ Fluent arguments$fluent_args"
+
+ #run the solver
+ /apps/cae/ANSYS/16.1/v161/fluent/bin/fluent $fluent_args > $outfile
+```
+<span>It runs the jobs out of the directory from which they are
+submitted (PBS_O_WORKDIR).</span>
+4. Running Fluent in parralel
+------
+[]()Fluent could be run in parallel only under Academic Research
+license. To do so this ANSYS Academic Research license must be placed
+before ANSYS CFD license in user preferences. To make this change
+[anslic_admin utility should be
+run](https://docs.it4i.cz/salomon/software/ansys/setting-license-preferences).
+Â
diff --git a/salomon/software/ansys/ansys-ls-dyna-pbs-file/at_download/ansysdyna.pbs b/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file.1
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/software/ansys/ansys-ls-dyna-pbs-file/at_download/ansysdyna.pbs
rename to docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file.1
diff --git a/salomon/software/ansys/ansysdyna.pbs b/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/at_download/file
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/software/ansys/ansysdyna.pbs
rename to docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/at_download/file
diff --git a/salomon/software/ansys/ansys-ls-dyna-pbs-file/view.html b/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/view.html
old mode 100755
new mode 100644
similarity index 61%
rename from salomon/software/ansys/ansys-ls-dyna-pbs-file/view.html
rename to docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/view.html
index 0eb3f78c4b38141f0b090126f8709742cc7a2a99..429fc0dbef80e4a255eaeac9cdc965638e541eae
--- a/salomon/software/ansys/ansys-ls-dyna-pbs-file/view.html
+++ b/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/view.html
@@ -10,45 +10,42 @@
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<title>ANSYS LS-DYNA PBS file — IT4I Docs</title>
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<span>Anselm Cluster Documentation</span>
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<a href="http://study.it4i.cz/">HPC Study</a>
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<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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<title>ANSYS LS-DYNA — IT4I Docs</title>
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- <a accesskey="2" href="ansys-ls-dyna.html#content">PĹ™ejĂt na obsah</a> |
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- <a accesskey="6" href="ansys-ls-dyna.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna#portal-globalnav">PĹ™ejĂt na navigaci</a>
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- <a href="../ansys.html">ANSYS</a>
+ <a href="https://docs.it4i.cz/salomon/software/ansys">ANSYS</a>
<span class="breadcrumbSeparator">
/
@@ -249,7 +246,7 @@
<p><a class="external-link" href="http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/Explicit+Dynamics/ANSYS+LS-DYNA" target="_blank" title="">ANSYS LS-DYNA</a> software provides convenient and easy-to-use access to the technology-rich, time-tested explicit solver without the need to contend with the complex input requirements of this sophisticated program. Introduced in 1996, ANSYS LS-DYNA capabilities have helped customers in numerous industries to resolve highly intricate design issues. <span>ANSYS Mechanical users have been able take advantage of complex explicit solutions for a long time utilizing the traditional ANSYS Parametric Design Language (APDL) environment. <span>These explicit capabilities are available to ANSYS Workbench users as well. The Workbench platform is a powerful, comprehensive, easy-to-use environment for engineering simulation. CAD import from all sources, geometry cleanup, automatic meshing, solution, parametric optimization, result visualization and comprehensive report generation are all available within a single fully interactive modern graphical user environment.</span></span></p>
<p><span>To run ANSYS LS-DYNA in batch mode you can utilize/modify the default ansysdyna.pbs script and execute it via the qsub command.</span></p>
<pre class=" ">#!/bin/bash<br />#PBS -l nodes=2:ppn=24<br />#PBS -q qprod<br />#PBS -N DYNA-Project<br />#PBS -A OPEN-0-0<br /><br />#! Mail to user when job terminate or abort<br />#PBS -m ae<br /><br />#!change the working directory (default is home directory)<br />#cd <working directory><br />WORK_DIR="/scratch/work/user<strong>/</strong>$USER"<br />cd $WORK_DIR<br /><br />echo Running on host `hostname`<br />echo Time is `date`<br />echo Directory is `pwd`<br />echo This jobs runs on the following processors:<br />echo `cat $PBS_NODEFILE`<br /><br />module load ANSYS<br /><br />#### Set number of processors per node<br />procs_per_host=24<br />#### Create host list<br />hl=""<br />for host in `cat $PBS_NODEFILE`<br />do<br /> if [ "$hl" = "" ]<br /> then hl="$host:$procs_per_host"<br /> else hl="${hl}:$host:$procs_per_host"<br /> fi<br />done<br /><br />echo Machines: $hl<br /><br /># prevent ANSYS from attempting to use scif0 interface<br />export MPI_IC_ORDER="UDAPL"<br /><br />lsdyna161 -dis -usessh -machines "$hl" i=input.k</pre>
-<p><span>Header of the pbs file (above) is common and description can be find </span><span> on <a target="_blank" title="" class="internal-link" href="../../resource-allocation-and-job-execution/job-submission-and-execution.html">this site</a>. <a class="external-link" href="http://www.svsfem.cz/" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</span></p>
+<p><span>Header of the pbs file (above) is common and description can be find </span><span> on <a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">this site</a>. <a class="external-link" href="http://www.svsfem.cz" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</span></p>
<p>Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common LS-DYNA .<strong>k</strong> file which is attached to the ansys solver via parameter i=</p>
<p class="exclamation">Without setting environment variable MPI_IC_ORDER="UDAPL", ANSYS will fail to run on nodes with Xeon Phi accelerator (it will use the virtual interface of Phi cards instead of the real InfiniBand interface and MPI will fail.</p>
<p><span><span><br /></span></span></p>
@@ -328,7 +325,7 @@
<dt class="portletHeader hiddenStructure">
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+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
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</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -392,7 +389,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -440,7 +437,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -472,7 +469,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -520,10 +517,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -539,7 +536,7 @@
- <a title="An engineering simulation software " class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -555,7 +552,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-mechanical-apdl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl">
<span>ANSYS MAPDL</span>
</a>
@@ -571,7 +568,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-cfx.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx">
<span>ANSYS CFX</span>
</a>
@@ -587,7 +584,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-fluent.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent">
<span>ANSYS Fluent</span>
</a>
@@ -603,7 +600,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="ansys-ls-dyna.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna">
<span>ANSYS LS-DYNA</span>
</a>
@@ -619,7 +616,7 @@
- <a title="" class="state-published contenttype-document" href="licensing.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/licensing">
<span>Licensing and Available Versions</span>
</a>
@@ -635,8 +632,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-mapdl-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS MAPDL PBS file</span>
</a>
@@ -651,8 +648,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-cfx-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS CFX PBS file</span>
</a>
@@ -667,8 +664,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-fluent-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS Fluent PBS file</span>
</a>
@@ -683,8 +680,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS LS-DYNA PBS file</span>
</a>
@@ -699,8 +696,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>LS-DYNA PBS file</span>
</a>
@@ -715,7 +712,7 @@
- <a title="" class="state-published contenttype-document" href="workbench.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/workbench">
<span>Workbench</span>
</a>
@@ -731,7 +728,7 @@
- <a title="" class="state-published contenttype-document" href="setting-license-preferences.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/setting-license-preferences">
<span>Setting license preferences</span>
</a>
@@ -756,7 +753,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -772,7 +769,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -788,7 +785,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -804,7 +801,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -820,7 +817,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -836,7 +833,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -852,7 +849,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -868,7 +865,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -884,7 +881,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -900,7 +897,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -925,7 +922,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -950,7 +947,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -966,7 +963,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
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- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -998,7 +995,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
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})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1087,7 +1084,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:19 GMT -->
</html>
diff --git a/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.md b/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.md
new file mode 100644
index 0000000000000000000000000000000000000000..04670fd4ea88d9937256eee5a4fdb773d4f614f9
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.md
@@ -0,0 +1,71 @@
+ANSYS LS-DYNA
+=============
+[ANSYS
+LS-DYNA](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/Explicit+Dynamics/ANSYS+LS-DYNA)
+software provides convenient and easy-to-use access to the
+technology-rich, time-tested explicit solver without the need to contend
+with the complex input requirements of this sophisticated program.
+Introduced in 1996, ANSYS LS-DYNA capabilities have helped customers in
+numerous industries to resolve highly intricate design
+issues. <span>ANSYS Mechanical users have been able take advantage of
+complex explicit solutions for a long time utilizing the traditional
+ANSYS Parametric Design Language (APDL) environment. <span>These
+explicit capabilities are available to ANSYS Workbench users as well.
+The Workbench platform is a powerful, comprehensive, easy-to-use
+environment for engineering simulation. CAD import from all sources,
+geometry cleanup, automatic meshing, solution, parametric optimization,
+result visualization and comprehensive report generation are all
+available within a single fully interactive modern graphical user
+environment.</span></span>
+<span>To run ANSYS LS-DYNA in batch mode you can utilize/modify the
+default ansysdyna.pbs script and execute it via the qsub command.</span>
+ #!/bin/bash
+ #PBS -l nodes=2:ppn=24
+ #PBS -q qprod
+ #PBS -N DYNA-Project
+ #PBS -A OPEN-0-0
+ #! Mail to user when job terminate or abort
+ #PBS -m ae
+ #!change the working directory (default is home directory)
+ #cd <working directory>
+ WORK_DIR="/scratch/work/user/$USER"
+ cd $WORK_DIR
+ echo Running on host `hostname`
+ echo Time is `date`
+ echo Directory is `pwd`
+ echo This jobs runs on the following processors:
+ echo `cat $PBS_NODEFILE`
+ module load ANSYS
+ #### Set number of processors per node
+ procs_per_host=24
+ #### Create host list
+ hl=""
+ for host in `cat $PBS_NODEFILE`
+ do
+ if [ "$hl" = "" ]
+ then hl="$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
+ fi
+ done
+ echo Machines$hl
+ # prevent ANSYS from attempting to use scif0 interface
+ export MPI_IC_ORDER="UDAPL"
+ lsdyna161 -dis -usessh -machines "$hl" i=input.k
+<span>Header of the pbs file (above) is common and description can be
+find </span><span> on [this
+site](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution).
+[SVS FEM](http://www.svsfem.cz) recommends to utilize
+sources by keywordsnodes, ppn. These keywords allows to address
+directly the number of nodes (computers) and cores (ppn) which will be
+utilized in the job. Also the rest of code assumes such structure of
+allocated resources.</span>
+Working directory has to be created before sending pbs job into the
+queue. Input file should be in working directory or full path to input
+file has to be specified. Input file has to be defined by common LS-DYNA
+.**k** file which is attached to the ansys solver via parameter i=
+Without setting environment variable MPI_IC_ORDER="UDAPL", ANSYS will
+fail to run on nodes with Xeon Phi accelerator (it will use the virtual
+interface of Phi cards instead of the real InfiniBand interface and MPI
+will fail.
+<span><span>
+</span></span>
diff --git a/salomon/software/ansys/ansys-mapdl-pbs-file/at_download/mapdl.pbs b/docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file.1
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/software/ansys/ansys-mapdl-pbs-file/at_download/mapdl.pbs
rename to docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file.1
diff --git a/salomon/software/ansys/mapdl.pbs b/docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/at_download/file
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/software/ansys/mapdl.pbs
rename to docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/at_download/file
diff --git a/salomon/software/ansys/ansys-mapdl-pbs-file/view.html b/docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view.html
old mode 100755
new mode 100644
similarity index 61%
rename from salomon/software/ansys/ansys-mapdl-pbs-file/view.html
rename to docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view.html
index d3240de9f8d9903bc87a5dadc237922515336c2d..b8d8fe90667e3ee637108e23f9af6031e5d65bf2
--- a/salomon/software/ansys/ansys-mapdl-pbs-file/view.html
+++ b/docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view.html
@@ -10,45 +10,42 @@
-
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>ANSYS MAPDL PBS file — IT4I Docs</title>
- <link rel="canonical" href="../mapdl.pbs" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="view.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="view.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../../index.html">
- <img src="../../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../../ansys.html">ANSYS</a>
+ <a href="https://docs.it4i.cz/salomon/software/ansys">ANSYS</a>
<span class="breadcrumbSeparator">
/
@@ -250,8 +247,8 @@
- <a href="at_download/mapdl.pbs">
- <img src="../../../../sh.png" alt="shell script icon" />
+ <a href="https://docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/at_download/file">
+ <img src="https://docs.it4i.cz/sh.png" alt="shell script icon" />
mapdl.pbs
</a>
<span class="discreet">
@@ -313,7 +310,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -329,7 +326,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -345,7 +342,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -361,7 +358,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -377,7 +374,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -393,7 +390,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -409,7 +406,7 @@
- <a title="" class="state-published contenttype-document" href="../../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -425,7 +422,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -441,7 +438,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -457,7 +454,7 @@
- <a title="" class="state-published contenttype-document" href="../../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -473,7 +470,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -489,7 +486,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -505,10 +502,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -524,7 +521,7 @@
- <a title="An engineering simulation software " class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../ansys.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -540,7 +537,7 @@
- <a title="" class="state-published contenttype-document" href="../ansys-mechanical-apdl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl">
<span>ANSYS MAPDL</span>
</a>
@@ -556,7 +553,7 @@
- <a title="" class="state-published contenttype-document" href="../ansys-cfx.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx">
<span>ANSYS CFX</span>
</a>
@@ -572,7 +569,7 @@
- <a title="" class="state-published contenttype-document" href="../ansys-fluent.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent">
<span>ANSYS Fluent</span>
</a>
@@ -588,7 +585,7 @@
- <a title="" class="state-published contenttype-document" href="../ansys-ls-dyna.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna">
<span>ANSYS LS-DYNA</span>
</a>
@@ -604,7 +601,7 @@
- <a title="" class="state-published contenttype-document" href="../licensing.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/licensing">
<span>Licensing and Available Versions</span>
</a>
@@ -620,8 +617,8 @@
- <a title="" class="state-missing-value navTreeCurrentItem navTreeCurrentNode contenttype-file" href="view.html">
- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value navTreeCurrentItem navTreeCurrentNode contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS MAPDL PBS file</span>
</a>
@@ -636,8 +633,8 @@
- <a title="" class="state-missing-value contenttype-file" href="../ansys-cfx-pbs-file/view.html">
- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS CFX PBS file</span>
</a>
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- <a title="" class="state-missing-value contenttype-file" href="../ansys-fluent-pbs-file/view.html">
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<span>LS-DYNA PBS file</span>
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<span>PRACE User Support</span>
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<span>Anselm Cluster Documentation</span>
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<span>Changelog</span>
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+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
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<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
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diff --git a/docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view.md b/docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view.md
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<title>ANSYS MAPDL — IT4I Docs</title>
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- <a accesskey="6" href="ansys-mechanical-apdl.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
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<p><span><strong><a class="external-link" href="http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics" target="_blank" title="">ANSYS Multiphysics</a></strong> software offers a comprehensive product solution for both multiphysics and single-physics analysis. The product includes structural, thermal, fluid and both high- and low-frequency electromagnetic analysis. The product also contains solutions for both direct and sequentially coupled physics problems including direct coupled-field elements and the ANSYS multi-field solver.</span></p>
<p><span>To run ANSYS MAPDL in batch mode you can utilize/modify the default mapdl.pbs script and execute it via the qsub command.</span></p>
<pre class=" ">#!/bin/bash<br />#PBS -l nodes=2:ppn=24<br />#PBS -q qprod<br />#PBS -N ANSYS-Project<br />#PBS -A OPEN-0-0<br /><br />#! Mail to user when job terminate or abort<br />#PBS -m ae<br /><br />#!change the working directory (default is home directory)<br />#cd <working directory> (working directory must exists)<br />WORK_DIR="/scratch/work/user/$USER"<br />cd $WORK_DIR<br /><br />echo Running on host `hostname`<br />echo Time is `date`<br />echo Directory is `pwd`<br />echo This jobs runs on the following processors:<br />echo `cat $PBS_NODEFILE`<br /><br />module load ANSYS/16.1<br /><br />#### Set number of processors per host listing<br />procs_per_host=24<br />#### Create host list<br />hl=""<br />for host in `cat $PBS_NODEFILE`<br />do<br /> if [ "$hl" = "" ]<br /> then hl="$host:$procs_per_host"<br /> else hl="${hl}:$host:$procs_per_host"<br /> fi<br />done<br /><br />echo Machines: $hl<br /><br /># prevent ANSYS from attempting to use scif0 interface<br />export MPI_IC_ORDER="UDAPL"<br /><br />#-i input.dat includes the input of analysis in APDL format<br />#-o file.out is output file from ansys where all text outputs will be redirected <br />#-p the name of license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial), aa_r_dy=Academic AUTODYN)<br />ansys161 -b -dis -usessh -p aa_r -i input.dat -o file.out -machines "$hl" -dir $WORK_DIR</pre>
-<p>Header of the PBS file (above) is common and description can be find on <a target="_blank" title="" class="internal-link" href="../../resource-allocation-and-job-execution/job-submission-and-execution.html">this site</a>. <a class="external-link" href="http://www.svsfem.cz/" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
+<p>Header of the PBS file (above) is common and description can be find on <a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">this site</a>. <a class="external-link" href="http://www.svsfem.cz" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
<p>Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common APDL file which is attached to the ansys solver via parameter -i</p>
-<p><strong>License</strong> should be selected by parameter -p. Licensed products are the following: aa_r (ANSYS <strong>Academic</strong> Research), ane3fl (ANSYS Multiphysics)-<strong>Commercial</strong>, aa_r_dy (ANSYS <strong>Academic</strong> AUTODYN)<span> <br /><a target="_self" title="" class="internal-link" href="licensing.html">More about licensing here</a><br /></span></p>
+<p><strong>License</strong> should be selected by parameter -p. Licensed products are the following: aa_r (ANSYS <strong>Academic</strong> Research), ane3fl (ANSYS Multiphysics)-<strong>Commercial</strong>, aa_r_dy (ANSYS <strong>Academic</strong> AUTODYN)<span> <br /><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/ansys/licensing">More about licensing here</a><br /></span></p>
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@@ -391,7 +388,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -407,7 +404,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -423,7 +420,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -439,7 +436,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -455,7 +452,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -471,7 +468,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -487,7 +484,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -503,7 +500,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -519,10 +516,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -538,7 +535,7 @@
- <a title="An engineering simulation software " class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -554,7 +551,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="ansys-mechanical-apdl.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl">
<span>ANSYS MAPDL</span>
</a>
@@ -570,7 +567,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-cfx.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx">
<span>ANSYS CFX</span>
</a>
@@ -586,7 +583,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-fluent.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent">
<span>ANSYS Fluent</span>
</a>
@@ -602,7 +599,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-ls-dyna.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna">
<span>ANSYS LS-DYNA</span>
</a>
@@ -618,7 +615,7 @@
- <a title="" class="state-published contenttype-document" href="licensing.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/licensing">
<span>Licensing and Available Versions</span>
</a>
@@ -634,8 +631,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-mapdl-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS MAPDL PBS file</span>
</a>
@@ -650,8 +647,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-cfx-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS CFX PBS file</span>
</a>
@@ -666,8 +663,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-fluent-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS Fluent PBS file</span>
</a>
@@ -682,8 +679,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS LS-DYNA PBS file</span>
</a>
@@ -698,8 +695,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>LS-DYNA PBS file</span>
</a>
@@ -714,7 +711,7 @@
- <a title="" class="state-published contenttype-document" href="workbench.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/workbench">
<span>Workbench</span>
</a>
@@ -730,7 +727,7 @@
- <a title="" class="state-published contenttype-document" href="setting-license-preferences.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/setting-license-preferences">
<span>Setting license preferences</span>
</a>
@@ -755,7 +752,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -771,7 +768,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -787,7 +784,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -803,7 +800,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -819,7 +816,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -835,7 +832,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -851,7 +848,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -867,7 +864,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -883,7 +880,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -899,7 +896,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -924,7 +921,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -949,7 +946,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -965,7 +962,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -981,7 +978,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -997,7 +994,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1036,14 +1033,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1065,12 +1062,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1086,7 +1083,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:19 GMT -->
</html>
diff --git a/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.md b/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.md
new file mode 100644
index 0000000000000000000000000000000000000000..442d38b9b591128ad0d163503da84af566ff0160
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.md
@@ -0,0 +1,66 @@
+ANSYS MAPDL
+===========
+<span>**[ANSYS
+Multiphysics](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics)**
+software offers a comprehensive product solution for both multiphysics
+and single-physics analysis. The product includes structural, thermal,
+fluid and both high- and low-frequency electromagnetic analysis. The
+product also contains solutions for both direct and sequentially coupled
+physics problems including direct coupled-field elements and the ANSYS
+multi-field solver.</span>
+<span>To run ANSYS MAPDL in batch mode you can utilize/modify the
+default mapdl.pbs script and execute it via the qsub command.</span>
+ #!/bin/bash
+ #PBS -l nodes=2:ppn=24
+ #PBS -q qprod
+ #PBS -N ANSYS-Project
+ #PBS -A OPEN-0-0
+ #! Mail to user when job terminate or abort
+ #PBS -m ae
+ #!change the working directory (default is home directory)
+ #cd <working directory> (working directory must exists)
+ WORK_DIR="/scratch/work/user/$USER"
+ cd $WORK_DIR
+ echo Running on host `hostname`
+ echo Time is `date`
+ echo Directory is `pwd`
+ echo This jobs runs on the following processors:
+ echo `cat $PBS_NODEFILE`
+ module load ANSYS/16.1
+ #### Set number of processors per host listing
+ procs_per_host=24
+ #### Create host list
+ hl=""
+ for host in `cat $PBS_NODEFILE`
+ do
+ if [ "$hl" = "" ]
+ then hl="$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
+ fi
+ done
+ echo Machines$hl
+ # prevent ANSYS from attempting to use scif0 interface
+ export MPI_IC_ORDER="UDAPL"
+ #-i input.dat includes the input of analysis in APDL format
+ #-o file.out is output file from ansys where all text outputs will be redirected
+ #-p the name of license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial), aa_r_dy=Academic AUTODYN)
+ ansys161 -b -dis -usessh -p aa_r -i input.dat -o file.out -machines "$hl" -dir $WORK_DIR
+Header of the PBS file (above) is common and description can be find on
+[this
+site](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution).
+[SVS FEM](http://www.svsfem.cz) recommends to utilize
+sources by keywordsnodes, ppn. These keywords allows to address
+directly the number of nodes (computers) and cores (ppn) which will be
+utilized in the job. Also the rest of code assumes such structure of
+allocated resources.
+Working directory has to be created before sending pbs job into the
+queue. Input file should be in working directory or full path to input
+file has to be specified. Input file has to be defined by common APDL
+file which is attached to the ansys solver via parameter -i
+**License** should be selected by parameter -p. Licensed products are
+the followingaa_r (ANSYS **Academic** Research), ane3fl (ANSYS
+Multiphysics)-**Commercial**, aa_r_dy (ANSYS **Academic**
+AUTODYN)<span>
+[More about licensing
+here](https://docs.it4i.cz/salomon/software/ansys/licensing)
+</span>
diff --git a/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.html b/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.html
new file mode 100644
index 0000000000000000000000000000000000000000..09bda6ba2f377f92606c4ce35e96a7099a369a4e
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.html
@@ -0,0 +1,1077 @@
+
+<!DOCTYPE html>
+
+<html xmlns="http://www.w3.org/1999/xhtml" lang="cs">
+
+
+
+
+
+
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+
+<head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+
+ <base href="https://docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl" /><!--[if lt IE 7]></base><![endif]-->
+
+
+
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+
+
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
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+
+
+<title>Overview of ANSYS Products — IT4I Docs</title>
+
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/ansys" />
+
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
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+ if (typeof($.datepicker) != "undefined"){
+ $.datepicker.setDefaults(
+ jQuery.extend($.datepicker.regional['cs'],
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+ <meta name="generator" content="Plone - http://plone.org" />
+
+</head>
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+<div id="visual-portal-wrapper">
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+ Overview of ANSYS Products
+ </h1>
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+ <p><strong><a class="external-link" href="http://www.svsfem.cz/" target="_blank" title="">SVS FEM</a></strong> as <em><strong><a class="external-link" href="http://www.ansys.com/" target="_self" title="">ANSYS Channel partner</a></strong></em> for Czech Republic provided all ANSYS licenses for all clusters and supports of all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent, Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging to problem of ANSYS functionality contact please <a class="email-link" href="mailto:hotline@svsfem.cz?subject=Ostrava%20-%20ANSELM" target="_self" title="">hotline@svsfem.cz</a></p>
+<p>The clusters provides as commercial as academic variants. Academic variants are distinguished by "<strong>Academic...</strong>" word in the name of  license or by two letter preposition "<strong>aa_</strong>" in the license feature name. Change of license is realized on command line respectively directly in user's pbs file (see individual products). <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/ansys/licensing">More about licensing here</a></p>
+<p>To load the latest version of any ANSYS product (Mechanical, Fluent, CFX, MAPDL,...) load the module:</p>
+<pre class=" ">$ module load ANSYS</pre>
+<p>ANSYS supports interactive regime, but due to assumed solution of extremely difficult tasks it is not recommended.</p>
+<p>If user needs to work in interactive regime we recommend to configure the RSM service on the client machine which allows to forward the solution to the clusters directly from the client's Workbench project (see ANSYS RSM service).</p>
+
+ </div>
+
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+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl">
+
+ <span>ANSYS MAPDL</span>
+ </a>
+
+
+
+
+</li>
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+
+<li class="navTreeItem visualNoMarker section-ansys-cfx">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx">
+
+ <span>ANSYS CFX</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ansys-fluent">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent">
+
+ <span>ANSYS Fluent</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ansys-ls-dyna">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna">
+
+ <span>ANSYS LS-DYNA</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-licensing">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/licensing">
+
+ <span>Licensing and Available Versions</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ansys-mapdl-pbs-file">
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+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
+ <span>ANSYS MAPDL PBS file</span>
+ </a>
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+
+
+
+</li>
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+<li class="navTreeItem visualNoMarker section-ansys-cfx-pbs-file">
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+
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+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
+ <span>ANSYS CFX PBS file</span>
+ </a>
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+
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+</li>
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+<li class="navTreeItem visualNoMarker section-ansys-fluent-pbs-file">
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+
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+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
+ <span>ANSYS Fluent PBS file</span>
+ </a>
+
+
+
+
+</li>
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+
+<li class="navTreeItem visualNoMarker section-ansys-ls-dyna-pbs-file">
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+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
+ <span>ANSYS LS-DYNA PBS file</span>
+ </a>
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+<li class="navTreeItem visualNoMarker section-ls-dyna-pbs-file">
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+
+
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+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
+ <span>LS-DYNA PBS file</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-workbench">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/workbench">
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+ <span>Workbench</span>
+ </a>
+
+
+
+
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+
+<li class="navTreeItem visualNoMarker section-setting-license-preferences">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/setting-license-preferences">
+
+ <span>Setting license preferences</span>
+ </a>
+
+
+
+
+</li>
+
+
+
+
+ </ul>
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-comsol">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
+
+ <span>COMSOL</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-debuggers">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
+
+ <span>Debuggers and profilers</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-chemistry">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
+
+ <span>Chemistry, Physics and Materials science</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-intel-suite">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
+
+ <span>Intel Parallel studio</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-mpi-1">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
+
+ <span>MPI</span>
+ </a>
+
+
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+
+</li>
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+<li class="navTreeItem visualNoMarker navTreeFolderish section-numerical-languages">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
+
+ <span>Numerical languages</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-compilers">
+
+
+
+
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
+
+ <span>Compilers</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-intel-xeon-phi">
+
+
+
+
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
+
+ <span>Intel Xeon Phi</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-java">
+
+
+
+
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
+
+ <span>Java</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-operating-system">
+
+
+
+
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
+
+ <span>Operating System</span>
+ </a>
+
+
+
+
+</li>
+
+
+
+
+ </ul>
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-prace">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
+
+ <span>PRACE User Support</span>
+ </a>
+
+
+
+
+</li>
+
+
+
+
+ </ul>
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-anselm-cluster-documentation">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
+
+ <span>Anselm Cluster Documentation</span>
+ </a>
+
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
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+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
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+
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+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
+
+ <span>PBSPro Documentation</span>
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+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<!-- End Piwik Code -->
+<!-- nagios_check_http_expect_string -->
+
+<div id="viewlet-cookiepolicy" style="display:none">
+ <h1 id="tlspu_cookiepolicy_title">This Site Uses Cookies</h1>
+ <p id="tlspu_cookiepolicy_message">We may use cookies to record some preference settings and to analyse how you use our web site. We may also use external analysis systems which may set additional cookies to perform their analysis. These cookies are integral to our web site. You can delete or disable these cookies in your web browser if you wish but then our site may not work correctly.</p>
+ <form id="tlspu_cookiepolicy_form">
+ <input type="checkbox" id="tlspu_cookiepolicy_agreed" value="confirmed" />
+ <label for="tlspu_cookiepolicy_agreed">I have read and understood this message.</label>
+ <button disabled="disabled" id="tlspu_cookiepolicy_button" value="hide">Hide this message</button>
+ </form>
+</div>
+
+<script type="text/javascript">
+/*
+*/
+</script>
+
+<div id="portal-footer">
+ <p>
+ <a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
+ <a href="http://prace.it4i.cz/">HPC & PRACE</a>
+ <a href="http://study.it4i.cz/">HPC Study</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
+ <a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
+ <a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
+ </p>
+ <!-- nagios_check_http_expect_string -->
+</div>
+
+ </div>
+ </div>
+
+ <!-- TODO -->
+ <!-- nagios_check_http_expect_string -->
+ <!-- TODO -->
+
+</div>
+</body>
+</html>
+
diff --git a/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md b/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md
new file mode 100644
index 0000000000000000000000000000000000000000..7b9535924fdf95994646696efcf45adcb8f0bfc9
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md
@@ -0,0 +1,25 @@
+Overview of ANSYS Products
+==========================
+**[SVS FEM](http://www.svsfem.cz/)** as ***[ANSYS
+Channel partner](http://www.ansys.com/)***Â for Czech
+Republic provided all ANSYS licenses for all clusters and supports of
+all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent,
+Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging
+to problem of ANSYS functionality contact
+please [hotline@svsfem.cz](mailto:hotline@svsfem.cz?subject=Ostrava%20-%20ANSELM){.email-link}
+The clusters provides as commercial as academic variants. Academic
+variants are distinguished by "**Academic...**" word in the name of
+Â license or by two letter preposition "**aa_**" in the license feature
+name. Change of license is realized on command line respectively
+directly in user's pbs file (see individual products). [More about
+licensing
+here](https://docs.it4i.cz/salomon/software/ansys/licensing)
+To load the latest version of any ANSYS product (Mechanical, Fluent,
+CFX, MAPDL,...) load the module:
+ $ module load ANSYS
+ANSYS supports interactive regime, but due to assumed solution of
+extremely difficult tasks it is not recommended.
+If user needs to work in interactive regime we recommend to configure
+the RSM service on the client machine which allows to forward the
+solution to the clusters directly from the client's Workbench project
+(see ANSYS RSM service).
diff --git a/salomon/software/ansys/licensing.html b/docs.it4i.cz/salomon/software/ansys/licensing.html
old mode 100755
new mode 100644
similarity index 64%
rename from salomon/software/ansys/licensing.html
rename to docs.it4i.cz/salomon/software/ansys/licensing.html
index ab269569423981cddd5ee2011465947d06286a12..1941de8416ebdc7d0174b51cd18e58058556ba9e
--- a/salomon/software/ansys/licensing.html
+++ b/docs.it4i.cz/salomon/software/ansys/licensing.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/ansys/licensing by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:19 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/ansys/licensing" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/IEFixes-cachekey-ec9b60024fd235ff2c883b4b54db91cb.css" />
<![endif]-->
- <style type="text/css" media="screen">@import url(../../../portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Licensing and Available Versions — IT4I Docs</title>
- <link rel="canonical" href="licensing.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/ansys/licensing" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="licensing.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/ansys/licensing#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="licensing.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/ansys/licensing#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../ansys.html">ANSYS</a>
+ <a href="https://docs.it4i.cz/salomon/software/ansys">ANSYS</a>
<span class="breadcrumbSeparator">
/
@@ -262,7 +259,7 @@
<li>17.0</li>
</ul>
<h2>License Preferences</h2>
-<p>Please <a target="_self" title="" class="internal-link" href="setting-license-preferences.html">see this page to set license preferences</a>.</p>
+<p>Please <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/ansys/setting-license-preferences">see this page to set license preferences</a>.</p>
<p>Â </p>
</div>
@@ -339,7 +336,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -355,7 +352,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -371,7 +368,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -387,7 +384,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -403,7 +400,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -419,7 +416,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -435,7 +432,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -451,7 +448,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -467,7 +464,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -483,7 +480,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -499,7 +496,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -515,7 +512,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -531,10 +528,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -550,7 +547,7 @@
- <a title="An engineering simulation software " class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -566,7 +563,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-mechanical-apdl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl">
<span>ANSYS MAPDL</span>
</a>
@@ -582,7 +579,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-cfx.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx">
<span>ANSYS CFX</span>
</a>
@@ -598,7 +595,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-fluent.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent">
<span>ANSYS Fluent</span>
</a>
@@ -614,7 +611,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-ls-dyna.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna">
<span>ANSYS LS-DYNA</span>
</a>
@@ -630,7 +627,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="licensing.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/licensing">
<span>Licensing and Available Versions</span>
</a>
@@ -646,8 +643,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-mapdl-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS MAPDL PBS file</span>
</a>
@@ -662,8 +659,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-cfx-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS CFX PBS file</span>
</a>
@@ -678,8 +675,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-fluent-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS Fluent PBS file</span>
</a>
@@ -694,8 +691,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS LS-DYNA PBS file</span>
</a>
@@ -710,8 +707,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>LS-DYNA PBS file</span>
</a>
@@ -726,7 +723,7 @@
- <a title="" class="state-published contenttype-document" href="workbench.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/workbench">
<span>Workbench</span>
</a>
@@ -742,7 +739,7 @@
- <a title="" class="state-published contenttype-document" href="setting-license-preferences.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/setting-license-preferences">
<span>Setting license preferences</span>
</a>
@@ -767,7 +764,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -783,7 +780,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -799,7 +796,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -815,7 +812,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -831,7 +828,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -847,7 +844,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -863,7 +860,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -879,7 +876,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -895,7 +892,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -911,7 +908,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -936,7 +933,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -961,7 +958,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -977,7 +974,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -993,7 +990,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1009,7 +1006,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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(function() {
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</div>
</body>
-
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</html>
diff --git a/docs.it4i.cz/salomon/software/ansys/licensing.md b/docs.it4i.cz/salomon/software/ansys/licensing.md
new file mode 100644
index 0000000000000000000000000000000000000000..475c2915e3bcea08d71d228dfb39c997082c4a1e
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/ansys/licensing.md
@@ -0,0 +1,32 @@
+Licensing and Available Versions
+================================
+ANSYS licence can be used by:
+------
+- all persons in the carrying out of the CE IT4Innovations Project (In
+ addition to the primary licensee, which is VSB - Technical
+ University of Ostrava, users are CE IT4Innovations third parties -
+ CE IT4Innovations project partners, particularly the University of
+ Ostrava, the Brno University of Technology - Faculty of Informatics,
+ the Silesian University in Opava, Institute of Geonics AS CR.)
+- <span id="result_box" class="short_text"><span class="hps">all
+ persons</span> <span class="hps">who have a valid</span> <span
+ class="hps">license</span></span>
+- <span id="result_box" class="short_text"><span class="hps">students
+ of</span> <span class="hps">the Technical University</span></span>
+ANSYS Academic Research
+The licence intended to be used for science and research, publications,
+students’ projects (academic licence).
+ANSYS COM
+---------
+The licence intended to be used for science and research, publications,
+students’ projects, commercial research with no commercial use
+restrictions.
+Available Versions
+------------------
+- 16.1
+- 17.0
+License Preferences
+-------------------
+Please [see this page to set license
+preferences](https://docs.it4i.cz/salomon/software/ansys/setting-license-preferences).
+Â
diff --git a/salomon/software/ansys/ls-dyna-pbs-file/at_download/lsdyna.pbs b/docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file.1
old mode 100755
new mode 100644
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rename from salomon/software/ansys/ls-dyna-pbs-file/at_download/lsdyna.pbs
rename to docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file.1
diff --git a/salomon/software/ansys/lsdyna.pbs b/docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/at_download/file
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/software/ansys/lsdyna.pbs
rename to docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/at_download/file
diff --git a/salomon/software/ansys/ls-dyna-pbs-file/view.html b/docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/view.html
old mode 100755
new mode 100644
similarity index 61%
rename from salomon/software/ansys/ls-dyna-pbs-file/view.html
rename to docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/view.html
index 1a126bf03f83133b4ab1b9b5ec4fc2026fc05a20..5136295ce9c648e833c2710ce6b3bd3578e39377
--- a/salomon/software/ansys/ls-dyna-pbs-file/view.html
+++ b/docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/view.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>LS-DYNA PBS file — IT4I Docs</title>
- <link rel="canonical" href="../lsdyna.pbs" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="view.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/view#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="view.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/view#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../../index.html">
- <img src="../../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../../ansys.html">ANSYS</a>
+ <a href="https://docs.it4i.cz/salomon/software/ansys">ANSYS</a>
<span class="breadcrumbSeparator">
/
@@ -250,8 +247,8 @@
- <a href="at_download/lsdyna.pbs">
- <img src="../../../../sh.png" alt="shell script icon" />
+ <a href="https://docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/at_download/file">
+ <img src="https://docs.it4i.cz/sh.png" alt="shell script icon" />
lsdyna.pbs
</a>
<span class="discreet">
@@ -313,7 +310,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -329,7 +326,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -345,7 +342,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -361,7 +358,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -377,7 +374,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -393,7 +390,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -409,7 +406,7 @@
- <a title="" class="state-published contenttype-document" href="../../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -425,7 +422,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -441,7 +438,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -457,7 +454,7 @@
- <a title="" class="state-published contenttype-document" href="../../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -473,7 +470,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -489,7 +486,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -505,10 +502,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -524,7 +521,7 @@
- <a title="An engineering simulation software " class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../ansys.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -540,7 +537,7 @@
- <a title="" class="state-published contenttype-document" href="../ansys-mechanical-apdl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl">
<span>ANSYS MAPDL</span>
</a>
@@ -556,7 +553,7 @@
- <a title="" class="state-published contenttype-document" href="../ansys-cfx.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx">
<span>ANSYS CFX</span>
</a>
@@ -572,7 +569,7 @@
- <a title="" class="state-published contenttype-document" href="../ansys-fluent.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent">
<span>ANSYS Fluent</span>
</a>
@@ -588,7 +585,7 @@
- <a title="" class="state-published contenttype-document" href="../ansys-ls-dyna.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna">
<span>ANSYS LS-DYNA</span>
</a>
@@ -604,7 +601,7 @@
- <a title="" class="state-published contenttype-document" href="../licensing.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/licensing">
<span>Licensing and Available Versions</span>
</a>
@@ -620,8 +617,8 @@
- <a title="" class="state-missing-value contenttype-file" href="../ansys-mapdl-pbs-file/view.html">
- <img width="16" height="16" src="../../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
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<span>ANSYS LS-DYNA PBS file</span>
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<span>LS-DYNA PBS file</span>
</a>
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<span>Workbench</span>
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<span>Setting license preferences</span>
</a>
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<span>COMSOL</span>
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</a>
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<span>Java</span>
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</a>
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<span>PRACE User Support</span>
</a>
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<span>Anselm Cluster Documentation</span>
</a>
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<span>Changelog</span>
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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diff --git a/docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/view.md b/docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/view.md
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old mode 100755
new mode 100644
similarity index 60%
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rename to docs.it4i.cz/salomon/software/ansys/setting-license-preferences.html
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<title>Setting license preferences — IT4I Docs</title>
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- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
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<script type="text/javascript">
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
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<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="setting-license-preferences.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/ansys/setting-license-preferences#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="setting-license-preferences.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/ansys/setting-license-preferences#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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<div id="portal-advanced-search" class="hiddenStructure">
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+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
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</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../ansys.html">ANSYS</a>
+ <a href="https://docs.it4i.cz/salomon/software/ansys">ANSYS</a>
<span class="breadcrumbSeparator">
/
@@ -251,13 +248,13 @@
<p>Launch the ANSLIC_ADMIN utility in a graphical environment:</p>
<pre class=" "> $ANSYSLIC_DIR/lic_admin/anslic_admin</pre>
<p>ANSLIC_ADMIN Utility will be run</p>
-<p><a target="_blank" title="" class="internal-link" href="Fluent_Licence_1.jpg"><img title="Fluent_Licence_1.jpg" class="image-inline" alt="Fluent_Licence_1.jpg" src="Fluent_Licence_1.jpg/%40%40images/0203aca4-d4f8-4372-ab71-432fcf15df43.jpg" /></a></p>
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<p>Â </p>
<p>ANSYS Academic Research license should be moved up to the top or down to the bottom of the list.</p>
<p>Â </p>
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</a>
@@ -381,7 +378,7 @@
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+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -397,7 +394,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -413,7 +410,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -429,7 +426,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -445,7 +442,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -461,7 +458,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -477,7 +474,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -493,7 +490,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -509,7 +506,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -525,10 +522,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -544,7 +541,7 @@
- <a title="An engineering simulation software " class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -560,7 +557,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-mechanical-apdl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl">
<span>ANSYS MAPDL</span>
</a>
@@ -576,7 +573,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-cfx.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx">
<span>ANSYS CFX</span>
</a>
@@ -592,7 +589,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-fluent.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent">
<span>ANSYS Fluent</span>
</a>
@@ -608,7 +605,7 @@
- <a title="" class="state-published contenttype-document" href="ansys-ls-dyna.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna">
<span>ANSYS LS-DYNA</span>
</a>
@@ -624,7 +621,7 @@
- <a title="" class="state-published contenttype-document" href="licensing.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/licensing">
<span>Licensing and Available Versions</span>
</a>
@@ -640,8 +637,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-mapdl-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS MAPDL PBS file</span>
</a>
@@ -656,8 +653,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-cfx-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS CFX PBS file</span>
</a>
@@ -672,8 +669,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-fluent-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS Fluent PBS file</span>
</a>
@@ -688,8 +685,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ansys-ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS LS-DYNA PBS file</span>
</a>
@@ -704,8 +701,8 @@
- <a title="" class="state-missing-value contenttype-file" href="ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>LS-DYNA PBS file</span>
</a>
@@ -720,7 +717,7 @@
- <a title="" class="state-published contenttype-document" href="workbench.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/workbench">
<span>Workbench</span>
</a>
@@ -736,7 +733,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="setting-license-preferences.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/setting-license-preferences">
<span>Setting license preferences</span>
</a>
@@ -761,7 +758,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -777,7 +774,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -793,7 +790,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -809,7 +806,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -825,7 +822,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -841,7 +838,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -857,7 +854,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -873,7 +870,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -889,7 +886,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -905,7 +902,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -930,7 +927,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -955,7 +952,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -971,7 +968,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -987,7 +984,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1003,7 +1000,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1042,14 +1039,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1071,12 +1068,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1092,7 +1089,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.md b/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.md
new file mode 100644
index 0000000000000000000000000000000000000000..a7a2bb2097cbbf3ccfe0e1a651dceed47db70040
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.md
@@ -0,0 +1,21 @@
+Setting license preferences
+===========================
+Some ANSYS tools allow you to explicitly specify usage of academic or
+commercial licenses in the command line (eg. <span
+class="monospace">ansys161 -p aa_r</span>Â to select Academic Research
+license). However, we have observed that not all tools obey this option
+and choose commercial license.
+Thus you need to configure preferred license order with ANSLIC_ADMIN.
+Please follow these steps and move Academic Research license to the  top
+or bottom of the list accordingly.
+Launch the ANSLIC_ADMIN utility in a graphical environment:
+ $ANSYSLIC_DIR/lic_admin/anslic_admin
+ANSLIC_ADMIN Utility will be run
+[](https://docs.it4i.cz/salomon/software/ansys/Fluent_Licence_1.jpg)
+[](https://docs.it4i.cz/salomon/software/ansys/Fluent_Licence_2.jpg)
+[](https://docs.it4i.cz/salomon/software/ansys/Fluent_Licence_3.jpg)
+Â
+ANSYS Academic Research license should be moved up to the top or down to
+the bottom of the list.
+Â
+[](https://docs.it4i.cz/salomon/software/ansys/Fluent_Licence_4.jpg)
diff --git a/salomon/software/ansys/workbench.html b/docs.it4i.cz/salomon/software/ansys/workbench.html
old mode 100755
new mode 100644
similarity index 65%
rename from salomon/software/ansys/workbench.html
rename to docs.it4i.cz/salomon/software/ansys/workbench.html
index 4f42f0117ffeced06db97510c8f63a72e2abfa6e..c83f88a3635c446f69c3a56fc849811dbfc8aceb
--- a/salomon/software/ansys/workbench.html
+++ b/docs.it4i.cz/salomon/software/ansys/workbench.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/ansys/workbench by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:22 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/ansys/workbench" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/IEFixes-cachekey-ec9b60024fd235ff2c883b4b54db91cb.css" />
<![endif]-->
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+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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- <script type="text/javascript" src="../../../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Workbench — IT4I Docs</title>
- <link rel="canonical" href="workbench.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/ansys/workbench" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="workbench.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/ansys/workbench#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="workbench.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/ansys/workbench#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../ansys.html">ANSYS</a>
+ <a href="https://docs.it4i.cz/salomon/software/ansys">ANSYS</a>
<span class="breadcrumbSeparator">
/
@@ -248,7 +245,7 @@
<div id="parent-fieldname-text-816fbedc79e54237b689a2bdf784a2af" class="">
<h2 class=" ">Workbench Batch Mode</h2>
<p>It is possible to run Workbench scripts in batch mode. You need to configure solvers of individual components to run in parallel mode. Open your project in Workbench. Then, for example, in Mechanical, go to Tools - Solve Process Settings ..., click Advanced button as shown on the screenshot.</p>
-<p><img title="" class="image-inline" alt="" src="AMsetPar1.png/%40%40images/a34a45cc-9385-4f05-b12e-efadf1bd93bb.png" /></p>
+<p><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/salomon/software/ansys/AMsetPar1.png/@@images/a34a45cc-9385-4f05-b12e-efadf1bd93bb.png" /></p>
<p>Enable Distribute Solution checkbox and enter number of cores (eg. 48 to run on two Salomon nodes). If you want the job to run on more then 1 node, you must also provide a so called MPI appfile. In the Additional Command Line Arguments input field, enter :</p>
<pre class=" ">-mpifile /path/to/my/job/mpifile.txt</pre>
<p>Where /path/to/my/job is the directory where your project is saved. We will create the file mpifile.txt programatically later in the batch script. For more information, refer to <em>ANSYS Mechanical APDL Parallel Processing</em> <em>Guide</em>.</p>
@@ -368,7 +365,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -384,7 +381,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -400,7 +397,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -416,7 +413,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -432,7 +429,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -448,7 +445,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -464,7 +461,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -480,7 +477,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -496,7 +493,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -512,7 +509,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -528,7 +525,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -544,7 +541,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -560,10 +557,10 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -579,7 +576,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="An engineering simulation software " class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -595,7 +592,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published contenttype-document" href="ansys-mechanical-apdl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl">
<span>ANSYS MAPDL</span>
</a>
@@ -611,7 +608,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published contenttype-document" href="ansys-cfx.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx">
<span>ANSYS CFX</span>
</a>
@@ -627,7 +624,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published contenttype-document" href="ansys-fluent.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent">
<span>ANSYS Fluent</span>
</a>
@@ -643,7 +640,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published contenttype-document" href="ansys-ls-dyna.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna">
<span>ANSYS LS-DYNA</span>
</a>
@@ -659,7 +656,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published contenttype-document" href="licensing.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/licensing">
<span>Licensing and Available Versions</span>
</a>
@@ -675,8 +672,8 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-missing-value contenttype-file" href="ansys-mapdl-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS MAPDL PBS file</span>
</a>
@@ -691,8 +688,8 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-missing-value contenttype-file" href="ansys-cfx-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS CFX PBS file</span>
</a>
@@ -707,8 +704,8 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-missing-value contenttype-file" href="ansys-fluent-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS Fluent PBS file</span>
</a>
@@ -723,8 +720,8 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-missing-value contenttype-file" href="ansys-ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>ANSYS LS-DYNA PBS file</span>
</a>
@@ -739,8 +736,8 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-missing-value contenttype-file" href="ls-dyna-pbs-file/view.html">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor" />
+ <a class="state-missing-value contenttype-file" title="" href="https://docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/view">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
<span>LS-DYNA PBS file</span>
</a>
@@ -755,7 +752,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="workbench.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/workbench">
<span>Workbench</span>
</a>
@@ -771,7 +768,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published contenttype-document" href="setting-license-preferences.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/ansys/setting-license-preferences">
<span>Setting license preferences</span>
</a>
@@ -796,7 +793,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -812,7 +809,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -828,7 +825,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -844,7 +841,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -860,7 +857,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -876,7 +873,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -892,7 +889,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -908,7 +905,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -924,7 +921,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -940,7 +937,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -965,7 +962,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -990,7 +987,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -1006,7 +1003,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1022,7 +1019,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1038,7 +1035,7 @@ runwb2 -R jou6.wbjn -B -F test9.wbpj
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1077,14 +1074,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1106,12 +1103,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1127,7 +1124,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/ansys/workbench by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:23 GMT -->
</html>
diff --git a/docs.it4i.cz/salomon/software/ansys/workbench.md b/docs.it4i.cz/salomon/software/ansys/workbench.md
new file mode 100644
index 0000000000000000000000000000000000000000..af6d2dbdd09159dd88797af2a4c2485f7fd2fdc7
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/ansys/workbench.md
@@ -0,0 +1,56 @@
+Workbench
+=========
+Workbench Batch Mode
+--------------------
+It is possible to run Workbench scripts in batch mode. You need to
+configure solvers of individual components to run in parallel mode. Open
+your project in Workbench. Then, for example, in Mechanical, go to Tools
+- Solve Process Settings ..., click Advanced button as shown on the
+screenshot.
+
+Enable Distribute Solution checkbox and enter number of cores (eg. 48 to
+run on two Salomon nodes). If you want the job to run on more then 1
+node, you must also provide a so called MPI appfile. In the Additional
+Command Line Arguments input field, enter :
+ -mpifile /path/to/my/job/mpifile.txt
+Where /path/to/my/job is the directory where your project is saved. We
+will create the file mpifile.txt programatically later in the batch
+script. For more information, refer to *ANSYS Mechanical APDL Parallel
+Processing* *Guide*.
+Now, save the project and close Workbench. We will use this script to
+launch the job:
+ #!/bin/bash
+ #PBS -l select=2:ncpus=24
+ #PBS -q qprod
+ #PBS -N test9_mpi_2
+ #PBS -A OPEN-0-0
+ # Mail to user when job terminate or abort
+ #PBS -m a
+ # change the working directory
+ WORK_DIR="$PBS_O_WORKDIR"
+ cd $WORK_DIR
+ echo Running on host `hostname`
+ echo Time is `date`
+ echo Directory is `pwd`
+ echo This jobs runs on the following nodes:
+ echo `cat $PBS_NODEFILE`
+ module load ANSYS
+ #### Set number of processors per host listing
+ procs_per_host=24
+ #### Create MPI appfile
+ echo -n "" > mpifile.txt
+ for host in `cat $PBS_NODEFILE`
+ do
+ echo "-h $host -np $procs_per_host $ANSYS160_DIR/bin/ansysdis161 -dis" >> mpifile.txt
+ done
+ #-i input.dat includes the input of analysis in APDL format
+ #-o file.out is output file from ansys where all text outputs will be redirected
+ #-p the name of license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial), aa_r_dy=Academic AUTODYN)
+ # prevent using scsif0 interface on accelerated nodes
+ export MPI_IC_ORDER="UDAPL"
+ # spawn remote process using SSH (default is RSH)
+ export MPI_REMSH="/usr/bin/ssh"
+ runwb2 -R jou6.wbjn -B -F test9.wbpj
+The solver settings are saved in file solvehandlers.xml, which is not
+located in the project directory. Verify your solved settings when
+uploading a project from your local computer.
diff --git a/salomon/software/chemistry.html b/docs.it4i.cz/salomon/software/chemistry.html
old mode 100755
new mode 100644
similarity index 65%
rename from salomon/software/chemistry.html
rename to docs.it4i.cz/salomon/software/chemistry.html
index 2e013256dfefece150e144ff10792ec86f0526c1..592d32e53a67946132b94e59c12b95dd7145b410
--- a/salomon/software/chemistry.html
+++ b/docs.it4i.cz/salomon/software/chemistry.html
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/chemistry/" /><!--[if lt IE 7]></base><![endif]-->
<meta content="Tools for computational chemistry." name="description" />
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- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
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<title>Chemistry, Physics and Materials science — IT4I Docs</title>
- <link rel="canonical" href="chemistry.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/chemistry" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="chemistry.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/chemistry#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="chemistry.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/chemistry#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
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</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -249,7 +246,7 @@
<span class="summary">
- <a href="chemistry/molpro.html" class="contenttype-document state-published url">Molpro</a>
+ <a href="https://docs.it4i.cz/salomon/software/chemistry/molpro" class="contenttype-document state-published url">Molpro</a>
</span>
<span class="documentByLine">
@@ -275,7 +272,7 @@
<span class="summary">
- <a href="chemistry/nwchem.html" class="contenttype-document state-published url">NWChem</a>
+ <a href="https://docs.it4i.cz/salomon/software/chemistry/nwchem" class="contenttype-document state-published url">NWChem</a>
</span>
<span class="documentByLine">
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<span class="summary">
- <a href="chemistry/phono3py.html" class="contenttype-document state-published url">Phono3py</a>
+ <a href="https://docs.it4i.cz/salomon/software/chemistry/phono3py" class="contenttype-document state-published url">Phono3py</a>
</span>
<span class="documentByLine">
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<span class="summary">
- <a href="chemistry/phono3py-input.html" class="contenttype-folder state-published url">Phono3py Input</a>
+ <a href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input" class="contenttype-folder state-published url">Phono3py Input</a>
</span>
<span class="documentByLine">
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<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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<span>What's New</span>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
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- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -557,7 +554,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -605,10 +602,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
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- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
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- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
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- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
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- <a title="Tools for computational chemistry." class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -688,7 +685,7 @@
- <a title="Molpro is a complete system of ab initio programs for molecular electronic structure calculations." class="state-published contenttype-document" href="chemistry/molpro.html">
+ <a class="state-published contenttype-document" title="Molpro is a complete system of ab initio programs for molecular electronic structure calculations." href="https://docs.it4i.cz/salomon/software/chemistry/molpro">
<span>Molpro</span>
</a>
@@ -704,7 +701,7 @@
- <a title="High-Performance Computational Chemistry" class="state-published contenttype-document" href="chemistry/nwchem.html">
+ <a class="state-published contenttype-document" title="High-Performance Computational Chemistry" href="https://docs.it4i.cz/salomon/software/chemistry/nwchem">
<span>NWChem</span>
</a>
@@ -720,8 +717,8 @@
- <a title="
-" class="state-published contenttype-document" href="chemistry/phono3py.html">
+ <a class="state-published contenttype-document" title="
+" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py">
<span>Phono3py</span>
</a>
@@ -737,7 +734,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="chemistry/phono3py-input.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input">
<span>Phono3py Input</span>
</a>
@@ -762,7 +759,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -778,7 +775,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -794,7 +791,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -810,7 +807,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -826,7 +823,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -842,7 +839,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -858,7 +855,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -883,7 +880,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -908,7 +905,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -924,7 +921,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -940,7 +937,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -956,7 +953,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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diff --git a/docs.it4i.cz/salomon/software/chemistry.md b/docs.it4i.cz/salomon/software/chemistry.md
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old mode 100755
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similarity index 68%
rename from salomon/software/chemistry/molpro.html
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<title>Molpro — IT4I Docs</title>
- <link rel="canonical" href="molpro.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/chemistry/molpro" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
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@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="molpro.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/chemistry/molpro#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="molpro.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/chemistry/molpro#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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<div id="portal-advanced-search" class="hiddenStructure">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
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+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
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- <a href="../chemistry.html">Chemistry, Physics and Materials science</a>
+ <a href="https://docs.it4i.cz/salomon/software/chemistry">Chemistry, Physics and Materials science</a>
<span class="breadcrumbSeparator">
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@@ -293,7 +290,7 @@
<h2 class=" ">Running</h2>
<p>Molpro is compiled for parallel execution using MPI and OpenMP. By default, Molpro reads the number of allocated nodes from PBS and launches a data server on one node. On the remaining allocated nodes, compute processes are launched, one process per node, each with 16 threads. You can modify this behavior by using -n, -t and helper-server options. Please refer to the <a class="external-link" href="http://www.molpro.net/info/2010.1/doc/manual/node9.html" target="_self" title="">Molpro documentation</a> for more details. </p>
<p class="exclamation">The OpenMP parallelization in Molpro is limited and has been observed to produce limited scaling. We therefore recommend to use MPI parallelization only. This can be achieved by passing option <span class="monospace">mpiprocs=24:ompthreads=1</span> to PBS.</p>
-<p>You are advised to use the -d option to point to a directory in <a target="_self" title="" class="internal-link" href="../../storage.html">SCRATCH filesystem</a>. Molpro can produce a large amount of temporary data during its run, and it is important that these are placed in the fast scratch filesystem.</p>
+<p>You are advised to use the -d option to point to a directory in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/storage">SCRATCH filesystem</a>. Molpro can produce a large amount of temporary data during its run, and it is important that these are placed in the fast scratch filesystem.</p>
<h3 class=" ">Example jobscript</h3>
<pre class=" ">#PBS -A IT4I-0-0<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=24:mpiprocs=24:ompthreads=1<br /><br />cd $PBS_O_WORKDIR<br /><br /># load Molpro module<br />module add Molpro/2010.1-patch-57-intel2015b<br /><br /># create a directory in the SCRATCH filesystem<br />mkdir -p /scratch/work/user/$USER/$PBS_JOBID<br /><br /># copy an example input<br />cp /apps/all/Molpro/2010.1-patch57/molprop_2010_1_Linux_x86_64_i8/examples/caffeine_opt_diis.com .<br /><br /># run Molpro with default options<br /><span>molpro -d /scratch/work/user/$USER/$PBS_JOBID caffeine_opt_diis.com<br /><br /># delete scratch directory<br />rm -rf /scratch/work/user/$USER/$PBS_JOBIDÂ </span></pre>
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<dt class="portletHeader hiddenStructure">
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -451,7 +448,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -467,7 +464,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -483,7 +480,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
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<span>Network</span>
</a>
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- <a title="In this section we provide overview of installed software and its usage.
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-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
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<span>Software</span>
</a>
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- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -598,7 +595,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
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- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -630,7 +627,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
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- <a title="Molpro is a complete system of ab initio programs for molecular electronic structure calculations." class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="molpro.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="Molpro is a complete system of ab initio programs for molecular electronic structure calculations." href="https://docs.it4i.cz/salomon/software/chemistry/molpro">
<span>Molpro</span>
</a>
@@ -662,7 +659,7 @@
- <a title="High-Performance Computational Chemistry" class="state-published contenttype-document" href="nwchem.html">
+ <a class="state-published contenttype-document" title="High-Performance Computational Chemistry" href="https://docs.it4i.cz/salomon/software/chemistry/nwchem">
<span>NWChem</span>
</a>
@@ -678,8 +675,8 @@
- <a title="
-" class="state-published contenttype-document" href="phono3py.html">
+ <a class="state-published contenttype-document" title="
+" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py">
<span>Phono3py</span>
</a>
@@ -695,7 +692,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="phono3py-input.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input">
<span>Phono3py Input</span>
</a>
@@ -720,7 +717,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -736,7 +733,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -752,7 +749,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -768,7 +765,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -784,7 +781,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -800,7 +797,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -816,7 +813,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -841,7 +838,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -866,7 +863,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -882,7 +879,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -898,7 +895,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -914,7 +911,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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(function() {
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
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})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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diff --git a/docs.it4i.cz/salomon/software/chemistry/molpro.md b/docs.it4i.cz/salomon/software/chemistry/molpro.md
new file mode 100644
index 0000000000000000000000000000000000000000..cd7dbf7c8ca72508fdb3449a46f52800d0b48964
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+++ b/docs.it4i.cz/salomon/software/chemistry/molpro.md
@@ -0,0 +1,67 @@
+Molpro
+======
+Molpro is a complete system of ab initio programs for molecular
+electronic structure calculations.
+About Molpro
+------------
+Molpro is a software package used for accurate ab-initio quantum
+chemistry calculations. More information can be found at the [official
+webpage](http://www.molpro.net/).
+License
+-------
+Molpro software package is available only to users that have a valid
+license. Please contact support to enable access to Molpro if you have a
+valid license appropriate for running on our cluster (eg. <span>academic
+research group licence, parallel execution).</span>
+<span>To run Molpro, you need to have a valid license token present in
+"<span class="monospace">$HOME/.molpro/token"</span></span>. You can
+download the token from [Molpro
+website](https://www.molpro.net/licensee/?portal=licensee).
+Installed version
+-----------------
+Currently on Salomon is installed version 2010.1, patch level 57,
+parallel version compiled with Intel compilers and Intel MPI.
+Compilation parameters are default :
+ Parameter Value
+ --- ------
+ <span>max number of atoms</span> 200
+ <span>max number of valence orbitals</span> 300
+ <span>max number of basis functions</span> 4095
+ <span>max number of states per symmmetry</span> 20
+ <span>max number of state symmetries</span> 16
+ <span>max number of records</span> 200
+ <span>max number of primitives</span> <span>maxbfn x [2]</span>
+Â
+Running
+-------
+Molpro is compiled for parallel execution using MPI and OpenMP. By
+default, Molpro reads the number of allocated nodes from PBS and
+launches a data server on one node. On the remaining allocated nodes,
+compute processes are launched, one process per node, each with 16
+threads. You can modify this behavior by using -n, -t and helper-server
+options. Please refer to the [Molpro
+documentation](http://www.molpro.net/info/2010.1/doc/manual/node9.html)
+for more details.Â
+The OpenMP parallelization in Molpro is limited and has been observed to
+produce limited scaling. We therefore recommend to use MPI
+parallelization only. This can be achieved by passing option <span
+class="monospace">mpiprocs=24:ompthreads=1</span> to PBS.
+You are advised to use the -d option to point to a directory in [SCRATCH
+filesystem](https://docs.it4i.cz/salomon/storage).
+Molpro can produce a large amount of temporary data during its run, and
+it is important that these are placed in the fast scratch filesystem.
+### Example jobscript
+ #PBS -A IT4I-0-0
+ #PBS -q qprod
+ #PBS -l select=1:ncpus=24:mpiprocs=24:ompthreads=1
+ cd $PBS_O_WORKDIR
+ # load Molpro module
+ module add Molpro/2010.1-patch-57-intel2015b
+ # create a directory in the SCRATCH filesystem
+ mkdir -p /scratch/work/user/$USER/$PBS_JOBID
+ # copy an example input
+ cp /apps/all/Molpro/2010.1-patch57/molprop_2010_1_Linux_x86_64_i8/examples/caffeine_opt_diis.com .
+ # run Molpro with default options
+ molpro -d /scratch/work/user/$USER/$PBS_JOBID caffeine_opt_diis.com
+ # delete scratch directory
+ rm -rf /scratch/work/user/$USER/$PBS_JOBIDÂ
diff --git a/salomon/software/chemistry/nwchem.html b/docs.it4i.cz/salomon/software/chemistry/nwchem.html
old mode 100755
new mode 100644
similarity index 66%
rename from salomon/software/chemistry/nwchem.html
rename to docs.it4i.cz/salomon/software/chemistry/nwchem.html
index bb82abd5d78f30bdb6e16253bb5ebfc7aa9f330f..719b33fcc9b7c319cf485050406d2c1f94bd76d0
--- a/salomon/software/chemistry/nwchem.html
+++ b/docs.it4i.cz/salomon/software/chemistry/nwchem.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/chemistry/nwchem by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:25 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/chemistry/nwchem" /><!--[if lt IE 7]></base><![endif]-->
<meta content="High-Performance Computational Chemistry" name="description" />
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>NWChem — IT4I Docs</title>
- <link rel="canonical" href="nwchem.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/chemistry/nwchem" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="nwchem.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/chemistry/nwchem#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="nwchem.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/chemistry/nwchem#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
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- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../chemistry.html">Chemistry, Physics and Materials science</a>
+ <a href="https://docs.it4i.cz/salomon/software/chemistry">Chemistry, Physics and Materials science</a>
<span class="breadcrumbSeparator">
/
@@ -269,7 +266,7 @@
<p>Please refer to <a class="external-link" href="http://www.nwchem-sw.org/index.php/Release62:Top-level" target="_self" title="">the documentation</a>Â and in the input file set the following directives :</p>
<ul>
<li><span>MEMORY : controls the amount of memory NWChem will use</span></li>
-<li><span>SCRATCH_DIR : set this to a directory in <a target="_self" title="" class="internal-link" href="../../storage.html">SCRATCH filesystem</a> (or run the calculation completely in a scratch directory). For certain calculations, it might be advisable to reduce I/O by forcing "direct" mode, eg. "scf direct"</span></li>
+<li><span>SCRATCH_DIR : set this to a directory in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/storage">SCRATCH filesystem</a> (or run the calculation completely in a scratch directory). For certain calculations, it might be advisable to reduce I/O by forcing "direct" mode, eg. "scf direct"</span></li>
</ul>
</div>
@@ -346,7 +343,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -362,7 +359,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -378,7 +375,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -394,7 +391,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -410,7 +407,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -426,7 +423,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -442,7 +439,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -458,7 +455,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -474,7 +471,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -490,7 +487,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -506,7 +503,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -522,7 +519,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -538,10 +535,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -557,7 +554,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -573,7 +570,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -589,7 +586,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -605,7 +602,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -621,7 +618,7 @@
- <a title="Molpro is a complete system of ab initio programs for molecular electronic structure calculations." class="state-published contenttype-document" href="molpro.html">
+ <a class="state-published contenttype-document" title="Molpro is a complete system of ab initio programs for molecular electronic structure calculations." href="https://docs.it4i.cz/salomon/software/chemistry/molpro">
<span>Molpro</span>
</a>
@@ -637,7 +634,7 @@
- <a title="High-Performance Computational Chemistry" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="nwchem.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="High-Performance Computational Chemistry" href="https://docs.it4i.cz/salomon/software/chemistry/nwchem">
<span>NWChem</span>
</a>
@@ -653,8 +650,8 @@
- <a title="
-" class="state-published contenttype-document" href="phono3py.html">
+ <a class="state-published contenttype-document" title="
+" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py">
<span>Phono3py</span>
</a>
@@ -670,7 +667,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="phono3py-input.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input">
<span>Phono3py Input</span>
</a>
@@ -695,7 +692,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -711,7 +708,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -727,7 +724,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -743,7 +740,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -759,7 +756,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -775,7 +772,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -791,7 +788,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -816,7 +813,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -841,7 +838,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -857,7 +854,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -873,7 +870,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -889,7 +886,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -978,7 +975,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/chemistry/nwchem by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:25 GMT -->
</html>
diff --git a/docs.it4i.cz/salomon/software/chemistry/nwchem.md b/docs.it4i.cz/salomon/software/chemistry/nwchem.md
new file mode 100644
index 0000000000000000000000000000000000000000..625eb93bcd905b4e3b758bacc030e0f7f5613a6a
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/chemistry/nwchem.md
@@ -0,0 +1,46 @@
+NWChem
+======
+High-Performance Computational Chemistry
+<span>Introduction</span>
+--
+<span>NWChem aims to provide its users with computational chemistry
+tools that are scalable both in their ability to treat large scientific
+computational chemistry problems efficiently, and in their use of
+available parallel computing resources from high-performance parallel
+supercomputers to conventional workstation clusters.</span>
+[Homepage](http://www.nwchem-sw.org/index.php/Main_Page)
+Installed versions
+------------------
+The following versions are currently installed :Â
+- <span>NWChem/6.3.revision2-2013-10-17-Python-2.7.8, current release.
+ Compiled with Intel compilers, MKL and Intel MPI</span>
+ Â
+- <span>NWChem/6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.8</span>
+For a current list of installed versions, execute :Â
+ module avail NWChem
+The recommend to use version 6.5. Version 6.3 fails on Salomon nodes
+with accelerator, because it attempts to communicate over scif0
+interface. In 6.5 this is avoided by
+setting ARMCI_OPENIB_DEVICE=mlx4_0, this setting is included in the
+module.
+Running
+-------
+NWChem is compiled for parallel MPI execution. Normal procedure for MPI
+jobs applies. Sample jobscript :
+ #PBS -A IT4I-0-0
+ #PBS -q qprod
+ #PBS -l select=1:ncpus=24:mpiprocs=24
+ cd $PBS_O_WORKDIR
+ module add NWChem/6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.8
+ mpirun nwchem h2o.nw
+<span>Options</span>
+--------------------
+Please refer to [the
+documentation](http://www.nwchem-sw.org/index.php/Release62:Top-level)Â and
+in the input file set the following directives :
+- <span>MEMORY controls the amount of memory NWChem will use</span>
+- <span>SCRATCH_DIR set this to a directory in [SCRATCH
+ filesystem](https://docs.it4i.cz/salomon/storage)Â (or
+ run the calculation completely in a scratch directory). For certain
+ calculations, it might be advisable to reduce I/O by forcing
+ "direct" mode, eg. "scf direct"</span>
diff --git a/salomon/software/chemistry/phono3py-input.html b/docs.it4i.cz/salomon/software/chemistry/phono3py-input.html
old mode 100755
new mode 100644
similarity index 60%
rename from salomon/software/chemistry/phono3py-input.html
rename to docs.it4i.cz/salomon/software/chemistry/phono3py-input.html
index cc7acf2d655b7fd5fcc962417ab97da8bc0cd3d8..e6e3c1c136f4775335f964d7049d7136b47f4212
--- a/salomon/software/chemistry/phono3py-input.html
+++ b/docs.it4i.cz/salomon/software/chemistry/phono3py-input.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/chemistry/phono3py-input by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:28 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Phono3py Input — IT4I Docs</title>
- <link rel="canonical" href="phono3py-input.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="phono3py-input.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="phono3py-input.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../chemistry.html">Chemistry, Physics and Materials science</a>
+ <a href="https://docs.it4i.cz/salomon/software/chemistry">Chemistry, Physics and Materials science</a>
<span class="breadcrumbSeparator">
/
@@ -256,8 +253,8 @@
<dt class="">
<span class="summary">
- <img width="16" height="16" src="../../../application.png" alt="Soubor text/vnd.wap.si" />
- <a href="phono3py-input/poscar-si/view.html" class="contenttype-file state-missing-value url">POSCAR Si</a>
+ <img width="16" height="16" src="https://docs.it4i.cz/application.png" alt="Soubor text/vnd.wap.si" />
+ <a href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/poscar-si/view" class="contenttype-file state-missing-value url">POSCAR Si</a>
</span>
<span class="documentByLine">
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<dt class="">
<span class="summary">
- <img width="16" height="16" src="../../../application.png" alt="Soubor" />
- <a href="phono3py-input/KPOINTS/view.html" class="contenttype-file state-missing-value url">KPOINTS</a>
+ <img width="16" height="16" src="https://docs.it4i.cz/application.png" alt="Soubor" />
+ <a href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/KPOINTS/view" class="contenttype-file state-missing-value url">KPOINTS</a>
</span>
<span class="documentByLine">
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<dt class="">
<span class="summary">
- <img width="16" height="16" src="../../../application.png" alt="Soubor" />
- <a href="phono3py-input/POTCAR/view.html" class="contenttype-file state-missing-value url">POTCAR</a>
+ <img width="16" height="16" src="https://docs.it4i.cz/application.png" alt="Soubor" />
+ <a href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/POTCAR/view" class="contenttype-file state-missing-value url">POTCAR</a>
</span>
<span class="documentByLine">
@@ -334,8 +331,8 @@
<dt class="">
<span class="summary">
- <img width="16" height="16" src="../../../application.png" alt="Soubor" />
- <a href="phono3py-input/INCAR/view.html" class="contenttype-file state-missing-value url">INCAR</a>
+ <img width="16" height="16" src="https://docs.it4i.cz/application.png" alt="Soubor" />
+ <a href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/INCAR/view" class="contenttype-file state-missing-value url">INCAR</a>
</span>
<span class="documentByLine">
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<dt class="">
<span class="summary">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor shell script" />
- <a href="phono3py-input/run.sh/view.html" class="contenttype-file state-missing-value url">run.sh</a>
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor shell script" />
+ <a href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/run.sh/view" class="contenttype-file state-missing-value url">run.sh</a>
</span>
<span class="documentByLine">
@@ -386,8 +383,8 @@
<dt class="">
<span class="summary">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor shell script" />
- <a href="phono3py-input/submit.sh/view.html" class="contenttype-file state-missing-value url">submit.sh</a>
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor shell script" />
+ <a href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/submit.sh/view" class="contenttype-file state-missing-value url">submit.sh</a>
</span>
<span class="documentByLine">
@@ -412,8 +409,8 @@
<dt class="">
<span class="summary">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor shell script" />
- <a href="phono3py-input/prepare.sh/view.html" class="contenttype-file state-missing-value url">prepare.sh</a>
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor shell script" />
+ <a href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/prepare.sh/view" class="contenttype-file state-missing-value url">prepare.sh</a>
</span>
<span class="documentByLine">
@@ -438,8 +435,8 @@
<dt class="">
<span class="summary">
- <img width="16" height="16" src="../../../sh.png" alt="Soubor shell script" />
- <a href="phono3py-input/gofree-cond1.sh/view.html" class="contenttype-file state-missing-value url">gofree-cond1.sh</a>
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor shell script" />
+ <a href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/gofree-cond1.sh/view" class="contenttype-file state-missing-value url">gofree-cond1.sh</a>
</span>
<span class="documentByLine">
@@ -524,7 +521,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -540,7 +537,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -556,7 +553,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -572,7 +569,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -588,7 +585,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -604,7 +601,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -620,7 +617,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -636,7 +633,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -652,7 +649,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -668,7 +665,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -684,7 +681,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -700,7 +697,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -716,10 +713,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -735,7 +732,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -751,7 +748,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -767,7 +764,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -783,7 +780,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -799,7 +796,7 @@
- <a title="Molpro is a complete system of ab initio programs for molecular electronic structure calculations." class="state-published contenttype-document" href="molpro.html">
+ <a class="state-published contenttype-document" title="Molpro is a complete system of ab initio programs for molecular electronic structure calculations." href="https://docs.it4i.cz/salomon/software/chemistry/molpro">
<span>Molpro</span>
</a>
@@ -815,7 +812,7 @@
- <a title="High-Performance Computational Chemistry" class="state-published contenttype-document" href="nwchem.html">
+ <a class="state-published contenttype-document" title="High-Performance Computational Chemistry" href="https://docs.it4i.cz/salomon/software/chemistry/nwchem">
<span>NWChem</span>
</a>
@@ -831,8 +828,8 @@
- <a title="
-" class="state-published contenttype-document" href="phono3py.html">
+ <a class="state-published contenttype-document" title="
+" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py">
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
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+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../../../salomon.html">Dokumentace pro Salomon</a>
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<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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<title>KPOINTS — IT4I Docs</title>
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<title>POTCAR — IT4I Docs</title>
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POTCAR
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<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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<title>gofree-cond1.sh — IT4I Docs</title>
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+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
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<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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old mode 100755
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rename from salomon/software/chemistry/phono3py-input/submit.sh/view.html
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<title>submit.sh — IT4I Docs</title>
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<pre class="prettyprint lang-sh">$ module load phono3py/0.9.14-ictce-7.3.5-Python-2.7.9</pre>
<h2>Example of calculating thermal conductivity of Si using VASP code.</h2>
<h3>Calculating force constants</h3>
-<p>One needs to calculate second order and third order force constants using the diamond structure of silicon stored in <a target="_self" title="" class="internal-link" href="phono3py-input/POSCAR">POSCAR</a>Â (the same form as in VASP) using single displacement calculations within supercell.</p>
+<p>One needs to calculate second order and third order force constants using the diamond structure of silicon stored in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/poscar-si">POSCAR</a>Â (the same form as in VASP) using single displacement calculations within supercell.</p>
<pre class="prettyprint lang-sh">$ cat POSCAR<br />Â Si<br />Â Â 1.0<br />Â Â Â Â 5.4335600309153529Â Â Â 0.0000000000000000Â Â Â 0.0000000000000000<br />Â Â Â Â 0.0000000000000000Â Â Â 5.4335600309153529Â Â Â 0.0000000000000000<br />Â Â Â Â 0.0000000000000000Â Â Â 0.0000000000000000Â Â Â 5.4335600309153529<br />Â Si<br />Â Â 8<br />Direct<br />Â Â 0.8750000000000000Â 0.8750000000000000Â 0.8750000000000000<br />Â Â 0.8750000000000000Â 0.3750000000000000Â 0.3750000000000000<br />Â Â 0.3750000000000000Â 0.8750000000000000Â 0.3750000000000000<br />Â Â 0.3750000000000000Â 0.3750000000000000Â 0.8750000000000000<br />Â Â 0.1250000000000000Â 0.1250000000000000Â 0.1250000000000000<br />Â Â 0.1250000000000000Â 0.6250000000000000Â 0.6250000000000000<br />Â Â 0.6250000000000000Â 0.1250000000000000Â 0.6250000000000000<br />Â Â 0.6250000000000000Â 0.6250000000000000Â 0.1250000000000000<br /><br /></pre>
<h3>Generating displacement using 2x2x2 supercell for both second and third order force constants</h3>
<pre class="prettyprint lang-sh">$ <span class="n">phono3py</span> <span class="o">-</span><span class="n">d</span> <span class="o">--</span><span class="n">dim</span><span class="o">=</span><span class="s2">"2 2 2"</span> <span class="o">-</span><span class="n">c</span> <span class="n">POSCAR</span><span class="o"></span><span class="n"></span></pre>
<p class=" "><span class="n">111 displacements is created stored in <span class="n">disp_fc3.yaml</span>, and the structure input files with this displacements are POSCAR-00XXX, where the XXX=111.<br /></span></p>
<pre class="prettyprint lang-sh"><span class="n">disp_fc3.yaml POSCAR-00008 POSCAR-00017 POSCAR-00026 POSCAR-00035 POSCAR-00044 POSCAR-00053 POSCAR-00062 POSCAR-00071 POSCAR-00080 POSCAR-00089 POSCAR-00098 POSCAR-00107<br />POSCAR        POSCAR-00009 POSCAR-00018 POSCAR-00027 POSCAR-00036 POSCAR-00045 POSCAR-00054 POSCAR-00063 POSCAR-00072 POSCAR-00081 POSCAR-00090 POSCAR-00099 POSCAR-00108<br />POSCAR-00001  POSCAR-00010 POSCAR-00019 POSCAR-00028 POSCAR-00037 POSCAR-00046 POSCAR-00055 POSCAR-00064 POSCAR-00073 POSCAR-00082 POSCAR-00091 POSCAR-00100 POSCAR-00109<br />POSCAR-00002  POSCAR-00011 POSCAR-00020 POSCAR-00029 POSCAR-00038 POSCAR-00047 POSCAR-00056 POSCAR-00065 POSCAR-00074 POSCAR-00083 POSCAR-00092 POSCAR-00101 POSCAR-00110<br />POSCAR-00003  POSCAR-00012 POSCAR-00021 POSCAR-00030 POSCAR-00039 POSCAR-00048 POSCAR-00057 POSCAR-00066 POSCAR-00075 POSCAR-00084 POSCAR-00093 POSCAR-00102 POSCAR-00111<br />POSCAR-00004  POSCAR-00013 POSCAR-00022 POSCAR-00031 POSCAR-00040 POSCAR-00049 POSCAR-00058 POSCAR-00067 POSCAR-00076 POSCAR-00085 POSCAR-00094 POSCAR-00103<br />POSCAR-00005  POSCAR-00014 POSCAR-00023 POSCAR-00032 POSCAR-00041 POSCAR-00050 POSCAR-00059 POSCAR-00068 POSCAR-00077 POSCAR-00086 POSCAR-00095 POSCAR-00104<br />POSCAR-00006  POSCAR-00015 POSCAR-00024 POSCAR-00033 POSCAR-00042 POSCAR-00051 POSCAR-00060 POSCAR-00069 POSCAR-00078 POSCAR-00087 POSCAR-00096 POSCAR-00105<br />POSCAR-00007  POSCAR-00016 POSCAR-00025 POSCAR-00034 POSCAR-00043 POSCAR-00052 POSCAR-00061 POSCAR-00070 POSCAR-00079 POSCAR-00088 POSCAR-00097 POSCAR-00106</span></pre>
-<p class=" "><span class="n"> For each displacement the forces needs to be calculated, i.e. in form of the output file of VASP (vasprun.xml). For a single VASP calculations one needs <a target="_self" title="" class="internal-link" href="phono3py-input/KPOINTS">KPOINTS</a>, <a target="_self" title="" class="internal-link" href="phono3py-input/POTCAR">POTCAR</a>, <a target="_self" title="" class="internal-link" href="phono3py-input/INCAR">INCAR</a> in your case directory (where you have POSCARS) and those 111 displacements calculations can be generated by <a target="_self" title="" class="internal-link" href="phono3py-input/prepare.sh">prepare.sh</a> script. Then each of the single 111 calculations is submitted <a target="_self" title="" class="internal-link" href="phono3py-input/run.sh">run.sh</a> by <a target="_self" title="" class="internal-link" href="phono3py-input/submit.sh">submit.sh</a>.</span></p>
+<p class=" "><span class="n"> For each displacement the forces needs to be calculated, i.e. in form of the output file of VASP (vasprun.xml). For a single VASP calculations one needs <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/KPOINTS">KPOINTS</a>, <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/POTCAR">POTCAR</a>, <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/INCAR">INCAR</a> in your case directory (where you have POSCARS) and those 111 displacements calculations can be generated by <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/prepare.sh">prepare.sh</a> script. Then each of the single 111 calculations is submitted <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/run.sh">run.sh</a> by <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/submit.sh">submit.sh</a>.</span></p>
<pre class="prettyprint lang-sh"><span class="n">$./prepare.sh<br />$ls<br />disp-00001Â disp-00009Â disp-00017Â disp-00025Â disp-00033Â disp-00041Â disp-00049Â disp-00057Â disp-00065Â disp-00073Â disp-00081Â disp-00089Â disp-00097Â disp-00105Â Â Â Â INCAR<br />disp-00002Â disp-00010Â disp-00018Â disp-00026Â disp-00034Â disp-00042Â disp-00050Â disp-00058Â disp-00066Â disp-00074Â disp-00082Â disp-00090Â disp-00098Â disp-00106Â Â Â Â KPOINTS<br />disp-00003Â disp-00011Â disp-00019Â disp-00027Â disp-00035Â disp-00043Â disp-00051Â disp-00059Â disp-00067Â disp-00075Â disp-00083Â disp-00091Â disp-00099Â disp-00107Â Â Â Â POSCAR<br />disp-00004Â disp-00012Â disp-00020Â disp-00028Â disp-00036Â disp-00044Â disp-00052Â disp-00060Â disp-00068Â disp-00076Â disp-00084Â disp-00092Â disp-00100Â disp-00108Â Â Â Â POTCAR<br />disp-00005Â disp-00013Â disp-00021Â disp-00029Â disp-00037Â disp-00045Â disp-00053Â disp-00061Â disp-00069Â disp-00077Â disp-00085Â disp-00093Â disp-00101Â disp-00109Â Â Â Â prepare.sh<br />disp-00006Â disp-00014Â disp-00022Â disp-00030Â disp-00038Â disp-00046Â disp-00054Â disp-00062Â disp-00070Â disp-00078Â disp-00086Â disp-00094Â disp-00102Â disp-00110Â Â Â Â run.sh<br />disp-00007Â disp-00015Â disp-00023Â disp-00031Â disp-00039Â disp-00047Â disp-00055Â disp-00063Â disp-00071Â disp-00079Â disp-00087Â disp-00095Â disp-00103Â disp-00111Â Â Â Â submit.sh<br />disp-00008Â disp-00016Â disp-00024Â disp-00032Â disp-00040Â disp-00048Â disp-00056Â disp-00064Â disp-00072Â disp-00080Â disp-00088Â disp-00096Â disp-00104Â disp_fc3.yaml<br /></span></pre>
<p class=" "><span class="n">Taylor your run.sh script to fit into your project and other needs and submit all 111 calculations using submit.sh script</span></p>
<pre class="prettyprint lang-sh"><span class="n">$ ./submit.sh</span></pre>
@@ -283,7 +280,7 @@
<pre class="prettyprint lang-sh">$ grep grid_point ir_grid_points.yaml<br />num_reduced_ir_grid_points: 35<br />ir_grid_points:Â # [address, weight]<br />- grid_point: 0<br />- grid_point: 1<br />- grid_point: 2<br />- grid_point: 3<br />- grid_point: 4<br />- grid_point: 10<br />- grid_point: 11<br />- grid_point: 12<br />- grid_point: 13<br />- grid_point: 20<br />- grid_point: 21<br />- grid_point: 22<br />- grid_point: 30<br />- grid_point: 31<br />- grid_point: 40<br />- grid_point: 91<br />- grid_point: 92<br />- grid_point: 93<br />- grid_point: 94<br />- grid_point: 101<br />- grid_point: 102<br />- grid_point: 103<br />- grid_point: 111<br />- grid_point: 112<br />- grid_point: 121<br />- grid_point: 182<br />- grid_point: 183<br />- grid_point: 184<br />- grid_point: 192<br />- grid_point: 193<br />- grid_point: 202<br />- grid_point: 273<br />- grid_point: 274<br />- grid_point: 283<br />- grid_point: 364</pre>
<p>one finds which grid points needed to be calculated, for instance using following</p>
<pre class="prettyprint lang-sh"><span class="n">$ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCARÂ --sigma 0.1 --br --write-gamma --gp="0 1 2</span></pre>
-<p><span class="n">one calculates grid points 0, 1, 2. To automize one can use for instance scripts to submit 5 points in series, see <a target="_self" title="" class="internal-link" href="phono3py-input/gofree-cond1.sh">gofree-cond1.sh </a></span></p>
+<p><span class="n">one calculates grid points 0, 1, 2. To automize one can use for instance scripts to submit 5 points in series, see <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/gofree-cond1.sh">gofree-cond1.sh </a></span></p>
<pre class="prettyprint lang-sh"><span class="n">$ qsub gofree-cond1.sh</span></pre>
<p><span class="n">Finally the thermal conductivity result is produced by grouping single conductivity per grid calculations using </span></p>
<pre class="prettyprint lang-sh"><span class="n">$ <span class="n">phono3py</span> <span class="o">--</span><span class="n">fc3</span> <span class="o">--</span><span class="n">fc2</span> <span class="o">--</span><span class="n">dim</span><span class="o">=</span><span class="s2">"2 2 2"</span> <span class="o">--</span><span class="n">mesh</span><span class="o">=</span><span class="s2">"</span>9 9 9" <span class="o">--</span><span class="n">br</span> <span class="o">--</span><span class="n">read_gamma</span></span></pre>
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@@ -791,7 +788,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -807,7 +804,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -832,7 +829,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -857,7 +854,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -873,7 +870,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -889,7 +886,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -905,7 +902,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -944,14 +941,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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@@ -994,7 +991,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/salomon/software/chemistry/phono3py.md b/docs.it4i.cz/salomon/software/chemistry/phono3py.md
similarity index 58%
rename from salomon/software/chemistry/phono3py.md
rename to docs.it4i.cz/salomon/software/chemistry/phono3py.md
index 5c9b5bba30b85dc8de907a95133bef64de80410b..5c34f9576f597ddd06c2cbf12bf7c0e18b8903eb 100644
--- a/salomon/software/chemistry/phono3py.md
+++ b/docs.it4i.cz/salomon/software/chemistry/phono3py.md
@@ -1,7 +1,6 @@
Phono3py
========
-
-
+
 Introduction
-------------
This GPL software calculates phonon-phonon interactions via the third
@@ -9,19 +8,19 @@ order force constants. It allows to obtain lattice thermal conductivity,
phonon lifetime/linewidth, imaginary part of self energy at the lowest
order, joint density of states (JDOS) and weighted-JDOS. For details see
Phys. Rev. B 91, 094306 (2015) and
-http//atztogo.github.io/phono3py/index.html
-
+http://atztogo.github.io/phono3py/index.html
Load the phono3py/0.9.14-ictce-7.3.5-Python-2.7.9 module
``` {.prettyprint .lang-sh}
$ module load phono3py/0.9.14-ictce-7.3.5-Python-2.7.9
```
Example of calculating thermal conductivity of Si using VASP code.
-------------------------------------------------------------------
+--------------------
### Calculating force constants
One needs to calculate second order and third order force constants
using the diamond structure of silicon stored in
-[POSCAR](phono3py-input/POSCAR)Â (the same form as in
-VASP) using single displacement calculations within supercell.
+[POSCAR](https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/poscar-si)Â
+(the same form as in VASP) using single displacement calculations within
+supercell.
``` {.prettyprint .lang-sh}
$ cat POSCAR
 Si
@@ -45,9 +44,10 @@ Direct
``` {.prettyprint .lang-sh}
$ phono3py -d --dim="2 2 2" -c POSCAR
```
-111 displacements is created stored in
-class="n">disp_fc3.yaml, and the structure input files with this
+<span class="n">111 displacements is created stored in <span
+class="n">disp_fc3.yaml</span>, and the structure input files with this
displacements are POSCAR-00XXX, where the XXX=111.
+</span>
``` {.prettyprint .lang-sh}
disp_fc3.yaml POSCAR-00008 POSCAR-00017 POSCAR-00026 POSCAR-00035 POSCAR-00044 POSCAR-00053 POSCAR-00062 POSCAR-00071 POSCAR-00080 POSCAR-00089 POSCAR-00098 POSCAR-00107
POSCARÂ Â Â Â Â Â Â Â POSCAR-00009Â POSCAR-00018Â POSCAR-00027Â POSCAR-00036Â POSCAR-00045Â POSCAR-00054Â POSCAR-00063Â POSCAR-00072Â POSCAR-00081Â POSCAR-00090Â POSCAR-00099Â POSCAR-00108
@@ -59,17 +59,19 @@ POSCAR-00005Â Â POSCAR-00014Â POSCAR-00023Â POSCAR-00032Â POSCAR-00041Â POS
POSCAR-00006Â Â POSCAR-00015Â POSCAR-00024Â POSCAR-00033Â POSCAR-00042Â POSCAR-00051Â POSCAR-00060Â POSCAR-00069Â POSCAR-00078Â POSCAR-00087Â POSCAR-00096Â POSCAR-00105
POSCAR-00007Â Â POSCAR-00016Â POSCAR-00025Â POSCAR-00034Â POSCAR-00043Â POSCAR-00052Â POSCAR-00061Â POSCAR-00070Â POSCAR-00079Â POSCAR-00088Â POSCAR-00097Â POSCAR-00106
```
- For each displacement the forces needs to be
+<span class="n"> For each displacement the forces needs to be
calculated, i.e. in form of the output file of VASP (vasprun.xml). For a
single VASP calculations one needs
-[KPOINTS](phono3py-input/KPOINTS),
-[POTCAR](phono3py-input/POTCAR),
-[INCAR](phono3py-input/INCAR) in your case directory
-(where you have POSCARS) and those 111 displacements calculations can be
-generated by [prepare.sh](phono3py-input/prepare.sh)
+[KPOINTS](https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/KPOINTS),
+[POTCAR](https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/POTCAR),
+[INCAR](https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/INCAR)
+in your case directory (where you have POSCARS) and those 111
+displacements calculations can be generated by
+[prepare.sh](https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/prepare.sh)
script. Then each of the single 111 calculations is submitted
-[run.sh](phono3py-input/run.sh) by
-[submit.sh](phono3py-input/submit.sh).
+[run.sh](https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/run.sh)
+by
+[submit.sh](https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/submit.sh).</span>
``` {.prettyprint .lang-sh}
$./prepare.sh
$ls
@@ -82,142 +84,89 @@ disp-00006Â disp-00014Â disp-00022Â disp-00030Â disp-00038Â disp-00046Â di
disp-00007Â disp-00015Â disp-00023Â disp-00031Â disp-00039Â disp-00047Â disp-00055Â disp-00063Â disp-00071Â disp-00079Â disp-00087Â disp-00095Â disp-00103Â disp-00111Â Â Â Â submit.sh
disp-00008Â disp-00016Â disp-00024Â disp-00032Â disp-00040Â disp-00048Â disp-00056Â disp-00064Â disp-00072Â disp-00080Â disp-00088Â disp-00096Â disp-00104Â disp_fc3.yaml
```
-Taylor your run.sh script to fit into your project and
+<span class="n">Taylor your run.sh script to fit into your project and
other needs and submit all 111 calculations using submit.sh
-script
+script</span>
``` {.prettyprint .lang-sh}
$ ./submit.sh
```
-Collecting results and post-processing with phono3py
----------------------------------------------------------------------------
-Once all jobs are finished and vasprun.xml is created in
-each disp-XXXXX directory the collection is done by
+<span class="n">Collecting results and post-processing with phono3py</span>
+------
+<span class="n">Once all jobs are finished and vasprun.xml is created in
+each disp-XXXXX directory the collection is done by </span>
``` {.prettyprint .lang-sh}
$ phono3py --cf3 disp-{00001..00111}/vasprun.xml
```
-and
+<span class="n"><span class="n">and
`disp_fc2.yaml, FORCES_FC2`{.docutils .literal}, `FORCES_FC3`{.docutils
-.literal} and disp_fc3.yaml should appear and put into the hdf
-format by
+.literal}</span> and disp_fc3.yaml should appear and put into the hdf
+format by </span>
``` {.prettyprint .lang-sh}
$ phono3py --dim="2 2 2" -c POSCAR
```
resulting in `fc2.hdf5`{.docutils .literal} and `fc3.hdf5`{.docutils
.literal}
### Thermal conductivity
-The phonon lifetime calculations takes some time,
-however is independent on grid points, so could be splitted
+<span class="pre">The phonon lifetime calculations takes some time,
+however is independent on grid points, so could be splitted:
+</span>
``` {.prettyprint .lang-sh}
$ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" --sigma 0.1 --wgp
```
-### Inspecting ir_grid_points.yaml
+### <span class="n">Inspecting ir_grid_points.yaml</span>
``` {.prettyprint .lang-sh}
$ grep grid_point ir_grid_points.yaml
-num_reduced_ir_grid_points 35
-ir_grid_points # [address, weight]
-- grid_point 0
-- grid_point 1
-- grid_point 2
-- grid_point 3
-- grid_point 4
-- grid_point 10
-- grid_point 11
-- grid_point 12
-- grid_point 13
-- grid_point 20
-- grid_point 21
-- grid_point 22
-- grid_point 30
-- grid_point 31
-- grid_point 40
-- grid_point 91
-- grid_point 92
-- grid_point 93
-- grid_point 94
-- grid_point 101
-- grid_point 102
-- grid_point 103
-- grid_point 111
-- grid_point 112
-- grid_point 121
-- grid_point 182
-- grid_point 183
-- grid_point 184
-- grid_point 192
-- grid_point 193
-- grid_point 202
-- grid_point 273
-- grid_point 274
-- grid_point 283
-- grid_point 364
+num_reduced_ir_grid_points35
+ir_grid_points:Â # [address, weight]
+- grid_point0
+- grid_point1
+- grid_point2
+- grid_point3
+- grid_point4
+- grid_point10
+- grid_point11
+- grid_point12
+- grid_point13
+- grid_point20
+- grid_point21
+- grid_point22
+- grid_point30
+- grid_point31
+- grid_point40
+- grid_point91
+- grid_point92
+- grid_point93
+- grid_point94
+- grid_point101
+- grid_point102
+- grid_point103
+- grid_point111
+- grid_point112
+- grid_point121
+- grid_point182
+- grid_point183
+- grid_point184
+- grid_point192
+- grid_point193
+- grid_point202
+- grid_point273
+- grid_point274
+- grid_point283
+- grid_point364
```
one finds which grid points needed to be calculated, for instance using
following
``` {.prettyprint .lang-sh}
$ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCARÂ --sigma 0.1 --br --write-gamma --gp="0 1 2
```
-one calculates grid points 0, 1, 2. To automize one can
+<span class="n">one calculates grid points 0, 1, 2. To automize one can
use for instance scripts to submit 5 points in series, see
-[gofree-cond1.sh](phono3py-input/gofree-cond1.sh)
+[gofree-cond1.sh](https://docs.it4i.cz/salomon/software/chemistry/phono3py-input/gofree-cond1.sh)</span>
``` {.prettyprint .lang-sh}
$ qsub gofree-cond1.sh
```
-Finally the thermal conductivity result is produced by
-grouping single conductivity per grid calculations usingÂ
+<span class="n">Finally the thermal conductivity result is produced by
+grouping single conductivity per grid calculations using </span>
``` {.prettyprint .lang-sh}
$ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" --br --read_gamma
```
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old mode 100755
new mode 100644
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rename from salomon/software/compilers.html
rename to docs.it4i.cz/salomon/software/compilers.html
index 195d4106818816f340e5da16d6d24ff46bbc6968..66255030ce755dda1b63d44ddf26eba098f4cf67
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+++ b/docs.it4i.cz/salomon/software/compilers.html
@@ -10,45 +10,42 @@
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<title>Compilers — IT4I Docs</title>
- <link rel="canonical" href="compilers.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/compilers" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="compilers.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/compilers#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="compilers.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/compilers#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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@@ -125,13 +122,13 @@
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<div id="portal-advanced-search" class="hiddenStructure">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -261,7 +258,7 @@
<li>PGI</li>
</ul>
<h2 class=" ">Intel Compilers</h2>
-<p class=" ">For information about the usage of Intel Compilers and other Intel products, please read the <a target="_self" title="" class="internal-link" href="intel-suite.html">Intel Parallel studio</a> page.</p>
+<p class=" ">For information about the usage of Intel Compilers and other Intel products, please read the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite">Intel Parallel studio</a> page.</p>
<h2 class=" ">PGI Compilers</h2>
<p>The Portland Group Cluster Development Kit (PGI CDK) is available.</p>
<pre>$ module load PGI<br />$ pgcc -v<br />$ pgc++ -v<br />$ pgf77 -v<br />$ pgf90 -v<br />$ pgf95 -v<br />$ pghpf -v</pre>
@@ -308,9 +305,9 @@
<pre class=" ">$ qsub -I -q qprod -A PROJECT_ID -l select=2:ncpus=24 <br />$ module add bupc<br />$ upcrun -n 48 ./hello.upc.x</pre>
<p class=" ">Â For more informations see the man pages.</p>
<h2 class=" ">Java</h2>
-<p>For information how to use Java (runtime and/or compiler), please read the <a target="_self" title="" class="internal-link" href="java.html">Java page</a>.</p>
+<p>For information how to use Java (runtime and/or compiler), please read the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/java">Java page</a>.</p>
<p class="hiddenForView">nVidia CUDA</p>
-<p class="hiddenForView">For information how to work with nVidia CUDA, please read the <a target="_self" title="" class="internal-link" href="../../anselm-cluster-documentation/software/nvidia-cuda.html">nVidia CUDA page</a>.</p>
+<p class="hiddenForView">For information how to work with nVidia CUDA, please read the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">nVidia CUDA page</a>.</p>
</div>
@@ -386,7 +383,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -402,7 +399,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -418,7 +415,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -434,7 +431,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -450,7 +447,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -466,7 +463,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -482,7 +479,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -498,7 +495,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -514,7 +511,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -530,7 +527,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -546,7 +543,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -562,7 +559,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -578,10 +575,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -597,7 +594,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -613,7 +610,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -629,7 +626,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -645,7 +642,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -661,7 +658,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -677,7 +674,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -693,7 +690,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -709,7 +706,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="compilers.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -725,7 +722,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -741,7 +738,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -757,7 +754,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -782,7 +779,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -807,7 +804,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -823,7 +820,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -839,7 +836,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -855,7 +852,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -894,14 +891,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -923,12 +920,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -944,7 +941,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/compilers by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:33 GMT -->
</html>
diff --git a/salomon/software/compilers.md b/docs.it4i.cz/salomon/software/compilers.md
similarity index 61%
rename from salomon/software/compilers.md
rename to docs.it4i.cz/salomon/software/compilers.md
index 9c16541110eb4f0b5e4f9fb0728bbf9ae5bed809..3cf8ab3113fe1bc198e8ccddda4846af8a66b058 100644
--- a/salomon/software/compilers.md
+++ b/docs.it4i.cz/salomon/software/compilers.md
@@ -1,23 +1,26 @@
-
-
+Compilers
+=========
+Available compilers, including GNU, INTEL and UPC compilers
+
There are several compilers for different programming languages
-available on the cluster
+available on the cluster:
- C/C++
- Fortran 77/90/95/HPF
- Unified Parallel C
- Java
-The C/C++ and Fortran compilers are provided by
-Opensource
+The C/C++ and Fortran compilers are provided by:
+Opensource:
- GNU GCC
- Clang/LLVM
-Commercial licenses
+Commercial licenses:
- Intel
- PGI
Intel Compilers
---------------
For information about the usage of Intel Compilers and other Intel
products, please read the [Intel Parallel
-studio](intel-suite.html) page.
+studio](https://docs.it4i.cz/salomon/software/intel-suite)
+page.
PGI Compilers
-------------
The Portland Group Cluster Development Kit (PGI CDK) is available.
@@ -35,21 +38,21 @@ PGDBG OpenMP/MPI debugger and PGPROF OpenMP/MPI profiler are available
$ pgdbg &
$ pgprof &
For more information, see the [PGI
-page](http//www.pgroup.com/products/pgicdk.htm).
+page](http://www.pgroup.com/products/pgicdk.htm).
GNU
---
For compatibility reasons there are still available the original (old
4.4.7-11) versions of GNU compilers as part of the OS. These are
accessible in the search path by default.
It is strongly recommended to use the up to date version which comes
-with the module GCC
+with the module GCC:
$ module load GCC
$ gcc -v
$ g++ -v
$ gfortran -v
With the module loaded two environment variables are predefined. One for
maximum optimizations on the cluster's architecture, and the other for
-debugging purposes
+debugging purposes:
$ echo $OPTFLAGS
-O3 -march=native
$ echo $DEBUGFLAGS
@@ -58,7 +61,7 @@ For more information about the possibilities of the compilers, please
see the man pages.
Unified Parallel C
------------------
-UPC is supported by two compiler/runtime implementations
+UPC is supported by two compiler/runtime implementations:
- GNU - SMP/multi-threading support only
- Berkley - multi-node support as well as SMP/multi-threading support
### GNU UPC Compiler
@@ -70,8 +73,8 @@ gupc
Simple program to test the compiler
$ cat count.upc
/* hello.upc - a simple UPC example */
- #include
- #include
+ #include <upc.h>
+ #include <stdio.h>
int main() {
 if (MYTHREAD == 0) {
   printf("Welcome to GNU UPC!!!n");
@@ -97,11 +100,11 @@ implementation of UPC network "ibv". For testing/debugging using
multiple nodes, the "mpi" UPC network is recommended. Please note, that
**the selection of the network is done at the compile time** and not at
runtime (as expected)!
-Example UPC code
+Example UPC code:
$ cat hello.upc
/* hello.upc - a simple UPC example */
- #include
- #include
+ #include <upc.h>
+ #include <stdio.h>
int main() {
 if (MYTHREAD == 0) {
   printf("Welcome to Berkeley UPC!!!n");
@@ -116,58 +119,16 @@ To run the example with 5 threads issue
$ upcrun -n 5 ./hello.upc.x
To run the example on two compute nodes using all 48 cores, with 48
threads, issue
- $ qsub -I -q qprod -A PROJECT_ID -l select=2ncpus=24
+ $ qsub -I -q qprod -A PROJECT_ID -l select=2:ncpus=24
$ module add bupc
$ upcrun -n 48 ./hello.upc.x
 For more informations see the man pages.
Java
----
For information how to use Java (runtime and/or compiler), please read
-the [Java page](java.html).
+the [Java
+page](https://docs.it4i.cz/salomon/software/java).
nVidia CUDA
For information how to work with nVidia CUDA, please read the [nVidia
CUDA
-page](../../anselm-cluster-documentation/software/nvidia-cuda.html).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
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- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [List of Available
- Modules](../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage.html)
-
- - [Network](../network-1.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
+page](https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda).
diff --git a/salomon/software/comsol.html b/docs.it4i.cz/salomon/software/comsol.html
old mode 100755
new mode 100644
similarity index 72%
rename from salomon/software/comsol.html
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/comsol/comsol-multiphysics" /><!--[if lt IE 7]></base><![endif]-->
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<title>COMSOL Multiphysics® — IT4I Docs</title>
- <link rel="canonical" href="comsol.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/comsol" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
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<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="comsol.html#content">PĹ™ejĂt na obsah</a> |
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- <a accesskey="6" href="comsol.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/comsol#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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@@ -153,7 +150,7 @@
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+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
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@@ -241,7 +238,7 @@
<div id="parent-fieldname-text-a2a39285512b4de285187d84e6cea9f3" class="">
<h2 class=" "><span><span>Introduction<br /></span></span></h2>
-<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/" target="_self" title="">COMSOL</a></span></span><span><span> is a powerful environment for modelling and solving various engineering and scientific problems based on partial differential equations. COMSOL is designed to solve coupled or multiphysics phenomena. For many standard engineering problems COMSOL provides add-on products such as electrical, mechanical, fluid flow, and chemical applications.</span></span></p>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com" target="_self" title="">COMSOL</a></span></span><span><span> is a powerful environment for modelling and solving various engineering and scientific problems based on partial differential equations. COMSOL is designed to solve coupled or multiphysics phenomena. For many standard engineering problems COMSOL provides add-on products such as electrical, mechanical, fluid flow, and chemical applications.</span></span></p>
<ul>
<li>
<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/structural-mechanics-module" target="_self" title="">Structural Mechanics Module</a>, </span></span></p>
@@ -274,14 +271,14 @@
<pre class="prettyprint lang-sh"><span><span>$ module load COMSOL/51-EDU</span></span></pre>
<p align="JUSTIFY"><span><span>By default the </span></span><span><span><b>EDU variant</b></span></span><span><span> will be loaded. If user needs other version or variant, load the particular version. To obtain the list of available versions use</span></span></p>
<pre class="prettyprint lang-sh"><span><span>$ module avail <span><span>COMSOL</span></span></span></span></pre>
-<p align="JUSTIFY"><span><span>If user needs to prepare COMSOL jobs in the interactive mode it is recommend to use COMSOL on the compute nodes via PBS Pro scheduler. In order run the COMSOL Desktop GUI on Windows is recommended to use the <a target="_self" title="" class="internal-link" href="../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html">Virtual Network Computing (VNC)</a>.</span></span></p>
+<p align="JUSTIFY"><span><span>If user needs to prepare COMSOL jobs in the interactive mode it is recommend to use COMSOL on the compute nodes via PBS Pro scheduler. In order run the COMSOL Desktop GUI on Windows is recommended to use the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">Virtual Network Computing (VNC)</a>.</span></span></p>
<pre class="prettyprint lang-sh"><span><span><span>$ xhost +<br />$ qsub -I -X</span></span></span><span><span><span><span> </span></span></span></span><span><span><span>-A</span></span></span><span><span> </span></span><span><span><span><span>PROJECT_ID </span></span></span></span><span><span><span>-q </span></span></span><span><span><span><span>qprod</span></span></span></span><span><span><span> -l </span></span></span><span><span><span><span>select=1:ppn=24</span><br />$ module load </span></span></span><span><span>COMSOL<span><br />$ </span></span></span><span><span>comsol<br /></span></span></pre>
<p align="JUSTIFY"><span><span>To run COMSOL in batch mode, without the COMSOL Desktop GUI environment, user can utilized the default (comsol.pbs) job script and execute it via the qsub command.</span></span></p>
<pre class="prettyprint lang-sh"><span><span>#!/bin/bash<br />#PBS -l select=3:ppn=24<br />#PBS -q qprod<br />#PBS -N JOB_NAME<br />#PBS -A PROJECT_ID<br /><br />cd /scratch/work/user<strong>/</strong>$USER/ || exit<br /><br />echo Time is `date`<br />echo Directory is `pwd`<br />echo '***PBS_NODEFILE***START*******'<br />cat $PBS_NODEFILE<br />echo '***PBS_NODEFILE***END*********'<br /><br />text_nodes < cat $PBS_NODEFILE<br /><br />module load COMSOL<br /># module load COMSOL/51-EDU<br /><br />ntask=$(wc -l $PBS_NODEFILE)<br /><br />comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log<br /><br /></span></span></pre>
<p align="JUSTIFY"><span><span>Working directory has to be created before sending the (comsol.pbs) job script into the queue. Input file (name_input_f.mph) has to be in working directory or full path to input file has to be specified. The appropriate path to the temp directory of the job has to be set by command option (-tmpdir).</span></span></p>
<h2 class=" ">LiveLink™<i> </i>for MATLAB<sup>®</sup></h2>
<p align="JUSTIFY"><span><span>COMSOL is the software package for the numerical solution of the partial differential equations. LiveLink for MATLAB allows connection to the COMSOL</span></span><span><span><sup><span><span><span><span><span><span><span><b>®</b></span></span></span></span></span></span></span></sup></span></span><span><span> API (Application Programming Interface) with the benefits of the programming language and computing environment of the MATLAB. </span></span></p>
-<p align="JUSTIFY"><span><span>LiveLink for MATLAB is available in both </span></span><span><span><b>EDU</b></span></span><span><span> and </span></span><span><span><b>COM</b></span></span><span><span> </span></span><span><span><b>variant</b></span></span><span><span> of the COMSOL release. On the clusters 1 commercial (</span></span><span><span><b>COM</b></span></span><span><span>) license and the 5 educational (</span></span><span><span><b>EDU</b></span></span><span><span>) licenses of LiveLink for MATLAB (please see the <a target="_self" title="" class="internal-link" href="../../acl_users/credentials_cookie_auth/require_logind8a8.html">ISV Licenses</a>) are available. Following example shows how to start COMSOL model from MATLAB via LiveLink in the interactive mode.</span></span></p>
+<p align="JUSTIFY"><span><span>LiveLink for MATLAB is available in both </span></span><span><span><b>EDU</b></span></span><span><span> and </span></span><span><span><b>COM</b></span></span><span><span> </span></span><span><span><b>variant</b></span></span><span><span> of the COMSOL release. On the clusters 1 commercial (</span></span><span><span><b>COM</b></span></span><span><span>) license and the 5 educational (</span></span><span><span><b>EDU</b></span></span><span><span>) licenses of LiveLink for MATLAB (please see the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/isv_licenses">ISV Licenses</a>) are available. Following example shows how to start COMSOL model from MATLAB via LiveLink in the interactive mode.</span></span></p>
<pre class="prettyprint lang-sh">$ xhost +<br />$ qsub -I -X -A PROJECT_ID -q qexp -l select=1:ppn=24<br />$ module load MATLAB<br />$ module load COMSOL<br />$ comsol server MATLAB</pre>
<p align="JUSTIFY"><span><span>At the first time to launch the LiveLink for MATLAB (client-MATLAB/server-COMSOL connection) the login and password is requested and this information is not requested again.</span></span></p>
<p align="JUSTIFY"><span><span>To run LiveLink for MATLAB in batch mode with (comsol_matlab.pbs) job script you can utilize/modify the following script and execute it via the qsub command.</span></span></p>
@@ -362,7 +359,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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<span>Salomon Cluster Documentation</span>
</a>
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<span>Hardware Overview</span>
</a>
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<span>Accessing the Cluster</span>
</a>
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<span>Environment and Modules</span>
</a>
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- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
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<span>Resource Allocation and Job Execution</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -554,10 +551,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
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- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -589,7 +586,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -605,7 +602,7 @@
- <a title="" class="state-published contenttype-document" href="comsol/licensing-and-available-versions.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions">
<span>Licensing and Available Versions</span>
</a>
@@ -630,7 +627,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -646,7 +643,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -662,7 +659,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -678,7 +675,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -694,7 +691,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -710,7 +707,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -726,7 +723,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -742,7 +739,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -758,7 +755,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -783,7 +780,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -808,7 +805,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -824,7 +821,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -840,7 +837,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -856,7 +853,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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diff --git a/docs.it4i.cz/salomon/software/comsol.md b/docs.it4i.cz/salomon/software/comsol.md
new file mode 100644
index 0000000000000000000000000000000000000000..5a7ac7c3614a0c8b1017864d3dedb6ece1b65275
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/comsol.md
@@ -0,0 +1,162 @@
+COMSOL Multiphysics®
+====================
+
+<span><span>Introduction
+</span></span>
+--
+<span><span>[COMSOL](http://www.comsol.com)</span></span><span><span>
+is a powerful environment for modelling and solving various engineering
+and scientific problems based on partial differential equations. COMSOL
+is designed to solve coupled or multiphysics phenomena. For many
+standard engineering problems COMSOL provides add-on products such as
+electrical, mechanical, fluid flow, and chemical
+applications.</span></span>
+- <span><span>[Structural Mechanics
+ Module](http://www.comsol.com/structural-mechanics-module),
+ </span></span>
+- <span><span>[Heat Transfer
+ Module](http://www.comsol.com/heat-transfer-module),
+ </span></span>
+- <span><span>[CFD
+ Module](http://www.comsol.com/cfd-module),
+ </span></span>
+- <span><span>[Acoustics
+ Module](http://www.comsol.com/acoustics-module),
+ </span></span>
+- <span><span>and [many
+ others](http://www.comsol.com/products)</span></span>
+<span><span>COMSOL also allows an
+</span></span><span><span><span><span>interface support for
+equation-based modelling of
+</span></span></span></span><span><span>partial differential
+equations.</span></span>
+<span><span>Execution
+</span></span>
+----------------------
+<span><span>On the clusters COMSOL is available in the latest stable
+version. There are two variants of the release:</span></span>
+- <span><span>**Non commercial**</span></span><span><span> or so
+ called </span></span><span><span>**EDU
+ variant**</span></span><span><span>, which can be used for research
+ and educational purposes.</span></span>
+- <span><span>**Commercial**</span></span><span><span> or so called
+ </span></span><span><span>**COM variant**</span></span><span><span>,
+ which can used also for commercial activities.
+ </span></span><span><span>**COM variant**</span></span><span><span>
+ has only subset of features compared to the
+ </span></span><span><span>**EDU
+ variant**</span></span><span><span> available. <span
+ class="internal-link"><span id="result_box" class="short_text"><span
+ class="hps">More</span> <span class="hps">about
+ licensing</span> will be posted <span class="hps">here
+ soon</span>.</span></span>
+ </span></span>
+<span><span>To load the of COMSOL load the module</span></span>
+``` {.prettyprint .lang-sh}
+$ module load COMSOL/51-EDU
+```
+<span><span>By default the </span></span><span><span>**EDU
+variant**</span></span><span><span> will be loaded. If user needs other
+version or variant, load the particular version. To obtain the list of
+available versions use</span></span>
+``` {.prettyprint .lang-sh}
+$ module avail COMSOL
+```
+<span><span>If user needs to prepare COMSOL jobs in the interactive mode
+it is recommend to use COMSOL on the compute nodes via PBS Pro
+scheduler. In order run the COMSOL Desktop GUI on Windows is recommended
+to use the [Virtual Network Computing
+(VNC)](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc).</span></span>
+``` {.prettyprint .lang-sh}
+$ xhost +
+$ qsub -I -X -A PROJECT_ID -q qprod -l select=1:ppn=24
+$ module load COMSOL
+$ comsol
+```
+<span><span>To run COMSOL in batch mode, without the COMSOL Desktop GUI
+environment, user can utilized the default (comsol.pbs) job script and
+execute it via the qsub command.</span></span>
+``` {.prettyprint .lang-sh}
+#!/bin/bash
+#PBS -l select=3:ppn=24
+#PBS -q qprod
+#PBS -N JOB_NAME
+#PBS -AÂ PROJECT_ID
+cd /scratch/work/user/$USER/ || exit
+echo Time is `date`
+echo Directory is `pwd`
+echo '***PBS_NODEFILE***START*******'
+cat $PBS_NODEFILE
+echo '***PBS_NODEFILE***END*********'
+text_nodes < cat $PBS_NODEFILE
+module load COMSOL
+# module load COMSOL/51-EDU
+ntask=$(wc -l $PBS_NODEFILE)
+comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log
+```
+<span><span>Working directory has to be created before sending the
+(comsol.pbs) job script into the queue. Input file (name_input_f.mph)
+has to be in working directory or full path to input file has to be
+specified. The appropriate path to the temp directory of the job has to
+be set by command option (-tmpdir).</span></span>
+LiveLink™* *for MATLAB^®^
+--
+<span><span>COMSOL is the software package for the numerical solution of
+the partial differential equations. LiveLink for MATLAB allows
+connection to the
+COMSOL</span></span><span><span>^<span><span><span><span><span><span><span>**®**</span></span></span></span></span></span></span>^</span></span><span><span>
+API (Application Programming Interface) with the benefits of the
+programming language and computing environment of the MATLAB.
+</span></span>
+<span><span>LiveLink for MATLAB is available in both
+</span></span><span><span>**EDU**</span></span><span><span> and
+</span></span><span><span>**COM**</span></span><span><span>
+</span></span><span><span>**variant**</span></span><span><span> of the
+COMSOL release. On the clusters 1 commercial
+(</span></span><span><span>**COM**</span></span><span><span>) license
+and the 5 educational
+(</span></span><span><span>**EDU**</span></span><span><span>) licenses
+of LiveLink for MATLAB (please see the [ISV
+Licenses](https://docs.it4i.cz/salomon/software/isv_licenses))
+are available. Following example shows how to start COMSOL model from
+MATLAB via LiveLink in the interactive mode.</span></span>
+``` {.prettyprint .lang-sh}
+$ xhost +
+$ qsub -I -X -A PROJECT_ID -q qexp -l select=1:ppn=24
+$ module load MATLAB
+$ module load COMSOL
+$ comsol server MATLAB
+```
+<span><span>At the first time to launch the LiveLink for MATLAB
+(client-MATLAB/server-COMSOL connection) the login and password is
+requested and this information is not requested again.</span></span>
+<span><span>To run LiveLink for MATLAB in batch mode with
+(comsol_matlab.pbs) job script you can utilize/modify the following
+script and execute it via the qsub command.</span></span>
+``` {.prettyprint .lang-sh}
+#!/bin/bash
+#PBS -l select=3:ppn=24
+#PBS -q qprod
+#PBS -N JOB_NAME
+#PBS -AÂ PROJECT_ID
+cd /scratch/work/user/$USER || exit
+echo Time is `date`
+echo Directory is `pwd`
+echo '***PBS_NODEFILE***START*******'
+cat $PBS_NODEFILE
+echo '***PBS_NODEFILE***END*********'
+text_nodes < cat $PBS_NODEFILE
+module load MATLAB
+module load COMSOL/51-EDU
+ntask=$(wc -l $PBS_NODEFILE)
+comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/work/user/$USER/work &
+cd /apps/cae/COMSOL/51/mli
+matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/work/user/$USER/work; test_job"
+```
+This example shows how to run Livelink for MATLAB with following
+configuration3 nodes and 16 cores per node. Working directory has to
+be created before submitting (comsol_matlab.pbs) job script into the
+queue. Input file (test_job.m) has to be in working directory or full
+path to input file has to be specified. The Matlab command option (-r
+”mphstart”) created a connection with a COMSOL server using the default
+port number.
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+
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+ <div id="parent-fieldname-text-a2a39285512b4de285187d84e6cea9f3" class="">
+ <h2 class=" "><span><span>Introduction<br /></span></span></h2>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com" target="_self" title="">COMSOL</a></span></span><span><span> is a powerful environment for modelling and solving various engineering and scientific problems based on partial differential equations. COMSOL is designed to solve coupled or multiphysics phenomena. For many standard engineering problems COMSOL provides add-on products such as electrical, mechanical, fluid flow, and chemical applications.</span></span></p>
+<ul>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/structural-mechanics-module" target="_self" title="">Structural Mechanics Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/heat-transfer-module" target="_self" title="">Heat Transfer Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/cfd-module" target="_self" title="">CFD Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/acoustics-module" target="_self" title="">Acoustics Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span>and <a class="external-link" href="http://www.comsol.com/products" target="_self" title="">many others</a></span></span></p>
+</li>
+</ul>
+<p align="JUSTIFY"><span><span>COMSOL also allows an </span></span><span><span><span><span>interface support for equation-based modelling of </span></span></span></span><span><span>partial differential equations.</span></span></p>
+<h2 class=" "><span><span>Execution<br /></span></span></h2>
+<p align="JUSTIFY"><span><span>On the clusters COMSOL is available in the latest stable version. There are two variants of the release:</span></span></p>
+<ul>
+<li>
+<p align="JUSTIFY"><span><span><b>Non commercial</b></span></span><span><span> or so called </span></span><span><span><b>EDU variant</b></span></span><span><span>, which can be used for research and educational purposes.</span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><b>Commercial</b></span></span><span><span> or so called </span></span><span><span><b>COM variant</b></span></span><span><span>, which can used also for commercial activities. </span></span><span><span><b>COM variant</b></span></span><span><span> has only subset of features compared to the </span></span><span><span><b>EDU variant</b></span></span><span><span> available. <span class="internal-link"><span class="short_text" id="result_box"><span class="hps">More</span> <span class="hps">about licensing</span> will be posted <span class="hps">here soon</span>.</span></span><br /></span></span></p>
+</li>
+</ul>
+<p align="JUSTIFY"><span><span>To load the of COMSOL load the module</span></span></p>
+<pre class="prettyprint lang-sh"><span><span>$ module load COMSOL/51-EDU</span></span></pre>
+<p align="JUSTIFY"><span><span>By default the </span></span><span><span><b>EDU variant</b></span></span><span><span> will be loaded. If user needs other version or variant, load the particular version. To obtain the list of available versions use</span></span></p>
+<pre class="prettyprint lang-sh"><span><span>$ module avail <span><span>COMSOL</span></span></span></span></pre>
+<p align="JUSTIFY"><span><span>If user needs to prepare COMSOL jobs in the interactive mode it is recommend to use COMSOL on the compute nodes via PBS Pro scheduler. In order run the COMSOL Desktop GUI on Windows is recommended to use the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">Virtual Network Computing (VNC)</a>.</span></span></p>
+<pre class="prettyprint lang-sh"><span><span><span>$ xhost +<br />$ qsub -I -X</span></span></span><span><span><span><span> </span></span></span></span><span><span><span>-A</span></span></span><span><span> </span></span><span><span><span><span>PROJECT_ID </span></span></span></span><span><span><span>-q </span></span></span><span><span><span><span>qprod</span></span></span></span><span><span><span> -l </span></span></span><span><span><span><span>select=1:ppn=24</span><br />$ module load </span></span></span><span><span>COMSOL<span><br />$ </span></span></span><span><span>comsol<br /></span></span></pre>
+<p align="JUSTIFY"><span><span>To run COMSOL in batch mode, without the COMSOL Desktop GUI environment, user can utilized the default (comsol.pbs) job script and execute it via the qsub command.</span></span></p>
+<pre class="prettyprint lang-sh"><span><span>#!/bin/bash<br />#PBS -l select=3:ppn=24<br />#PBS -q qprod<br />#PBS -N JOB_NAME<br />#PBS -A PROJECT_ID<br /><br />cd /scratch/work/user<strong>/</strong>$USER/ || exit<br /><br />echo Time is `date`<br />echo Directory is `pwd`<br />echo '***PBS_NODEFILE***START*******'<br />cat $PBS_NODEFILE<br />echo '***PBS_NODEFILE***END*********'<br /><br />text_nodes < cat $PBS_NODEFILE<br /><br />module load COMSOL<br /># module load COMSOL/51-EDU<br /><br />ntask=$(wc -l $PBS_NODEFILE)<br /><br />comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log<br /><br /></span></span></pre>
+<p align="JUSTIFY"><span><span>Working directory has to be created before sending the (comsol.pbs) job script into the queue. Input file (name_input_f.mph) has to be in working directory or full path to input file has to be specified. The appropriate path to the temp directory of the job has to be set by command option (-tmpdir).</span></span></p>
+<h2 class=" ">LiveLink™<i> </i>for MATLAB<sup>®</sup></h2>
+<p align="JUSTIFY"><span><span>COMSOL is the software package for the numerical solution of the partial differential equations. LiveLink for MATLAB allows connection to the COMSOL</span></span><span><span><sup><span><span><span><span><span><span><span><b>®</b></span></span></span></span></span></span></span></sup></span></span><span><span> API (Application Programming Interface) with the benefits of the programming language and computing environment of the MATLAB. </span></span></p>
+<p align="JUSTIFY"><span><span>LiveLink for MATLAB is available in both </span></span><span><span><b>EDU</b></span></span><span><span> and </span></span><span><span><b>COM</b></span></span><span><span> </span></span><span><span><b>variant</b></span></span><span><span> of the COMSOL release. On the clusters 1 commercial (</span></span><span><span><b>COM</b></span></span><span><span>) license and the 5 educational (</span></span><span><span><b>EDU</b></span></span><span><span>) licenses of LiveLink for MATLAB (please see the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/isv_licenses">ISV Licenses</a>) are available. Following example shows how to start COMSOL model from MATLAB via LiveLink in the interactive mode.</span></span></p>
+<pre class="prettyprint lang-sh">$ xhost +<br />$ qsub -I -X -A PROJECT_ID -q qexp -l select=1:ppn=24<br />$ module load MATLAB<br />$ module load COMSOL<br />$ comsol server MATLAB</pre>
+<p align="JUSTIFY"><span><span>At the first time to launch the LiveLink for MATLAB (client-MATLAB/server-COMSOL connection) the login and password is requested and this information is not requested again.</span></span></p>
+<p align="JUSTIFY"><span><span>To run LiveLink for MATLAB in batch mode with (comsol_matlab.pbs) job script you can utilize/modify the following script and execute it via the qsub command.</span></span></p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -l select=3:ppn=24<br />#PBS -q qprod<br />#PBS -N JOB_NAME<br />#PBS -AÂ PROJECT_ID<br /><br />cd /scratch/work/user/$USER || exit<br /><br />echo Time is `date`<br />echo Directory is `pwd`<br />echo '***PBS_NODEFILE***START*******'<br />cat $PBS_NODEFILE<br />echo '***PBS_NODEFILE***END*********'<br /><br />text_nodes < cat $PBS_NODEFILE<br /><br />module load MATLAB<br />module load COMSOL/51-EDU<br /><br />ntask=$(wc -l $PBS_NODEFILE)<br /><br />comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/<strong>work/user/</strong>$USER/work &<br />cd /apps/cae/COMSOL/51/mli<br />matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/<strong>work/user/</strong>$USER/work; test_job"</pre>
+<p>This example shows how to run Livelink for MATLAB with following configuration: 3 nodes and 16 cores per node. Working directory has to be created before submitting (comsol_matlab.pbs) job script into the queue. Input file (test_job.m) has to be in working directory or full path to input file has to be specified. The Matlab command option (-r ”mphstart”) created a connection with a COMSOL server using the default port number.<br /><br /></p>
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diff --git a/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.md b/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.md
new file mode 100644
index 0000000000000000000000000000000000000000..5a7ac7c3614a0c8b1017864d3dedb6ece1b65275
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.md
@@ -0,0 +1,162 @@
+COMSOL Multiphysics®
+====================
+
+<span><span>Introduction
+</span></span>
+--
+<span><span>[COMSOL](http://www.comsol.com)</span></span><span><span>
+is a powerful environment for modelling and solving various engineering
+and scientific problems based on partial differential equations. COMSOL
+is designed to solve coupled or multiphysics phenomena. For many
+standard engineering problems COMSOL provides add-on products such as
+electrical, mechanical, fluid flow, and chemical
+applications.</span></span>
+- <span><span>[Structural Mechanics
+ Module](http://www.comsol.com/structural-mechanics-module),
+ </span></span>
+- <span><span>[Heat Transfer
+ Module](http://www.comsol.com/heat-transfer-module),
+ </span></span>
+- <span><span>[CFD
+ Module](http://www.comsol.com/cfd-module),
+ </span></span>
+- <span><span>[Acoustics
+ Module](http://www.comsol.com/acoustics-module),
+ </span></span>
+- <span><span>and [many
+ others](http://www.comsol.com/products)</span></span>
+<span><span>COMSOL also allows an
+</span></span><span><span><span><span>interface support for
+equation-based modelling of
+</span></span></span></span><span><span>partial differential
+equations.</span></span>
+<span><span>Execution
+</span></span>
+----------------------
+<span><span>On the clusters COMSOL is available in the latest stable
+version. There are two variants of the release:</span></span>
+- <span><span>**Non commercial**</span></span><span><span> or so
+ called </span></span><span><span>**EDU
+ variant**</span></span><span><span>, which can be used for research
+ and educational purposes.</span></span>
+- <span><span>**Commercial**</span></span><span><span> or so called
+ </span></span><span><span>**COM variant**</span></span><span><span>,
+ which can used also for commercial activities.
+ </span></span><span><span>**COM variant**</span></span><span><span>
+ has only subset of features compared to the
+ </span></span><span><span>**EDU
+ variant**</span></span><span><span> available. <span
+ class="internal-link"><span id="result_box" class="short_text"><span
+ class="hps">More</span> <span class="hps">about
+ licensing</span> will be posted <span class="hps">here
+ soon</span>.</span></span>
+ </span></span>
+<span><span>To load the of COMSOL load the module</span></span>
+``` {.prettyprint .lang-sh}
+$ module load COMSOL/51-EDU
+```
+<span><span>By default the </span></span><span><span>**EDU
+variant**</span></span><span><span> will be loaded. If user needs other
+version or variant, load the particular version. To obtain the list of
+available versions use</span></span>
+``` {.prettyprint .lang-sh}
+$ module avail COMSOL
+```
+<span><span>If user needs to prepare COMSOL jobs in the interactive mode
+it is recommend to use COMSOL on the compute nodes via PBS Pro
+scheduler. In order run the COMSOL Desktop GUI on Windows is recommended
+to use the [Virtual Network Computing
+(VNC)](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc).</span></span>
+``` {.prettyprint .lang-sh}
+$ xhost +
+$ qsub -I -X -A PROJECT_ID -q qprod -l select=1:ppn=24
+$ module load COMSOL
+$ comsol
+```
+<span><span>To run COMSOL in batch mode, without the COMSOL Desktop GUI
+environment, user can utilized the default (comsol.pbs) job script and
+execute it via the qsub command.</span></span>
+``` {.prettyprint .lang-sh}
+#!/bin/bash
+#PBS -l select=3:ppn=24
+#PBS -q qprod
+#PBS -N JOB_NAME
+#PBS -AÂ PROJECT_ID
+cd /scratch/work/user/$USER/ || exit
+echo Time is `date`
+echo Directory is `pwd`
+echo '***PBS_NODEFILE***START*******'
+cat $PBS_NODEFILE
+echo '***PBS_NODEFILE***END*********'
+text_nodes < cat $PBS_NODEFILE
+module load COMSOL
+# module load COMSOL/51-EDU
+ntask=$(wc -l $PBS_NODEFILE)
+comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log
+```
+<span><span>Working directory has to be created before sending the
+(comsol.pbs) job script into the queue. Input file (name_input_f.mph)
+has to be in working directory or full path to input file has to be
+specified. The appropriate path to the temp directory of the job has to
+be set by command option (-tmpdir).</span></span>
+LiveLink™* *for MATLAB^®^
+--
+<span><span>COMSOL is the software package for the numerical solution of
+the partial differential equations. LiveLink for MATLAB allows
+connection to the
+COMSOL</span></span><span><span>^<span><span><span><span><span><span><span>**®**</span></span></span></span></span></span></span>^</span></span><span><span>
+API (Application Programming Interface) with the benefits of the
+programming language and computing environment of the MATLAB.
+</span></span>
+<span><span>LiveLink for MATLAB is available in both
+</span></span><span><span>**EDU**</span></span><span><span> and
+</span></span><span><span>**COM**</span></span><span><span>
+</span></span><span><span>**variant**</span></span><span><span> of the
+COMSOL release. On the clusters 1 commercial
+(</span></span><span><span>**COM**</span></span><span><span>) license
+and the 5 educational
+(</span></span><span><span>**EDU**</span></span><span><span>) licenses
+of LiveLink for MATLAB (please see the [ISV
+Licenses](https://docs.it4i.cz/salomon/software/isv_licenses))
+are available. Following example shows how to start COMSOL model from
+MATLAB via LiveLink in the interactive mode.</span></span>
+``` {.prettyprint .lang-sh}
+$ xhost +
+$ qsub -I -X -A PROJECT_ID -q qexp -l select=1:ppn=24
+$ module load MATLAB
+$ module load COMSOL
+$ comsol server MATLAB
+```
+<span><span>At the first time to launch the LiveLink for MATLAB
+(client-MATLAB/server-COMSOL connection) the login and password is
+requested and this information is not requested again.</span></span>
+<span><span>To run LiveLink for MATLAB in batch mode with
+(comsol_matlab.pbs) job script you can utilize/modify the following
+script and execute it via the qsub command.</span></span>
+``` {.prettyprint .lang-sh}
+#!/bin/bash
+#PBS -l select=3:ppn=24
+#PBS -q qprod
+#PBS -N JOB_NAME
+#PBS -AÂ PROJECT_ID
+cd /scratch/work/user/$USER || exit
+echo Time is `date`
+echo Directory is `pwd`
+echo '***PBS_NODEFILE***START*******'
+cat $PBS_NODEFILE
+echo '***PBS_NODEFILE***END*********'
+text_nodes < cat $PBS_NODEFILE
+module load MATLAB
+module load COMSOL/51-EDU
+ntask=$(wc -l $PBS_NODEFILE)
+comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/work/user/$USER/work &
+cd /apps/cae/COMSOL/51/mli
+matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/work/user/$USER/work; test_job"
+```
+This example shows how to run Livelink for MATLAB with following
+configuration3 nodes and 16 cores per node. Working directory has to
+be created before submitting (comsol_matlab.pbs) job script into the
+queue. Input file (test_job.m) has to be in working directory or full
+path to input file has to be specified. The Matlab command option (-r
+”mphstart”) created a connection with a COMSOL server using the default
+port number.
diff --git a/salomon/software/comsol/licensing-and-available-versions.html b/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.html
old mode 100755
new mode 100644
similarity index 67%
rename from salomon/software/comsol/licensing-and-available-versions.html
rename to docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.html
index 79ffeb738698b47f04b264667978c6f230fa0867..6312a4373e259b477676298fd1f655d8d3f01db6
--- a/salomon/software/comsol/licensing-and-available-versions.html
+++ b/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:25 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Licensing and Available Versions — IT4I Docs</title>
- <link rel="canonical" href="licensing-and-available-versions.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="licensing-and-available-versions.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="licensing-and-available-versions.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../comsol.html">COMSOL</a>
+ <a href="https://docs.it4i.cz/salomon/software/comsol">COMSOL</a>
<span class="breadcrumbSeparator">
/
@@ -335,7 +332,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -351,7 +348,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -367,7 +364,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -383,7 +380,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -399,7 +396,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -415,7 +412,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -431,7 +428,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -447,7 +444,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -463,7 +460,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -479,7 +476,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -495,7 +492,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -511,7 +508,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -527,10 +524,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -546,7 +543,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -562,7 +559,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -578,7 +575,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="licensing-and-available-versions.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions">
<span>Licensing and Available Versions</span>
</a>
@@ -603,7 +600,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -619,7 +616,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -635,7 +632,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -651,7 +648,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -667,7 +664,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -683,7 +680,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -699,7 +696,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -715,7 +712,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -731,7 +728,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -756,7 +753,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -781,7 +778,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -797,7 +794,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -813,7 +810,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -829,7 +826,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
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+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -897,12 +894,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -918,7 +915,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:25 GMT -->
</html>
diff --git a/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.md b/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.md
new file mode 100644
index 0000000000000000000000000000000000000000..66e530b4bcbddfa9b7bbb75ab4db713edddb34bd
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.md
@@ -0,0 +1,31 @@
+Licensing and Available Versions
+================================
+Comsol licence can be used by:
+-------
+- all persons in the carrying out of the CE IT4Innovations Project (In
+ addition to the primary licensee, which is VSB - Technical
+ University of Ostrava, users are CE IT4Innovations third parties -
+ CE IT4Innovations project partners, particularly the University of
+ Ostrava, the Brno University of Technology - Faculty of Informatics,
+ the Silesian University in Opava, Institute of Geonics AS CR.)
+- <span id="result_box" class="short_text"><span class="hps">all
+ persons</span> <span class="hps">who have a valid</span> <span
+ class="hps">license</span></span>
+- <span id="result_box" class="short_text"><span class="hps">students
+ of</span> <span class="hps">the Technical University</span></span>
+Comsol EDU Network Licence
+---
+The licence intended to be used for science and research, publications,
+students’ projects, teaching (academic licence).
+Comsol COM Network Licence
+---
+The licence intended to be used for science and research, publications,
+students’ projects, commercial research with no commercial use
+restrictions. <span id="result_box"><span class="hps">E</span><span
+class="hps">nables</span> <span class="hps">the solution</span> <span
+class="hps">of at least</span> <span class="hps">one job</span> <span
+class="hps">by one user</span> <span class="hps">in one</span> <span
+class="hps">program start.</span></span>
+Available Versions
+------------------
+- ver. 51
diff --git a/salomon/software/debuggers/summary.html b/docs.it4i.cz/salomon/software/debuggers.1.html
old mode 100755
new mode 100644
similarity index 64%
rename from salomon/software/debuggers/summary.html
rename to docs.it4i.cz/salomon/software/debuggers.1.html
index fe8152bc1407e2500f1716b1ab1f86a8d8a376a5..537ce39041d034ba49bd6ebac074998b51e97eef
--- a/salomon/software/debuggers/summary.html
+++ b/docs.it4i.cz/salomon/software/debuggers.1.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/debuggers/summary by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:05 GMT -->
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- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Debuggers and profilers summary — IT4I Docs</title>
- <link rel="canonical" href="../debuggers.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/debuggers" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="summary.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/debuggers#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="summary.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/debuggers#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -244,25 +241,25 @@
<p>We provide state of the art programms and tools to develop, profile and debug HPC codes at IT4Innovations.<br />On these pages, we provide an overview of the profiling and debugging tools available on Anslem at IT4I.</p>
<h2 class=" ">Intel debugger</h2>
<p class="exclamation">Intel debugger is no longer available since Parallel Studio version 2015</p>
-<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a target="_self" title="" class="internal-link" href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html">X display</a> for running the GUI.</p>
+<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">X display</a> for running the GUI.</p>
<pre class=" ">$ module load intel<br />$ idb</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="../intel-suite/intel-debugger.html">Intel Debugger</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger">Intel Debugger</a> page.</p>
<h2 class=" ">Allinea Forge (DDT/MAP)</h2>
<p>Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel Xeon Phi accelerators. DDT provides all the standard debugging features (stack trace, breakpoints, watches, view variables, threads etc.) for every thread running as part of your program, or for every process - even if these processes are distributed across a cluster using an MPI implementation.</p>
<pre class=" ">$ module load Forge<br />$ forge</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="allinea-ddt.html">Allinea DDT</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt">Allinea DDT</a> page.</p>
<h2 class=" ">Allinea Performance Reports</h2>
<p>Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs. Our license is limited to 64 MPI processes.</p>
<pre class=" ">$ module load PerformanceReports/6.0 <br />$ perf-report mpirun -n 64 ./my_application argument01 argument02</pre>
-<p class=" ">Read more at the <a target="_self" title="" class="internal-link" href="allinea-performance-reports.html">Allinea Performance Reports</a> page.</p>
+<p class=" ">Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports">Allinea Performance Reports</a> page.</p>
<h2 class=" ">RougeWave Totalview</h2>
<p>TotalView is a source- and machine-level debugger for multi-process, multi-threaded programs. Its wide range of tools provides ways to analyze, organize, and test programs, making it easy to isolate and identify problems in individual threads and processes in programs of great complexity.</p>
<pre class=" ">$ module load TotalView/8.15.4-6-linux-x86-64<br />$ totalview</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="total-view.html">Totalview</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/total-view">Totalview</a> page.</p>
<h2 class=" ">Vampir trace analyzer</h2>
<p>Vampir is a GUI trace analyzer for traces in OTF format.</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="vampir.html">Vampir</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">Vampir</a> page.</p>
</div>
@@ -338,7 +335,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -354,7 +351,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -370,7 +367,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -386,7 +383,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -402,7 +399,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -418,7 +415,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -434,7 +431,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -450,7 +447,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -466,7 +463,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -482,7 +479,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -498,7 +495,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -514,7 +511,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -530,10 +527,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -549,7 +546,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -565,7 +562,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -581,7 +578,7 @@
- <a title="A collection of development tools" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -597,7 +594,7 @@
- <a title="" class="state-published contenttype-document" href="aislinn.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/aislinn">
<span>Aislinn</span>
</a>
@@ -613,7 +610,7 @@
- <a title="" class="state-published contenttype-document" href="allinea-ddt.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
@@ -629,7 +626,7 @@
- <a title="quick application profiling" class="state-published contenttype-document" href="allinea-performance-reports.html">
+ <a class="state-published contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -645,7 +642,7 @@
- <a title="" class="state-published contenttype-document" href="intel-vtune-amplifier.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier XE</span>
</a>
@@ -661,7 +658,7 @@
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published contenttype-document" href="total-view.html">
+ <a class="state-published contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/salomon/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -677,7 +674,7 @@
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/salomon/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -693,7 +690,7 @@
- <a title="" class="state-published contenttype-document" href="vampir.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -718,7 +715,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -734,7 +731,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -750,7 +747,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -766,7 +763,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -782,7 +779,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -798,7 +795,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -814,7 +811,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -830,7 +827,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -855,7 +852,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -880,7 +877,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -896,7 +893,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -912,7 +909,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -928,7 +925,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
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})();
</script>
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</html>
diff --git a/docs.it4i.cz/salomon/software/debuggers.1.md b/docs.it4i.cz/salomon/software/debuggers.1.md
new file mode 100644
index 0000000000000000000000000000000000000000..ec7667feb2fd66fa8ca0de417ec15619311ed117
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/debuggers.1.md
@@ -0,0 +1,69 @@
+Debuggers and profilers summary
+===============================
+
+Introduction
+------------
+We provide state of the art programms and tools to develop, profile and
+debug HPC codes at IT4Innovations.
+On these pages, we provide an overview of the profiling and debugging
+tools available on Anslem at IT4I.
+Intel debugger
+--------------
+Intel debugger is no longer available since Parallel Studio version 2015
+The intel debugger version 13.0 is available, via module intel. The
+debugger works for applications compiled with C and C++ compiler and the
+ifort fortran 77/90/95 compiler. The debugger provides java GUI
+environment. Use [X
+display](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc)
+for running the GUI.
+ $ module load intel
+ $ idb
+Read more at the [Intel
+Debugger](https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger)
+page.
+Allinea Forge (DDT/MAP)
+Allinea DDT, is a commercial debugger primarily for debugging parallel
+MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel
+Xeon Phi accelerators. DDT provides all the standard debugging features
+(stack trace, breakpoints, watches, view variables, threads etc.) for
+every thread running as part of your program, or for every process -
+even if these processes are distributed across a cluster using an MPI
+implementation.
+ $ module load Forge
+ $ forge
+Read more at the [Allinea
+DDT](https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt)
+page.
+Allinea Performance Reports
+----
+Allinea Performance Reports characterize the performance of HPC
+application runs. After executing your application through the tool, a
+synthetic HTML report is generated automatically, containing information
+about several metrics along with clear behavior statements and hints to
+help you improve the efficiency of your runs. Our license is limited to
+64 MPI processes.
+ $ module load PerformanceReports/6.0
+ $ perf-report mpirun -n 64 ./my_application argument01 argument02
+Read more at the [Allinea Performance
+Reports](https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports)
+page.
+RougeWave Totalview
+-------------------
+TotalView is a source- and machine-level debugger for multi-process,
+multi-threaded programs. Its wide range of tools provides ways to
+analyze, organize, and test programs, making it easy to isolate and
+identify problems in individual threads and processes in programs of
+great complexity.
+ $ module load TotalView/8.15.4-6-linux-x86-64
+ $ totalview
+Read more at the
+[Totalview](https://docs.it4i.cz/salomon/software/debuggers/total-view)
+page.
+Vampir trace analyzer
+---------------------
+Vampir is a GUI trace analyzer for traces in OTF format.
+ $ module load Vampir/8.5.0
+ $ vampir
+Read more at the
+[Vampir](https://docs.it4i.cz/salomon/software/debuggers/vampir)
+page.
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<head>
@@ -43,13 +40,11 @@
<body>
<div id="content-core">
- <a href="view.html"><span>Zpět na portál</span><br /><img src="image.png" alt="Vampir screenshot" title="Vampir screenshot" height="647" width="1071" /></a>
+ <a href="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/view"><span>Zpět na portál</span><br /><img src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/image" alt="Vampir screenshot" title="Vampir screenshot" height="647" width="1071" /></a>
</div>
</body>
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</html>
diff --git a/docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/image_view_fullscreen.md b/docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/image_view_fullscreen.md
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<title>Vampir screenshot — IT4I Docs</title>
- <link rel="canonical" href="../Snimek%20obrazovky%202016-07-08%20v%2012.33.35.png" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png" />
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+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
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<div id="portal-header">
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+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/view#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="view.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/view#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<div id="portal-personaltools-wrapper">
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</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
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- <img src="../../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
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@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../../debuggers.html">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/salomon/software/debuggers">Debuggers and profilers</a>
<span class="breadcrumbSeparator">
/
@@ -242,8 +239,8 @@
<div id="content-core">
- <a href="image_view_fullscreen.html">
- <img src="image_preview.png" alt="Vampir screenshot" title="Vampir screenshot" height="241" width="400" />
+ <a href="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/image_view_fullscreen">
+ <img src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/image_preview" alt="Vampir screenshot" title="Vampir screenshot" height="241" width="400" />
<br />
</a>
@@ -254,16 +251,16 @@
<span>202 KB</span>
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- <img alt="Zobrazit obrázek" title="Zobrazit obrázek" src="../../../../search_icon.png" />
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<span>ZobrazenĂ</span>
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- <img alt="Stáhnout obrázek" title="Stáhnout obrázek" src="../../../../download_icon.png" />
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<span>Salomon Cluster Documentation</span>
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<span>Hardware Overview</span>
</a>
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<span>Accessing the Cluster</span>
</a>
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<span>Environment and Modules</span>
</a>
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<span>List of Available Modules</span>
</a>
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<span>Resource Allocation and Job Execution</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../../compute-nodes.html">
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<span>Compute Nodes</span>
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<span>Storage</span>
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<span>Software</span>
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</a>
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<span>Debuggers and profilers</span>
</a>
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<span>Aislinn</span>
</a>
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<span>Allinea Forge (DDT,MAP)</span>
</a>
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<span>Allinea Performance Reports</span>
</a>
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</a>
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<span>Total View</span>
</a>
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- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="../valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/salomon/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
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<span>Vampir</span>
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+ <img width="16" height="16" src="https://docs.it4i.cz/png.png" alt="Obrázek PNG image" />
<span>Vampir screenshot</span>
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- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../../chemistry.html">
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<span>Chemistry, Physics and Materials science</span>
</a>
@@ -727,7 +724,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
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<span>MPI</span>
</a>
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<span>Numerical languages</span>
</a>
@@ -775,7 +772,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -791,7 +788,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -807,7 +804,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
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- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -848,7 +845,7 @@
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<span>PRACE User Support</span>
</a>
@@ -873,7 +870,7 @@
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<span>Anselm Cluster Documentation</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
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- <a title="" class="state-published contenttype-collection" href="../../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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<title>Aislinn — IT4I Docs</title>
- <link rel="canonical" href="aislinn.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/debuggers/aislinn" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
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<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="aislinn.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/debuggers/aislinn#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="aislinn.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/debuggers/aislinn#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<div id="portal-personaltools-wrapper">
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
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- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../debuggers.html">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/salomon/software/debuggers">Debuggers and profilers</a>
<span class="breadcrumbSeparator">
/
@@ -430,7 +427,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -446,7 +443,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -462,7 +459,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -478,7 +475,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -494,7 +491,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -510,7 +507,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -526,7 +523,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -542,7 +539,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -558,7 +555,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -574,7 +571,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -590,7 +587,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -606,7 +603,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -622,10 +619,10 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -641,7 +638,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -657,7 +654,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -673,7 +670,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="A collection of development tools" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -689,7 +686,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="aislinn.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/aislinn">
<span>Aislinn</span>
</a>
@@ -705,7 +702,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="" class="state-published contenttype-document" href="allinea-ddt.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
@@ -721,7 +718,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="quick application profiling" class="state-published contenttype-document" href="allinea-performance-reports.html">
+ <a class="state-published contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -737,7 +734,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="" class="state-published contenttype-document" href="intel-vtune-amplifier.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier XE</span>
</a>
@@ -753,7 +750,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published contenttype-document" href="total-view.html">
+ <a class="state-published contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/salomon/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -769,7 +766,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/salomon/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -785,7 +782,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="" class="state-published contenttype-document" href="vampir.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -810,7 +807,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -826,7 +823,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -842,7 +839,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -858,7 +855,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -874,7 +871,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -890,7 +887,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -906,7 +903,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -922,7 +919,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -947,7 +944,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -972,7 +969,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -988,7 +985,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -1004,7 +1001,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1020,7 +1017,7 @@ communicator management. Unfortunately, MPI-IO and one-side communication is not
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1059,14 +1056,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1088,12 +1085,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1109,7 +1106,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/debuggers/aislinn by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:08 GMT -->
</html>
diff --git a/salomon/software/debuggers/aislinn.md b/docs.it4i.cz/salomon/software/debuggers/aislinn.md
similarity index 61%
rename from salomon/software/debuggers/aislinn.md
rename to docs.it4i.cz/salomon/software/debuggers/aislinn.md
index 8163e484cc6020a30342011b229411056a5e3638..b9ce1b6c76a6eed04de7c99aeffaeec05b436a88 100644
--- a/salomon/software/debuggers/aislinn.md
+++ b/docs.it4i.cz/salomon/software/debuggers/aislinn.md
@@ -1,3 +1,4 @@
+Aislinn
=======
- Aislinn is a dynamic verifier for MPI programs. For a fixed input it
covers all possible runs with respect to nondeterminism introduced
@@ -7,17 +8,17 @@
misuse of MPI, and resource leaks.
- Aislinn is open-source software; you can use it without any
licensing limitations.
-- Web page of the project
+- Web page of the project<http://verif.cs.vsb.cz/aislinn/>
Note
Aislinn is software developed at IT4Innovations and some parts are still
considered experimental. If you have any questions or experienced any
-problems, please contact the author .
+problems, please contact the author<stanislav.bohm@vsb.cz>.
### Usage
Let us have the following program that contains a bug that is not
-manifested in all runs
+manifested in all runs:
``` {.literal-block}
-#include
-#include
+#include <mpi.h>
+#include <stdlib.h>
int main(int argc, char **argv) {
int rank;
MPI_Init(&argc, &argv);
@@ -42,12 +43,12 @@ int main(int argc, char **argv) {
return 0;
}
```
-The program does the following process 0 receives two messages from
+The program does the followingprocess 0 receives two messages from
anyone and processes 1 and 2 send a message to process 0. If a message
from process 1 is received first, then the run does not expose the
error. If a message from process 2 is received first, then invalid
memory write occurs at line 16.
-To verify this program by Aislinn, we first load Aislinn itself
+To verify this program by Aislinn, we first load Aislinn itself:
``` {.literal-block}
$ module load aislinn
```
@@ -68,19 +69,19 @@ specifies that we want to verify our program for the case of three MPI
processes
``` {.literal-block}
$ aislinn -p 3 ./test
-==AN== INFO Aislinn v0.3.0
-==AN== INFO Found error 'Invalid write'
-==AN== INFO 1 error(s) found
-==AN== INFO Report written into 'report.html'
+==AN== INFOAislinn v0.3.0
+==AN== INFOFound error 'Invalid write'
+==AN== INFO1 error(s) found
+==AN== INFOReport written into 'report.html'
```
Aislinn found an error and produced HTML report. To view it, we can use
-any browser, e.g.
+any browser, e.g.:
> $ firefox report.html
At the beginning of the report there are some basic summaries of the
verification. In the second part (depicted in the following picture),
the error is described.
-
-It shows us
+
+It shows us:
> - Error occurs in process 0 in test.cpp on line 16.
> - Stdout and stderr streams are empty. (The program does not
> write anything).
@@ -105,7 +106,7 @@ limitations.
not interacts with the system in some unusual ways (e.g.
opening sockets).
There are also some limitations bounded to the current version and they
-will be removed in the future
+will be removed in the future:
- All files containing MPI calls have to be recompiled by MPI
implementation provided by Aislinn. The files that does not contain
MPI calls, they do not have to recompiled. Aislinn MPI
@@ -117,66 +118,3 @@ will be removed in the future
`OMP_NUM_THREADS`{.docutils .literal} to 1).
- There are some limitations for using files, but if the program just
reads inputs and writes results, it is ok.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
- .navTreeFolderish
- .contenttype-folder}
- - [Aislinn](aislinn.html)
-
-
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
- - [Intel VTune Amplifier
- XE](intel-vtune-amplifier.html)
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
diff --git a/salomon/software/debuggers/allinea-performance-reports.html b/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.html
old mode 100755
new mode 100644
similarity index 64%
rename from salomon/software/debuggers/allinea-performance-reports.html
rename to docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.html
index 851edccd554b8b22033a124b56fcc0ac302c77e8..1dca99a8c9f0c4900e6aa2f32cc142e76427b2b7
--- a/salomon/software/debuggers/allinea-performance-reports.html
+++ b/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:08 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports" /><!--[if lt IE 7]></base><![endif]-->
<meta content="quick application profiling" name="description" />
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<title>Allinea Performance Reports — IT4I Docs</title>
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<div id="portal-header">
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- <a accesskey="2" href="allinea-performance-reports.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="allinea-performance-reports.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<div id="portal-advanced-search" class="hiddenStructure">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
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@@ -173,7 +170,7 @@
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- <a href="../debuggers.html">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/salomon/software/debuggers">Debuggers and profilers</a>
<span class="breadcrumbSeparator">
/
@@ -262,9 +259,9 @@
<p class=" ">The module sets up environment variables, required for using the Allinea Performance Reports. </p>
<h2 class=" ">Usage</h2>
<p class="callout">Use the the perf-report wrapper on your (MPI) program.</p>
-<p>Instead of <a target="_self" title="" class="internal-link" href="../mpi-1.html">running your MPI program the usual way</a>, use the the perf report wrapper:</p>
+<p>Instead of <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/mpi-1">running your MPI program the usual way</a>, use the the perf report wrapper:</p>
<pre class=" ">$ perf-report mpirun ./mympiprog.x</pre>
-<p class=" ">The mpi program will run as usual. The perf-report creates two additional files, in *.txt and *.html format, containing the performance report. Note that <span class="internal-link">demanding MPI codes should be run within </span><a target="_self" title="" class="internal-link" href="../../resource-allocation-and-job-execution/job-submission-and-execution.html"><span class="internal-link">the queue system</span></a>.</p>
+<p class=" ">The mpi program will run as usual. The perf-report creates two additional files, in *.txt and *.html format, containing the performance report. Note that <span class="internal-link">demanding MPI codes should be run within </span><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution"><span class="internal-link">the queue system</span></a>.</p>
<h2 class=" ">Example</h2>
<p class=" ">In this example, we will be profiling the mympiprog.x MPI program, using Allinea performance reports. Assume that the code is compiled with intel compilers and linked against intel MPI library:</p>
<p class=" ">First, we allocate some nodes via the express queue:</p>
@@ -273,7 +270,7 @@
<pre class=" ">$ module load intel impi PerfReports/6.0<br />$ mpirun ./mympiprog.x</pre>
<p class=" ">Now lets profile the code:</p>
<pre class=" ">$ perf-report mpirun ./mympiprog.x</pre>
-<p class=" ">Performance report files <a target="_self" title="" class="internal-link" href="mympiprog_32p_2014-10-15_16-56.txt">mympiprog_32p*.txt</a> and <a target="_self" title="" class="internal-link" href="mympiprog_32p_2014-10-15_16-56.html">mympiprog_32p*.html</a> were created. We can see that the code is very efficient on MPI and is CPU bounded.</p>
+<p class=" ">Performance report files <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.txt">mympiprog_32p*.txt</a> and <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.html">mympiprog_32p*.html</a> were created. We can see that the code is very efficient on MPI and is CPU bounded.</p>
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<span>Salomon Cluster Documentation</span>
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<span>Accessing the Cluster</span>
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<span>Environment and Modules</span>
</a>
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- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
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<span>Resource Allocation and Job Execution</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
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<span>Compute Nodes</span>
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<span>Storage</span>
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<span>Network</span>
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- <a title="In this section we provide overview of installed software and its usage.
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-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
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<span>Software</span>
</a>
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<span>ANSYS</span>
</a>
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- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
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+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
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- <a title="" class="state-published contenttype-document" href="aislinn.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/aislinn">
<span>Aislinn</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
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- <a title="quick application profiling" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="allinea-performance-reports.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -656,7 +653,7 @@
- <a title="" class="state-published contenttype-document" href="intel-vtune-amplifier.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier XE</span>
</a>
@@ -672,7 +669,7 @@
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published contenttype-document" href="total-view.html">
+ <a class="state-published contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/salomon/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -688,7 +685,7 @@
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/salomon/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -704,7 +701,7 @@
- <a title="" class="state-published contenttype-document" href="vampir.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -729,7 +726,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -745,7 +742,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -761,7 +758,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -777,7 +774,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -793,7 +790,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -809,7 +806,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -825,7 +822,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -841,7 +838,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -866,7 +863,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -891,7 +888,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -907,7 +904,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -923,7 +920,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -939,7 +936,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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})();
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-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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diff --git a/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.md b/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.md
new file mode 100644
index 0000000000000000000000000000000000000000..3b0b5db6a349278f03a1699529825f293f90335f
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.md
@@ -0,0 +1,52 @@
+Allinea Performance Reports
+===========================
+quick application profiling
+
+Introduction
+------------
+Allinea Performance Reports characterize the performance of HPC
+application runs. After executing your application through the tool, a
+synthetic HTML report is generated automatically, containing information
+about several metrics along with clear behavior statements and hints to
+help you improve the efficiency of your runs.
+The Allinea Performance Reports is most useful in profiling MPI
+programs.
+Our license is limited to 64 MPI processes.
+Modules
+-------
+Allinea Performance Reports version 6.0 is available
+ $ module load PerformanceReports/6.0
+The module sets up environment variables, required for using the Allinea
+Performance Reports.Â
+Usage
+-----
+Use the the perf-report wrapper on your (MPI) program.
+Instead of [running your MPI program the usual
+way](https://docs.it4i.cz/salomon/software/mpi-1), use
+the the perf report wrapper:
+ $ perf-report mpirun ./mympiprog.x
+The mpi program will run as usual. The perf-report creates two
+additional files, in *.txt and *.html format, containing the
+performance report. Note that <span class="internal-link">demanding MPI
+codes should be run within </span>[<span class="internal-link">the queue
+system</span>](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution).
+Example
+-------
+In this example, we will be profiling the mympiprog.x MPI program, using
+Allinea performance reports. Assume that the code is compiled with intel
+compilers and linked against intel MPI library:
+First, we allocate some nodes via the express queue:
+ $ qsub -q qexp -l select=2:ppn=24:mpiprocs=24:ompthreads=1 -I
+ qsubwaiting for job 262197.dm2 to start
+ qsubjob 262197.dm2 ready
+Then we load the modules and run the program the usual way:
+ $ module load intel impi PerfReports/6.0
+ $ mpirun ./mympiprog.x
+Now lets profile the code:
+ $ perf-report mpirun ./mympiprog.x
+Performance report files
+[mympiprog_32p*.txt](https://docs.it4i.cz/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.txt)
+and
+[mympiprog_32p*.html](https://docs.it4i.cz/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.html)
+were created. We can see that the code is very efficient on MPI and is
+CPU bounded.
diff --git a/salomon/software/debuggers/ddt1.png b/docs.it4i.cz/salomon/software/debuggers/ddt1.png
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/software/debuggers/ddt1.png
rename to docs.it4i.cz/salomon/software/debuggers/ddt1.png
diff --git a/salomon/software/debuggers/intel-vtune-amplifier.html b/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.html
old mode 100755
new mode 100644
similarity index 70%
rename from salomon/software/debuggers/intel-vtune-amplifier.html
rename to docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.html
index eaf651e7de9ee90db97157f535ce25a674736b06..edbb591a6199859a8f970469d3b8516e0dd294ad
--- a/salomon/software/debuggers/intel-vtune-amplifier.html
+++ b/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.html
@@ -10,45 +10,42 @@
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Intel VTune Amplifier XE — IT4I Docs</title>
- <link rel="canonical" href="intel-vtune-amplifier.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="intel-vtune-amplifier.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="intel-vtune-amplifier.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
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- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../debuggers.html">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/salomon/software/debuggers">Debuggers and profilers</a>
<span class="breadcrumbSeparator">
/
@@ -259,7 +256,7 @@
<li>Power usage analysis - frequency and sleep states.</li>
</ul>
<div></div>
-<div><a target="_blank" title="" class="internal-link" href="Snimek%20obrazovky%202015-03-03%20v%2015.50.36.png"><img title="VTune Amplifier" class="image-inline" alt="screenshot" src="vtune-amplifier/%40%40images/7ca8748b-69ad-4b53-9667-29c2fdaa8913.png" /></a></div>
+<div><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/software/debuggers/vtune-amplifier"><img alt="screenshot" class="image-inline" title="VTune Amplifier" src="https://docs.it4i.cz/salomon/software/debuggers/vtune-amplifier/@@images/7ca8748b-69ad-4b53-9667-29c2fdaa8913.png" /></a></div>
<h2 class=" ">Usage</h2>
<p><span>To profile an application with VTune Amplifier, special kernel modules need to be loaded. The modules are not loaded on the login nodes, thus direct profiling on login nodes is not possible. By default, the kernel modules ale not loaded on compute nodes neither. In order to have the modules loaded, you need to specify vtune=version PBS resource at job submit. The version is the same as for <em>environment module</em>. For example to use <span class="monospace">VTune/2016_update1</span>:</span></p>
<pre><span>$ qsub -q qexp -A OPEN-0-0 -I -l select=1,vtune=2016_update1</span></pre>
@@ -371,7 +368,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
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<span>What's New</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -435,7 +432,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -451,7 +448,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -467,7 +464,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -483,7 +480,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -499,7 +496,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -515,7 +512,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -547,7 +544,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
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- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
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- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
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- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
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- <a title="A collection of development tools" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
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- <a title="" class="state-published contenttype-document" href="aislinn.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/aislinn">
<span>Aislinn</span>
</a>
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- <a title="" class="state-published contenttype-document" href="allinea-ddt.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
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- <a title="quick application profiling" class="state-published contenttype-document" href="allinea-performance-reports.html">
+ <a class="state-published contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -678,7 +675,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="intel-vtune-amplifier.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier XE</span>
</a>
@@ -694,7 +691,7 @@
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published contenttype-document" href="total-view.html">
+ <a class="state-published contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/salomon/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -710,7 +707,7 @@
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/salomon/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -726,7 +723,7 @@
- <a title="" class="state-published contenttype-document" href="vampir.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -751,7 +748,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -767,7 +764,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -783,7 +780,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
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- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -815,7 +812,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
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- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -847,7 +844,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -863,7 +860,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -888,7 +885,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
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- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -961,7 +958,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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diff --git a/salomon/software/debuggers/intel-vtune-amplifier.md b/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.md
similarity index 50%
rename from salomon/software/debuggers/intel-vtune-amplifier.md
rename to docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.md
index 13f2dc0bf5d4da8eb6279d0efa91126e432cea29..6b53ac22565b09b1ab906298c2cf0085f6472a23 100644
--- a/salomon/software/debuggers/intel-vtune-amplifier.md
+++ b/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.md
@@ -1,48 +1,47 @@
Intel VTune Amplifier XE
========================
-
-
+
Introduction
------------
-Intel*® *VTune™ Amplifier, part of Intel Parallel studio, is a GUI
+Intel*® *VTune™ <span>Amplifier, part of Intel Parallel studio, is a GUI
profiling tool designed for Intel processors. It offers a graphical
performance analysis of single core and multithreaded applications. A
-highlight of the features
+highlight of the features:</span>
- Hotspot analysis
- Locks and waits analysis
- Low level specific counters, such as branch analysis and memory
bandwidth
- Power usage analysis - frequency and sleep states.
-[](Snimek%20obrazovky%202015-03-03%20v%2015.50.36.png)
+[](https://docs.it4i.cz/salomon/software/debuggers/vtune-amplifier)
Usage
-----
-To profile an application with VTune Amplifier, special kernel
+<span>To profile an application with VTune Amplifier, special kernel
modules need to be loaded. The modules are not loaded on the login
nodes, thus direct profiling on login nodes is not possible. By default,
the kernel modules ale not loaded on compute nodes neither. In order to
have the modules loaded, you need to specify vtune=version PBS resource
at job submit. The version is the same as for *environment module*. For
-example to use
-class="monospace">VTune/2016_update1
+example to use <span
+class="monospace">VTune/2016_update1</span>:</span>
$ qsub -q qexp -A OPEN-0-0 -I -l select=1,vtune=2016_update1
After that, you can verify the modules sep*, pax and vtsspp are present
-in the kernel
+in the kernel :
$ lsmod | grep -e sep -e pax -e vtsspp
vtsspp 362000 0
sep3_15 546657 0
pax 4312 0
-To launch the GUI, first load the module
+To launch the GUI, first load the module:
$ module add VTune/2016_update1
-and launch the GUI
+<span class="s1">and launch the GUI :</span>
$Â amplxe-gui
-The GUI will open in new window. Click on "*New Project...*" to
+<span>The GUI will open in new window. Click on "*New Project...*" to
create a new project. After clicking *OK*, a new window with project
-properties will appear. Â At "*Application*", select the bath to your
+properties will appear. Â At "*Application:*", select the bath to your
binary you want to profile (the binary should be compiled with -g flag).
Some additional options such as command line arguments can be selected.
-At "*Managed code profiling mode*" select "*Native*" (unless you want
+At "*Managed code profiling mode:*" select "*Native*" (unless you want
to profile managed mode .NET/Mono applications). After clicking *OK*,
-your project is created.
+your project is created.</span>
To run a new analysis, click "*New analysis...*". You will see a list of
possible analysis. Some of them will not be possible on the current CPU
(eg. Intel Atom analysis is not possible on Sandy bridge CPU), the GUI
@@ -58,7 +57,7 @@ profiling without interactive graphical jobs. To perform a remote
analysis, launch a GUI somewhere, open the new analysis window and then
click the button "*Command line*" in bottom right corner. It will show
the command line needed to perform the selected analysis.
-The command line will look like this
+The command line will look like this:
/apps/all/VTune/2016_update1/vtune_amplifier_xe_2016.1.1.434111/bin64/amplxe-cl -collect advanced-hotspots -app-working-dir /home/sta545/tmp -- /home/sta545/tmp/sgemm
Copy the line to clipboard and then you can paste it in your jobscript
or in command line. After the collection is run, open the GUI once
@@ -83,81 +82,18 @@ might be impossible and you will get errors like "ERROR connecting to
MIC card". In this case please contact our support to reboot the MIC
card.
You may also use remote analysis to collect data from the MIC and then
-analyze it in the GUI later
-Native launch
- $ /apps/all/VTune/2016_update1/vtune_amplifier_xe_2016.1.1.434111/bin64/amplxe-cl -target-system mic-native0 -collect advanced-hotspots -- /home/sta545/tmp/vect-add-mic
-Host launch
- $ /apps/all/VTune/2016_update1/vtune_amplifier_xe_2016.1.1.434111/bin64/amplxe-cl -target-system mic-host-launch0 -collect advanced-hotspots -- /home/sta545/tmp/sgemm
+analyze it in the GUI later :
+Native launch:
+ $ /apps/all/VTune/2016_update1/vtune_amplifier_xe_2016.1.1.434111/bin64/amplxe-cl -target-system mic-native:0 -collect advanced-hotspots -- /home/sta545/tmp/vect-add-mic
+Host launch:
+ $ /apps/all/VTune/2016_update1/vtune_amplifier_xe_2016.1.1.434111/bin64/amplxe-cl -target-system mic-host-launch:0 -collect advanced-hotspots -- /home/sta545/tmp/sgemm
You can obtain this command line by pressing the "Command line..."
button on Analysis Type screen.Â
References
----------
-1. Â Performance
- Tuning for Intel® Xeon Phi™ Coprocessors
-2.  Intel®
- VTune™ Amplifier Support
-3. Â Linux
- user guide
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
- .navTreeFolderish
- .contenttype-folder}
- - [Aislinn](aislinn.html)
-
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
- - [Intel VTune Amplifier
- XE](intel-vtune-amplifier.html)
-
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
+1. <span><https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf>Â Performance
+ Tuning for Intel® Xeon Phi™ Coprocessors</span>
+2. <span><https://software.intel.com/en-us/intel-vtune-amplifier-xe-support/documentation> <span>Intel®
+ VTune™ Amplifier Support</span></span>
+3. <span><span><https://software.intel.com/en-us/amplifier_help_linux>Â Linux
+ user guide</span></span>
diff --git a/anselm-cluster-documentation/software/debuggers/mympiprog_32p_2014-10-15_16-56.html b/docs.it4i.cz/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.html
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>mympiprog.x - Performance Report</title>
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diff --git a/docs.it4i.cz/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.md b/docs.it4i.cz/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.md
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old mode 100755
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<title>IT4I Docs</title>
- <link rel="canonical" href="../../index.html" />
+ <link rel="canonical" href="https://docs.it4i.cz" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
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+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
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<script type="text/javascript">
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- <link rel="alternate" href="../../RSS" title="IT4I Docs - RSS 1.0" type="application/rss+xml" />
+ <link rel="alternate" href="https://docs.it4i.cz/RSS" title="IT4I Docs - RSS 1.0" type="application/rss+xml" />
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@@ -79,7 +76,7 @@
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+ <script type="text/javascript" src="https://docs.it4i.cz/login.js">
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@@ -96,9 +93,9 @@
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<p class="hiddenStructure">
- <a accesskey="2" href="require_loginc71d.html?came_from=https%3A//docs.it4i.cz/salomon/software/debuggers/score-p#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/acl_users/credentials_cookie_auth/require_login?came_from=https%3A//docs.it4i.cz/salomon/software/debuggers/score-p#content">PĹ™ejĂt na obsah</a> |
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<div id="portal-advanced-search" class="hiddenStructure">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
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- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
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<title>Debuggers and profilers summary — IT4I Docs</title>
- <link rel="canonical" href="debuggers.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/debuggers" />
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- <a accesskey="6" href="debuggers.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/debuggers/summary#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
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+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
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@@ -244,25 +241,25 @@
<p>We provide state of the art programms and tools to develop, profile and debug HPC codes at IT4Innovations.<br />On these pages, we provide an overview of the profiling and debugging tools available on Anslem at IT4I.</p>
<h2 class=" ">Intel debugger</h2>
<p class="exclamation">Intel debugger is no longer available since Parallel Studio version 2015</p>
-<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a target="_self" title="" class="internal-link" href="../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html">X display</a> for running the GUI.</p>
+<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">X display</a> for running the GUI.</p>
<pre class=" ">$ module load intel<br />$ idb</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="intel-suite/intel-debugger.html">Intel Debugger</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger">Intel Debugger</a> page.</p>
<h2 class=" ">Allinea Forge (DDT/MAP)</h2>
<p>Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel Xeon Phi accelerators. DDT provides all the standard debugging features (stack trace, breakpoints, watches, view variables, threads etc.) for every thread running as part of your program, or for every process - even if these processes are distributed across a cluster using an MPI implementation.</p>
<pre class=" ">$ module load Forge<br />$ forge</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="debuggers/allinea-ddt.html">Allinea DDT</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt">Allinea DDT</a> page.</p>
<h2 class=" ">Allinea Performance Reports</h2>
<p>Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs. Our license is limited to 64 MPI processes.</p>
<pre class=" ">$ module load PerformanceReports/6.0 <br />$ perf-report mpirun -n 64 ./my_application argument01 argument02</pre>
-<p class=" ">Read more at the <a target="_self" title="" class="internal-link" href="debuggers/allinea-performance-reports.html">Allinea Performance Reports</a> page.</p>
+<p class=" ">Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports">Allinea Performance Reports</a> page.</p>
<h2 class=" ">RougeWave Totalview</h2>
<p>TotalView is a source- and machine-level debugger for multi-process, multi-threaded programs. Its wide range of tools provides ways to analyze, organize, and test programs, making it easy to isolate and identify problems in individual threads and processes in programs of great complexity.</p>
<pre class=" ">$ module load TotalView/8.15.4-6-linux-x86-64<br />$ totalview</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="debuggers/total-view.html">Totalview</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/total-view">Totalview</a> page.</p>
<h2 class=" ">Vampir trace analyzer</h2>
<p>Vampir is a GUI trace analyzer for traces in OTF format.</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="debuggers/vampir.html">Vampir</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">Vampir</a> page.</p>
</div>
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<dt class="portletHeader hiddenStructure">
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<span>What's New</span>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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<span>Salomon Cluster Documentation</span>
</a>
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<span>Hardware Overview</span>
</a>
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<span>Accessing the Cluster</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
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<span>Environment and Modules</span>
</a>
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- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -482,7 +479,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
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<span>Network</span>
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- <a title="In this section we provide overview of installed software and its usage.
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-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
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<span>Software</span>
</a>
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- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -565,7 +562,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -581,7 +578,7 @@
- <a title="A collection of development tools" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -597,7 +594,7 @@
- <a title="" class="state-published contenttype-document" href="debuggers/aislinn.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/aislinn">
<span>Aislinn</span>
</a>
@@ -613,7 +610,7 @@
- <a title="" class="state-published contenttype-document" href="debuggers/allinea-ddt.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
@@ -629,7 +626,7 @@
- <a title="quick application profiling" class="state-published contenttype-document" href="debuggers/allinea-performance-reports.html">
+ <a class="state-published contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -645,7 +642,7 @@
- <a title="" class="state-published contenttype-document" href="debuggers/intel-vtune-amplifier.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier XE</span>
</a>
@@ -661,7 +658,7 @@
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published contenttype-document" href="debuggers/total-view.html">
+ <a class="state-published contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/salomon/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -677,7 +674,7 @@
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="debuggers/valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/salomon/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -693,7 +690,7 @@
- <a title="" class="state-published contenttype-document" href="debuggers/vampir.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -718,7 +715,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -734,7 +731,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -750,7 +747,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -766,7 +763,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -782,7 +779,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -798,7 +795,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -814,7 +811,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -830,7 +827,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -855,7 +852,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -880,7 +877,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -896,7 +893,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -912,7 +909,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -928,7 +925,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</div>
</body>
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</html>
diff --git a/docs.it4i.cz/salomon/software/debuggers/summary.md b/docs.it4i.cz/salomon/software/debuggers/summary.md
new file mode 100644
index 0000000000000000000000000000000000000000..ec7667feb2fd66fa8ca0de417ec15619311ed117
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/debuggers/summary.md
@@ -0,0 +1,69 @@
+Debuggers and profilers summary
+===============================
+
+Introduction
+------------
+We provide state of the art programms and tools to develop, profile and
+debug HPC codes at IT4Innovations.
+On these pages, we provide an overview of the profiling and debugging
+tools available on Anslem at IT4I.
+Intel debugger
+--------------
+Intel debugger is no longer available since Parallel Studio version 2015
+The intel debugger version 13.0 is available, via module intel. The
+debugger works for applications compiled with C and C++ compiler and the
+ifort fortran 77/90/95 compiler. The debugger provides java GUI
+environment. Use [X
+display](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc)
+for running the GUI.
+ $ module load intel
+ $ idb
+Read more at the [Intel
+Debugger](https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger)
+page.
+Allinea Forge (DDT/MAP)
+Allinea DDT, is a commercial debugger primarily for debugging parallel
+MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel
+Xeon Phi accelerators. DDT provides all the standard debugging features
+(stack trace, breakpoints, watches, view variables, threads etc.) for
+every thread running as part of your program, or for every process -
+even if these processes are distributed across a cluster using an MPI
+implementation.
+ $ module load Forge
+ $ forge
+Read more at the [Allinea
+DDT](https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt)
+page.
+Allinea Performance Reports
+----
+Allinea Performance Reports characterize the performance of HPC
+application runs. After executing your application through the tool, a
+synthetic HTML report is generated automatically, containing information
+about several metrics along with clear behavior statements and hints to
+help you improve the efficiency of your runs. Our license is limited to
+64 MPI processes.
+ $ module load PerformanceReports/6.0
+ $ perf-report mpirun -n 64 ./my_application argument01 argument02
+Read more at the [Allinea Performance
+Reports](https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports)
+page.
+RougeWave Totalview
+-------------------
+TotalView is a source- and machine-level debugger for multi-process,
+multi-threaded programs. Its wide range of tools provides ways to
+analyze, organize, and test programs, making it easy to isolate and
+identify problems in individual threads and processes in programs of
+great complexity.
+ $ module load TotalView/8.15.4-6-linux-x86-64
+ $ totalview
+Read more at the
+[Totalview](https://docs.it4i.cz/salomon/software/debuggers/total-view)
+page.
+Vampir trace analyzer
+---------------------
+Vampir is a GUI trace analyzer for traces in OTF format.
+ $ module load Vampir/8.5.0
+ $ vampir
+Read more at the
+[Vampir](https://docs.it4i.cz/salomon/software/debuggers/vampir)
+page.
diff --git a/salomon/software/debuggers/total-view.html b/docs.it4i.cz/salomon/software/debuggers/total-view.html
old mode 100755
new mode 100644
similarity index 69%
rename from salomon/software/debuggers/total-view.html
rename to docs.it4i.cz/salomon/software/debuggers/total-view.html
index 151f598d6383af610c441355d67649680fa507cc..877b96e85210aaccad3038ea9c8c494606a4faf7
--- a/salomon/software/debuggers/total-view.html
+++ b/docs.it4i.cz/salomon/software/debuggers/total-view.html
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/debuggers/total-view" /><!--[if lt IE 7]></base><![endif]-->
<meta content="TotalView is a GUI-based source code multi-process, multi-thread debugger. " name="description" />
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Total View — IT4I Docs</title>
- <link rel="canonical" href="total-view.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/debuggers/total-view" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="total-view.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/debuggers/total-view#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="total-view.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/debuggers/total-view#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
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- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../debuggers.html">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/salomon/software/debuggers">Debuggers and profilers</a>
<span class="breadcrumbSeparator">
/
@@ -265,7 +262,7 @@
<h2 class=" ">Starting a Job with TotalView</h2>
<p>Be sure to log in with an X window forwarding enabled. This could mean using the -X in the ssh:Â </p>
<pre class=" ">ssh -X username@salomon.it4i.cz </pre>
-<p>Other options is to access login node using VNC. Please see the detailed information on how to use graphic user interface on Anselm <a target="_self" title="" class="internal-link" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html#VNC">here</a>.</p>
+<p>Other options is to access login node using VNC. Please see the detailed information on how to use graphic user interface on Anselm <a title="" class="internal-link" target="_self" href="resolveuid/11e53ad0d2fd4c5187537f4baeedff33#VNC">here</a>.</p>
<p>From the login node an interactive session with X windows forwarding (-X option) can be started by following command:</p>
<pre class=" ">qsub -I -X -A NONE-0-0 -q qexp -lselect=1:ncpus=24:mpiprocs=24,walltime=01:00:00 </pre>
<p>Then launch the debugger with the totalview command followed by the name of the executable to debug.</p>
@@ -283,9 +280,9 @@
<p>Now you can run the parallel debugger using:</p>
<pre class=" ">mpirun -tv -n 5 ./test_debug</pre>
<p>When following dialog appears click on "Yes"</p>
-<p><a target="_blank" title="" class="internal-link" href="totalview1.png"><img title="" class="image-inline" alt="" src="totalview1.png/%40%40images/45a91b6e-7f4d-4084-a5ba-d1ee703adaa1.png" /></a></p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/software/debuggers/totalview1.png"><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/salomon/software/debuggers/totalview1.png/@@images/45a91b6e-7f4d-4084-a5ba-d1ee703adaa1.png" /></a></p>
<p>At this point the main TotalView GUI window will appear and you can insert the breakpoints and start debugging:</p>
-<p><a target="_blank" title="" class="internal-link" href="totalview2.png"><img title="" class="image-inline" alt="" src="totalview2.png" /></a></p>
+<p><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/software/debuggers/totalview2.png"><img alt="" class="image-inline" title="" src="https://docs.it4i.cz/salomon/software/debuggers/totalview2.png" /></a></p>
<h3 class=" ">Debugging a parallel code - option 2</h3>
<p>Other option to start new parallel debugging session from a command line is to let TotalView to execute mpirun by itself. In this case user has to specify a MPI implementation used to compile the source code. </p>
<p>The following example shows how to start debugging session with Intel MPI:</p>
@@ -369,7 +366,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -385,7 +382,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -401,7 +398,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -417,7 +414,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -433,7 +430,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -449,7 +446,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -465,7 +462,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -481,7 +478,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -497,7 +494,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -513,7 +510,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -529,7 +526,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -545,7 +542,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -561,10 +558,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -580,7 +577,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -596,7 +593,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -612,7 +609,7 @@
- <a title="A collection of development tools" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -628,7 +625,7 @@
- <a title="" class="state-published contenttype-document" href="aislinn.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/aislinn">
<span>Aislinn</span>
</a>
@@ -644,7 +641,7 @@
- <a title="" class="state-published contenttype-document" href="allinea-ddt.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
@@ -660,7 +657,7 @@
- <a title="quick application profiling" class="state-published contenttype-document" href="allinea-performance-reports.html">
+ <a class="state-published contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -676,7 +673,7 @@
- <a title="" class="state-published contenttype-document" href="intel-vtune-amplifier.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier XE</span>
</a>
@@ -692,7 +689,7 @@
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="total-view.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/salomon/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -708,7 +705,7 @@
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/salomon/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -724,7 +721,7 @@
- <a title="" class="state-published contenttype-document" href="vampir.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -749,7 +746,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -765,7 +762,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -781,7 +778,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -797,7 +794,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -813,7 +810,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -829,7 +826,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -845,7 +842,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -861,7 +858,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -886,7 +883,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -911,7 +908,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -927,7 +924,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -943,7 +940,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -959,7 +956,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -1027,12 +1024,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</div>
</body>
-
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</html>
diff --git a/docs.it4i.cz/salomon/software/debuggers/total-view.md b/docs.it4i.cz/salomon/software/debuggers/total-view.md
new file mode 100644
index 0000000000000000000000000000000000000000..09090e2a4425b05fba843532ef4403e41091e544
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/debuggers/total-view.md
@@ -0,0 +1,99 @@
+Total View
+==========
+TotalView is a GUI-based source code multi-process, multi-thread
+debugger.
+License and Limitations for cluster Users
+------------------
+On the cluster users can debug OpenMP or MPI code that runs up to 64
+parallel processes. These limitation means that:
+Â Â Â 1 user can debug up 64 processes, or
+Â Â Â 32 users can debug 2 processes, etc.
+Debugging of GPU accelerated codes is also supported.
+You can check the status of the licenses
+[here](https://extranet.it4i.cz/rsweb/anselm/license/totalview).
+Compiling Code to run with TotalView
+-------------
+### Modules
+Load all necessary modules to compile the code. For example:
+ module load intel
+ module load impi  ... or ... module load OpenMPI/X.X.X-icc
+Load the TotalView module:
+ module load TotalView/8.15.4-6-linux-x86-64
+Compile the code:
+ mpicc -g -O0 -o test_debug test.c
+ mpif90 -g -O0 -o test_debug test.f
+### Compiler flags
+Before debugging, you need to compile your code with theses flags:
+**-g** Generates extra debugging information usable by GDB. -g3
+includes even more debugging information. This option is available for
+GNU and INTEL C/C++ and Fortran compilers.
+**-O0** Suppress all optimizations.
+Starting a Job with TotalView
+------
+Be sure to log in with an X window forwarding enabled. This could mean
+using the -X in the ssh:Â
+ ssh -X username@salomon.it4i.cz
+Other options is to access login node using VNC. Please see the detailed
+information on how to use graphic user interface on Anselm
+[here](resolveuid/11e53ad0d2fd4c5187537f4baeedff33#VNC).
+From the login node an interactive session with X windows forwarding (-X
+option) can be started by following command:
+ qsub -I -X -A NONE-0-0 -q qexp -lselect=1:ncpus=24:mpiprocs=24,walltime=01:00:00
+Then launch the debugger with the totalview command followed by the name
+of the executable to debug.
+### Debugging a serial code
+To debug a serial code use:
+ totalview test_debug
+### Debugging a parallel code - option 1
+To debug a parallel code compiled with <span>**OpenMPI**</span> you need
+to setup your TotalView environment:Â
+**Please note:** To be able to run parallel debugging procedure from the
+command line without stopping the debugger in the mpiexec source code
+you have to add the following function to your **~/.tvdrc** file:
+ proc mpi_auto_run_starter {loaded_id} {
+ Â Â Â set starter_programs {mpirun mpiexec orterun}
+ Â Â Â set executable_name [TV::symbol get $loaded_id full_pathname]
+ Â Â Â set file_component [file tail $executable_name]
+ Â Â Â if {[lsearch -exact $starter_programs $file_component] != -1} {
+ Â Â Â Â Â Â Â puts "**************************************"
+ Â Â Â Â Â Â Â puts "Automatically starting $file_component"
+ Â Â Â Â Â Â Â puts "**************************************"
+ Â Â Â Â Â Â Â dgo
+ Â Â Â }
+ }
+ # Append this function to TotalView's image load callbacks so that
+ # TotalView run this program automatically.
+ dlappend TV::image_load_callbacks mpi_auto_run_starter
+The source code of this function can be also found in
+ /apps/all/OpenMPI/1.10.1-GNU-4.9.3-2.25/etc/openmpi-totalview.tcl
+You can also add only following line to you ~/.tvdrc file instead of
+the entire function:
+**source /apps/all/OpenMPI/1.10.1-GNU-4.9.3-2.25/etc/openmpi-totalview.tcl**
+You need to do this step only once. See also [OpenMPI FAQ
+entry](https://www.open-mpi.org/faq/?category=running#run-with-tv)
+Now you can run the parallel debugger using:
+ mpirun -tv -n 5 ./test_debug
+When following dialog appears click on "Yes"
+[](https://docs.it4i.cz/salomon/software/debuggers/totalview1.png)
+At this point the main TotalView GUI window will appear and you can
+insert the breakpoints and start debugging:
+[](https://docs.it4i.cz/salomon/software/debuggers/totalview2.png)
+### Debugging a parallel code - option 2
+Other option to start new parallel debugging session from a command line
+is to let TotalView to execute mpirun by itself. In this case user has
+to specify a MPI implementation used to compile the source code.Â
+The following example shows how to start debugging session with Intel
+MPI:
+ module load intel/2015b-intel-2015b impi/5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25 TotalView/8.15.4-6-linux-x86-64
+ totalview -mpi "Intel MPI-Hydra" -np 8 ./hello_debug_impi
+After running previous command you will see the same window as shown in
+the screenshot above.
+More information regarding the command line parameters of the TotalView
+can be found TotalView Reference Guide, Chapter 7TotalView Command
+Syntax. Â
+Documentation
+-------------
+[1] The [TotalView
+documentation](http://www.roguewave.com/support/product-documentation/totalview-family.aspx#totalview)
+web page is a good resource for learning more about some of the advanced
+TotalView features.
diff --git a/salomon/software/debuggers/totalview1.png.txt b/docs.it4i.cz/salomon/software/debuggers/totalview1.png
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/software/debuggers/totalview1.png.txt
rename to docs.it4i.cz/salomon/software/debuggers/totalview1.png
diff --git a/salomon/software/debuggers/totalview2.png b/docs.it4i.cz/salomon/software/debuggers/totalview2.png
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/software/debuggers/totalview2.png
rename to docs.it4i.cz/salomon/software/debuggers/totalview2.png
diff --git a/salomon/software/debuggers/valgrind.html b/docs.it4i.cz/salomon/software/debuggers/valgrind.html
old mode 100755
new mode 100644
similarity index 76%
rename from salomon/software/debuggers/valgrind.html
rename to docs.it4i.cz/salomon/software/debuggers/valgrind.html
index 7d162a7e6ece47448242db23f10f00b87b9ee906..bacbf5513684bfb8e6084fdc4917cb4ec496e42f
--- a/salomon/software/debuggers/valgrind.html
+++ b/docs.it4i.cz/salomon/software/debuggers/valgrind.html
@@ -10,45 +10,42 @@
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-<!-- Mirrored from docs.it4i.cz/salomon/software/debuggers/valgrind by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:10 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/debuggers/valgrind" /><!--[if lt IE 7]></base><![endif]-->
<meta content="Valgrind is a tool for memory debugging and profiling." name="description" />
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Valgrind — IT4I Docs</title>
- <link rel="canonical" href="valgrind.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/debuggers/valgrind" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="valgrind.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/debuggers/valgrind#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="valgrind.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/debuggers/valgrind#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../debuggers.html">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/salomon/software/debuggers">Debuggers and profilers</a>
<span class="breadcrumbSeparator">
/
@@ -264,7 +261,7 @@
<p>There are two versions of Valgrind available on the cluster.</p>
<ul>
<li><span>Version 3.8.1, installed by operating system vendor in </span><span class="monospace">/usr/bin/valgrind. </span><span>This version is available by default, without the need to load any module. This version however does not provide additional MPI support. Also, it does not support AVX2 instructions, <strong>debugging of an AVX2-enabled executable with this version will fail</strong></span></li>
-<li><span><span>Version 3.11.0 built by ICC with support for Intel MPI, available in <a target="_self" title="" class="internal-link" href="../../environment-and-modules.html">module</a>Â </span></span><span class="monospace">Valgrind/3.11.0-intel-2015b. </span>After loading the module, this version replaces the default valgrind.</li>
+<li><span><span>Version 3.11.0 built by ICC with support for Intel MPI, available in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/environment-and-modules">module</a>Â </span></span><span class="monospace">Valgrind/3.11.0-intel-2015b. </span>After loading the module, this version replaces the default valgrind.</li>
<li>Version 3.11.0 built by GCC with support for Open MPI, module <span class="monospace">Valgrind/3.11.0-foss-2015b</span></li>
</ul>
<h2 class=" ">Usage</h2>
@@ -370,7 +367,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -386,7 +383,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -402,7 +399,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -418,7 +415,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -434,7 +431,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -450,7 +447,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -466,7 +463,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -482,7 +479,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -498,7 +495,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -514,7 +511,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -530,7 +527,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -546,7 +543,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -562,10 +559,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -581,7 +578,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -597,7 +594,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -613,7 +610,7 @@
- <a title="A collection of development tools" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -629,7 +626,7 @@
- <a title="" class="state-published contenttype-document" href="aislinn.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/aislinn">
<span>Aislinn</span>
</a>
@@ -645,7 +642,7 @@
- <a title="" class="state-published contenttype-document" href="allinea-ddt.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
@@ -661,7 +658,7 @@
- <a title="quick application profiling" class="state-published contenttype-document" href="allinea-performance-reports.html">
+ <a class="state-published contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -677,7 +674,7 @@
- <a title="" class="state-published contenttype-document" href="intel-vtune-amplifier.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier XE</span>
</a>
@@ -693,7 +690,7 @@
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published contenttype-document" href="total-view.html">
+ <a class="state-published contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/salomon/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -709,7 +706,7 @@
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="valgrind.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/salomon/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -725,7 +722,7 @@
- <a title="" class="state-published contenttype-document" href="vampir.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -750,7 +747,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -766,7 +763,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -782,7 +779,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -798,7 +795,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -814,7 +811,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -830,7 +827,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -846,7 +843,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -862,7 +859,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -887,7 +884,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -912,7 +909,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -928,7 +925,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -944,7 +941,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -960,7 +957,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -999,14 +996,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -1028,12 +1025,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1049,7 +1046,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/docs.it4i.cz/salomon/software/debuggers/valgrind.md b/docs.it4i.cz/salomon/software/debuggers/valgrind.md
new file mode 100644
index 0000000000000000000000000000000000000000..2fef5871c7e9450843cf5aa82893a396cab38f62
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/debuggers/valgrind.md
@@ -0,0 +1,257 @@
+Valgrind
+========
+Valgrind is a tool for memory debugging and profiling.
+About Valgrind
+--------------
+Valgrind is an open-source tool, used mainly for debuggig memory-related
+problems, such as memory leaks, use of uninitalized memory etc. in C/C++
+applications. The toolchain was however extended over time with more
+functionality, such as debugging of threaded applications, cache
+profiling, not limited only to C/C++.
+Valgind is an extremely useful tool for debugging memory errors such as
+[off-by-one](http://en.wikipedia.org/wiki/Off-by-one_error).
+Valgrind uses a virtual machine and dynamic recompilation of binary
+code, because of that, you can expect that programs being debugged by
+Valgrind run 5-100 times slower.
+The main tools available in Valgrind are :
+- **Memcheck**, the original, must used and default tool. Verifies
+ memory access in you program and can detect use of unitialized
+ memory, out of bounds memory access, memory leaks, double free, etc.
+- **Massif**, a heap profiler.
+- **Hellgrind** and **DRD** can detect race conditions in
+ multi-threaded applications.
+- **Cachegrind**, a cache profiler.
+- **Callgrind**, a callgraph analyzer.
+- For a full list and detailed documentation, please refer to the
+ [official Valgrind
+ documentation](http://valgrind.org/docs/).
+Installed versions
+------------------
+There are two versions of Valgrind available on the cluster.
+- <span>Version 3.8.1, installed by operating system vendor
+ in </span><span class="monospace">/usr/bin/valgrind.
+ </span><span>This version is available by default, without the need
+ to load any module. This version however does not provide additional
+ MPI support. Also, it does not support AVX2 instructions,
+ **debugging of an AVX2-enabled executable with this version will
+ fail**</span>
+- <span><span>Version 3.11.0 built by ICC with support for Intel MPI,
+ available in
+ [module](https://docs.it4i.cz/salomon/environment-and-modules)Â </span></span><span
+ class="monospace">Valgrind/3.11.0-intel-2015b. </span>After loading
+ the module, this version replaces the default valgrind.
+- Version 3.11.0 built by GCC with support for Open MPI, module <span
+ class="monospace">Valgrind/3.11.0-foss-2015b</span>
+Usage
+-----
+Compile the application which you want to debug as usual. It is
+advisable to add compilation flags <span class="monospace">-g </span>(to
+add debugging information to the binary so that you will see original
+source code lines in the output) and <span class="monospace">-O0</span>
+(to disable compiler optimizations).Â
+For example, lets look at this C code, which has two problems :
+ #include <stdlib.h>
+ void f(void)
+ {
+ int* x = malloc(10 * sizeof(int));
+ x[10] = 0; // problem 1heap block overrun
+ } // problem 2memory leak -- x not freed
+ int main(void)
+ {
+ f();
+ return 0;
+ }
+Now, compile it with Intel compiler :
+ $ module add intel
+ $ icc -g valgrind-example.c -o valgrind-exampleÂ
+Now, lets run it with Valgrind. The syntax is :
+<span class="monospace">valgrind [valgrind options] <your program
+binary> [your program options]</span>
+If no Valgrind options are specified, Valgrind defaults to running
+Memcheck tool. Please refer to the Valgrind documentation for a full
+description of command line options.
+ $ valgrind ./valgrind-example
+ ==12652== Memcheck, a memory error detector
+ ==12652== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
+ ==12652== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info
+ ==12652== Command./valgrind-example
+ ==12652==
+ ==12652== Invalid write of size 4
+ ==12652== at 0x40053Ef (valgrind-example.c:6)
+ ==12652== by 0x40054Emain (valgrind-example.c:11)
+ ==12652== Address 0x5861068 is 0 bytes after a block of size 40 alloc'd
+ ==12652== at 0x4C27AAAmalloc (vg_replace_malloc.c:291)
+ ==12652== by 0x400528f (valgrind-example.c:5)
+ ==12652== by 0x40054Emain (valgrind-example.c:11)
+ ==12652==
+ ==12652==
+ ==12652== HEAP SUMMARY:
+ ==12652== in use at exit40 bytes in 1 blocks
+ ==12652== total heap usage1 allocs, 0 frees, 40 bytes allocated
+ ==12652==
+ ==12652== LEAK SUMMARY:
+ ==12652== definitely lost40 bytes in 1 blocks
+ ==12652== indirectly lost0 bytes in 0 blocks
+ ==12652== possibly lost0 bytes in 0 blocks
+ ==12652== still reachable0 bytes in 0 blocks
+ ==12652== suppressed0 bytes in 0 blocks
+ ==12652== Rerun with --leak-check=full to see details of leaked memory
+ ==12652==
+ ==12652== For counts of detected and suppressed errors, rerun with-v
+ ==12652== ERROR SUMMARY1 errors from 1 contexts (suppressed6 from 6)
+In the output we can see that Valgrind has detected both errors - the
+off-by-one memory access at line 5 and a memory leak of 40 bytes. If we
+want a detailed analysis of the memory leak, we need to run Valgrind
+with <span class="monospace">--leak-check=full</span> option :
+ $ valgrind --leak-check=full ./valgrind-example
+ ==23856== Memcheck, a memory error detector
+ ==23856== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.
+ ==23856== Using Valgrind-3.6.0 and LibVEX; rerun with -h for copyright info
+ ==23856== Command./valgrind-example
+ ==23856==
+ ==23856== Invalid write of size 4
+ ==23856== at 0x40067Ef (valgrind-example.c:6)
+ ==23856== by 0x40068Emain (valgrind-example.c:11)
+ ==23856== Address 0x66e7068 is 0 bytes after a block of size 40 alloc'd
+ ==23856== at 0x4C26FDEmalloc (vg_replace_malloc.c:236)
+ ==23856== by 0x400668f (valgrind-example.c:5)
+ ==23856== by 0x40068Emain (valgrind-example.c:11)
+ ==23856==
+ ==23856==
+ ==23856== HEAP SUMMARY:
+ ==23856== in use at exit40 bytes in 1 blocks
+ ==23856== total heap usage1 allocs, 0 frees, 40 bytes allocated
+ ==23856==
+ ==23856== 40 bytes in 1 blocks are definitely lost in loss record 1 of 1
+ ==23856== at 0x4C26FDEmalloc (vg_replace_malloc.c:236)
+ ==23856== by 0x400668f (valgrind-example.c:5)
+ ==23856== by 0x40068Emain (valgrind-example.c:11)
+ ==23856==
+ ==23856== LEAK SUMMARY:
+ ==23856== definitely lost40 bytes in 1 blocks
+ ==23856== indirectly lost0 bytes in 0 blocks
+ ==23856== possibly lost0 bytes in 0 blocks
+ ==23856== still reachable0 bytes in 0 blocks
+ ==23856== suppressed0 bytes in 0 blocks
+ ==23856==
+ ==23856== For counts of detected and suppressed errors, rerun with-v
+ ==23856== ERROR SUMMARY2 errors from 2 contexts (suppressed6 from 6)
+Now we can see that the memory leak is due to the <span
+class="monospace">malloc()</span> at line 6.
+<span>Usage with MPI</span>
+----
+Although Valgrind is not primarily a parallel debugger, it can be used
+to debug parallel applications as well. When launching your parallel
+applications, prepend the valgrind command. For example :
+ $ mpirun -np 4 valgrind myapplication
+The default version without MPI support will however report a large
+number of false errors in the MPI library, such as :
+ ==30166== Conditional jump or move depends on uninitialised value(s)
+ ==30166== at 0x4C287E8strlen (mc_replace_strmem.c:282)
+ ==30166== by 0x55443BDI_MPI_Processor_model_number (init_interface.c:427)
+ ==30166== by 0x55439E0I_MPI_Processor_arch_code (init_interface.c:171)
+ ==30166== by 0x558D5AEMPID_nem_impi_init_shm_configuration (mpid_nem_impi_extensions.c:1091)
+ ==30166== by 0x5598F4CMPID_nem_init_ckpt (mpid_nem_init.c:566)
+ ==30166== by 0x5598B65MPID_nem_init (mpid_nem_init.c:489)
+ ==30166== by 0x539BD75MPIDI_CH3_Init (ch3_init.c:64)
+ ==30166== by 0x5578743MPID_Init (mpid_init.c:193)
+ ==30166== by 0x554650AMPIR_Init_thread (initthread.c:539)
+ ==30166== by 0x553369FPMPI_Init (init.c:195)
+ ==30166== by 0x4008BDmain (valgrind-example-mpi.c:18)
+so it is better to use the MPI-enabled valgrind from module. The MPI
+versions requires library :Â
+<span
+class="monospace">$EBROOTVALGRIND/lib/valgrind/libmpiwrap-amd64-linux.so</span>
+which must be included in the<span class="monospace"> LD_PRELOAD
+</span>environment variable.
+Lets look at this MPI example :
+ #include <stdlib.h>
+ #include <mpi.h>Â
+ int main(int argc, char *argv[])
+ {
+ Â Â Â Â Â int *data = malloc(sizeof(int)*99);
+ Â Â Â Â Â MPI_Init(&argc, &argv);
+ Â Â Â Â MPI_Bcast(data, 100, MPI_INT, 0, MPI_COMM_WORLD);
+ Â Â Â Â Â MPI_Finalize();Â
+ Â Â Â Â Â Â Â return 0;
+ }
+There are two errors - use of uninitialized memory and invalid length of
+the buffer. Lets debug it with valgrind :
+ $ module add intel impi
+ $ mpiicc -g valgrind-example-mpi.c -o valgrind-example-mpi
+ $ module add Valgrind/3.11.0-intel-2015b
+ $ mpirun -np 2 -env LD_PRELOAD $EBROOTVALGRIND/lib/valgrind/libmpiwrap-amd64-linux.so valgrind ./valgrind-example-mpi
+Prints this output (note that there is output printed for every
+launched MPI process)
+ ==31318== Memcheck, a memory error detector
+ ==31318== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
+ ==31318== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info
+ ==31318== Command./valgrind-example-mpi
+ ==31318==
+ ==31319== Memcheck, a memory error detector
+ ==31319== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
+ ==31319== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info
+ ==31319== Command./valgrind-example-mpi
+ ==31319==
+ valgrind MPI wrappers 31319Active for pid 31319
+ valgrind MPI wrappers 31319Try MPIWRAP_DEBUG=help for possible options
+ valgrind MPI wrappers 31318Active for pid 31318
+ valgrind MPI wrappers 31318Try MPIWRAP_DEBUG=help for possible options
+ ==31319== Unaddressable byte(s) found during client check request
+ ==31319== at 0x4E35974check_mem_is_addressable_untyped (libmpiwrap.c:960)
+ ==31319== by 0x4E5D0FEPMPI_Bcast (libmpiwrap.c:908)
+ ==31319== by 0x400911main (valgrind-example-mpi.c:20)
+ ==31319== Address 0x69291cc is 0 bytes after a block of size 396 alloc'd
+ ==31319== at 0x4C27AAAmalloc (vg_replace_malloc.c:291)
+ ==31319== by 0x4007BCmain (valgrind-example-mpi.c:8)
+ ==31319==
+ ==31318== Uninitialised byte(s) found during client check request
+ ==31318== at 0x4E3591Dcheck_mem_is_defined_untyped (libmpiwrap.c:952)
+ ==31318== by 0x4E5D06DPMPI_Bcast (libmpiwrap.c:908)
+ ==31318== by 0x400911main (valgrind-example-mpi.c:20)
+ ==31318== Address 0x6929040 is 0 bytes inside a block of size 396 alloc'd
+ ==31318== at 0x4C27AAAmalloc (vg_replace_malloc.c:291)
+ ==31318== by 0x4007BCmain (valgrind-example-mpi.c:8)
+ ==31318==
+ ==31318== Unaddressable byte(s) found during client check request
+ ==31318== at 0x4E3591Dcheck_mem_is_defined_untyped (libmpiwrap.c:952)
+ ==31318== by 0x4E5D06DPMPI_Bcast (libmpiwrap.c:908)
+ ==31318== by 0x400911main (valgrind-example-mpi.c:20)
+ ==31318== Address 0x69291cc is 0 bytes after a block of size 396 alloc'd
+ ==31318== at 0x4C27AAAmalloc (vg_replace_malloc.c:291)
+ ==31318== by 0x4007BCmain (valgrind-example-mpi.c:8)
+ ==31318==
+ ==31318==
+ ==31318== HEAP SUMMARY:
+ ==31318== in use at exit3,172 bytes in 67 blocks
+ ==31318== total heap usage191 allocs, 124 frees, 81,203 bytes allocated
+ ==31318==
+ ==31319==
+ ==31319== HEAP SUMMARY:
+ ==31319== in use at exit3,172 bytes in 67 blocks
+ ==31319== total heap usage175 allocs, 108 frees, 48,435 bytes allocated
+ ==31319==
+ ==31318== LEAK SUMMARY:
+ ==31318== definitely lost408 bytes in 3 blocks
+ ==31318== indirectly lost256 bytes in 1 blocks
+ ==31318== possibly lost0 bytes in 0 blocks
+ ==31318== still reachable2,508 bytes in 63 blocks
+ ==31318== suppressed0 bytes in 0 blocks
+ ==31318== Rerun with --leak-check=full to see details of leaked memory
+ ==31318==
+ ==31318== For counts of detected and suppressed errors, rerun with-v
+ ==31318== Use --track-origins=yes to see where uninitialised values come from
+ ==31318== ERROR SUMMARY2 errors from 2 contexts (suppressed4 from 4)
+ ==31319== LEAK SUMMARY:
+ ==31319== definitely lost408 bytes in 3 blocks
+ ==31319== indirectly lost256 bytes in 1 blocks
+ ==31319== possibly lost0 bytes in 0 blocks
+ ==31319== still reachable2,508 bytes in 63 blocks
+ ==31319== suppressed0 bytes in 0 blocks
+ ==31319== Rerun with --leak-check=full to see details of leaked memory
+ ==31319==
+ ==31319== For counts of detected and suppressed errors, rerun with-v
+ ==31319== ERROR SUMMARY1 errors from 1 contexts (suppressed4 from 4)
+We can see that Valgrind has reported use of unitialised memory on the
+master process (which reads the array to be broadcasted) and use of
+unaddresable memory on both processes.
diff --git a/salomon/software/debuggers/vampir.html b/docs.it4i.cz/salomon/software/debuggers/vampir.html
old mode 100755
new mode 100644
similarity index 63%
rename from salomon/software/debuggers/vampir.html
rename to docs.it4i.cz/salomon/software/debuggers/vampir.html
index 85218463c7ac52f0f765aec37f13c09f0b6652e6..4dbcfaf4f5b98b72467f8a9a1dd3c070567e6fa1
--- a/salomon/software/debuggers/vampir.html
+++ b/docs.it4i.cz/salomon/software/debuggers/vampir.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/debuggers/vampir by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:02 GMT -->
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
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<title>Vampir — IT4I Docs</title>
- <link rel="canonical" href="vampir.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/debuggers/vampir" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="vampir.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/debuggers/vampir#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="vampir.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/debuggers/vampir#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
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-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../debuggers.html">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/salomon/software/debuggers">Debuggers and profilers</a>
<span class="breadcrumbSeparator">
/
@@ -246,8 +243,8 @@
<div id="parent-fieldname-text-50ee0f8999e14a08822bd423d24de7ef" class="">
- <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a target="_self" title="" class="internal-link" href="../../../acl_users/credentials_cookie_auth/require_loginc71d.html">Score-P</a>) first to collect the traces.</p>
-<h2 class=" "><img title="Vampir screenshot" class="image-inline" alt="Vampir screenshot" src="Snmekobrazovky20160708v12.33.35.png/%40%40images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
+ <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/debuggers/score-p">Score-P</a>) first to collect the traces.</p>
+<h2 class=" "><img alt="Vampir screenshot" class="image-inline" title="Vampir screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" /></h2>
<h2 class=" ">Installed versions</h2>
<p>Version 8.5.0 is currently installed as module <span class="monospace">Vampir/8.5.0</span> :</p>
<pre>$ module load Vampir/8.5.0<br />$ vampir &</pre>
@@ -255,7 +252,7 @@
<p>You can find the detailed user manual in PDF format in <span class="monospace">$EBROOTVAMPIR/doc/vampir-manual.pdf</span></p>
<h2>References</h2>
<ol>
-<li><a class="external-link" href="https://www.vampir.eu/" target="_self" title="">https://www.vampir.eu</a></li>
+<li><a class="external-link" href="https://www.vampir.eu" target="_self" title="">https://www.vampir.eu</a></li>
</ol>
<h2></h2>
@@ -333,7 +330,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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@@ -349,7 +346,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -365,7 +362,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -381,7 +378,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -397,7 +394,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -413,7 +410,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -429,7 +426,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -445,7 +442,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -461,7 +458,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -477,7 +474,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -493,7 +490,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -509,7 +506,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -525,10 +522,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -544,7 +541,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -560,7 +557,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -576,7 +573,7 @@
- <a title="A collection of development tools" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -592,7 +589,7 @@
- <a title="" class="state-published contenttype-document" href="aislinn.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/aislinn">
<span>Aislinn</span>
</a>
@@ -608,7 +605,7 @@
- <a title="" class="state-published contenttype-document" href="allinea-ddt.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
@@ -624,7 +621,7 @@
- <a title="quick application profiling" class="state-published contenttype-document" href="allinea-performance-reports.html">
+ <a class="state-published contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -640,7 +637,7 @@
- <a title="" class="state-published contenttype-document" href="intel-vtune-amplifier.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier XE</span>
</a>
@@ -656,7 +653,7 @@
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published contenttype-document" href="total-view.html">
+ <a class="state-published contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/salomon/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -672,7 +669,7 @@
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/salomon/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -688,7 +685,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="vampir.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -713,7 +710,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -729,7 +726,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -745,7 +742,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -761,7 +758,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -777,7 +774,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -793,7 +790,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -809,7 +806,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -825,7 +822,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -850,7 +847,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -875,7 +872,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -891,7 +888,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -907,7 +904,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -923,7 +920,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1012,7 +1009,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/debuggers/vampir by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:04 GMT -->
</html>
diff --git a/docs.it4i.cz/salomon/software/debuggers/vampir.md b/docs.it4i.cz/salomon/software/debuggers/vampir.md
new file mode 100644
index 0000000000000000000000000000000000000000..363d24bec314eaee26b69cb81f03118c73674bb4
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/debuggers/vampir.md
@@ -0,0 +1,23 @@
+Vampir
+======
+Vampir is a commercial trace analysis and visualisation tool. It can
+work with traces in OTF and OTF2 formats. It does not have the
+functionality to collect traces, you need to use a trace collection tool
+(such as
+[Score-P](https://docs.it4i.cz/salomon/software/debuggers/score-p))
+first to collect the traces.
+
+------
+Installed versions
+------------------
+Version 8.5.0 is currently installed as module <span
+class="monospace">Vampir/8.5.0</span> :
+ $ module load Vampir/8.5.0
+ $ vampir &
+User manual
+-----------
+You can find the detailed user manual in PDF format in <span
+class="monospace">$EBROOTVAMPIR/doc/vampir-manual.pdf</span>
+References
+----------
+1. <https://www.vampir.eu>
diff --git a/salomon/software/debuggers/Snimek obrazovky 2015-03-03 v 15.50.36.png b/docs.it4i.cz/salomon/software/debuggers/vtune-amplifier
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/software/debuggers/Snimek obrazovky 2015-03-03 v 15.50.36.png
rename to docs.it4i.cz/salomon/software/debuggers/vtune-amplifier
diff --git a/salomon/software/intel-suite.html b/docs.it4i.cz/salomon/software/intel-suite.html
old mode 100755
new mode 100644
similarity index 65%
rename from salomon/software/intel-suite.html
rename to docs.it4i.cz/salomon/software/intel-suite.html
index 2bf021bd3c2e6cb11b1fcdc5b8fbed802cf7f3d0..b43b31fd9d27ee0efab5634bbdbd4d40d2cf000f
--- a/salomon/software/intel-suite.html
+++ b/docs.it4i.cz/salomon/software/intel-suite.html
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction" /><!--[if lt IE 7]></base><![endif]-->
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- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
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<title>Intel Parallel Studio — IT4I Docs</title>
- <link rel="canonical" href="intel-suite.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/intel-suite" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="intel-suite.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/intel-suite#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="intel-suite.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/intel-suite#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
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- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -273,24 +270,24 @@
<h2 class=" ">Intel compilers</h2>
<p>The Intel compilers version 131.3 are available, via module iccifort/2013.5.192-GCC-4.8.3. The compilers include the icc C and C++ compiler and the ifort fortran 77/90/95 compiler.</p>
<pre class=" ">$ module load intel<br />$ icc -v<br />$ ifort -v</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="intel-suite/intel-compilers.html">Intel Compilers</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-compilers">Intel Compilers</a> page.</p>
<h2 class=" ">Intel debugger</h2>
<p class="exclamation">IDB is no longer available since Parallel Studio 2015.</p>
-<p>Â The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a target="_self" title="" class="internal-link" href="../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html">X display</a> for running the GUI.</p>
+<p>Â The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">X display</a> for running the GUI.</p>
<pre class=" ">$ module load intel<br />$ idb</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="intel-suite/intel-debugger.html">Intel Debugger</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger">Intel Debugger</a> page.</p>
<h2 class=" ">Intel Math Kernel Library</h2>
<p>Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, extensively threaded and optimized for maximum performance. Intel MKL unites and provides these basic components: BLAS, LAPACK, ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and many more.</p>
<pre class=" ">$ module load imkl</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="intel-suite/intel-mkl.html">Intel MKL</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-mkl">Intel MKL</a> page.</p>
<h2 class=" ">Intel Integrated Performance Primitives</h2>
<p>Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is available, via module ipp. The IPP is a library of highly optimized algorithmic building blocks for media and data applications. This includes signal, image and frame processing algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many more.</p>
<pre class=" ">$ module load ipp</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="intel-suite/intel-integrated-performance-primitives.html">Intel IPP</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives">Intel IPP</a> page.</p>
<h2 class=" ">Intel Threading Building Blocks</h2>
<p>Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. It is designed to promote scalable data parallel programming. Additionally, it fully supports nested parallelism, so you can build larger parallel components from smaller parallel components. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner.</p>
<pre class=" ">$ module load tbb</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="intel-suite/intel-tbb.html">Intel TBB</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb">Intel TBB</a> page.</p>
</div>
@@ -366,7 +363,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -382,7 +379,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -398,7 +395,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -414,7 +411,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -430,7 +427,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -446,7 +443,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -462,7 +459,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -478,7 +475,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -494,7 +491,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -510,7 +507,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -526,7 +523,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -542,7 +539,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -558,10 +555,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -577,7 +574,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -593,7 +590,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -625,7 +622,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
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<span>Intel Parallel studio</span>
</a>
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<span>Intel Compilers</span>
</a>
@@ -673,7 +670,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger">
<span>Intel Debugger</span>
</a>
@@ -689,7 +686,7 @@
- <a title="" class="state-published contenttype-document" href="intel-suite/intel-mkl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-mkl">
<span>Intel MKL</span>
</a>
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- <a title="" class="state-published contenttype-document" href="intel-suite/intel-integrated-performance-primitives.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives">
<span>Intel IPP</span>
</a>
@@ -721,7 +718,7 @@
- <a title="" class="state-published contenttype-document" href="intel-suite/intel-tbb.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb">
<span>Intel TBB</span>
</a>
@@ -737,7 +734,7 @@
- <a title="" class="state-published contenttype-document" href="intel-suite/intel-trace-analyzer-and-collector.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector">
<span>Intel Trace Analyzer and Collector</span>
</a>
@@ -753,7 +750,7 @@
- <a title="" class="state-published contenttype-document" href="intel-suite/intel-advisor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-advisor">
<span>Intel Advisor</span>
</a>
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- <a title="" class="state-published contenttype-document" href="intel-suite/intel-inspector.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-inspector">
<span>Intel Inspector</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
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<span>Numerical languages</span>
</a>
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<span>Compilers</span>
</a>
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<span>Intel Xeon Phi</span>
</a>
@@ -858,7 +855,7 @@
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+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
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+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -899,7 +896,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -924,7 +921,7 @@
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<span>Anselm Cluster Documentation</span>
</a>
@@ -940,7 +937,7 @@
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<span>Links</span>
</a>
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+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -972,7 +969,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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})();
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</html>
diff --git a/docs.it4i.cz/salomon/software/intel-suite.md b/docs.it4i.cz/salomon/software/intel-suite.md
new file mode 100644
index 0000000000000000000000000000000000000000..01daba67ed047a3ccdd229242906476624a594da
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/intel-suite.md
@@ -0,0 +1,77 @@
+Intel Parallel Studio
+=====================
+
+The Salomon cluster provides following elements of the Intel Parallel
+Studio XE
+ Intel Parallel Studio XE
+ ---
+ Intel Compilers
+ Intel Debugger
+ Intel MKL Library
+ Intel Integrated Performance Primitives Library
+ Intel Threading Building Blocks Library
+ Intel Trace Analyzer and Collector
+ Intel Advisor
+ Intel Inspector
+Intel compilers
+---------------
+The Intel compilers version 131.3 are available, via module
+iccifort/2013.5.192-GCC-4.8.3. The compilers include the icc C and C++
+compiler and the ifort fortran 77/90/95 compiler.
+ $ module load intel
+ $ icc -v
+ $ ifort -v
+Read more at the [Intel
+Compilers](https://docs.it4i.cz/salomon/software/intel-suite/intel-compilers)
+page.
+Intel debugger
+--------------
+IDB is no longer available since Parallel Studio 2015.
+Â The intel debugger version 13.0 is available, via module intel. The
+debugger works for applications compiled with C and C++ compiler and the
+ifort fortran 77/90/95 compiler. The debugger provides java GUI
+environment. Use [X
+display](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc)
+for running the GUI.
+ $ module load intel
+ $ idb
+Read more at the [Intel
+Debugger](https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger)
+page.
+Intel Math Kernel Library
+--
+Intel Math Kernel Library (Intel MKL) is a library of math kernel
+subroutines, extensively threaded and optimized for maximum performance.
+Intel MKL unites and provides these basic componentsBLAS, LAPACK,
+ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and
+many more.
+ $ module load imkl
+Read more at the [Intel
+MKL](https://docs.it4i.cz/salomon/software/intel-suite/intel-mkl)
+page.
+Intel Integrated Performance Primitives
+----------------
+Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX
+is available, via module ipp. The IPP is a library of highly optimized
+algorithmic building blocks for media and data applications. This
+includes signal, image and frame processing algorithms, such as FFT,
+FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many
+more.
+ $ module load ipp
+Read more at the [Intel
+IPP](https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives)
+page.
+Intel Threading Building Blocks
+--------
+Intel Threading Building Blocks (Intel TBB) is a library that supports
+scalable parallel programming using standard ISO C++ code. It does not
+require special languages or compilers. It is designed to promote
+scalable data parallel programming. Additionally, it fully supports
+nested parallelism, so you can build larger parallel components from
+smaller parallel components. To use the library, you specify tasks, not
+threads, and let the library map tasks onto threads in an efficient
+manner.
+ $ module load tbb
+Read more at the [Intel
+TBB](https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb)
+page.
diff --git a/salomon/software/intel-suite/Snmekobrazovky20151204v15.35.12.png/@@images/fb3b3ac2-a88f-4e55-a25e-23f1da2200cb.png b/docs.it4i.cz/salomon/software/intel-suite/Snmekobrazovky20151204v15.35.12.png/@@images/fb3b3ac2-a88f-4e55-a25e-23f1da2200cb.png
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rename from salomon/software/intel-suite/intel-advisor.html
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/intel-suite/intel-advisor" /><!--[if lt IE 7]></base><![endif]-->
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<title>Intel Advisor — IT4I Docs</title>
- <link rel="canonical" href="intel-advisor.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-advisor" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="intel-advisor.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-advisor#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="intel-advisor.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-advisor#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
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/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../intel-suite.html">Intel Parallel studio</a>
+ <a href="https://docs.it4i.cz/salomon/software/intel-suite">Intel Parallel studio</a>
<span class="breadcrumbSeparator">
/
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<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -367,7 +364,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -383,7 +380,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -399,7 +396,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -415,7 +412,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -431,7 +428,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -447,7 +444,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -463,7 +460,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -479,7 +476,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -495,7 +492,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -511,7 +508,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -527,7 +524,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -543,10 +540,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -562,7 +559,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -578,7 +575,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -594,7 +591,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -610,7 +607,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -626,7 +623,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -642,7 +639,7 @@
- <a title="" class="state-published contenttype-document" href="intel-compilers.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-compilers">
<span>Intel Compilers</span>
</a>
@@ -658,7 +655,7 @@
- <a title="" class="state-published contenttype-document" href="intel-debugger.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger">
<span>Intel Debugger</span>
</a>
@@ -674,7 +671,7 @@
- <a title="" class="state-published contenttype-document" href="intel-mkl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-mkl">
<span>Intel MKL</span>
</a>
@@ -690,7 +687,7 @@
- <a title="" class="state-published contenttype-document" href="intel-integrated-performance-primitives.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives">
<span>Intel IPP</span>
</a>
@@ -706,7 +703,7 @@
- <a title="" class="state-published contenttype-document" href="intel-tbb.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb">
<span>Intel TBB</span>
</a>
@@ -722,7 +719,7 @@
- <a title="" class="state-published contenttype-document" href="intel-trace-analyzer-and-collector.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector">
<span>Intel Trace Analyzer and Collector</span>
</a>
@@ -738,7 +735,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="intel-advisor.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-advisor">
<span>Intel Advisor</span>
</a>
@@ -754,7 +751,7 @@
- <a title="" class="state-published contenttype-document" href="intel-inspector.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-inspector">
<span>Intel Inspector</span>
</a>
@@ -779,7 +776,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -795,7 +792,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -811,7 +808,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -827,7 +824,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -843,7 +840,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -859,7 +856,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -884,7 +881,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -909,7 +906,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -925,7 +922,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -941,7 +938,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -957,7 +954,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1046,7 +1043,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
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-
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</html>
diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.md b/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.md
new file mode 100644
index 0000000000000000000000000000000000000000..043b023a1a868cfc03575cbf891fa7abc0f1fa02
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.md
@@ -0,0 +1,39 @@
+Intel Advisor
+=============
+is tool aiming to assist you in vectorization and threading of your
+code. You can use it to profile your application and identify
+loops, that could benefit from vectorization and/or threading
+parallelism.
+Installed versions
+------------------
+The following versions are currently available on Salomon as modules:
+ ---------------
+ **Version** **Module**
+ 2016 Update 2 Advisor/2016_update2
+ ---------------
+Usage
+-----
+Your program should be compiled with -g switch to include symbol names.
+You should compile with -O2 or higher to see code that is already
+vectorized by the compiler.
+Profiling is possible either directly from the GUI, or from command
+line.
+To profile from GUI, launch Advisor:
+ $ advixe-gui
+Then select menu File -> New -> Project. Choose a directory to
+save project data to. After clicking OK, Project properties window will
+appear, where you can configure path to your binary, launch arguments,
+working directory etc. After clicking OK, the project is ready.
+In the left pane, you can switch between Vectorization and Threading
+workflows. Each has several possible steps which you can execute by
+clicking Collect button. Alternatively, you can click on Command Line,
+to see the command line required to run the analysis directly from
+command line.
+References
+----------
+1. [Intel® Advisor 2015 TutorialFind Where to Add Parallelism - C++
+ Sample](https://software.intel.com/en-us/advisorxe_2015_tut_lin_c)
+2. [Product
+ page](https://software.intel.com/en-us/intel-advisor-xe)
+3. [Documentation](https://software.intel.com/en-us/intel-advisor-2016-user-guide-linux)
+Â
diff --git a/salomon/software/intel-suite/intel-compilers.html b/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.html
old mode 100755
new mode 100644
similarity index 68%
rename from salomon/software/intel-suite/intel-compilers.html
rename to docs.it4i.cz/salomon/software/intel-suite/intel-compilers.html
index f067bca274c05d9bf887623ac343688ec751ba91..0cab1ef9476ff56d099824404f4fadbc2e9c61e6
--- a/salomon/software/intel-suite/intel-compilers.html
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/intel-suite/intel-compilers" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<title>Intel Compilers — IT4I Docs</title>
- <link rel="canonical" href="intel-compilers.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-compilers" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="intel-compilers.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-compilers#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="intel-compilers.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-compilers#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
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- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
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/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../intel-suite.html">Intel Parallel studio</a>
+ <a href="https://docs.it4i.cz/salomon/software/intel-suite">Intel Parallel studio</a>
<span class="breadcrumbSeparator">
/
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<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
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<span class="portletTopRight"></span>
</dt>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -372,7 +369,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -388,7 +385,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -404,7 +401,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -420,7 +417,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -436,7 +433,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -452,7 +449,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -468,7 +465,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -484,7 +481,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -500,7 +497,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -516,7 +513,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -532,10 +529,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -551,7 +548,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -567,7 +564,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -583,7 +580,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -599,7 +596,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -615,7 +612,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -631,7 +628,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="intel-compilers.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-compilers">
<span>Intel Compilers</span>
</a>
@@ -647,7 +644,7 @@
- <a title="" class="state-published contenttype-document" href="intel-debugger.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger">
<span>Intel Debugger</span>
</a>
@@ -663,7 +660,7 @@
- <a title="" class="state-published contenttype-document" href="intel-mkl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-mkl">
<span>Intel MKL</span>
</a>
@@ -679,7 +676,7 @@
- <a title="" class="state-published contenttype-document" href="intel-integrated-performance-primitives.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives">
<span>Intel IPP</span>
</a>
@@ -695,7 +692,7 @@
- <a title="" class="state-published contenttype-document" href="intel-tbb.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb">
<span>Intel TBB</span>
</a>
@@ -711,7 +708,7 @@
- <a title="" class="state-published contenttype-document" href="intel-trace-analyzer-and-collector.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector">
<span>Intel Trace Analyzer and Collector</span>
</a>
@@ -727,7 +724,7 @@
- <a title="" class="state-published contenttype-document" href="intel-advisor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-advisor">
<span>Intel Advisor</span>
</a>
@@ -743,7 +740,7 @@
- <a title="" class="state-published contenttype-document" href="intel-inspector.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-inspector">
<span>Intel Inspector</span>
</a>
@@ -768,7 +765,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -784,7 +781,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -800,7 +797,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -816,7 +813,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -832,7 +829,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -848,7 +845,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -873,7 +870,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -898,7 +895,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -914,7 +911,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -930,7 +927,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -946,7 +943,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -985,14 +982,14 @@ var _paq = _paq || [];
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_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -1014,12 +1011,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1035,7 +1032,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
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</html>
diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.md b/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.md
new file mode 100644
index 0000000000000000000000000000000000000000..6017e153ae7c241fb61e7ab6948e5da5bd044ca2
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.md
@@ -0,0 +1,57 @@
+Intel Compilers
+===============
+
+The Intel compilers in multiple versions are available, via module
+intel. The compilers include the icc C and C++ compiler and the ifort
+fortran 77/90/95 compiler.
+ $ module load intel
+ $ icc -v
+ $ ifort -v
+The intel compilers provide for vectorization of the code, via the AVX2
+instructions and support threading parallelization via OpenMP
+For maximum performance on the Salomon cluster compute nodes, compile
+your programs using the AVX2 instructions, with reporting where the
+vectorization was used. We recommend following compilation options for
+high performance
+ $ icc -ipo -O3 -xCORE-AVX2 -qopt-report1 -qopt-report-phase=vec myprog.c mysubroutines.c -o myprog.x
+ $ ifort -ipo -O3 -xCORE-AVX2 -qopt-report1 -qopt-report-phase=vec myprog.f mysubroutines.f -o myprog.x
+In this example, we compile the program enabling interprocedural
+optimizations between source files (-ipo), aggresive loop optimizations
+(-O3) and vectorization (-xCORE-AVX2)
+The compiler recognizes the omp, simd, vector and ivdep pragmas for
+OpenMP parallelization and AVX2 vectorization. Enable the OpenMP
+parallelization by the **-openmp** compiler switch.
+ $ icc -ipo -O3 -xCORE-AVX2 -qopt-report1 -qopt-report-phase=vec -openmp myprog.c mysubroutines.c -o myprog.x
+ $ ifort -ipo -O3 -xCORE-AVX2 -qopt-report1 -qopt-report-phase=vec -openmp myprog.f mysubroutines.f -o myprog.x
+Read more
+at <https://software.intel.com/en-us/intel-cplusplus-compiler-16.0-user-and-reference-guide>
+Sandy Bridge/Ivy Bridge/Haswell binary compatibility
+------
+Anselm nodes are currently equipped with Sandy Bridge CPUs, while
+Salomon compute nodes are equipped with Haswell based architecture. The
+UV1 SMP compute server has Ivy Bridge CPUs, which are equivalent to
+Sandy Bridge (only smaller manufacturing technology). <span>The new
+processors are backward compatible with the Sandy Bridge nodes, so all
+programs that ran on the Sandy Bridge processors, should also run on the
+new Haswell nodes. </span><span>To get optimal performance out of the
+Haswell processors a program should make use of the
+special </span><span>AVX2 instructions for this processor. One can do
+this by recompiling codes with the compiler
+flags </span><span>designated to invoke these instructions. For the
+Intel compiler suite, there are two ways of
+doing </span><span>this:</span>
+- <span>Using compiler flag (both for Fortran and C)<span
+ class="monospace">-xCORE-AVX2</span>. This will create a
+ binary </span><span class="s1">with AVX2 instructions, specifically
+ for the Haswell processors. Note that the
+ executable </span><span>will not run on Sandy Bridge/Ivy
+ Bridge nodes.</span>
+- <span>Using compiler flags (both for Fortran and C)<span
+ class="monospace">-xAVX -axCORE-AVX2</span>. This
+ will </span><span>generate multiple, feature specific auto-dispatch
+ code paths for Intel® processors, if there is </span><span>a
+ performance benefit. So this binary will run both on Sandy
+ Bridge/Ivy Bridge and Haswell </span><span>processors. During
+ runtime it will be decided which path to follow, dependent on
+ which </span><span>processor you are running on. In general this
+ will result in larger binaries.</span>
diff --git a/salomon/software/intel-suite/intel-debugger.html b/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.html
old mode 100755
new mode 100644
similarity index 66%
rename from salomon/software/intel-suite/intel-debugger.html
rename to docs.it4i.cz/salomon/software/intel-suite/intel-debugger.html
index 7da7b1ed0e375af4f9e0bd693b114e9d684cc073..b8dfe553539a0b3de78ffd94aebed8fa0825a2e0
--- a/salomon/software/intel-suite/intel-debugger.html
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.html
@@ -10,45 +10,42 @@
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
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<title>Intel Debugger — IT4I Docs</title>
- <link rel="canonical" href="intel-debugger.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="intel-debugger.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="intel-debugger.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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@@ -125,13 +122,13 @@
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../intel-suite.html">Intel Parallel studio</a>
+ <a href="https://docs.it4i.cz/salomon/software/intel-suite">Intel Parallel studio</a>
<span class="breadcrumbSeparator">
/
@@ -252,18 +249,18 @@
<div id="parent-fieldname-text-ff4d5c2722fa49e98c78dc41f37e63d8" class="">
<p class="exclamation">IDB is no longer available since Intel Parallel Studio 2015</p>
<h2 class=" ">Debugging serial applications</h2>
-<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a target="_self" title="" class="internal-link" href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html">X display</a> for running the GUI.</p>
+<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">X display</a> for running the GUI.</p>
<pre class=" ">$ module load intel/2014.06<br />$ module load Java<br />$ idb</pre>
<p>The debugger may run in text mode. To debug in text mode, use</p>
<pre class=" ">$ idbc</pre>
-<p>To debug on the compute nodes, module intel must be loaded. <br />The GUI on compute nodes may be accessed using the same way as in <a target="_self" title="" class="internal-link" href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html">the GUI section </a></p>
+<p>To debug on the compute nodes, module intel must be loaded. <br />The GUI on compute nodes may be accessed using the same way as in <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">the GUI section </a></p>
<p>Example:</p>
<pre class=" ">$ qsub -q qexp -l select=1:ncpus=24 -X -I<br />qsub: waiting for job 19654.srv11 to start<br />qsub: job 19654.srv11 ready<br /><br />$ module load intel<br />$ module load Java<br />$ icc -O0 -g myprog.c -o myprog.x<br />$ idb ./myprog.x</pre>
<p>In this example, we allocate 1 full compute node, compile program myprog.c with debugging options -O0 -g and run the idb debugger interactively on the myprog.x executable. The GUI access is via X11 port forwarding provided by the PBS workload manager.</p>
<h2 class=" ">Debugging parallel applications</h2>
<p>Intel debugger is capable of debugging multithreaded and MPI parallel programs as well.</p>
<h3 class=" ">Small number of MPI ranks</h3>
-<p>For debugging small number of MPI ranks, you may execute and debug each rank in separate xterm terminal (do not forget the <a target="_self" title="" class="internal-link" href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html">X display</a>). Using Intel MPI, this may be done in following way:</p>
+<p>For debugging small number of MPI ranks, you may execute and debug each rank in separate xterm terminal (do not forget the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">X display</a>). Using Intel MPI, this may be done in following way:</p>
<pre class=" ">$ qsub -q qexp -l select=2:ncpus=24 -X -I<br />qsub: waiting for job 19654.srv11 to start<br />qsub: job 19655.srv11 ready<br /><br />$ module load intel impi<br />$ mpirun -ppn 1 -hostfile $PBS_NODEFILE --enable-x xterm -e idbc ./mympiprog.x</pre>
<p>In this example, we allocate 2 full compute node, run xterm on each node and start idb debugger in command line mode, debugging two ranks of mympiprog.x application. The xterm will pop up for each rank, with idb prompt ready. The example is not limited to use of Intel MPI</p>
<h3 class=" ">Large number of MPI ranks</h3>
@@ -348,7 +345,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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@@ -364,7 +361,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
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</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -396,7 +393,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -412,7 +409,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -428,7 +425,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -444,7 +441,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -460,7 +457,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -476,7 +473,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -492,7 +489,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -508,7 +505,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -524,7 +521,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -540,10 +537,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -559,7 +556,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -575,7 +572,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -591,7 +588,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -607,7 +604,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -623,7 +620,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -639,7 +636,7 @@
- <a title="" class="state-published contenttype-document" href="intel-compilers.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-compilers">
<span>Intel Compilers</span>
</a>
@@ -655,7 +652,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="intel-debugger.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger">
<span>Intel Debugger</span>
</a>
@@ -671,7 +668,7 @@
- <a title="" class="state-published contenttype-document" href="intel-mkl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-mkl">
<span>Intel MKL</span>
</a>
@@ -687,7 +684,7 @@
- <a title="" class="state-published contenttype-document" href="intel-integrated-performance-primitives.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives">
<span>Intel IPP</span>
</a>
@@ -703,7 +700,7 @@
- <a title="" class="state-published contenttype-document" href="intel-tbb.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb">
<span>Intel TBB</span>
</a>
@@ -719,7 +716,7 @@
- <a title="" class="state-published contenttype-document" href="intel-trace-analyzer-and-collector.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector">
<span>Intel Trace Analyzer and Collector</span>
</a>
@@ -735,7 +732,7 @@
- <a title="" class="state-published contenttype-document" href="intel-advisor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-advisor">
<span>Intel Advisor</span>
</a>
@@ -751,7 +748,7 @@
- <a title="" class="state-published contenttype-document" href="intel-inspector.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-inspector">
<span>Intel Inspector</span>
</a>
@@ -776,7 +773,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -792,7 +789,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -808,7 +805,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -824,7 +821,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -840,7 +837,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -856,7 +853,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -881,7 +878,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -906,7 +903,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -922,7 +919,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -938,7 +935,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -954,7 +951,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1043,7 +1040,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
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-
-<!-- Mirrored from docs.it4i.cz/salomon/software/intel-suite/intel-debugger by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:10 GMT -->
</html>
diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.md b/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.md
new file mode 100644
index 0000000000000000000000000000000000000000..020094925f0cf72345b4b2076152d02b46d6ba92
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.md
@@ -0,0 +1,72 @@
+Intel Debugger
+==============
+
+IDB is no longer available since Intel Parallel Studio 2015
+Debugging serial applications
+------
+The intel debugger version 13.0 is available, via module intel. The
+debugger works for applications compiled with C and C++ compiler and the
+ifort fortran 77/90/95 compiler. The debugger provides java GUI
+environment. Use [X
+display](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc)
+for running the GUI.
+ $ module load intel/2014.06
+ $ module load Java
+ $ idb
+The debugger may run in text mode. To debug in text mode, use
+ $ idbc
+To debug on the compute nodes, module intel must be loaded.
+The GUI on compute nodes may be accessed using the same way as in [the
+GUI
+section](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc)
+Example:
+ $ qsub -q qexp -l select=1:ncpus=24 -X -I
+ qsubwaiting for job 19654.srv11 to start
+ qsubjob 19654.srv11 ready
+ $ module load intel
+ $ module load Java
+ $ icc -O0 -g myprog.c -o myprog.x
+ $ idb ./myprog.x
+In this example, we allocate 1 full compute node, compile program
+myprog.c with debugging options -O0 -g and run the idb debugger
+interactively on the myprog.x executable. The GUI access is via X11 port
+forwarding provided by the PBS workload manager.
+Debugging parallel applications
+--------
+Intel debugger is capable of debugging multithreaded and MPI parallel
+programs as well.
+### Small number of MPI ranks
+For debugging small number of MPI ranks, you may execute and debug each
+rank in separate xterm terminal (do not forget the [X
+display](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc)).
+Using Intel MPI, this may be done in following way:
+ $ qsub -q qexp -l select=2:ncpus=24 -X -I
+ qsubwaiting for job 19654.srv11 to start
+ qsubjob 19655.srv11 ready
+ $ module load intel impi
+ $ mpirun -ppn 1 -hostfile $PBS_NODEFILE --enable-x xterm -e idbc ./mympiprog.x
+In this example, we allocate 2 full compute node, run xterm on each node
+and start idb debugger in command line mode, debugging two ranks of
+mympiprog.x application. The xterm will pop up for each rank, with idb
+prompt ready. The example is not limited to use of Intel MPI
+### Large number of MPI ranks
+Run the idb debugger from within the MPI debug option. This will cause
+the debugger to bind to all ranks and provide aggregated outputs across
+the ranks, pausing execution automatically just after startup. You may
+then set break points and step the execution manually. Using Intel MPI:
+ $ qsub -q qexp -l select=2:ncpus=24 -X -I
+ qsubwaiting for job 19654.srv11 to start
+ qsubjob 19655.srv11 ready
+ $ module load intel impi
+ $ mpirun -n 48 -idb ./mympiprog.x
+### Debugging multithreaded application
+Run the idb debugger in GUI mode. The menu Parallel contains number of
+tools for debugging multiple threads. One of the most useful tools is
+the **Serialize Execution** tool, which serializes execution of
+concurrent threads for easy orientation and identification of
+concurrency related bugs.
+Further information
+-------------------
+Exhaustive manual on idb features and usage is published at Intel
+website,
+<https://software.intel.com/sites/products/documentation/doclib/iss/2013/compiler/cpp-lin/>
diff --git a/salomon/software/intel-suite/intel-inspector.html b/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.html
old mode 100755
new mode 100644
similarity index 67%
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<title>Intel Inspector — IT4I Docs</title>
- <link rel="canonical" href="intel-inspector.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-inspector" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
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<div id="portal-header">
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+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-inspector#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="intel-inspector.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-inspector#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
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<div id="portal-advanced-search" class="hiddenStructure">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
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<span id="breadcrumbs-3" dir="ltr">
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<dt class="portletHeader hiddenStructure">
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</a>
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<span>Salomon Cluster Documentation</span>
</a>
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<span>Hardware Overview</span>
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<span>Accessing the Cluster</span>
</a>
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<span>Environment and Modules</span>
</a>
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<span>List of Available Modules</span>
</a>
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<span>Resource Allocation and Job Execution</span>
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<span>Compute Nodes</span>
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<span>Network</span>
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<span>Software</span>
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<span>ANSYS</span>
</a>
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<span>COMSOL</span>
</a>
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<span>Debuggers and profilers</span>
</a>
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<span>Chemistry, Physics and Materials science</span>
</a>
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- <a title="The Intel Parallel Studio XE" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-compilers">
<span>Intel Compilers</span>
</a>
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- <a title="" class="state-published contenttype-document" href="intel-debugger.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger">
<span>Intel Debugger</span>
</a>
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<span>Intel MKL</span>
</a>
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- <a title="" class="state-published contenttype-document" href="intel-integrated-performance-primitives.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives">
<span>Intel IPP</span>
</a>
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- <a title="" class="state-published contenttype-document" href="intel-tbb.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb">
<span>Intel TBB</span>
</a>
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- <a title="" class="state-published contenttype-document" href="intel-trace-analyzer-and-collector.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector">
<span>Intel Trace Analyzer and Collector</span>
</a>
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- <a title="" class="state-published contenttype-document" href="intel-advisor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-advisor">
<span>Intel Advisor</span>
</a>
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- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="intel-inspector.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-inspector">
<span>Intel Inspector</span>
</a>
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- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -797,7 +794,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -813,7 +810,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -829,7 +826,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -845,7 +842,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
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- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -886,7 +883,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -927,7 +924,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -943,7 +940,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
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- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
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})();
</script>
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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</html>
diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.md b/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.md
new file mode 100644
index 0000000000000000000000000000000000000000..eb960e36d3926c6ff025e21b7f462f9af870a207
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.md
@@ -0,0 +1,45 @@
+Intel Inspector
+===============
+Intel Inspector is a dynamic memory and threading error checking tool
+for C/C++/Fortran applications. It can detect issues such as memory
+leaks, invalid memory references, uninitalized variables, race
+conditions, deadlocks etc.
+Installed versions
+------------------
+The following versions are currently available on Salomon as modules:
+ --------------- --
+ **Version** **Module**
+ 2016 Update 1 Inspector/2016_update1
+ --------------- --
+Usage
+-----
+Your program should be compiled with -g switch to include symbol names.
+Optimizations can be turned on.
+Debugging is possible either directly from the GUI, or from command
+line.
+### GUI mode
+To debug from GUI, launch Inspector:
+ $ inspxe-gui &
+Then select menu File -> New -> Project. Choose a directory to
+save project data to. After clicking OK, Project properties window will
+appear, where you can configure path to your binary, launch arguments,
+working directory etc. After clicking OK, the project is ready.
+In the main pane, you can start a predefined analysis type or define
+your own. Click Start to start the analysis. Alternatively, you can
+click on Command Line, to see the command line required to run the
+analysis directly from command line.
+### Batch mode
+Analysis can be also run from command line in batch mode. Batch mode
+analysis is run with command <span class="monospace">inspxe-cl</span>.
+To obtain the required parameters, either consult the documentation or
+you can configure the analysis in the GUI and then click "Command Line"
+button in the lower right corner to the respective command line.
+Results obtained from batch mode can be then viewed in the GUI by
+selecting File -> Open -> Result...
+References
+----------
+1. [Product
+ page](https://software.intel.com/en-us/intel-inspector-xe)
+2. [Documentation and Release
+ Notes](https://software.intel.com/en-us/intel-inspector-xe-support/documentation)
+3. [Tutorials](https://software.intel.com/en-us/articles/inspectorxe-tutorials)
diff --git a/salomon/software/intel-suite/intel-integrated-performance-primitives.html b/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.html
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--- a/salomon/software/intel-suite/intel-integrated-performance-primitives.html
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ <base href="https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives" /><!--[if lt IE 7]></base><![endif]-->
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<title>Intel IPP — IT4I Docs</title>
- <link rel="canonical" href="intel-integrated-performance-primitives.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives" />
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<div id="portal-header">
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- <a accesskey="2" href="intel-integrated-performance-primitives.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="intel-integrated-performance-primitives.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
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<div id="portal-advanced-search" class="hiddenStructure">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
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</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
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+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
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</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../intel-suite.html">Intel Parallel studio</a>
+ <a href="https://docs.it4i.cz/salomon/software/intel-suite">Intel Parallel studio</a>
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<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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<span>What's New</span>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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<span>Hardware Overview</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
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- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
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<span>Storage</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
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<span>Network</span>
</a>
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- <a title="In this section we provide overview of installed software and its usage.
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<span>Software</span>
</a>
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<span>ANSYS</span>
</a>
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<span>COMSOL</span>
</a>
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<span>Debuggers and profilers</span>
</a>
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- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
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<span>Chemistry, Physics and Materials science</span>
</a>
@@ -614,7 +611,7 @@
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+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-compilers">
<span>Intel Compilers</span>
</a>
@@ -646,7 +643,7 @@
- <a title="" class="state-published contenttype-document" href="intel-debugger.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger">
<span>Intel Debugger</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-mkl">
<span>Intel MKL</span>
</a>
@@ -678,7 +675,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="intel-integrated-performance-primitives.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives">
<span>Intel IPP</span>
</a>
@@ -694,7 +691,7 @@
- <a title="" class="state-published contenttype-document" href="intel-tbb.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb">
<span>Intel TBB</span>
</a>
@@ -710,7 +707,7 @@
- <a title="" class="state-published contenttype-document" href="intel-trace-analyzer-and-collector.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector">
<span>Intel Trace Analyzer and Collector</span>
</a>
@@ -726,7 +723,7 @@
- <a title="" class="state-published contenttype-document" href="intel-advisor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-advisor">
<span>Intel Advisor</span>
</a>
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- <a title="" class="state-published contenttype-document" href="intel-inspector.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-inspector">
<span>Intel Inspector</span>
</a>
@@ -767,7 +764,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -783,7 +780,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -799,7 +796,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -815,7 +812,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -831,7 +828,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -847,7 +844,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -872,7 +869,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -897,7 +894,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -913,7 +910,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -929,7 +926,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -945,7 +942,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.md b/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.md
new file mode 100644
index 0000000000000000000000000000000000000000..19091f58369e2eb8b0adb5880a8ffd98e3e05e22
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.md
@@ -0,0 +1,72 @@
+Intel IPP
+=========
+
+Intel Integrated Performance Primitives
+----------------
+Intel Integrated Performance Primitives, version 9.0.1, compiled for
+AVX2 vector instructions is available, via module ipp. The IPP is a very
+rich library of highly optimized algorithmic building blocks for media
+and data applications. This includes signal, image and frame processing
+algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough
+transform, Sum, MinMax, as well as cryptographic functions, linear
+algebra functions and many more.
+Check out IPP before implementing own math functions for data
+processing, it is likely already there.
+ $ module load ipp
+The module sets up environment variables, required for linking and
+running ipp enabled applications.
+IPP example
+-----------
+ #include "ipp.h"
+ #include <stdio.h>
+ int main(int argc, char* argv[])
+ {
+ const IppLibraryVersion *lib;
+ Ipp64u fm;
+ IppStatus status;
+ status= ippInit(); //IPP initialization with the best optimization layer
+ if( status != ippStsNoErr ) {
+ printf("IppInit() Error:n");
+ printf("%sn", ippGetStatusString(status) );
+ return -1;
+ }
+ //Get version info
+ lib = ippiGetLibVersion();
+ printf("%s %sn", lib->Name, lib->Version);
+ //Get CPU features enabled with selected library level
+ fm=ippGetEnabledCpuFeatures();
+ printf("SSE :%cn",(fm>>1)&1?'Y':'N');
+ printf("SSE2 :%cn",(fm>>2)&1?'Y':'N');
+ printf("SSE3 :%cn",(fm>>3)&1?'Y':'N');
+ printf("SSSE3 :%cn",(fm>>4)&1?'Y':'N');
+ printf("SSE41 :%cn",(fm>>6)&1?'Y':'N');
+ printf("SSE42 :%cn",(fm>>7)&1?'Y':'N');
+ printf("AVX :%cn",(fm>>8)&1 ?'Y':'N');
+ printf("AVX2 :%cn", (fm>>15)&1 ?'Y':'N' );
+ printf("----------n");
+ printf("OS Enabled AVX :%cn", (fm>>9)&1 ?'Y':'N');
+ printf("AES :%cn", (fm>>10)&1?'Y':'N');
+ printf("CLMUL :%cn", (fm>>11)&1?'Y':'N');
+ printf("RDRAND :%cn", (fm>>13)&1?'Y':'N');
+ printf("F16C :%cn", (fm>>14)&1?'Y':'N');
+ return 0;
+ }
+Â Compile above example, using any compiler and the ipp module.
+ $ module load intel
+ $ module load ipp
+ $ icc testipp.c -o testipp.x -lippi -lipps -lippcore
+You will need the ipp module loaded to run the ipp enabled executable.
+This may be avoided, by compiling library search paths into the
+executable
+ $ module load intel
+ $ module load ipp
+ $ icc testipp.c -o testipp.x -Wl,-rpath=$LIBRARY_PATH -lippi -lipps -lippcore
+Code samples and documentation
+-------
+Intel provides number of [Code Samples for
+IPP](https://software.intel.com/en-us/articles/code-samples-for-intel-integrated-performance-primitives-library),
+illustrating use of IPP.
+Read full documentation on IPP [on Intel
+website,](http://software.intel.com/sites/products/search/search.php?q=&x=15&y=6&product=ipp&version=7.1&docos=lin)
+in particular the [IPP Reference
+manual.](http://software.intel.com/sites/products/documentation/doclib/ipp_sa/71/ipp_manual/index.htm)
diff --git a/salomon/software/intel-suite/intel-mkl.html b/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.html
old mode 100755
new mode 100644
similarity index 72%
rename from salomon/software/intel-suite/intel-mkl.html
rename to docs.it4i.cz/salomon/software/intel-suite/intel-mkl.html
index 380b74ad235abcc49719a9b25038ebc8aaa41291..eb8d9c2f82a90b8848e0391d6396d944ac5928a0
--- a/salomon/software/intel-suite/intel-mkl.html
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/intel-suite/intel-mkl by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:31 GMT -->
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<title>Intel MKL — IT4I Docs</title>
- <link rel="canonical" href="intel-mkl.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-mkl" />
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="intel-mkl.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-mkl#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="intel-mkl.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-mkl#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
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<div id="portal-advanced-search" class="hiddenStructure">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
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@@ -153,7 +150,7 @@
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+ <a href="https://docs.it4i.cz/salomon/software/intel-suite">Intel Parallel studio</a>
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@@ -308,7 +305,7 @@
<pre class=" ">$ module load GCC<br />$ module load imkl<br />$ cp -a $MKL_EXAMPLES/cblas /tmp/<br />$ cd /tmp/cblas<br /> <br />$ gcc -w source/cblas_dgemmx.c source/common_func.c -o cblas_dgemmx.x \<br />-lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lm<br /><br />$ ./cblas_dgemmx.x data/cblas_dgemmx.d</pre>
<p>In this example, we compile, link and run the cblas_dgemm example, using LP64 interface to threaded MKL and gnu OMP threads implementation.</p>
<h2 class=" ">MKL and MIC accelerators</h2>
-<p>The Intel MKL is capable to automatically offload the computations o the MIC accelerator. See section <a target="_self" title="" class="internal-link" href="../intel-xeon-phi.html">Intel Xeon Phi</a> for details.</p>
+<p>The Intel MKL is capable to automatically offload the computations o the MIC accelerator. See section <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">Intel Xeon Phi</a> for details.</p>
<h2 class=" ">LAPACKE C Interface</h2>
<p>MKL includes LAPACKE C Interface to LAPACK. For some reason, although Intel is the author of LAPACKE, the LAPACKE header files are not present in MKL. For this reason, we have prepared <span class="monospace">LAPACKE</span> module, which includes Intel's LAPACKE headers from official LAPACK, which you can use to compile code using LAPACKE interface against MKL.</p>
<h2 class=" ">Further reading</h2>
@@ -388,7 +385,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
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@@ -420,7 +417,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -436,7 +433,7 @@
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+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -452,7 +449,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -468,7 +465,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -484,7 +481,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -500,7 +497,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -516,7 +513,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
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</a>
@@ -532,7 +529,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -548,7 +545,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -564,7 +561,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
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@@ -580,10 +577,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -599,7 +596,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -615,7 +612,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -631,7 +628,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -647,7 +644,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -663,7 +660,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -679,7 +676,7 @@
- <a title="" class="state-published contenttype-document" href="intel-compilers.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-compilers">
<span>Intel Compilers</span>
</a>
@@ -695,7 +692,7 @@
- <a title="" class="state-published contenttype-document" href="intel-debugger.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger">
<span>Intel Debugger</span>
</a>
@@ -711,7 +708,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="intel-mkl.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-mkl">
<span>Intel MKL</span>
</a>
@@ -727,7 +724,7 @@
- <a title="" class="state-published contenttype-document" href="intel-integrated-performance-primitives.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives">
<span>Intel IPP</span>
</a>
@@ -743,7 +740,7 @@
- <a title="" class="state-published contenttype-document" href="intel-tbb.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb">
<span>Intel TBB</span>
</a>
@@ -759,7 +756,7 @@
- <a title="" class="state-published contenttype-document" href="intel-trace-analyzer-and-collector.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector">
<span>Intel Trace Analyzer and Collector</span>
</a>
@@ -775,7 +772,7 @@
- <a title="" class="state-published contenttype-document" href="intel-advisor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-advisor">
<span>Intel Advisor</span>
</a>
@@ -791,7 +788,7 @@
- <a title="" class="state-published contenttype-document" href="intel-inspector.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-inspector">
<span>Intel Inspector</span>
</a>
@@ -816,7 +813,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -832,7 +829,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -848,7 +845,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -864,7 +861,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -880,7 +877,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -896,7 +893,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -921,7 +918,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -946,7 +943,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -962,7 +959,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -978,7 +975,7 @@
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+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -994,7 +991,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
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-var u="http://extranet.it4i.cz/piwik/";
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
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- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
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@@ -1083,7 +1080,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
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-
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</html>
diff --git a/salomon/software/intel-suite/intel-mkl.md b/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.md
similarity index 61%
rename from salomon/software/intel-suite/intel-mkl.md
rename to docs.it4i.cz/salomon/software/intel-suite/intel-mkl.md
index ce22742be19173bae024427596a808f9e1841f72..65c1148e0db98f4570ab59a7dbd54742e2f32bb0 100644
--- a/salomon/software/intel-suite/intel-mkl.md
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.md
@@ -1,44 +1,44 @@
+Intel MKL
=========
-
-
+
Intel Math Kernel Library
--------------------------
+--
Intel Math Kernel Library (Intel MKL) is a library of math kernel
subroutines, extensively threaded and optimized for maximum performance.
-Intel MKL provides these basic math kernels
+Intel MKL provides these basic math kernels:
[]()
--
+- <div id="d4841e18">
[]()BLAS (level 1, 2, and 3) and LAPACK linear algebra routines,
offering vector, vector-matrix, and matrix-matrix operations.
--
+- <div id="d4841e21">
[]()The PARDISO direct sparse solver, an iterative sparse solver,
and supporting sparse BLAS (level 1, 2, and 3) routines for solving
sparse systems of equations.
--
+- <div id="d4841e24">
[]()ScaLAPACK distributed processing linear algebra routines for
Linux* and Windows* operating systems, as well as the Basic Linear
Algebra Communications Subprograms (BLACS) and the Parallel Basic
Linear Algebra Subprograms (PBLAS).
--
+- <div id="d4841e27">
[]()Fast Fourier transform (FFT) functions in one, two, or three
dimensions with support for mixed radices (not limited to sizes that
are powers of 2), as well as distributed versions of
these functions.
--
+- <div id="d4841e30">
[]()Vector Math Library (VML) routines for optimized mathematical
operations on vectors.
--
+- <div id="d4841e34">
[]()Vector Statistical Library (VSL) routines, which offer
high-performance vectorized random number generators (RNG) for
several probability distributions, convolution and correlation
routines, and summary statistics functions.
--
+- <div id="d4841e37">
[]()Data Fitting Library, which provides capabilities for
spline-based approximation of functions, derivatives and integrals
@@ -46,7 +46,7 @@ Intel MKL provides these basic math kernels
- Extended Eigensolver, a shared memory version of an eigensolver
based on the Feast Eigenvalue Solver.
For details see the [Intel MKL Reference
-Manual](http//software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mklman/index.htm).
+Manual](http://software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mklman/index.htm).
Intel MKL version 11.2.3.187 is available on the cluster
$ module load imkl
The module sets up environment variables, required for linking and
@@ -61,16 +61,16 @@ integer type (necessary for indexing large arrays, with more than
2^31^-1 elements), whereas the LP64 libraries index arrays with the
32-bit integer type.
Interface Integer type
- ----------- -----------------------------------------------
+ ----------- -
LP64 32-bit, int, integer(kind=4), MPI_INT
ILP64 64-bit, long int, integer(kind=8), MPI_INT64
### Linking
Linking Intel MKL libraries may be complex. Intel [mkl link line
-advisor](http//software.intel.com/en-us/articles/intel-mkl-link-line-advisor)
+advisor](http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor)
helps. See also [examples](#examples) below.
You will need the mkl module loaded to run the mkl enabled executable.
This may be avoided, by compiling library search paths into the
-executable. Include rpath on the compile line
+executable. Include rpath on the compile line:
$ icc .... -Wl,-rpath=$LIBRARY_PATH ...
### Threading
Advantage in using Intel MKL library is that it brings threaded
@@ -97,7 +97,7 @@ compiled program for multi-threaded matrix multiplication.
$ make sointel64 function=cblas_dgemm
In this example, we compile, link and run the cblas_dgemm example,
demonstrating use of MKL example suite installed on clusters.
-### Example MKL and Intel compiler
+### ExampleMKL and Intel compiler
$ module load intel
$ module load imkl
$ cp -a $MKL_EXAMPLES/cblas /tmp/
@@ -107,12 +107,12 @@ demonstrating use of MKL example suite installed on clusters.
$ ./cblas_dgemmx.x data/cblas_dgemmx.d
In this example, we compile, link and run the cblas_dgemm example,
demonstrating use of MKL with icc -mkl option. Using the -mkl option is
-equivalent to
+equivalent to:
$ icc -w source/cblas_dgemmx.c source/common_func.c -o cblas_dgemmx.x
-I$MKL_INC_DIR -L$MKL_LIB_DIR -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5
In this example, we compile and link the cblas_dgemm example, using
LP64 interface to threaded MKL and Intel OMP threads implementation.
-### Example Intel MKL and GNU compiler
+### ExampleIntel MKL and GNU compiler
$ module load GCC
$ module load imkl
$ cp -a $MKL_EXAMPLES/cblas /tmp/
@@ -124,90 +124,22 @@ LP64 interface to threaded MKL and Intel OMP threads implementation.
In this example, we compile, link and run the cblas_dgemm example,
using LP64 interface to threaded MKL and gnu OMP threads implementation.
MKL and MIC accelerators
-------------------------
+-
The Intel MKL is capable to automatically offload the computations o the
MIC accelerator. See section [Intel Xeon
-Phi](../intel-xeon-phi.html) for details.
+Phi](https://docs.it4i.cz/salomon/software/intel-xeon-phi)
+for details.
LAPACKE C Interface
-------------------
MKL includes LAPACKE C Interface to LAPACK. For some reason, although
Intel is the author of LAPACKE, the LAPACKE header files are not present
-in MKL. For this reason, we have prepared
-class="monospace">LAPACKE module, which includes Intel's LAPACKE
+in MKL. For this reason, we have prepared <span
+class="monospace">LAPACKE</span> module, which includes Intel's LAPACKE
headers from official LAPACK, which you can use to compile code using
LAPACKE interface against MKL.
Further reading
---------------
Read more on [Intel
-website](http//software.intel.com/en-us/intel-mkl), in
+website](http://software.intel.com/en-us/intel-mkl), in
particular the [MKL users
-guide](https//software.intel.com/en-us/intel-mkl/documentation/linux).
-------------------------------------------------------------------------
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- .navTreeFolderish
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-
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diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.html b/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.html
new file mode 100644
index 0000000000000000000000000000000000000000..34e25b4c12c69b9f6d50f33f551434c6a12f18c6
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+ <div id="parent-fieldname-text-20d9f0898b694621a77070007f3bf715" class="">
+ <p>The Salomon cluster provides following elements of the Intel Parallel Studio XE</p>
+<table class="listing">
+<tbody>
+<tr><th>Intel Parallel Studio XE</th></tr>
+<tr class="even">
+<td>Intel Compilers</td>
+</tr>
+<tr class="odd">
+<td>Intel Debugger</td>
+</tr>
+<tr class="even">
+<td>Intel MKL Library</td>
+</tr>
+<tr class="odd">
+<td>Intel Integrated Performance Primitives Library</td>
+</tr>
+<tr class="even">
+<td>Intel Threading Building Blocks Library</td>
+</tr>
+<tr class="even">
+<td>Intel Trace Analyzer and Collector</td>
+</tr>
+<tr class="even">
+<td>Intel Advisor</td>
+</tr>
+<tr class="even">
+<td>Intel Inspector</td>
+</tr>
+</tbody>
+</table>
+<h2 class=" ">Intel compilers</h2>
+<p>The Intel compilers version 131.3 are available, via module iccifort/2013.5.192-GCC-4.8.3. The compilers include the icc C and C++ compiler and the ifort fortran 77/90/95 compiler.</p>
+<pre class=" ">$ module load intel<br />$ icc -v<br />$ ifort -v</pre>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-compilers">Intel Compilers</a> page.</p>
+<h2 class=" ">Intel debugger</h2>
+<p class="exclamation">IDB is no longer available since Parallel Studio 2015.</p>
+<p>Â The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">X display</a> for running the GUI.</p>
+<pre class=" ">$ module load intel<br />$ idb</pre>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger">Intel Debugger</a> page.</p>
+<h2 class=" ">Intel Math Kernel Library</h2>
+<p>Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, extensively threaded and optimized for maximum performance. Intel MKL unites and provides these basic components: BLAS, LAPACK, ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and many more.</p>
+<pre class=" ">$ module load imkl</pre>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-mkl">Intel MKL</a> page.</p>
+<h2 class=" ">Intel Integrated Performance Primitives</h2>
+<p>Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is available, via module ipp. The IPP is a library of highly optimized algorithmic building blocks for media and data applications. This includes signal, image and frame processing algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many more.</p>
+<pre class=" ">$ module load ipp</pre>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives">Intel IPP</a> page.</p>
+<h2 class=" ">Intel Threading Building Blocks</h2>
+<p>Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. It is designed to promote scalable data parallel programming. Additionally, it fully supports nested parallelism, so you can build larger parallel components from smaller parallel components. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner.</p>
+<pre class=" ">$ module load tbb</pre>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb">Intel TBB</a> page.</p>
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diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.md b/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.md
new file mode 100644
index 0000000000000000000000000000000000000000..01daba67ed047a3ccdd229242906476624a594da
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.md
@@ -0,0 +1,77 @@
+Intel Parallel Studio
+=====================
+
+The Salomon cluster provides following elements of the Intel Parallel
+Studio XE
+ Intel Parallel Studio XE
+ ---
+ Intel Compilers
+ Intel Debugger
+ Intel MKL Library
+ Intel Integrated Performance Primitives Library
+ Intel Threading Building Blocks Library
+ Intel Trace Analyzer and Collector
+ Intel Advisor
+ Intel Inspector
+Intel compilers
+---------------
+The Intel compilers version 131.3 are available, via module
+iccifort/2013.5.192-GCC-4.8.3. The compilers include the icc C and C++
+compiler and the ifort fortran 77/90/95 compiler.
+ $ module load intel
+ $ icc -v
+ $ ifort -v
+Read more at the [Intel
+Compilers](https://docs.it4i.cz/salomon/software/intel-suite/intel-compilers)
+page.
+Intel debugger
+--------------
+IDB is no longer available since Parallel Studio 2015.
+Â The intel debugger version 13.0 is available, via module intel. The
+debugger works for applications compiled with C and C++ compiler and the
+ifort fortran 77/90/95 compiler. The debugger provides java GUI
+environment. Use [X
+display](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc)
+for running the GUI.
+ $ module load intel
+ $ idb
+Read more at the [Intel
+Debugger](https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger)
+page.
+Intel Math Kernel Library
+--
+Intel Math Kernel Library (Intel MKL) is a library of math kernel
+subroutines, extensively threaded and optimized for maximum performance.
+Intel MKL unites and provides these basic componentsBLAS, LAPACK,
+ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and
+many more.
+ $ module load imkl
+Read more at the [Intel
+MKL](https://docs.it4i.cz/salomon/software/intel-suite/intel-mkl)
+page.
+Intel Integrated Performance Primitives
+----------------
+Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX
+is available, via module ipp. The IPP is a library of highly optimized
+algorithmic building blocks for media and data applications. This
+includes signal, image and frame processing algorithms, such as FFT,
+FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many
+more.
+ $ module load ipp
+Read more at the [Intel
+IPP](https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives)
+page.
+Intel Threading Building Blocks
+--------
+Intel Threading Building Blocks (Intel TBB) is a library that supports
+scalable parallel programming using standard ISO C++ code. It does not
+require special languages or compilers. It is designed to promote
+scalable data parallel programming. Additionally, it fully supports
+nested parallelism, so you can build larger parallel components from
+smaller parallel components. To use the library, you specify tasks, not
+threads, and let the library map tasks onto threads in an efficient
+manner.
+ $ module load tbb
+Read more at the [Intel
+TBB](https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb)
+page.
diff --git a/salomon/software/intel-suite/intel-tbb.html b/docs.it4i.cz/salomon/software/intel-suite/intel-tbb.html
old mode 100755
new mode 100644
similarity index 66%
rename from salomon/software/intel-suite/intel-tbb.html
rename to docs.it4i.cz/salomon/software/intel-suite/intel-tbb.html
index 09327b03383e71f9a1b23e04fd950d8b80a725a5..93b4ecedbdbad19d3153408b06742797a9644a5c
--- a/salomon/software/intel-suite/intel-tbb.html
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-tbb.html
@@ -10,45 +10,42 @@
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
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<title>Intel TBB — IT4I Docs</title>
- <link rel="canonical" href="intel-tbb.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="intel-tbb.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="intel-tbb.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
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</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
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- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../intel-suite.html">Intel Parallel studio</a>
+ <a href="https://docs.it4i.cz/salomon/software/intel-suite">Intel Parallel studio</a>
<span class="breadcrumbSeparator">
/
@@ -251,7 +248,7 @@
<div id="parent-fieldname-text-f4f931ac0c334382a548cfe25eea3bd7" class="">
<h2 class=" ">Intel Threading Building Blocks</h2>
-<p>Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner. The tasks are executed by a runtime scheduler and may be offloaded to <a target="_self" title="" class="internal-link" href="../intel-xeon-phi.html">MIC accelerator</a>.</p>
+<p>Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner. The tasks are executed by a runtime scheduler and may be offloaded to <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">MIC accelerator</a>.</p>
<p>Intel TBB version 4.3.5.187 is available on the cluster.</p>
<pre class=" ">$ module load tbb</pre>
<p>The module sets up environment variables, required for linking and running tbb enabled applications.</p>
@@ -339,7 +336,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -355,7 +352,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -371,7 +368,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -387,7 +384,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -419,7 +416,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -435,7 +432,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -451,7 +448,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -467,7 +464,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -483,7 +480,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -499,7 +496,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -515,7 +512,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -531,10 +528,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -550,7 +547,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -566,7 +563,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -582,7 +579,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -598,7 +595,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -614,7 +611,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -630,7 +627,7 @@
- <a title="" class="state-published contenttype-document" href="intel-compilers.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-compilers">
<span>Intel Compilers</span>
</a>
@@ -646,7 +643,7 @@
- <a title="" class="state-published contenttype-document" href="intel-debugger.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger">
<span>Intel Debugger</span>
</a>
@@ -662,7 +659,7 @@
- <a title="" class="state-published contenttype-document" href="intel-mkl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-mkl">
<span>Intel MKL</span>
</a>
@@ -678,7 +675,7 @@
- <a title="" class="state-published contenttype-document" href="intel-integrated-performance-primitives.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives">
<span>Intel IPP</span>
</a>
@@ -694,7 +691,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="intel-tbb.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb">
<span>Intel TBB</span>
</a>
@@ -710,7 +707,7 @@
- <a title="" class="state-published contenttype-document" href="intel-trace-analyzer-and-collector.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector">
<span>Intel Trace Analyzer and Collector</span>
</a>
@@ -726,7 +723,7 @@
- <a title="" class="state-published contenttype-document" href="intel-advisor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-advisor">
<span>Intel Advisor</span>
</a>
@@ -742,7 +739,7 @@
- <a title="" class="state-published contenttype-document" href="intel-inspector.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-inspector">
<span>Intel Inspector</span>
</a>
@@ -767,7 +764,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -783,7 +780,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -799,7 +796,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -815,7 +812,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -831,7 +828,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -847,7 +844,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -872,7 +869,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -897,7 +894,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -913,7 +910,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -929,7 +926,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -945,7 +942,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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(function() {
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1034,7 +1031,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/intel-suite/intel-tbb by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:31 GMT -->
</html>
diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-tbb.md b/docs.it4i.cz/salomon/software/intel-suite/intel-tbb.md
new file mode 100644
index 0000000000000000000000000000000000000000..e9d6a07e7defce10acf7cdfeb98eb020ade671c6
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-tbb.md
@@ -0,0 +1,38 @@
+Intel TBB
+=========
+
+Intel Threading Building Blocks
+--------
+Intel Threading Building Blocks (Intel TBB) is a library that supports
+scalable parallel programming using standard ISO C++ code. It does not
+require special languages or compilers. To use the library, you specify
+tasks, not threads, and let the library map tasks onto threads in an
+efficient manner. The tasks are executed by a runtime scheduler and may
+be offloaded to [MIC
+accelerator](https://docs.it4i.cz/salomon/software/intel-xeon-phi).
+Intel TBB version 4.3.5.187 is available on the cluster.
+ $ module load tbb
+The module sets up environment variables, required for linking and
+running tbb enabled applications.
+Link the tbb library, using -ltbb
+Examples
+--------
+Number of examples, demonstrating use of TBB and its built-in schedulerÂ
+is available on Anselm, in the $TBB_EXAMPLES directory.
+ $ module load intel
+ $ module load tbb
+ $ cp -a $TBB_EXAMPLES/common $TBB_EXAMPLES/parallel_reduce /tmp/
+ $ cd /tmp/parallel_reduce/primes
+ $ icc -O2 -DNDEBUG -o primes.x main.cpp primes.cpp -ltbb
+ $ ./primes.x
+In this example, we compile, link and run the primes example,
+demonstrating use of parallel task-based reduce in computation of prime
+numbers.
+You will need the tbb module loaded to run the tbb enabled executable.
+This may be avoided, by compiling library search paths into the
+executable.
+ $ icc -O2 -o primes.x main.cpp primes.cpp -Wl,-rpath=$LIBRARY_PATH -ltbb
+Further reading
+---------------
+Read more on Intel website,
+<http://software.intel.com/sites/products/documentation/doclib/tbb_sa/help/index.htm>
diff --git a/salomon/software/intel-suite/intel-trace-analyzer-and-collector.html b/docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector.html
old mode 100755
new mode 100644
similarity index 64%
rename from salomon/software/intel-suite/intel-trace-analyzer-and-collector.html
rename to docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector.html
index f7be6cdc0594a843c6053fb353d08f3b5f944c93..d0eebafd79e07e9c1d19050383826d8cd38b366f
--- a/salomon/software/intel-suite/intel-trace-analyzer-and-collector.html
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector.html
@@ -10,45 +10,42 @@
-
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+ <base href="https://docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Intel Trace Analyzer and Collector — IT4I Docs</title>
- <link rel="canonical" href="intel-trace-analyzer-and-collector.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
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@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="intel-trace-analyzer-and-collector.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="intel-trace-analyzer-and-collector.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
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- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
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@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../intel-suite.html">Intel Parallel studio</a>
+ <a href="https://docs.it4i.cz/salomon/software/intel-suite">Intel Parallel studio</a>
<span class="breadcrumbSeparator">
/
@@ -255,15 +252,15 @@
<pre>$ module load itac/9.1.2.024<br />$ mpirun -trace myapp</pre>
<p class=" ">The trace will be saved in file myapp.stf in the current directory.</p>
<h2>Viewing traces</h2>
-<p>To view and analyze the trace, open ITAC GUI in a <a target="_self" title="" class="internal-link" href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html">graphical environment</a> :</p>
+<p>To view and analyze the trace, open ITAC GUI in a <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">graphical environment</a> :</p>
<pre>$ module load itac/9.1.2.024<br />$ traceanalyzer</pre>
<p class=" ">The GUI will launch and you can open the produced *.stf file.</p>
-<p class=" "><img title="Intel Trace Analyzer" class="image-inline" alt="Intel Trace Analyzer" src="Snmekobrazovky20151204v15.35.12.png/%40%40images/fb3b3ac2-a88f-4e55-a25e-23f1da2200cb.png" /></p>
+<p class=" "><img alt="Intel Trace Analyzer" class="image-inline" title="Intel Trace Analyzer" src="https://docs.it4i.cz/salomon/software/intel-suite/Snmekobrazovky20151204v15.35.12.png/@@images/fb3b3ac2-a88f-4e55-a25e-23f1da2200cb.png" /></p>
<p class=" ">Please refer to Intel documenation about usage of the GUI tool.</p>
<h2>References</h2>
<ol>
<li><a class="external-link" href="https://software.intel.com/en-us/get-started-with-itac-for-linux" target="_self" title="">Getting Started with Intel® Trace Analyzer and Collector</a></li>
-<li><a class="external-link" href="http://xn--intel trace analyzer and collector - documentation-g6b/" target="_self" title="">Intel® Trace Analyzer and Collector - Documentation</a></li>
+<li><a class="external-link" href="http://Intel® Trace Analyzer and Collector - Documentation" target="_self" title="">Intel® Trace Analyzer and Collector - Documentation</a></li>
</ol>
</div>
@@ -340,7 +337,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -356,7 +353,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -372,7 +369,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -388,7 +385,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -404,7 +401,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -420,7 +417,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -436,7 +433,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -452,7 +449,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -468,7 +465,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -484,7 +481,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -500,7 +497,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -516,7 +513,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -532,10 +529,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -551,7 +548,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -567,7 +564,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -583,7 +580,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -599,7 +596,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -615,7 +612,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -631,7 +628,7 @@
- <a title="" class="state-published contenttype-document" href="intel-compilers.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-compilers">
<span>Intel Compilers</span>
</a>
@@ -647,7 +644,7 @@
- <a title="" class="state-published contenttype-document" href="intel-debugger.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger">
<span>Intel Debugger</span>
</a>
@@ -663,7 +660,7 @@
- <a title="" class="state-published contenttype-document" href="intel-mkl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-mkl">
<span>Intel MKL</span>
</a>
@@ -679,7 +676,7 @@
- <a title="" class="state-published contenttype-document" href="intel-integrated-performance-primitives.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives">
<span>Intel IPP</span>
</a>
@@ -695,7 +692,7 @@
- <a title="" class="state-published contenttype-document" href="intel-tbb.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb">
<span>Intel TBB</span>
</a>
@@ -711,7 +708,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="intel-trace-analyzer-and-collector.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector">
<span>Intel Trace Analyzer and Collector</span>
</a>
@@ -727,7 +724,7 @@
- <a title="" class="state-published contenttype-document" href="intel-advisor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-advisor">
<span>Intel Advisor</span>
</a>
@@ -743,7 +740,7 @@
- <a title="" class="state-published contenttype-document" href="intel-inspector.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-inspector">
<span>Intel Inspector</span>
</a>
@@ -768,7 +765,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -784,7 +781,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -800,7 +797,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -816,7 +813,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -832,7 +829,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -848,7 +845,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -873,7 +870,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
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<span>PRACE User Support</span>
</a>
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<span>Anselm Cluster Documentation</span>
</a>
@@ -914,7 +911,7 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
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+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
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@@ -946,7 +943,7 @@
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+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md b/docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
new file mode 100644
index 0000000000000000000000000000000000000000..d9d4ee7a27a5e365a15aab6d41ef1f4d95f2131d
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
@@ -0,0 +1,38 @@
+Intel Trace Analyzer and Collector
+==================================
+Intel Trace Analyzer and Collector (ITAC) is a tool to collect and
+graphicaly analyze behaviour of MPI applications. It helps you to
+analyze communication patterns of your application, identify hotspots,
+perform correctnes checking (identify deadlocks, data corruption etc),
+simulate how your application would run on a different interconnect.Â
+ITAC is a offline analysis tool - first you run your application to
+collect a trace file, then you can open the trace in a GUI analyzer to
+view it.
+Installed version
+-----------------
+Currently on Salomon is version 9.1.2.024 available as module <span
+class="monospace">itac/9.1.2.024</span>
+Collecting traces
+-----------------
+ITAC can collect traces from applications that are using Intel MPI. To
+generate a trace, simply add -trace option to your mpirun command :
+ $ module load itac/9.1.2.024
+ $ mpirun -trace myapp
+The trace will be saved in file myapp.stf in the current directory.
+Viewing traces
+--------------
+To view and analyze the trace, open ITAC GUI in a [graphical
+environment](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc)
+:
+ $ module load itac/9.1.2.024
+ $ traceanalyzer
+The GUI will launch and you can open the produced *.stf file.
+
+Please refer to Intel documenation about usage of the GUI tool.
+References
+----------
+1. [Getting Started with Intel® Trace Analyzer and
+ Collector](https://software.intel.com/en-us/get-started-with-itac-for-linux)
+2. [Intel® Trace Analyzer and Collector -
+ Documentation](http://Intel®%20Trace%20Analyzer%20and%20Collector%20-%20Documentation)
diff --git a/salomon/software/intel-xeon-phi.html b/docs.it4i.cz/salomon/software/intel-xeon-phi.html
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<meta content="A guide to Intel Xeon Phi usage" name="description" />
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<title>Intel Xeon Phi — IT4I Docs</title>
- <link rel="canonical" href="intel-xeon-phi.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
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+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
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<script type="text/javascript">
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- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
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- <a accesskey="2" href="intel-xeon-phi.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="intel-xeon-phi.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
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</span>
<span id="breadcrumbs-1" dir="ltr">
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<dt class="portletHeader hiddenStructure">
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<span>Get Started with IT4Innovations</span>
</a>
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</a>
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<span>Resource Allocation and Job Execution</span>
</a>
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
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</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
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<span>Software</span>
</a>
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</a>
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<span>Chemistry, Physics and Materials science</span>
</a>
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</a>
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<span>Numerical languages</span>
</a>
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<span>Compilers</span>
</a>
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<span>Intel Xeon Phi</span>
</a>
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- <a title="Java on the cluster" class="state-published contenttype-document" href="java.html">
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</a>
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</a>
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- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
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</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
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- <a title="" class="state-published contenttype-document" href="../../links.html">
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</a>
@@ -1088,7 +1085,7 @@ Device No: 1, Device Name: mic1
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -1104,7 +1101,7 @@ Device No: 1, Device Name: mic1
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1143,14 +1140,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
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_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
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+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -1172,12 +1169,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
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- <a href="https://extranet.it4i.cz/">Extranet</a>
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+ <a href="https://extranet.it4i.cz">Extranet</a>
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- <a href="../../salomon.html">Dokumentace pro Salomon</a>
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@@ -1193,7 +1190,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
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diff --git a/salomon/software/intel-xeon-phi.md b/docs.it4i.cz/salomon/software/intel-xeon-phi.md
similarity index 64%
rename from salomon/software/intel-xeon-phi.md
rename to docs.it4i.cz/salomon/software/intel-xeon-phi.md
index e5ba1737a802a420338d05582f905272f32cf399..7dce1db70db512be0404dfff974fd27c6b55e2e9 100644
--- a/salomon/software/intel-xeon-phi.md
+++ b/docs.it4i.cz/salomon/software/intel-xeon-phi.md
@@ -1,13 +1,15 @@
-
-
+Intel Xeon Phi
+==============
+A guide to Intel Xeon Phi usage
+
Intel Xeon Phi accelerator can be programmed in several modes. The
default mode on the cluster is offload mode, but all modes described in
this document are supported.
Intel Utilities for Xeon Phi
-----------------------------
+-----
To get access to a compute node with Intel Xeon Phi accelerator, use the
PBS interactive session
- $ qsub -I -q qprod -l select=1ncpus=24accelerator=Truenaccelerators=2accelerator_model=phi7120 -A NONE-0-0
+ $ qsub -I -q qprod -l select=1:ncpus=24:accelerator=True:naccelerators=2:accelerator_model=phi7120 -A NONE-0-0
To set up the environment module "intel" has to be loaded, without
specifying the version, default version is loaded (at time of writing
this, it's 2015b)
@@ -16,108 +18,108 @@ Information about the hardware can be obtained by running
the micinfo program on the host.
$ /usr/bin/micinfo
The output of the "micinfo" utility executed on one of the cluster node
-is as follows. (note to get PCIe related details the command has to be
+is as follows. (noteto get PCIe related details the command has to be
run with root privileges)
MicInfo Utility Log
- Created Mon Aug 17 135559 2015
+ Created Mon Aug 17 13:55:59 2015
System Info
- HOST OS Linux
- OS Version 2.6.32-504.16.2.el6.x86_64
- Driver Version 3.4.1-1
- MPSS Version 3.4.1
- Host Physical Memory 131930 MB
- Device No 0, Device Name mic0
+ HOST OS Linux
+ OS Version 2.6.32-504.16.2.el6.x86_64
+ Driver Version 3.4.1-1
+ MPSS Version 3.4.1
+ Host Physical Memory 131930 MB
+ Device No0, Device Namemic0
Version
- Flash Version 2.1.02.0390
- SMC Firmware Version 1.16.5078
- SMC Boot Loader Version 1.8.4326
- uOS Version 2.6.38.8+mpss3.4.1
- Device Serial Number ADKC44601414
+ Flash Version 2.1.02.0390
+ SMC Firmware Version 1.16.5078
+ SMC Boot Loader Version 1.8.4326
+ uOS Version 2.6.38.8+mpss3.4.1
+ Device Serial Number ADKC44601414
Board
- Vendor ID 0x8086
- Device ID 0x225c
- Subsystem ID 0x7d95
- Coprocessor Stepping ID 2
- PCIe Width x16
- PCIe Speed 5 GT/s
- PCIe Max payload size 256 bytes
- PCIe Max read req size 512 bytes
- Coprocessor Model 0x01
- Coprocessor Model Ext 0x00
- Coprocessor Type 0x00
- Coprocessor Family 0x0b
- Coprocessor Family Ext 0x00
- Coprocessor Stepping C0
- Board SKU C0PRQ-7120 P/A/X/D
- ECC Mode Enabled
- SMC HW Revision Product 300W Passive CS
+ Vendor ID 0x8086
+ Device ID 0x225c
+ Subsystem ID 0x7d95
+ Coprocessor Stepping ID 2
+ PCIe Width x16
+ PCIe Speed 5 GT/s
+ PCIe Max payload size 256 bytes
+ PCIe Max read req size 512 bytes
+ Coprocessor Model 0x01
+ Coprocessor Model Ext 0x00
+ Coprocessor Type 0x00
+ Coprocessor Family 0x0b
+ Coprocessor Family Ext 0x00
+ Coprocessor Stepping C0
+ Board SKU C0PRQ-7120 P/A/X/D
+ ECC Mode Enabled
+ SMC HW Revision Product 300W Passive CS
Cores
- Total No of Active Cores 61
- Voltage 1007000 uV
- Frequency 1238095 kHz
+ Total No of Active Cores 61
+ Voltage 1007000 uV
+ Frequency 1238095 kHz
Thermal
- Fan Speed Control N/A
- Fan RPM N/A
- Fan PWM N/A
- Die Temp 60 C
+ Fan Speed Control N/A
+ Fan RPM N/A
+ Fan PWM N/A
+ Die Temp 60 C
GDDR
- GDDR Vendor Samsung
- GDDR Version 0x6
- GDDR Density 4096 Mb
- GDDR Size 15872 MB
- GDDR Technology GDDR5
- GDDR Speed 5.500000 GT/s
- GDDR Frequency 2750000 kHz
- GDDR Voltage 1501000 uV
- Device No 1, Device Name mic1
+ GDDR Vendor Samsung
+ GDDR Version 0x6
+ GDDR Density 4096 Mb
+ GDDR Size 15872 MB
+ GDDR Technology GDDR5
+ GDDR Speed 5.500000 GT/s
+ GDDR Frequency 2750000 kHz
+ GDDR Voltage 1501000 uV
+ Device No1, Device Namemic1
Version
- Flash Version 2.1.02.0390
- SMC Firmware Version 1.16.5078
- SMC Boot Loader Version 1.8.4326
- uOS Version 2.6.38.8+mpss3.4.1
- Device Serial Number ADKC44500454
+ Flash Version 2.1.02.0390
+ SMC Firmware Version 1.16.5078
+ SMC Boot Loader Version 1.8.4326
+ uOS Version 2.6.38.8+mpss3.4.1
+ Device Serial Number ADKC44500454
Board
- Vendor ID 0x8086
- Device ID 0x225c
- Subsystem ID 0x7d95
- Coprocessor Stepping ID 2
- PCIe Width x16
- PCIe Speed 5 GT/s
- PCIe Max payload size 256 bytes
- PCIe Max read req size 512 bytes
- Coprocessor Model 0x01
- Coprocessor Model Ext 0x00
- Coprocessor Type 0x00
- Coprocessor Family 0x0b
- Coprocessor Family Ext 0x00
- Coprocessor Stepping C0
- Board SKU C0PRQ-7120 P/A/X/D
- ECC Mode Enabled
- SMC HW Revision Product 300W Passive CS
+ Vendor ID 0x8086
+ Device ID 0x225c
+ Subsystem ID 0x7d95
+ Coprocessor Stepping ID 2
+ PCIe Width x16
+ PCIe Speed 5 GT/s
+ PCIe Max payload size 256 bytes
+ PCIe Max read req size 512 bytes
+ Coprocessor Model 0x01
+ Coprocessor Model Ext 0x00
+ Coprocessor Type 0x00
+ Coprocessor Family 0x0b
+ Coprocessor Family Ext 0x00
+ Coprocessor Stepping C0
+ Board SKU C0PRQ-7120 P/A/X/D
+ ECC Mode Enabled
+ SMC HW Revision Product 300W Passive CS
Cores
- Total No of Active Cores 61
- Voltage 998000 uV
- Frequency 1238095 kHz
+ Total No of Active Cores 61
+ Voltage 998000 uV
+ Frequency 1238095 kHz
Thermal
- Fan Speed Control N/A
- Fan RPM N/A
- Fan PWM N/A
- Die Temp 59 C
+ Fan Speed Control N/A
+ Fan RPM N/A
+ Fan PWM N/A
+ Die Temp 59 C
GDDR
- GDDR Vendor Samsung
- GDDR Version 0x6
- GDDR Density 4096 Mb
- GDDR Size 15872 MB
- GDDR Technology GDDR5
- GDDR Speed 5.500000 GT/s
- GDDR Frequency 2750000 kHz
- GDDR Voltage 1501000 uV
+ GDDR Vendor Samsung
+ GDDR Version 0x6
+ GDDR Density 4096 Mb
+ GDDR Size 15872 MB
+ GDDR Technology GDDR5
+ GDDR Speed 5.500000 GT/s
+ GDDR Frequency 2750000 kHz
+ GDDR Voltage 1501000 uV
Offload Mode
------------
To compile a code for Intel Xeon Phi a MPSS stack has to be installed on
the machine where compilation is executed. Currently the MPSS stack is
only installed on compute nodes equipped with accelerators.
- $ qsub -I -q qprod -l select=1ncpus=24accelerator=Truenaccelerators=2accelerator_model=phi7120 -A NONE-0-0
+ $ qsub -I -q qprod -l select=1:ncpus=24:accelerator=True:naccelerators=2:accelerator_model=phi7120 -A NONE-0-0
$ module load intel
For debugging purposes it is also recommended to set environment
variable "OFFLOAD_REPORT". Value can be set from 0 to 3, where higher
@@ -127,7 +129,7 @@ A very basic example of code that employs offload programming technique
is shown in the next listing. Please note that this code is sequential
and utilizes only single core of the accelerator.
$ vim source-offload.cpp
- #include
+ #include <iostream>
int main(int argc, char* argv[])
{
   const int niter = 100000;
@@ -138,7 +140,7 @@ and utilizes only single core of the accelerator.
       result += 4.0 / (t * t + 1.0);
   }
   result /= niter;
- Â Â Â stdcout << "Pi ~ " << result << 'n';
+ Â Â Â std::cout << "Pi ~ " << result << 'n';
}
To compile a code using Intel compiler run
$ icc source-offload.cpp -o bin-offload
@@ -149,7 +151,7 @@ One way of paralelization a code for Xeon Phi is using OpenMP
directives. The following example shows code for parallel vector
addition.Â
$ vim ./vect-add
- #include
+ #include <stdio.h>
typedef int T;
#define SIZE 1000
#pragma offload_attribute(push, target(mic))
@@ -213,52 +215,51 @@ vectorized in both host and accelerator. This can be enabled with
compiler option "-vec-report2". To compile and execute the code run
$ icc vect-add.c -openmp_report2 -vec-report2 -o vect-add
$ ./vect-add
-Some interesting compiler flags useful not only for code debugging are
+Some interesting compiler flags useful not only for code debugging are:
Debugging
 openmp_report[0|1|2] - controls the compiler based vectorization
diagnostic level
 vec-report[0|1|2] - controls the OpenMP parallelizer diagnostic
level
-
Performance ooptimization
 xhost - FOR HOST ONLY - to generate AVX (Advanced Vector Extensions)
instructions.
Automatic Offload using Intel MKL Library
------------------------------------------
+------------------
Intel MKL includes an Automatic Offload (AO) feature that enables
computationally intensive MKL functions called in user code to benefit
from attached Intel Xeon Phi coprocessors automatically and
transparently.
Behavioural of automatic offload mode is controlled by functions called
within the program or by environmental variables. Complete list of
-controls is listed [
-class="external-link">here](http//software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mkl_userguide_lnx/GUID-3DC4FC7D-A1E4-423D-9C0C-06AB265FFA86.htm).
+controls is listed [<span
+class="external-link">here</span>](http://software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mkl_userguide_lnx/GUID-3DC4FC7D-A1E4-423D-9C0C-06AB265FFA86.htm).
The Automatic Offload may be enabled by either an MKL function call
-within the code
+within the code:
mkl_mic_enable();
or by setting environment variable
$ export MKL_MIC_ENABLE=1
To get more information about automatic offload please refer to "[Using
Intel® MKL Automatic Offload on Intel ® Xeon Phi™
-Coprocessors](http//software.intel.com/sites/default/files/11MIC42_How_to_Use_MKL_Automatic_Offload_0.pdf)"
-white paper or [Intel MKL
-documentation](https//software.intel.com/en-us/articles/intel-math-kernel-library-documentation).
+Coprocessors](http://software.intel.com/sites/default/files/11MIC42_How_to_Use_MKL_Automatic_Offload_0.pdf)"
+white paper or [<span class="external-link">Intel MKL
+documentation</span>](https://software.intel.com/en-us/articles/intel-math-kernel-library-documentation).
### Automatic offload example #1
Following example show how to automatically offload an SGEMM (single
-precision - general matrix multiply) function to
+precision - g<span dir="auto">eneral matrix multiply</span>) function to
MIC coprocessor.
At first get an interactive PBS session on a node with MIC accelerator
and load "intel" module that automatically loads "mkl" module as well.
- $ qsub -I -q qprod -l select=1ncpus=24accelerator=Truenaccelerators=2accelerator_model=phi7120 -A NONE-0-0
+ $ qsub -I -q qprod -l select=1:ncpus=24:accelerator=True:naccelerators=2:accelerator_model=phi7120 -A NONE-0-0
$ module load intel
 The code can be copied to a file and compiled without any necessary
modification.Â
$ vim sgemm-ao-short.c
``` {.prettyprint .lang-cpp}
-#include
-#include
-#include
-#include
+#include <stdio.h>
+#include <stdlib.h>
+#include <malloc.h>
+#include <stdint.h>
#include "mkl.h"
int main(int argc, char **argv)
{
@@ -285,7 +286,7 @@ int main(int argc, char **argv)
       mkl_mic_enable();
      Â
       int ndevices = mkl_mic_get_device_count(); /* Number of MIC devices */
-       printf("Automatic Offload enabled %d MIC devices presentn",  ndevices);
+       printf("Automatic Offload enabled%d MIC devices presentn",  ndevices);
       printf("Computing SGEMM with automatic workdivisionn");
       sgemm(&transa, &transb, &N, &N, &N, &alpha, A, &N, B, &N, &beta, C, &N);
       /* Free the matrix memory */
@@ -294,20 +295,20 @@ int main(int argc, char **argv)
   return 0;
}
```
-Please note This example is simplified version of an example from MKL.
-The expanded version can be found here
+Please noteThis example is simplified version of an example from MKL.
+The expanded version can be found here:
**$MKL_EXAMPLES/mic_ao/blasc/source/sgemm.c**
-To compile a code using Intel compiler use
+To compile a code using Intel compiler use:
$ icc -mkl sgemm-ao-short.c -o sgemm
For debugging purposes enable the offload report to see more information
about automatic offloading.
$ export OFFLOAD_REPORT=2
The output of a code should look similar to following listing, where
-lines starting with [MKL] are generated by offload reporting
+lines starting with [MKL] are generated by offload reporting:
[user@r31u03n799 ~]$ ./sgemm
Computing SGEMM on the host
Enabling Automatic Offload
- Automatic Offload enabled 2 MIC devices present
+ Automatic Offload enabled2 MIC devices present
Computing SGEMM with automatic workdivision
[MKL] [MIC --] [AO Function]Â Â Â SGEMM
[MKL] [MIC --] [AO SGEMM Workdivision]Â Â Â 0.44 0.28 0.28
@@ -322,28 +323,28 @@ lines starting with [MKL] are generated by offload reporting
Done
Behavioral of automatic offload mode is controlled by functions called
within the program or by environmental variables. Complete list of
-controls is listed [
-class="external-link">here](http//software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mkl_userguide_lnx/GUID-3DC4FC7D-A1E4-423D-9C0C-06AB265FFA86.htm).
+controls is listed [<span
+class="external-link">here</span>](http://software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mkl_userguide_lnx/GUID-3DC4FC7D-A1E4-423D-9C0C-06AB265FFA86.htm).
To get more information about automatic offload please refer to "[Using
Intel® MKL Automatic Offload on Intel ® Xeon Phi™
-Coprocessors](http//software.intel.com/sites/default/files/11MIC42_How_to_Use_MKL_Automatic_Offload_0.pdf)"
-white paper or [Intel MKL
-documentation](https//software.intel.com/en-us/articles/intel-math-kernel-library-documentation).
+Coprocessors](http://software.intel.com/sites/default/files/11MIC42_How_to_Use_MKL_Automatic_Offload_0.pdf)"
+white paper or [<span class="external-link">Intel MKL
+documentation</span>](https://software.intel.com/en-us/articles/intel-math-kernel-library-documentation).
### Automatic offload example #2
In this example, we will demonstrate automatic offload control via an
environment vatiable MKL_MIC_ENABLE. The function DGEMM will be
offloaded.
At first get an interactive PBS session on a node with MIC accelerator.
- $ qsub -I -q qprod -l select=1ncpus=24accelerator=Truenaccelerators=2accelerator_model=phi7120 -A NONE-0-0
+ $ qsub -I -q qprod -l select=1:ncpus=24:accelerator=True:naccelerators=2:accelerator_model=phi7120 -A NONE-0-0
Once in, we enable the offload and run the Octave software. In octave,
we generate two large random matrices and let them multiply together.
$ export MKL_MIC_ENABLE=1
$ export OFFLOAD_REPORT=2
$ module load Octave/3.8.2-intel-2015b
$ octave -q
- octave1> A=rand(10000);
- octave2> B=rand(10000);
- octave3> C=A*B;
+ octave:1> A=rand(10000);
+ octave:2> B=rand(10000);
+ octave:3> C=A*B;
[MKL] [MIC --] [AO Function]Â Â Â DGEMM
[MKL] [MIC --] [AO DGEMM Workdivision]Â Â Â 0.14 0.43 0.43
[MKL] [MIC 00] [AO DGEMM CPU Time]Â Â Â 3.814714 seconds
@@ -354,7 +355,7 @@ we generate two large random matrices and let them multiply together.
[MKL] [MIC 01] [AO DGEMM MIC Time]Â Â Â 2.843016 seconds
[MKL] [MIC 01] [AO DGEMM CPU->MIC Data]Â Â Â 1145600000 bytes
[MKL] [MIC 01] [AO DGEMM MIC->CPU Data]Â Â Â 1382400000 bytes
- octave4> exit
+ octave:4> exit
On the example above we observe, that the DGEMM function workload was
split over CPU, MIC 0 and MIC 1, in the ratio 0.14 0.43 0.43. The matrix
multiplication was done on the CPU, accelerated by two Xeon Phi
@@ -366,20 +367,20 @@ without involvement of the host machine. Similarly to offload mode, the
code is compiled on the host computer with Intel compilers.
To compile a code user has to be connected to a compute with MIC and
load Intel compilers module. To get an interactive session on a compute
-node with an Intel Xeon Phi and load the module use following commandsÂ
- $ qsub -I -q qprod -l select=1ncpus=24accelerator=Truenaccelerators=2accelerator_model=phi7120 -A NONE-0-0
+node with an Intel Xeon Phi and load the module use following commands:Â
+ $ qsub -I -q qprod -l select=1:ncpus=24:accelerator=True:naccelerators=2:accelerator_model=phi7120 -A NONE-0-0
$ module load intel
Please note that particular version of the Intel module is specified.
This information is used later to specify the correct library paths.
To produce a binary compatible with Intel Xeon Phi architecture user has
to specify "-mmic" compiler flag. Two compilation examples are shown
below. The first example shows how to compile OpenMP parallel code
-"vect-add.c" for host only
+"vect-add.c" for host only:
$ icc -xhost -no-offload -fopenmp vect-add.c -o vect-add-host
-To run this code on host, use
+To run this code on host, use:
$ ./vect-add-host
The second example shows how to compile the same code for Intel Xeon
-Phi
+Phi:
$ icc -mmic -fopenmp vect-add.c -o vect-add-mic
### Execution of the Program in Native Mode on Intel Xeon Phi
The user access to the Intel Xeon Phi is through the SSH. Since user
@@ -387,128 +388,135 @@ home directories are mounted using NFS on the accelerator, users do not
have to copy binary files or libraries between the host and accelerator.
Â
Get the PATH of MIC enabled libraries for currently used Intel Compiler
-(here was icc/2015.3.187-GNU-5.1.0-2.25 used)
+(here was icc/2015.3.187-GNU-5.1.0-2.25 used) :
$ echo $MIC_LD_LIBRARY_PATH
/apps/all/icc/2015.3.187-GNU-5.1.0-2.25/composer_xe_2015.3.187/compiler/lib/mic
-To connect to the accelerator run
+To connect to the accelerator run:
$ ssh mic0
-If the code is sequential, it can be executed directly
+If the code is sequential, it can be executed directly:
mic0 $ ~/path_to_binary/vect-add-seq-mic
If the code is parallelized using OpenMP a set of additional libraries
is required for execution. To locate these libraries new path has to be
added to the LD_LIBRARY_PATH environment variable prior to the
-execution
- mic0 $ export LD_LIBRARY_PATH=/apps/all/icc/2015.3.187-GNU-5.1.0-2.25/composer_xe_2015.3.187/compiler/lib/mic$LD_LIBRARY_PATH
+execution:
+ mic0 $ export LD_LIBRARY_PATH=/apps/all/icc/2015.3.187-GNU-5.1.0-2.25/composer_xe_2015.3.187/compiler/lib/mic:$LD_LIBRARY_PATH
Please note that the path exported in the previous example contains path
to a specific compiler (here the version is 2015.3.187-GNU-5.1.0-2.25).
This version number has to match with the version number of the Intel
compiler module that was used to compile the code on the host computer.
For your information the list of libraries and their location required
-for execution of an OpenMP parallel code on Intel Xeon Phi is
-class="discreet visualHighlight">
-/apps/all/icc/2015.3.187-GNU-5.1.0-2.25/composer_xe_2015.3.187/compiler/lib/mic
-
+for execution of an OpenMP parallel code on Intel Xeon Phi is:<span
+class="discreet visualHighlight"></span>
+<span>/apps/all/icc/2015.3.187-GNU-5.1.0-2.25/composer_xe_2015.3.187/compiler/lib/mic
libiomp5.so
libimf.so
libsvml.so
libirng.so
libintlc.so.5
-Finally, to run the compiled code use
+</span>
+<span>Finally, to run the compiled code use</span>
$ ~/path_to_binary/vect-add-mic
-OpenCL
+<span>OpenCL</span>
-------------------
-OpenCL (Open Computing Language) is an open standard for
+<span>OpenCL (Open Computing Language) is an open standard for
general-purpose parallel programming for diverse mix of multi-core CPUs,
GPU coprocessors, and other parallel processors. OpenCL provides a
flexible execution model and uniform programming environment for
software developers to write portable code for systems running on both
the CPU and graphics processors or accelerators like the Intel® Xeon
-Phi.
-On Anselm OpenCL is installed only on compute nodes with MIC
+Phi.</span>
+<span>On Anselm OpenCL is installed only on compute nodes with MIC
accelerator, therefore OpenCL code can be compiled only on these nodes.
+</span>
module load opencl-sdk opencl-rt
-Always load "opencl-sdk" (providing devel files like headers) and
+<span>Always load "opencl-sdk" (providing devel files like headers) and
"opencl-rt" (providing dynamic library libOpenCL.so) modules to compile
and link OpenCL code. Load "opencl-rt" for running your compiled code.
-There are two basic examples of OpenCL code in the following
-directory
+</span>
+<span>There are two basic examples of OpenCL code in the following
+directory</span>
/apps/intel/opencl-examples/
-First example "CapsBasic" detects OpenCL compatible hardware, here
+<span>First example "CapsBasic" detects OpenCL compatible hardware, here
CPU and MIC, and prints basic information about the capabilities of
it.Â
+</span>
/apps/intel/opencl-examples/CapsBasic/capsbasic
-To compile and run the example copy it to your home directory, get
+<span>To compile and run the example copy it to your home directory, get
a PBS interactive session on of the nodes with MIC and run make for
compilation. Make files are very basic and shows how the OpenCL code can
-be compiled on Anselm.
+be compiled on Anselm. </span>
$ cp /apps/intel/opencl-examples/CapsBasic/* .
- $ qsub -I -q qprod -l select=1ncpus=24accelerator=Truenaccelerators=2accelerator_model=phi7120 -A NONE-0-0
+ $ qsub -I -q qprod -l select=1:ncpus=24:accelerator=True:naccelerators=2:accelerator_model=phi7120 -A NONE-0-0
$ make
-The compilation command for this example is
+<span>The compilation command for this example is</span>
$ g++ capsbasic.cpp -lOpenCL -o capsbasic -I/apps/intel/opencl/include/
-After executing the complied binary file, following output should
+<span>After executing the complied binary file, following output should
be displayed.
+</span>
./capsbasic
- Number of available platforms 1
- Platform names
+ Number of available platforms1
+ Platform names:
   [0] Intel(R) OpenCL [Selected]
- Number of devices available for each type
- Â Â Â CL_DEVICE_TYPE_CPU 1
- Â Â Â CL_DEVICE_TYPE_GPU 0
- Â Â Â CL_DEVICE_TYPE_ACCELERATOR 1
+ Number of devices available for each type:
+ Â Â Â CL_DEVICE_TYPE_CPU1
+ Â Â Â CL_DEVICE_TYPE_GPU0
+ Â Â Â CL_DEVICE_TYPE_ACCELERATOR1
*** Detailed information for each device ***
CL_DEVICE_TYPE_CPU[0]
- Â Â Â CL_DEVICE_NAMEÂ Â Â Â Â Â Â Intel(R) Xeon(R) CPU E5-2470 0 @ 2.30GHz
- Â Â Â CL_DEVICE_AVAILABLE 1
+ Â Â Â CL_DEVICE_NAME:Â Â Â Â Â Â Â Intel(R) Xeon(R) CPU E5-2470 0 @ 2.30GHz
+ Â Â Â CL_DEVICE_AVAILABLE1
...
CL_DEVICE_TYPE_ACCELERATOR[0]
- Â Â Â CL_DEVICE_NAME Intel(R) Many Integrated Core Acceleration Card
- Â Â Â CL_DEVICE_AVAILABLE 1
+ Â Â Â CL_DEVICE_NAMEIntel(R) Many Integrated Core Acceleration Card
+ Â Â Â CL_DEVICE_AVAILABLE1
...
-More information about this example can be found on Intel website
-
-The second example that can be found in
-"/apps/intel/opencl-examples" directory is General Matrix
+<span>More information about this example can be found on Intel website:
+<http://software.intel.com/en-us/vcsource/samples/caps-basic/>
+</span>
+<span>The second example that can be found in
+"/apps/intel/opencl-examples" </span><span>directory is General Matrix
Multiply. You can follow the the same procedure to download the example
to your directory and compile it.Â
+</span>
$ cp -r /apps/intel/opencl-examples/* .
- $ qsub -I -q qprod -l select=1ncpus=24accelerator=Truenaccelerators=2accelerator_model=phi7120 -A NONE-0-0
+ $ qsub -I -q qprod -l select=1:ncpus=24:accelerator=True:naccelerators=2:accelerator_model=phi7120 -A NONE-0-0
$ cd GEMM
$ make
-The compilation command for this example is
+<span>The compilation command for this example is</span>
$ g++ cmdoptions.cpp gemm.cpp ../common/basic.cpp ../common/cmdparser.cpp ../common/oclobject.cpp -I../common -lOpenCL -o gemm -I/apps/intel/opencl/include/
-To see the performance of Intel Xeon Phi performing the DGEMM run
-the example as follows
+<span>To see the performance of Intel Xeon Phi performing the DGEMM run
+the example as follows</span>
./gemm -d 1
- Platforms (1)
+ Platforms (1):
[0] Intel(R) OpenCL [Selected]
- Devices (2)
+ Devices (2):
[0] Intel(R) Xeon(R) CPU E5-2470 0 @ 2.30GHz
[1] Intel(R) Many Integrated Core Acceleration Card [Selected]
- Build program options "-DT=float -DTILE_SIZE_M=1 -DTILE_GROUP_M=16 -DTILE_SIZE_N=128 -DTILE_GROUP_N=1 -DTILE_SIZE_K=8"
- Running gemm_nn kernel with matrix size 3968x3968
- Memory row stride to ensure necessary alignment 15872 bytes
- Size of memory region for one matrix 62980096 bytes
+ Build program options"-DT=float -DTILE_SIZE_M=1 -DTILE_GROUP_M=16 -DTILE_SIZE_N=128 -DTILE_GROUP_N=1 -DTILE_SIZE_K=8"
+ Running gemm_nn kernel with matrix size3968x3968
+ Memory row stride to ensure necessary alignment15872 bytes
+ Size of memory region for one matrix62980096 bytes
Using alpha = 0.57599 and beta = 0.872412
...
- Host time 0.292953 sec.
- Host perf 426.635 GFLOPS
- Host time 0.293334 sec.
- Host perf 426.081 GFLOPS
+ Host time0.292953 sec.
+ Host perf426.635 GFLOPS
+ Host time0.293334 sec.
+ Host perf426.081 GFLOPS
...
-Please note GNU compiler is used to compile the OpenCL codes for
+<span>Please noteGNU compiler is used to compile the OpenCL codes for
Intel MIC. You do not need to load Intel compiler module.
-MPI
+</span>
+<span>MPI</span>
----------------
### Environment setup and compilation
To achieve best MPI performance always use following setup for Intel MPI
-on Xeon Phi accelerated nodes
- $ export I_MPI_FABRICS=shmdapl
+on Xeon Phi accelerated nodes:
+ $ export I_MPI_FABRICS=shm:dapl
$ export I_MPI_DAPL_PROVIDER_LIST=ofa-v2-mlx4_0-1u,ofa-v2-scif0,ofa-v2-mcm-1
This ensures, that MPI inside node will use SHMEM communication, between
HOST and Phi the IB SCIF will be used and between different nodes or
Phi's on diferent nodes a CCL-Direct proxy will be used.
-Please note Other FABRICS like tcp,ofa may be used (even combined with
+Please noteOther FABRICS like tcp,ofa may be used (even combined with
shm) but there's severe loss of performance (by order of magnitude).
Usage of single DAPL PROVIDER (e. g.
I_MPI_DAPL_PROVIDER=ofa-v2-mlx4_0-1u) will cause failure of
@@ -518,25 +526,25 @@ cause failure of any MPI communication, since those nodes don't have
SCIF device and there's no CCL-Direct proxy runnig.
Again an MPI code for Intel Xeon Phi has to be compiled on a compute
node with accelerator and MPSS software stack installed. To get to a
-compute node with accelerator use
- $ qsub -I -q qprod -l select=1ncpus=24accelerator=Truenaccelerators=2accelerator_model=phi7120 -A NONE-0-0
+compute node with accelerator use:
+ $ qsub -I -q qprod -l select=1:ncpus=24:accelerator=True:naccelerators=2:accelerator_model=phi7120 -A NONE-0-0
The only supported implementation of MPI standard for Intel Xeon Phi is
Intel MPI. To setup a fully functional development environment a
combination of Intel compiler and Intel MPI has to be used. On a host
-load following modules before compilation
+load following modules before compilation:
$ module load intel impi
-To compile an MPI code for host use
+To compile an MPI code for host use:
$ mpiicc -xhost -o mpi-test mpi-test.c
-To compile the same code for Intel Xeon Phi architecture use
+To compile the same code for Intel Xeon Phi architecture use:
$ mpiicc -mmic -o mpi-test-mic mpi-test.c
-Or, if you are using Fortran
+Or, if you are using Fortran :
$ mpiifort -mmic -o mpi-test-mic mpi-test.f90
An example of basic MPI version of "hello-world" example in C language,
that can be executed on both host and Xeon Phi is (can be directly copy
and pasted to a .c file)
``` {.prettyprint .lang-cpp}
-#include
-#include
+#include <stdio.h>
+#include <mpi.h>
int main (argc, argv)
    int argc;
    char *argv[];
@@ -554,31 +562,30 @@ int main (argc, argv)
}
```
### MPI programming models
-Intel MPI for the Xeon Phi coprocessors offers different MPI
-programming models
+<span>Intel MPI for the Xeon Phi coprocessors offers different MPI
+programming models:</span>
**Host-only model** - all MPI ranks reside on the host. The coprocessors
can be used by using offload pragmas. (Using MPI calls inside offloaded
code is not supported.)**
-
Coprocessor-only model** - all MPI ranks reside only on the
coprocessors.
-
**Symmetric model** - the MPI ranks reside on both the host and the
coprocessor. Most general MPI case.
-### Host-only model
-In this case all environment variables are set by modules,
-so to execute the compiled MPI program on a single node, use
+### <span>Host-only model</span>
+<span></span>In this case all environment variables are set by modules,
+so to execute the compiled MPI program on a single node, use:
$ mpirun -np 4 ./mpi-test
-The output should be similar to
+The output should be similar to:
Hello world from process 1 of 4 on host r38u31n1000
Hello world from process 3 of 4 on host r38u31n1000
Hello world from process 2 of 4 on host r38u31n1000
Hello world from process 0 of 4 on host r38u31n1000
### Coprocessor-only model
-There are two ways how to execute an MPI code on a single
-coprocessor 1.) lunch the program using "**mpirun**" from the
+<span>There are two ways how to execute an MPI code on a single
+coprocessor1.) lunch the program using "**mpirun**" from the
coprocessor; or 2.) lunch the task using "**mpiexec.hydra**" from a
host.
+</span>
**Execution on coprocessor**Â
Similarly to execution of OpenMP programs in native mode, since the
environmental module are not supported on MIC, user has to setup paths
@@ -587,32 +594,32 @@ by creating a "**.profile**" file in user's home directory. This file
sets up the environment on the MIC automatically once user access to the
accelerator through the SSH.
At first get the LD_LIBRARY_PATH for currenty used Intel Compiler and
-Intel MPI
+Intel MPI:
$ echo $MIC_LD_LIBRARY_PATH
- /apps/all/imkl/11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25/mkl/lib/mic/apps/all/imkl/11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25/lib/mic/apps/all/icc/2015.3.187-GNU-5.1.0-2.25/composer_xe_2015.3.187/compiler/lib/mic/
-Use it in your ~/.profile
+ /apps/all/imkl/11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25/mkl/lib/mic:/apps/all/imkl/11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25/lib/mic:/apps/all/icc/2015.3.187-GNU-5.1.0-2.25/composer_xe_2015.3.187/compiler/lib/mic/
+Use it in your ~/.profile:
$ vim ~/.profile
PS1='[u@h W]$ '
- export PATH=/usr/bin/usr/sbin/bin/sbin
+ export PATH=/usr/bin:/usr/sbin:/bin:/sbin
#IMPI
- export PATH=/apps/all/impi/5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25/mic/bin/$PATH
+ export PATH=/apps/all/impi/5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25/mic/bin/:$PATH
#OpenMP (ICC, IFORT), IMKL and IMPI
- export LD_LIBRARY_PATH=/apps/all/imkl/11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25/mkl/lib/mic/apps/all/imkl/11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25/lib/mic/apps/all/icc/2015.3.187-GNU-5.1.0-2.25/composer_xe_2015.3.187/compiler/lib/mic$LD_LIBRARY_PATH
-Please note
+ export LD_LIBRARY_PATH=/apps/all/imkl/11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25/mkl/lib/mic:/apps/all/imkl/11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25/lib/mic:/apps/all/icc/2015.3.187-GNU-5.1.0-2.25/composer_xe_2015.3.187/compiler/lib/mic:$LD_LIBRARY_PATH
+Please note:
 - this file sets up both environmental variable for both MPI and OpenMP
libraries.
 - this file sets up the paths to a particular version of Intel MPI
library and particular version of an Intel compiler. These versions have
to match with loaded modules.
To access a MIC accelerator located on a node that user is currently
-connected to, use
+connected to, use:
$ ssh mic0
-or in case you need specify a MIC accelerator on a particular node, use
+or in case you need specify a MIC accelerator on a particular node, use:
$ ssh r38u31n1000-mic0
To run the MPI code in parallel on multiple core of the accelerator,
-use
+use:
$ mpirun -np 4 ./mpi-test-mic
-The output should be similar to
+The output should be similar to:
Hello world from process 1 of 4 on host r38u31n1000-mic0
Hello world from process 2 of 4 on host r38u31n1000-mic0
Hello world from process 3 of 4 on host r38u31n1000-mic0
@@ -626,76 +633,78 @@ user has to specify library paths from the command line when calling
First step is to tell mpiexec that the MPI should be executed on a local
accelerator by setting up the environmental variable "I_MPI_MIC"
$ export I_MPI_MIC=1
-Now the MPI program can be executed as
+Now the MPI program can be executed as:
$ mpirun -genv LD_LIBRARY_PATH $MIC_LD_LIBRARY_PATH -host mic0 -n 4 ~/mpi-test-mic
or using mpirun
$ mpirun -genv LD_LIBRARY_PATH $MIC_LD_LIBRARY_PATH -host mic0 -n 4 ~/mpi-test-mic
-Please note
-Â - the full path to the binary has to specified (here
-"**~/mpi-test-mic**")
+Please note:
+Â - the full path to the binary has to specified (here:
+"**<span>~/mpi-test-mic</span>**")
 - the LD_LIBRARY_PATH has to match with Intel MPI module used to
compile the MPI code
-The output should be again similar to
+The output should be again similar to:
Hello world from process 1 of 4 on host r38u31n1000-mic0
Hello world from process 2 of 4 on host r38u31n1000-mic0
Hello world from process 3 of 4 on host r38u31n1000-mic0
Hello world from process 0 of 4 on host r38u31n1000-mic0
Please note that the "mpiexec.hydra" requires a file
-"**pmi_proxy**" from Intel MPI library to be copied to the
+"**<span>pmi_proxy</span>**" from Intel MPI library to be copied to the
MIC filesystem. If the file is missing please contact the system
administrators. A simple test to see if the file is present is to
-execute
+execute:
  $ ssh mic0 ls /bin/pmi_proxy
 /bin/pmi_proxy
**Â **
**Execution on host - MPI processes distributed over multiple
accelerators on multiple nodes**
-To get access to multiple nodes with MIC accelerator, user has to
+<span>To get access to multiple nodes with MIC accelerator, user has to
use PBS to allocate the resources. To start interactive session, that
allocates 2 compute nodes = 2 MIC accelerators run qsub command with
-following parameters
- $ qsub -I -q qprod -l select=2ncpus=24accelerator=Truenaccelerators=2accelerator_model=phi7120 -A NONE-0-0
+following parameters</span>
+ $ qsub -I -q qprod -l select=2:ncpus=24:accelerator=True:naccelerators=2:accelerator_model=phi7120 -A NONE-0-0
$ module load intel impi
-This command connects user through ssh to one of the nodes
-immediately. To see the other nodes that have been allocated use
+<span>This command connects user through ssh to one of the nodes
+immediately. To see the other nodes that have been allocated use:
+</span>
$ cat $PBS_NODEFILE
-For example
+<span>For example</span>
r38u31n1000.bullx
r38u32n1001.bullx
-This output means that the PBS allocated nodes r38u31n1000 and
+<span>This output means that the PBS allocated nodes r38u31n1000 and
r38u32n1001, which means that user has direct access to
-"**r38u31n1000-mic0**" and "**r38u32n1001-mic0**"
-accelerators.
-Please note At this point user can connect to any of the
-allocated nodes or any of the allocated MIC accelerators using ssh
-- to connect to the second node **$
-ssh r38u32n1001**
-- to connect to the accelerator on the first node from the first
-node **$ ssh
-r38u31n1000-mic0** or **
-class="monospace">$ ssh mic0**
+"**r38u31n1000-mic0**" and "**<span>r38u32n1001</span>-mic0**"
+accelerators.</span>
+<span>Please noteAt this point user can connect to any of the
+allocated nodes or any of the allocated MIC accelerators using ssh:
+- to connect to the second node **<span class="monospace">$
+ssh <span>r38u32n1001</span></span>**
+<span>- to connect to the accelerator on the first node from the first
+node<span class="monospace">**$ ssh
+<span>r38u31n1000</span>-mic0**</span></span> or **<span
+class="monospace">$ ssh mic0</span>**
**-** to connect to the accelerator on the second node from the first
-node **$ ssh
-r38u32n1001-mic0**
-At this point we expect that correct modules are loaded and binary
-is compiled. For parallel execution the mpiexec.hydra is used.
+node<span class="monospace">**$ ssh
+<span>r38u32n1001</span>-mic0**</span>
+</span>
+<span>At this point we expect that correct modules are loaded and binary
+is compiled. For parallel execution the mpiexec.hydra is used.</span>
Again the first step is to tell mpiexec that the MPI can be executed on
MIC accelerators by setting up the environmental variable "I_MPI_MIC",
don't forget to have correct FABRIC and PROVIDER defined.
$ export I_MPI_MIC=1
- $ export I_MPI_FABRICS=shmdapl
+ $ export I_MPI_FABRICS=shm:dapl
$ export I_MPI_DAPL_PROVIDER_LIST=ofa-v2-mlx4_0-1u,ofa-v2-scif0,ofa-v2-mcm-1
-The launch the MPI program use
+<span>The launch the MPI program use:</span>
$ mpirun -genv LD_LIBRARY_PATH $MIC_LD_LIBRARY_PATH
-host r38u31n1000-mic0 -n 4 ~/mpi-test-mic
- -host r38u32n1001-mic0 -n 6 ~/mpi-test-mic
-or using mpirun
+ -host r38u32n1001-mic0 -n 6 ~/mpi-test-mic
+or using mpirun:
$ mpirun -genv LD_LIBRARY_PATH
-host r38u31n1000-mic0 -n 4 ~/mpi-test-mic
- -host r38u32n1001-mic0 -n 6 ~/mpi-test-mic
+ -host r38u32n1001-mic0 -n 6 ~/mpi-test-mic
In this case four MPI processes are executed on accelerator
r38u31n1000-mic and six processes are executed on accelerator
-r38u32n1001-mic0. The sample output (sorted after execution) is
+r38u32n1001-mic0. The sample output (sorted after execution) is:
Hello world from process 0 of 10 on host r38u31n1000-mic0
Hello world from process 1 of 10 on host r38u31n1000-mic0
Hello world from process 2 of 10 on host r38u31n1000-mic0
@@ -706,45 +715,48 @@ r38u32n1001-mic0. The sample output (sorted after execution) is
Hello world from process 7 of 10 on host r38u32n1001-mic0
Hello world from process 8 of 10 on host r38u32n1001-mic0
Hello world from process 9 of 10 on host r38u32n1001-mic0
-The same way MPI program can be executed on multiple hostsÂ
+The same way MPI program can be executed on multiple hosts:Â
$ mpirun -genv LD_LIBRARY_PATH $MIC_LD_LIBRARY_PATH
-host r38u31n1000 -n 4 ~/mpi-test
- -host r38u32n1001 -n 6 ~/mpi-test
-### Symmetric model
-In a symmetric mode MPI programs are executed on both host
+ -host r38u32n1001 -n 6 ~/mpi-test
+### <span>Symmetric model </span>
+<span>In a symmetric mode MPI programs are executed on both host
computer(s) and MIC accelerator(s). Since MIC has a different
architecture and requires different binary file produced by the Intel
compiler two different files has to be compiled before MPI program is
-executed.
-In the previous section we have compiled two binary files, one for
+executed. </span>
+<span>In the previous section we have compiled two binary files, one for
hosts "**mpi-test**" and one for MIC accelerators "**mpi-test-mic**".
-These two binaries can be executed at once using mpiexec.hydra
+These two binaries can be executed at once using mpiexec.hydra:
+</span>
$ mpirun
-genv $MIC_LD_LIBRARY_PATH
-host r38u32n1001 -n 2 ~/mpi-test
- -host r38u32n1001-mic0 -n 2 ~/mpi-test-mic
+ -host r38u32n1001-mic0 -n 2 ~/mpi-test-mic
In this example the first two parameters (line 2 and 3) sets up required
environment variables for execution. The third line specifies binary
that is executed on host (here r38u32n1001) and the last line specifies
the binary that is execute on the accelerator (here r38u32n1001-mic0).
-The output of the program is
+<span>The output of the program is</span>
Hello world from process 0 of 4 on host r38u32n1001
Hello world from process 1 of 4 on host r38u32n1001
Hello world from process 2 of 4 on host r38u32n1001-mic0
Hello world from process 3 of 4 on host r38u32n1001-mic0
-The execution procedure can be simplified by using the mpirun
+<span>The execution procedure can be simplified by using the mpirun
command with the machine file a a parameter. Machine file contains list
of all nodes and accelerators that should used to execute MPI processes.
-An example of a machine file that uses 2 hosts (r38u32n1001
+</span>
+<span>An example of a machine file that uses 2 <span>hosts (r38u32n1001
and r38u33n1002) and 2 accelerators **(r38u32n1001-mic0** and
-**r38u33n1002-mic0**) to run 2 MPI processes
-on each of them
+**<span><span>r38u33n1002</span></span>-mic0**) to run 2 MPI processes
+on each</span> of them:
+</span>
$ cat hosts_file_mix
- r38u32n10012
- r38u32n1001-mic02
- r38u33n10022
- r38u33n1002-mic02
-In addition if a naming convention is set in a way that the name
+ r38u32n1001:2
+ r38u32n1001-mic0:2
+ r38u33n1002:2
+ r38u33n1002-mic0:2
+<span>In addition if a naming convention is set in a way that the name
of the binary for host is **"bin_name"**Â and the name of the binary
for the accelerator is **"bin_name-mic"** then by setting up the
environment variable **I_MPI_MIC_POSTFIX** to **"-mic"** user do not
@@ -752,15 +764,18 @@ have to specify the names of booth binaries. In this case mpirun needs
just the name of the host binary file (i.e. "mpi-test") and uses the
suffix to get a name of the binary for accelerator (i..e.
"mpi-test-mic").
+</span>
$ export I_MPI_MIC_POSTFIX=-mic
-Â To run the MPI code using mpirun and the machine file
-"hosts_file_mix" use
+Â <span>To run the MPI code using mpirun and the machine file
+"hosts_file_mix" use:
+</span>
$ mpirun
-genv LD_LIBRARY_PATH $MIC_LD_LIBRARY_PATH
-machinefile hosts_file_mix
~/mpi-test
-A possible output of the MPI "hello-world" example executed on two
-hosts and two accelerators is
+<span>A possible output of the MPI "hello-world" example executed on two
+hosts and two accelerators is:
+</span>
Hello world from process 0 of 8 on host r38u31n1000
Hello world from process 1 of 8 on host r38u31n1000
Hello world from process 2 of 8 on host r38u31n1000-mic0
@@ -772,12 +787,12 @@ hosts and two accelerators is
**Using the PBS automatically generated node-files
**
PBS also generates a set of node-files that can be used instead of
-manually creating a new one every time. Three node-files are genereated
-**Host only node-file**
+manually creating a new one every time. Three node-files are genereated:
+**Host only node-file:**
 - /lscratch/${PBS_JOBID}/nodefile-cn
-**MIC only node-file**
+**MIC only node-file**:
 - /lscratch/${PBS_JOBID}/nodefile-mic
-**Host and MIC node-file**
+**Host and MIC node-file**:
 - /lscratch/${PBS_JOBID}/nodefile-mix
Please note each host or accelerator is listed only per files. User has
to specify how many jobs should be executed per node using "-n"
@@ -786,48 +801,5 @@ Optimization
------------
For more details about optimization techniques please read Intel
document [Optimization and Performance Tuning for Intel® Xeon Phi™
-Coprocessors](http//software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization "http//software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization"){.external
+Coprocessors](http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization "http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization"){.external
.text}.
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- - [What's New](../../whats-new.html)
-
- - [Get Started with
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-
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- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [List of Available
- Modules](../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
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- - [ANSYS](ansys.html "An engineering simulation software ")
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diff --git a/acl_users/credentials_cookie_auth/require_login888f.html b/docs.it4i.cz/salomon/software/isv_licenses.html
old mode 100755
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--- a/acl_users/credentials_cookie_auth/require_login888f.html
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<title>IT4I Docs</title>
- <link rel="canonical" href="../../index.html" />
+ <link rel="canonical" href="https://docs.it4i.cz" />
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+ <a accesskey="2" href="https://docs.it4i.cz/acl_users/credentials_cookie_auth/require_login?came_from=https%3A//docs.it4i.cz/salomon/software/isv_licenses#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="require_login888f.html?came_from=https%3A//docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/acl_users/credentials_cookie_auth/require_login?came_from=https%3A//docs.it4i.cz/salomon/software/isv_licenses#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<div id="portal-advanced-search" class="hiddenStructure">
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+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
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<div id="login-form">
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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diff --git a/docs.it4i.cz/salomon/software/isv_licenses.md b/docs.it4i.cz/salomon/software/isv_licenses.md
new file mode 100644
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+ <base href="https://docs.it4i.cz/salomon/software/java" /><!--[if lt IE 7]></base><![endif]-->
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<title>Java — IT4I Docs</title>
- <link rel="canonical" href="java.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/java" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
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+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
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<script type="text/javascript">
@@ -64,7 +61,7 @@
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
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<div id="portal-header">
<p class="hiddenStructure">
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- <a accesskey="6" href="java.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/java#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<div id="portal-personaltools-wrapper">
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<div id="portal-advanced-search" class="hiddenStructure">
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- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
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</span>
<span id="breadcrumbs-1" dir="ltr">
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</span>
<span id="breadcrumbs-2" dir="ltr">
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+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
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/
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<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -357,7 +354,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -373,7 +370,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -389,7 +386,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -405,7 +402,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -421,7 +418,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -437,7 +434,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -453,7 +450,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -469,7 +466,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -485,7 +482,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -501,7 +498,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -517,10 +514,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -536,7 +533,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -552,7 +549,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -568,7 +565,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -584,7 +581,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -600,7 +597,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -616,7 +613,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -632,7 +629,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -648,7 +645,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -664,7 +661,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -680,7 +677,7 @@
- <a title="Java on the cluster" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="java.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -696,7 +693,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -721,7 +718,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -746,7 +743,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -762,7 +759,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -778,7 +775,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -794,7 +791,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/java by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:33 GMT -->
</html>
diff --git a/docs.it4i.cz/salomon/software/java.md b/docs.it4i.cz/salomon/software/java.md
new file mode 100644
index 0000000000000000000000000000000000000000..f691a0796ac6ba0def45375392cb1fb47a973a42
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/java.md
@@ -0,0 +1,22 @@
+Java
+====
+Java on the cluster
+
+Java is available on the cluster. Activate java by loading the Java
+module
+ $ module load Java
+Note that the Java module must be loaded on the compute nodes as well,
+in order to run java on compute nodes.
+Check for java version and path
+ $ java -version
+ $ which java
+With the module loaded, not only the runtime environment (JRE), but also
+the development environment (JDK) with the compiler is available.
+ $ javac -version
+ $ which javac
+Java applications may use MPI for interprocess communication, in
+conjunction with OpenMPI. Read more
+on <http://www.open-mpi.org/faq/?category=java>.
+This functionality is currently not supported on Anselm cluster. In case
+you require the java interface to MPI, please contact [cluster
+support](https://support.it4i.cz/rt/).
diff --git a/salomon/software/mpi-1.html b/docs.it4i.cz/salomon/software/mpi-1.html
old mode 100755
new mode 100644
similarity index 70%
rename from salomon/software/mpi-1.html
rename to docs.it4i.cz/salomon/software/mpi-1.html
index 187c0966c542b1db6b9ab3dfdcca2fa37849beb8..e853184e2feefda46dac88b7c343f3b4032696e7
--- a/salomon/software/mpi-1.html
+++ b/docs.it4i.cz/salomon/software/mpi-1.html
@@ -10,45 +10,42 @@
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/mpi-1/mpi" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>MPI — IT4I Docs</title>
- <link rel="canonical" href="mpi-1.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/mpi-1" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="mpi-1.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/mpi-1#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="mpi-1.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/mpi-1#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -285,7 +282,7 @@
</table>
<p>Examples:</p>
<pre class=" ">$ module load gompi/2015b</pre>
-<p>In this example, we activate the latest OpenMPI with latest GNU compilers (OpenMPI 1.8.6 and GCC 5.1). Please see more information about toolchains in section <a href="../environment-and-modules.html">Environment and Modules</a> .</p>
+<p>In this example, we activate the latest OpenMPI with latest GNU compilers (OpenMPI 1.8.6 and GCC 5.1). Please see more information about toolchains in section <a href="https://docs.it4i.cz/salomon/environment-and-modules">Environment and Modules</a> .</p>
<p>To use OpenMPI with the intel compiler suite, use</p>
<pre class=" ">$ module load iompi/2015.03</pre>
<p>In this example, the openmpi 1.8.6 using intel compilers is activated. It's used "iompi" toolchain.</p>
@@ -312,9 +309,9 @@
<p>In the previous two cases with one or two MPI processes per node, the operating system might still migrate OpenMP threads between cores. You want to avoid this by setting the KMP_AFFINITY or GOMP_CPU_AFFINITY environment variables.</p>
<p class=" "><strong class=" ">24 MPI</strong> processes per node, using 1 thread each bound to processor core is most suitable for highly scalable applications with low communication demand.</p>
<h3 class=" ">Running OpenMPI</h3>
-<p>The <a class="external-link" href="http://www.open-mpi.org/" target="_self" title=""><strong>OpenMPI 1.8.6</strong></a> is based on OpenMPI. Read more on <a target="_self" title="" class="internal-link" href="mpi-1/Running_OpenMPI.html">how to run OpenMPI</a> based MPI.</p>
+<p>The <a class="external-link" href="http://www.open-mpi.org/" target="_self" title=""><strong>OpenMPI 1.8.6</strong></a> is based on OpenMPI. Read more on <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI">how to run OpenMPI</a> based MPI.</p>
<p>Â </p>
-<p>The Intel MPI may run on the<a target="_self" title="" class="internal-link" href="intel-xeon-phi.html"> Intel Xeon Ph</a>i accelerators as well. Read more on <a target="_self" title="" class="internal-link" href="intel-xeon-phi.html">how to run Intel MPI on accelerators</a>.</p>
+<p>The Intel MPI may run on the<a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi"> Intel Xeon Ph</a>i accelerators as well. Read more on <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">how to run Intel MPI on accelerators</a>.</p>
</div>
@@ -390,7 +387,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -406,7 +403,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -422,7 +419,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -438,7 +435,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -454,7 +451,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -470,7 +467,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -486,7 +483,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -502,7 +499,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -518,7 +515,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -534,7 +531,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -550,7 +547,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -566,7 +563,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -582,10 +579,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -601,7 +598,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -617,7 +614,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -633,7 +630,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -649,7 +646,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -665,7 +662,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -681,7 +678,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -697,7 +694,7 @@
- <a title="" class="state-published contenttype-document" href="mpi-1/Running_OpenMPI.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI">
<span>Running OpenMPI</span>
</a>
@@ -713,7 +710,7 @@
- <a title="OpenMPI interface to Python" class="state-published contenttype-document" href="mpi-1/mpi4py-mpi-for-python.html">
+ <a class="state-published contenttype-document" title="OpenMPI interface to Python" href="https://docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python">
<span>MPI4Py (MPI for Python)</span>
</a>
@@ -738,7 +735,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -754,7 +751,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -770,7 +767,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -786,7 +783,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -802,7 +799,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -827,7 +824,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -852,7 +849,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -868,7 +865,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -884,7 +881,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -900,7 +897,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -939,14 +936,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -968,12 +965,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -989,7 +986,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/mpi-1 by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:33 GMT -->
</html>
diff --git a/salomon/software/mpi-1.md b/docs.it4i.cz/salomon/software/mpi-1.md
similarity index 62%
rename from salomon/software/mpi-1.md
rename to docs.it4i.cz/salomon/software/mpi-1.md
index 8249c5a7f5d5c022cbdc8192194df717257ec63d..553d8c78eb2098d52573a463319358226f1359db 100644
--- a/salomon/software/mpi-1.md
+++ b/docs.it4i.cz/salomon/software/mpi-1.md
@@ -1,10 +1,12 @@
-
+MPI
+===
+
Setting up MPI Environment
---------------------------
-The Salomon cluster provides several implementations of the MPI library
- -------------------------------------------------------------------------
+---
+The Salomon cluster provides several implementations of the MPI library:
+ ----
MPI Library Thread support
- ------------------------------------ ------------------------------------
+ ------------- -------------
**Intel MPI 4.1** Full thread support up to
MPI_THREAD_MULTIPLE
**Intel MPI 5.0** Full thread support up to
@@ -13,11 +15,11 @@ The Salomon cluster provides several implementations of the MPI library
MPI_THREAD_MULTIPLE, MPI-3.0
support
SGI MPT 2.12
- -------------------------------------------------------------------------
+ ----
MPI libraries are activated via the environment modules.
Look up section modulefiles/mpi in module avail
$ module avail
- ------------------------------ /apps/modules/mpi -------------------------------
+ ------- /apps/modules/mpi --------
impi/4.1.1.036-iccifort-2013.5.192
impi/4.1.1.036-iccifort-2013.5.192-GCC-4.8.3
impi/5.0.3.048-iccifort-2015.3.187
@@ -28,20 +30,20 @@ There are default compilers associated with any particular MPI
implementation. The defaults may be changed, the MPI libraries may be
used in conjunction with any compiler.
The defaults are selected via the modules in following way
- --------------------------------------------------------------------------
+ -----
Module MPI Compiler suite
- ------------------------ ------------------------ ------------------------
+ - - -
impi-5.0.3.048-iccifort- Intel MPI 5.0.3
2015.3.187
OpenMP-1.8.6-GNU-5.1.0-2 OpenMPI 1.8.6
.25
- --------------------------------------------------------------------------
-Examples
+ -----
+Examples:
$ module load gompi/2015b
In this example, we activate the latest OpenMPI with latest GNU
compilers (OpenMPI 1.8.6 and GCC 5.1). Please see more information about
toolchains in section [Environment and
-Modules](../environment-and-modules.html)Â .
+Modules](https://docs.it4i.cz/salomon/environment-and-modules)Â .
To use OpenMPI with the intel compiler suite, use
$ module load iompi/2015.03
In this example, the openmpi 1.8.6 using intel compilers is activated.
@@ -53,17 +55,17 @@ the mpi wrappers
$ mpicc -v
$ mpif77 -v
$ mpif90 -v
-When using Intel MPI, use the following MPI wrappers
+When using Intel MPI, use the following MPI wrappers:
$ mpicc
$ mpiifortÂ
Wrappers mpif90, mpif77 that are provided by Intel MPI are designed for
gcc and gfortran. You might be able to compile MPI code by them even
with Intel compilers, but you might run into problems (for example,
native MIC compilation with -mmic does not work with mpif90).
-Example program
+Example program:
// helloworld_mpi.c
- #include
- #include
+ #include <stdio.h>
+ #include<mpi.h>
int main(int argc, char **argv) {
int len;
int rank, size;
@@ -96,7 +98,7 @@ scratch /lscratch filesystem.
### Ways to run MPI programs
Optimal way to run an MPI program depends on its memory requirements,
memory access pattern and communication pattern.
-Consider these ways to run an MPI program
+Consider these ways to run an MPI program:
1. One MPI process per node, 24 threads per process
2. Two MPI processes per node, 12 threads per process
3. 24 MPI processes per node, 1 thread per process.
@@ -120,60 +122,12 @@ environment variables.
core is most suitable for highly scalable applications with low
communication demand.
### Running OpenMPI
-The [**OpenMPI 1.8.6**](http//www.open-mpi.org/) is
+The [**OpenMPI 1.8.6**](http://www.open-mpi.org/) is
based on OpenMPI. Read more on [how to run
-OpenMPI](mpi-1/Running_OpenMPI.html) based MPI.
+OpenMPI](https://docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI)
+based MPI.
Â
The Intel MPI may run on the[Intel Xeon
-Ph](intel-xeon-phi.html)i accelerators as well. Read
-more on [how to run Intel MPI on
-accelerators](intel-xeon-phi.html).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [List of Available
- Modules](../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage.html)
-
- - [Network](../network-1.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](chemistry.html "Tools for computational chemistry.")
+Ph](https://docs.it4i.cz/salomon/software/intel-xeon-phi)i
+accelerators as well. Read more on [how to run Intel MPI on
+accelerators](https://docs.it4i.cz/salomon/software/intel-xeon-phi).
diff --git a/salomon/software/mpi-1/Running_OpenMPI.html b/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.html
old mode 100755
new mode 100644
similarity index 75%
rename from salomon/software/mpi-1/Running_OpenMPI.html
rename to docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.html
index 896a578ec73e4830c8c3feda3812e1c0d91b5334..f234d48ce713a50dea3b0b2e379f0b91564fea81
--- a/salomon/software/mpi-1/Running_OpenMPI.html
+++ b/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:32 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Running OpenMPI — IT4I Docs</title>
- <link rel="canonical" href="Running_OpenMPI.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="Running_OpenMPI.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="Running_OpenMPI.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../mpi-1.html">MPI</a>
+ <a href="https://docs.it4i.cz/salomon/software/mpi-1">MPI</a>
<span class="breadcrumbSeparator">
/
@@ -413,7 +410,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -429,7 +426,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -445,7 +442,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -461,7 +458,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -477,7 +474,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -493,7 +490,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -509,7 +506,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -525,7 +522,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -541,7 +538,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -557,7 +554,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -573,7 +570,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -589,7 +586,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -605,10 +602,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -624,7 +621,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -640,7 +637,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -656,7 +653,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -672,7 +669,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -688,7 +685,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -704,7 +701,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -720,7 +717,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="Running_OpenMPI.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI">
<span>Running OpenMPI</span>
</a>
@@ -736,7 +733,7 @@
- <a title="OpenMPI interface to Python" class="state-published contenttype-document" href="mpi4py-mpi-for-python.html">
+ <a class="state-published contenttype-document" title="OpenMPI interface to Python" href="https://docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python">
<span>MPI4Py (MPI for Python)</span>
</a>
@@ -761,7 +758,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -777,7 +774,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -793,7 +790,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -809,7 +806,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -825,7 +822,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -850,7 +847,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -875,7 +872,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -891,7 +888,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -907,7 +904,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -923,7 +920,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -962,14 +959,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -991,12 +988,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1012,7 +1009,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:32 GMT -->
</html>
diff --git a/salomon/software/mpi-1/Running_OpenMPI.md b/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md
similarity index 61%
rename from salomon/software/mpi-1/Running_OpenMPI.md
rename to docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md
index 1f73ed09ea614304e9c725a8d886199d1e4db510..552565ad82993be6157db2d712f2e60bc0d1b84a 100644
--- a/salomon/software/mpi-1/Running_OpenMPI.md
+++ b/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md
@@ -1,17 +1,17 @@
+Running OpenMPI
===============
-
-
+
OpenMPI program execution
--------------------------
+--
The OpenMPI programs may be executed only via the PBS Workload manager,
by entering an appropriate queue. On the cluster, the **OpenMPI 1.8.6**
is OpenMPI based MPI implementation.
### Basic usage
Use the mpiexec to run the OpenMPI code.
-Example
- $ qsub -q qexp -l select=4ncpus=24 -I
- qsub waiting for job 15210.isrv5 to start
- qsub job 15210.isrv5 ready
+Example:
+ $ qsub -q qexp -l select=4:ncpus=24 -I
+ qsubwaiting for job 15210.isrv5 to start
+ qsubjob 15210.isrv5 ready
$ pwd
/home/username
$ module load OpenMPI
@@ -28,8 +28,8 @@ directive** to run up to 24 MPI tasks per each node.
In this example, we allocate 4 nodes via the express queue
interactively. We set up the openmpi environment and interactively run
the helloworld_mpi.x program.
-Note that the executable
-class="monospace">helloworld_mpi.x must be available within the
+Note that the executable <span
+class="monospace">helloworld_mpi.x</span> must be available within the
same path on all nodes. This is automatically fulfilled on the /home and
/scratch filesystem.
You need to preload the executable, if running on the local ramdisk /tmp
@@ -41,11 +41,11 @@ filesystem
Hello world! from rank 1 of 4 on host r1i0n5
Hello world! from rank 2 of 4 on host r1i0n6
Hello world! from rank 3 of 4 on host r1i0n7
-In this example, we assume the executable
-class="monospace">helloworld_mpi.x is present on compute node
+In this example, we assume the executable <span
+class="monospace">helloworld_mpi.x</span> is present on compute node
r1i0n17 on ramdisk. We call the mpiexec whith the **--preload-binary**
argument (valid for openmpi). The mpiexec will copy the executable from
-r1i0n17 to the /tmp/pbs.15210.isrv5
+r1i0n17 to the <span class="monospace">/tmp/pbs.15210.isrv5</span>
directory on r1i0n5, r1i0n6 and r1i0n7 and execute the program.
MPI process mapping may be controlled by PBS parameters.
The mpiprocs and ompthreads parameters allow for selection of number of
@@ -54,7 +54,7 @@ MPI process.
### One MPI process per node
Follow this example to run one MPI process per node, 24 threads per
process.Â
- $ qsub -q qexp -l select=4ncpus=24mpiprocs=1ompthreads=24 -I
+ $ qsub -q qexp -l select=4:ncpus=24:mpiprocs=1:ompthreads=24 -I
$ module load OpenMPI
$ mpiexec --bind-to-none ./helloworld_mpi.x
In this example, we demonstrate recommended way to run an MPI
@@ -63,7 +63,7 @@ on 4 nodes.
### Two MPI processes per node
Follow this example to run two MPI processes per node, 8 threads per
process. Note the options to mpiexec.
- $ qsub -q qexp -l select=4ncpus=24mpiprocs=2ompthreads=12 -I
+ $ qsub -q qexp -l select=4:ncpus=24:mpiprocs=2:ompthreads=12 -I
$ module load OpenMPI
$ mpiexec -bysocket -bind-to-socket ./helloworld_mpi.x
In this example, we demonstrate recommended way to run an MPI
@@ -73,7 +73,7 @@ node, on 4 nodes
### 24 MPI processes per node
Follow this example to run 24 MPI processes per node, 1 thread per
process. Note the options to mpiexec.
- $ qsub -q qexp -l select=4ncpus=24mpiprocs=24ompthreads=1 -I
+ $ qsub -q qexp -l select=4:ncpus=24:mpiprocs=24:ompthreads=1 -I
$ module load OpenMPI
$ mpiexec -bycore -bind-to-core ./helloworld_mpi.x
In this example, we demonstrate recommended way to run an MPI
@@ -84,16 +84,16 @@ Important! Bind every OpenMP thread to a core!
In the previous two examples with one or two MPI processes per node, the
operating system might still migrate OpenMP threads between cores. You
might want to avoid this by setting these environment variable for GCC
-OpenMP
+OpenMP:
$ export GOMP_CPU_AFFINITY="0-23"
-or this one for Intel OpenMP
+or this one for Intel OpenMP:
$ export KMP_AFFINITY=granularity=fine,compact,1,0
As of OpenMP 4.0 (supported by GCC 4.9 and later and Intel 14.0 and
-later) the following variables may be used for Intel or GCC
+later) the following variables may be used for Intel or GCC:
$ export OMP_PROC_BIND=true
$ export OMP_PLACES=coresÂ
-OpenMPI Process Mapping and Binding
-------------------------------------------------
+<span>OpenMPI Process Mapping and Binding</span>
+--
The mpiexec allows for precise selection of how the MPI processes will
be mapped to the computational nodes and how these processes will bind
to particular processor sockets and cores.
@@ -120,15 +120,15 @@ Exact control of MPI process placement and resource binding is provided
by specifying a rankfile
Appropriate binding may boost performance of your application.
Example rankfile
- rank 0=r1i0n7.smc.salomon.it4i.cz slot=10,1
- rank 1=r1i0n6.smc.salomon.it4i.cz slot=0*
- rank 2=r1i0n5.smc.salomon.it4i.cz slot=11-2
- rank 3=r1i0n17.smc.salomon slot=01,10-2
- rank 4=r1i0n6.smc.salomon.it4i.cz slot=0*,1*
+ rank 0=r1i0n7.smc.salomon.it4i.cz slot=1:0,1
+ rank 1=r1i0n6.smc.salomon.it4i.cz slot=0:*
+ rank 2=r1i0n5.smc.salomon.it4i.cz slot=1:1-2
+ rank 3=r1i0n17.smc.salomon slot=0:1,1:0-2
+ rank 4=r1i0n6.smc.salomon.it4i.cz slot=0:*,1:*
This rankfile assumes 5 ranks will be running on 4 nodes and provides
exact mapping and binding of the processes to the processor sockets and
cores
-Explanation
+Explanation:
rank 0 will be bounded to r1i0n7, socket1 core0 and core1
rank 1 will be bounded to r1i0n6, socket0, all cores
rank 2 will be bounded to r1i0n5, socket1, core1 and core2
@@ -136,11 +136,11 @@ rank 3 will be bounded to r1i0n17, socket0 core1, socket1 core0, core1,
core2
rank 4 will be bounded to r1i0n6, all cores on both sockets
$ mpiexec -n 5 -rf rankfile --report-bindings ./helloworld_mpi.x
- [r1i0n1711180] MCW rank 3 bound to socket 0[core 1] socket 1[core 0-2] [. B . . . . . . . . . .][B B B . . . . . . . . .] (slot list 01,10-2)
- [r1i0n709928] MCW rank 0 bound to socket 1[core 0-1] [. . . . . . . . . . . .][B B . . . . . . . . . .] (slot list 10,1)
- [r1i0n610395] MCW rank 1 bound to socket 0[core 0-7] [B B B B B B B B B B B B][. . . . . . . . . . . .] (slot list 0*)
- [r1i0n510406] MCW rank 2 bound to socket 1[core 1-2] [. . . . . . . . . . . .][. B B . . . . . . . . .] (slot list 11-2)
- [r1i0n610406] MCW rank 4 bound to socket 0[core 0-7] socket 1[core 0-7] [B B B B B B B B B B B B][B B B B B B B B B B B B] (slot list 0*,1*)
+ [r1i0n17:11180] MCW rank 3 bound to socket 0[core 1] socket 1[core 0-2][. B . . . . . . . . . .][B B B . . . . . . . . .] (slot list 0:1,1:0-2)
+ [r1i0n7:09928] MCW rank 0 bound to socket 1[core 0-1][. . . . . . . . . . . .][B B . . . . . . . . . .] (slot list 1:0,1)
+ [r1i0n6:10395] MCW rank 1 bound to socket 0[core 0-7][B B B B B B B B B B B B][. . . . . . . . . . . .] (slot list 0:*)
+ [r1i0n5:10406] MCW rank 2 bound to socket 1[core 1-2][. . . . . . . . . . . .][. B B . . . . . . . . .] (slot list 1:1-2)
+ [r1i0n6:10406] MCW rank 4 bound to socket 0[core 0-7] socket 1[core 0-7][B B B B B B B B B B B B][B B B B B B B B B B B B] (slot list 0:*,1:*)
Hello world! from rank 3 of 5 on host r1i0n17
Hello world! from rank 1 of 5 on host r1i0n6
Hello world! from rank 0 of 5 on host r1i0n7
@@ -155,75 +155,48 @@ It is users responsibility to provide correct number of ranks, sockets
and cores.
### Bindings verification
In all cases, binding and threading may be verified by executing for
-example
+example:
$ mpiexec -bysocket -bind-to-socket --report-bindings echo
$ mpiexec -bysocket -bind-to-socket numactl --show
$ mpiexec -bysocket -bind-to-socket echo $OMP_NUM_THREADS
Changes in OpenMPI 1.8
----------------------
Some options have changed in OpenMPI version 1.8.
-version 1.6.5
-version 1.8.1
---bind-to-none
---bind-to none
---bind-to-core
---bind-to core
---bind-to-socket
---bind-to socket
--bysocket
---map-by socket
--bycore
---map-by core
--pernode
---map-by ppr1node
-------------------------------------------------------------------------
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+<table>
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+<thead>
+<tr class="header">
+<th align="left">version 1.6.5</th>
+<th align="left">version 1.8.1</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left">--bind-to-none</td>
+<td align="left">--bind-to none</td>
+</tr>
+<tr class="even">
+<td align="left">--bind-to-core</td>
+<td align="left">--bind-to core</td>
+</tr>
+<tr class="odd">
+<td align="left">--bind-to-socket</td>
+<td align="left">--bind-to socket</td>
+</tr>
+<tr class="even">
+<td align="left">-bysocket</td>
+<td align="left">--map-by socket</td>
+</tr>
+<tr class="odd">
+<td align="left">-bycore</td>
+<td align="left">--map-by core</td>
+</tr>
+<tr class="even">
+<td align="left">-pernode</td>
+<td align="left"><p><span class="s1">--map-by ppr:1:node</span></p></td>
+</tr>
+</tbody>
+</table>
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+ <h2 class=" ">Setting up MPI Environment</h2>
+<p>The Salomon cluster provides several implementations of the MPI library:</p>
+<table class="listing">
+<tbody>
+<tr><th>MPI Library</th><th>Thread support</th></tr>
+<tr class="odd">
+<td><strong>Intel MPI 4.1</strong></td>
+<td>Full thread support up to MPI_THREAD_MULTIPLE</td>
+</tr>
+<tr class="odd">
+<td><strong>Intel MPI 5.0</strong></td>
+<td>Full thread support up to MPI_THREAD_MULTIPLE</td>
+</tr>
+<tr class="even">
+<td>OpenMPI 1.8.6</td>
+<td>Full thread support up to MPI_THREAD_MULTIPLE, MPI-3.0 support</td>
+</tr>
+<tr class="even">
+<td>SGI MPT 2.12</td>
+<td></td>
+</tr>
+</tbody>
+</table>
+<ul></ul>
+<p class="callout">MPI libraries are activated via the environment modules.</p>
+<p>Look up section modulefiles/mpi in module avail</p>
+<pre class=" ">$ module avail<br />------------------------------ /apps/modules/mpi -------------------------------<br />impi/4.1.1.036-iccifort-2013.5.192<br />impi/4.1.1.036-iccifort-2013.5.192-GCC-4.8.3<br />impi/5.0.3.048-iccifort-2015.3.187<br />impi/5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25<br />MPT/2.12<br />OpenMPI/1.8.6-GNU-5.1.0-2.25<br /><br /></pre>
+<p>There are default compilers associated with any particular MPI implementation. The defaults may be changed, the MPI libraries may be used in conjunction with any compiler.<br />The defaults are selected via the modules in following way</p>
+<table class="listing" summary="Modules selecting the MPI environment">
+<tbody>
+<tr><th>Module</th><th>MPI</th><th>Compiler suite</th></tr>
+<tr class="odd">
+<td>impi-5.0.3.048-iccifort-2015.3.187</td>
+<td>Intel MPI 5.0.3</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>OpenMP-1.8.6-GNU-5.1.0-2.25</td>
+<td>OpenMPI 1.8.6</td>
+<td></td>
+</tr>
+</tbody>
+</table>
+<p>Examples:</p>
+<pre class=" ">$ module load gompi/2015b</pre>
+<p>In this example, we activate the latest OpenMPI with latest GNU compilers (OpenMPI 1.8.6 and GCC 5.1). Please see more information about toolchains in section <a href="https://docs.it4i.cz/salomon/environment-and-modules">Environment and Modules</a> .</p>
+<p>To use OpenMPI with the intel compiler suite, use</p>
+<pre class=" ">$ module load iompi/2015.03</pre>
+<p>In this example, the openmpi 1.8.6 using intel compilers is activated. It's used "iompi" toolchain.</p>
+<h2 class=" ">Compiling MPI Programs</h2>
+<p class="callout">After setting up your MPI environment, compile your program using one of the mpi wrappers</p>
+<pre class=" ">$ mpicc -v<br />$ mpif77 -v<br />$ mpif90 -v</pre>
+<p>When using Intel MPI, use the following MPI wrappers:</p>
+<pre class=" ">$ mpicc<br />$ mpiifort </pre>
+<p>Wrappers mpif90, mpif77 that are provided by Intel MPI are designed for gcc and gfortran. You might be able to compile MPI code by them even with Intel compilers, but you might run into problems (for example, native MIC compilation with -mmic does not work with mpif90).</p>
+<p>Example program:</p>
+<pre class=" ">// helloworld_mpi.c<br />#include <stdio.h><br /><br />#include<mpi.h><br /><br />int main(int argc, char **argv) {<br /><br />int len;<br />int rank, size;<br />char node[MPI_MAX_PROCESSOR_NAME];<br /><br />// Initiate MPI<br />MPI_Init(&argc, &argv);<br />MPI_Comm_rank(MPI_COMM_WORLD,&rank);<br />MPI_Comm_size(MPI_COMM_WORLD,&size);<br /><br />// Get hostame and print<br />MPI_Get_processor_name(node,&len);<br />printf("Hello world! from rank %d of %d on host %s\n",rank,size,node);<br /><br />// Finalize and exit<br />MPI_Finalize();<br /><br />return 0;<br />}</pre>
+<p>Compile the above example with</p>
+<pre class=" ">$ mpicc helloworld_mpi.c -o helloworld_mpi.x</pre>
+<h2 class=" ">Running MPI Programs</h2>
+<p class="callout">The MPI program executable must be compatible with the loaded MPI module. <br />Always compile and execute using the very same MPI module.</p>
+<p>It is strongly discouraged to mix mpi implementations. Linking an application with one MPI implementation and running mpirun/mpiexec form other implementation may result in unexpected errors.</p>
+<p>The MPI program executable must be available within the same path on all nodes. This is automatically fulfilled on the /home and /scratch filesystem. You need to preload the executable, if running on the local scratch /lscratch filesystem.</p>
+<h3 class=" ">Ways to run MPI programs</h3>
+<p>Optimal way to run an MPI program depends on its memory requirements, memory access pattern and communication pattern.</p>
+<p class="callout">Consider these ways to run an MPI program:<br />1. One MPI process per node, 24 threads per process<br />2. Two MPI processes per node, 12 threads per process<br />3. 24 MPI processes per node, 1 thread per process.</p>
+<p class=" "><strong>One MPI</strong> process per node, using 24 threads, is most useful for memory demanding applications, that make good use of processor cache memory and are not memory bound. This is also a preferred way for communication intensive applications as one process per node enjoys full bandwidth access to the network interface. </p>
+<p class=" "><strong>Two MPI</strong> processes per node, using 12 threads each, bound to processor socket is most useful for memory bandwidth bound applications such as BLAS1 or FFT, with scalable memory demand. However, note that the two processes will share access to the network interface. The 12 threads and socket binding should ensure maximum memory access bandwidth and minimize communication, migration and numa effect overheads.</p>
+<p class="callout">Important! Bind every OpenMP thread to a core!</p>
+<p>In the previous two cases with one or two MPI processes per node, the operating system might still migrate OpenMP threads between cores. You want to avoid this by setting the KMP_AFFINITY or GOMP_CPU_AFFINITY environment variables.</p>
+<p class=" "><strong class=" ">24 MPI</strong> processes per node, using 1 thread each bound to processor core is most suitable for highly scalable applications with low communication demand.</p>
+<h3 class=" ">Running OpenMPI</h3>
+<p>The <a class="external-link" href="http://www.open-mpi.org/" target="_self" title=""><strong>OpenMPI 1.8.6</strong></a> is based on OpenMPI. Read more on <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI">how to run OpenMPI</a> based MPI.</p>
+<p>Â </p>
+<p>The Intel MPI may run on the<a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi"> Intel Xeon Ph</a>i accelerators as well. Read more on <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">how to run Intel MPI on accelerators</a>.</p>
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+<li class="navTreeItem visualNoMarker section-list_of_modules">
+
+
+
+
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
+
+ <span>List of Available Modules</span>
+ </a>
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+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-resource-allocation-and-job-execution">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
+
+ <span>Resource Allocation and Job Execution</span>
+ </a>
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+
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+</li>
+
+
+<li class="navTreeItem visualNoMarker section-compute-nodes">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
+
+ <span>Compute Nodes</span>
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+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-storage">
+
+
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+
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
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+ <span>Storage</span>
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+<li class="navTreeItem visualNoMarker navTreeFolderish section-network-1">
+
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+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
+
+ <span>Network</span>
+ </a>
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+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeItemInPath navTreeFolderish section-software">
+
+
+
+
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
+
+
+" href="https://docs.it4i.cz/salomon/software">
+
+ <span>Software</span>
+ </a>
+
+
+ <ul class="navTree navTreeLevel2">
+
+
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-ansys">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
+
+ <span>ANSYS</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-comsol">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
+
+ <span>COMSOL</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-debuggers">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
+
+ <span>Debuggers and profilers</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-chemistry">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
+
+ <span>Chemistry, Physics and Materials science</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-intel-suite">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
+
+ <span>Intel Parallel studio</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeCurrentNode navTreeFolderish section-mpi-1">
+
+
+
+
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
+
+ <span>MPI</span>
+ </a>
+
+
+ <ul class="navTree navTreeLevel3">
+
+
+
+
+<li class="navTreeItem visualNoMarker section-running_openmpi">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI">
+
+ <span>Running OpenMPI</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-mpi4py-mpi-for-python">
+
+
+
+
+ <a class="state-published contenttype-document" title="OpenMPI interface to Python" href="https://docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python">
+
+ <span>MPI4Py (MPI for Python)</span>
+ </a>
+
+
+
+
+</li>
+
+
+
+
+ </ul>
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-numerical-languages">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
+
+ <span>Numerical languages</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-compilers">
+
+
+
+
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
+
+ <span>Compilers</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-intel-xeon-phi">
+
+
+
+
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
+
+ <span>Intel Xeon Phi</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-java">
+
+
+
+
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
+
+ <span>Java</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-operating-system">
+
+
+
+
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
+
+ <span>Operating System</span>
+ </a>
+
+
+
+
+</li>
+
+
+
+
+ </ul>
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-prace">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
+
+ <span>PRACE User Support</span>
+ </a>
+
+
+
+
+</li>
+
+
+
+
+ </ul>
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-anselm-cluster-documentation">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
+
+ <span>Anselm Cluster Documentation</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-links">
+
+
+
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
+
+ <span>Links</span>
+ </a>
+
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+
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+</li>
+
+
+<li class="navTreeItem visualNoMarker section-changelog">
+
+
+
+
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
+
+ <span>Changelog</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-pbspro-documentation">
+
+
+
+
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
+
+ <span>PBSPro Documentation</span>
+ </a>
+
+
+
+
+</li>
+
+
+
+
+ </ul>
+ <span class="portletBottomLeft"></span>
+ <span class="portletBottomRight"></span>
+ </dd>
+</dl>
+
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diff --git a/docs.it4i.cz/salomon/software/mpi-1/mpi.md b/docs.it4i.cz/salomon/software/mpi-1/mpi.md
new file mode 100644
index 0000000000000000000000000000000000000000..553d8c78eb2098d52573a463319358226f1359db
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/mpi-1/mpi.md
@@ -0,0 +1,133 @@
+MPI
+===
+
+Setting up MPI Environment
+---
+The Salomon cluster provides several implementations of the MPI library:
+ ----
+ MPI Library Thread support
+ ------------- -------------
+ **Intel MPI 4.1** Full thread support up to
+ MPI_THREAD_MULTIPLE
+ **Intel MPI 5.0** Full thread support up to
+ MPI_THREAD_MULTIPLE
+ OpenMPI 1.8.6 Full thread support up to
+ MPI_THREAD_MULTIPLE, MPI-3.0
+ support
+ SGI MPT 2.12
+ ----
+MPI libraries are activated via the environment modules.
+Look up section modulefiles/mpi in module avail
+ $ module avail
+ ------- /apps/modules/mpi --------
+ impi/4.1.1.036-iccifort-2013.5.192
+ impi/4.1.1.036-iccifort-2013.5.192-GCC-4.8.3
+ impi/5.0.3.048-iccifort-2015.3.187
+ impi/5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25
+ MPT/2.12
+ OpenMPI/1.8.6-GNU-5.1.0-2.25
+There are default compilers associated with any particular MPI
+implementation. The defaults may be changed, the MPI libraries may be
+used in conjunction with any compiler.
+The defaults are selected via the modules in following way
+ -----
+ Module MPI Compiler suite
+ - - -
+ impi-5.0.3.048-iccifort- Intel MPI 5.0.3
+ 2015.3.187
+ OpenMP-1.8.6-GNU-5.1.0-2 OpenMPI 1.8.6
+ .25
+ -----
+Examples:
+ $ module load gompi/2015b
+In this example, we activate the latest OpenMPI with latest GNU
+compilers (OpenMPI 1.8.6 and GCC 5.1). Please see more information about
+toolchains in section [Environment and
+Modules](https://docs.it4i.cz/salomon/environment-and-modules)Â .
+To use OpenMPI with the intel compiler suite, use
+ $ module load iompi/2015.03
+In this example, the openmpi 1.8.6 using intel compilers is activated.
+It's used "iompi" toolchain.
+Compiling MPI Programs
+----------------------
+After setting up your MPI environment, compile your program using one of
+the mpi wrappers
+ $ mpicc -v
+ $ mpif77 -v
+ $ mpif90 -v
+When using Intel MPI, use the following MPI wrappers:
+ $ mpicc
+ $ mpiifortÂ
+Wrappers mpif90, mpif77 that are provided by Intel MPI are designed for
+gcc and gfortran. You might be able to compile MPI code by them even
+with Intel compilers, but you might run into problems (for example,
+native MIC compilation with -mmic does not work with mpif90).
+Example program:
+ // helloworld_mpi.c
+ #include <stdio.h>
+ #include<mpi.h>
+ int main(int argc, char **argv) {
+ int len;
+ int rank, size;
+ char node[MPI_MAX_PROCESSOR_NAME];
+ // Initiate MPI
+ MPI_Init(&argc, &argv);
+ MPI_Comm_rank(MPI_COMM_WORLD,&rank);
+ MPI_Comm_size(MPI_COMM_WORLD,&size);
+ // Get hostame and print
+ MPI_Get_processor_name(node,&len);
+ printf("Hello world! from rank %d of %d on host %sn",rank,size,node);
+ // Finalize and exit
+ MPI_Finalize();
+ return 0;
+ }
+Compile the above example with
+ $ mpicc helloworld_mpi.c -o helloworld_mpi.x
+Running MPI Programs
+--------------------
+The MPI program executable must be compatible with the loaded MPI
+module.
+Always compile and execute using the very same MPI module.
+It is strongly discouraged to mix mpi implementations. Linking an
+application with one MPI implementation and running mpirun/mpiexec form
+other implementation may result in unexpected errors.
+The MPI program executable must be available within the same path on all
+nodes. This is automatically fulfilled on the /home and /scratch
+filesystem. You need to preload the executable, if running on the local
+scratch /lscratch filesystem.
+### Ways to run MPI programs
+Optimal way to run an MPI program depends on its memory requirements,
+memory access pattern and communication pattern.
+Consider these ways to run an MPI program:
+1. One MPI process per node, 24 threads per process
+2. Two MPI processes per node, 12 threads per process
+3. 24 MPI processes per node, 1 thread per process.
+**One MPI** process per node, using 24 threads, is most useful for
+memory demanding applications, that make good use of processor cache
+memory and are not memory bound. This is also a preferred way for
+communication intensive applications as one process per node enjoys full
+bandwidth access to the network interface.Â
+**Two MPI** processes per node, using 12 threads each, bound to
+processor socket is most useful for memory bandwidth bound applications
+such as BLAS1 or FFT, with scalable memory demand. However, note that
+the two processes will share access to the network interface. The 12
+threads and socket binding should ensure maximum memory access bandwidth
+and minimize communication, migration and numa effect overheads.
+Important! Bind every OpenMP thread to a core!
+In the previous two cases with one or two MPI processes per node, the
+operating system might still migrate OpenMP threads between cores. You
+want to avoid this by setting the KMP_AFFINITY or GOMP_CPU_AFFINITY
+environment variables.
+**24 MPI** processes per node, using 1 thread each bound to processor
+core is most suitable for highly scalable applications with low
+communication demand.
+### Running OpenMPI
+The [**OpenMPI 1.8.6**](http://www.open-mpi.org/) is
+based on OpenMPI. Read more on [how to run
+OpenMPI](https://docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI)
+based MPI.
+Â
+The Intel MPI may run on the[Intel Xeon
+Ph](https://docs.it4i.cz/salomon/software/intel-xeon-phi)i
+accelerators as well. Read more on [how to run Intel MPI on
+accelerators](https://docs.it4i.cz/salomon/software/intel-xeon-phi).
diff --git a/salomon/software/mpi-1/mpi4py-mpi-for-python.html b/docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python.html
old mode 100755
new mode 100644
similarity index 69%
rename from salomon/software/mpi-1/mpi4py-mpi-for-python.html
rename to docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python.html
index 0afc61fa32cff1aacd032bffddd5f52fbb6be5ea..b6276d90eb501d68aea9a16428c8d89815406331
--- a/salomon/software/mpi-1/mpi4py-mpi-for-python.html
+++ b/docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python.html
@@ -10,45 +10,42 @@
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<title>MPI4Py (MPI for Python) — IT4I Docs</title>
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="mpi4py-mpi-for-python.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="mpi4py-mpi-for-python.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
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@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../mpi-1.html">MPI</a>
+ <a href="https://docs.it4i.cz/salomon/software/mpi-1">MPI</a>
<span class="breadcrumbSeparator">
/
@@ -262,7 +259,7 @@
<h2 class=" ">Execution</h2>
<p>You need to import MPI to your python program. Include the following line to the python script:</p>
<pre class=" ">from mpi4py import MPI</pre>
-<p>The MPI4Py enabled python programs <a target="_self" title="" class="internal-link" href="Running_OpenMPI.html">execute as any other OpenMPI</a> code.The simpliest way is to run</p>
+<p>The MPI4Py enabled python programs <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI">execute as any other OpenMPI</a> code.The simpliest way is to run</p>
<pre><span>$ mpiexec python <script>.py</span></pre>
<p><span>For example</span></p>
<pre>$ mpiexec python hello_world.py</pre>
@@ -349,7 +346,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -365,7 +362,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -381,7 +378,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -397,7 +394,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -413,7 +410,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -429,7 +426,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -445,7 +442,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -461,7 +458,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -477,7 +474,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -493,7 +490,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -509,7 +506,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -525,7 +522,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -541,10 +538,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -560,7 +557,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -576,7 +573,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -592,7 +589,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -608,7 +605,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -624,7 +621,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -640,7 +637,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -656,7 +653,7 @@
- <a title="" class="state-published contenttype-document" href="Running_OpenMPI.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI">
<span>Running OpenMPI</span>
</a>
@@ -672,7 +669,7 @@
- <a title="OpenMPI interface to Python" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="mpi4py-mpi-for-python.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="OpenMPI interface to Python" href="https://docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python">
<span>MPI4Py (MPI for Python)</span>
</a>
@@ -697,7 +694,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -713,7 +710,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -729,7 +726,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -745,7 +742,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -761,7 +758,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -786,7 +783,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -811,7 +808,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -827,7 +824,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -843,7 +840,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -859,7 +856,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['enableLinkTracking']);
(function() {
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -948,7 +945,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python.md b/docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python.md
new file mode 100644
index 0000000000000000000000000000000000000000..cba79e3e2113440f9543221ad5e990cdbf5b7781
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python.md
@@ -0,0 +1,69 @@
+MPI4Py (MPI for Python)
+=======================
+OpenMPI interface to Python
+
+Introduction
+------------
+MPI for Python provides bindings of the Message Passing Interface (MPI)
+standard for the Python programming language, allowing any Python
+program to exploit multiple processors.
+This package is constructed on top of the MPI-1/2 specifications and
+provides an object oriented interface which closely follows MPI-2 C++
+bindings. It supports point-to-point (sends, receives) and collective
+(broadcasts, scatters, gathers) communications of any picklable Python
+object, as well as optimized communications of Python object exposing
+the single-segment buffer interface (NumPy arrays, builtin
+bytes/string/array objects).
+On Anselm MPI4Py is available in standard Python modules.
+Modules
+-------
+MPI4Py is build for OpenMPI. Before you start with MPI4Py you need to
+load Python and OpenMPI modules. You can use toolchain, that loads
+Python and OpenMPI at once.
+ $ module load Python/2.7.9-foss-2015g
+Execution
+---------
+You need to import MPI to your python program. Include the following
+line to the python script:
+ from mpi4py import MPI
+The MPI4Py enabled python programs [execute as any other
+OpenMPI](https://docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI)
+code.The simpliest way is to run
+ $ mpiexec python <script>.py
+<span>For example</span>
+ $ mpiexec python hello_world.py
+Examples
+--------
+### Hello world!
+ from mpi4py import MPI
+ comm = MPI.COMM_WORLD
+ print "Hello! I'm rank %d from %d running in total..." % (comm.rank, comm.size)
+ comm.Barrier() Â # wait for everybody to synchronize
+### <span>Collective Communication with NumPy arrays</span>
+ from __future__ import division
+ from mpi4py import MPI
+ import numpy as np
+ comm = MPI.COMM_WORLD
+ print("-"*78)
+ print(" Running on %d cores" % comm.size)
+ print("-"*78)
+ comm.Barrier()
+ # Prepare a vector of N=5 elements to be broadcasted...
+ N = 5
+ if comm.rank == 0:
+ Â Â A = np.arange(N, dtype=np.float64) Â Â # rank 0 has proper data
+ else:
+ Â Â A = np.empty(N, dtype=np.float64) Â Â # all other just an empty array
+ # Broadcast A from rank 0 to everybody
+ comm.Bcast( [A, MPI.DOUBLE] )
+ # Everybody should now have the same...
+ print "[%02d] %s" % (comm.rank, A)
+Execute the above code as:
+ $ qsub -q qexp -l select=4:ncpus=24:mpiprocs=24:ompthreads=1 -I
+ $ module load Python/2.7.9-foss-2015g
+ $ mpiexec --map-by core --bind-to core python hello_world.py
+In this example, we run MPI4Py enabled code on 4 nodes, 24 cores per
+node (total of 96 processes), each python process is bound to a
+different core.
+More examples and documentation can be found on [MPI for Python
+webpage](https://pythonhosted.org/mpi4py/usrman/index.html).
diff --git a/salomon/software/numerical-languages.html b/docs.it4i.cz/salomon/software/numerical-languages.1.html
old mode 100755
new mode 100644
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rename from salomon/software/numerical-languages.html
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--- a/salomon/software/numerical-languages.html
+++ b/docs.it4i.cz/salomon/software/numerical-languages.1.html
@@ -10,45 +10,42 @@
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/numerical-languages/introduction" /><!--[if lt IE 7]></base><![endif]-->
<meta content="Interpreted languages for numerical computations and analysis" name="description" />
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- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<title>Numerical languages — IT4I Docs</title>
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+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/numerical-languages" />
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<div id="portal-header">
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- <a accesskey="2" href="numerical-languages.html#content">PĹ™ejĂt na obsah</a> |
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- <a accesskey="6" href="numerical-languages.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/numerical-languages#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
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+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
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<h2 class=" ">Matlab</h2>
<p>MATLAB<sup>®</sup> is a high-level language and interactive environment for numerical computation, visualization, and programming.</p>
<pre class=" ">$ module load MATLAB<br />$ matlab</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="numerical-languages/matlab.html">Matlab<span class="internal-link"></span> page</a>.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab">Matlab<span class="internal-link"></span> page</a>.</p>
<h2 class=" ">Octave</h2>
<p>GNU Octave is a high-level interpreted language, primarily intended for numerical computations. The Octave language is quite similar to Matlab so that most programs are easily portable.</p>
<pre class=" ">$ module load Octave<br />$ octave</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="numerical-languages/octave.html">Octave page</a>.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/numerical-languages/octave">Octave page</a>.</p>
<h2 class=" ">R</h2>
<p>The R is an interpreted language and environment for statistical computing and graphics.</p>
<pre class=" ">$ module load R<br />$ R</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="numerical-languages/r.html">R page</a>.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/numerical-languages/r">R page</a>.</p>
</div>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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<span>Hardware Overview</span>
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<span>Accessing the Cluster</span>
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<span>Environment and Modules</span>
</a>
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<span>List of Available Modules</span>
</a>
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+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
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<span>Storage</span>
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<span>Network</span>
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- <a title="In this section we provide overview of installed software and its usage.
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<span>Software</span>
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<span>ANSYS</span>
</a>
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- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
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<span>Debuggers and profilers</span>
</a>
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- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
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- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
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- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
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- <a title="Interpreted languages for numerical computations" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
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- <a title="" class="state-published contenttype-document" href="numerical-languages/matlab.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab">
<span>Matlab</span>
</a>
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- <a title="" class="state-published contenttype-document" href="numerical-languages/octave.html">
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<span>Octave</span>
</a>
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<span>R</span>
</a>
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- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
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- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -743,7 +740,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
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- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
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<span>Anselm Cluster Documentation</span>
</a>
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- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
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- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
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- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</html>
diff --git a/docs.it4i.cz/salomon/software/numerical-languages.1.md b/docs.it4i.cz/salomon/software/numerical-languages.1.md
new file mode 100644
index 0000000000000000000000000000000000000000..df50e0ee07651bcd6b2d1eac7e1f7be7cd2b99c0
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/numerical-languages.1.md
@@ -0,0 +1,33 @@
+Numerical languages
+===================
+Interpreted languages for numerical computations and analysis
+
+Introduction
+------------
+This section contains a collection of high-level interpreted languages,
+primarily intended for numerical computations.
+Matlab
+------
+MATLAB^®^ is a high-level language and interactive environment for
+numerical computation, visualization, and programming.
+ $ module load MATLAB
+ $ matlab
+Read more at the [Matlab<span class="internal-link"></span>
+page](https://docs.it4i.cz/salomon/software/numerical-languages/matlab).
+Octave
+------
+GNU Octave is a high-level interpreted language, primarily intended for
+numerical computations. The Octave language is quite similar to Matlab
+so that most programs are easily portable.
+ $ module load Octave
+ $ octave
+Read more at the [Octave
+page](https://docs.it4i.cz/salomon/software/numerical-languages/octave).
+R
+-
+The R is an interpreted language and environment for statistical
+computing and graphics.
+ $ module load R
+ $ R
+Read more at the [R
+page](https://docs.it4i.cz/salomon/software/numerical-languages/r).
diff --git a/docs.it4i.cz/salomon/software/numerical-languages/introduction.html b/docs.it4i.cz/salomon/software/numerical-languages/introduction.html
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+ <h2 class=" ">Introduction</h2>
+<p>This section contains a collection of high-level interpreted languages, primarily intended for numerical computations.</p>
+<h2 class=" ">Matlab</h2>
+<p>MATLAB<sup>®</sup> is a high-level language and interactive environment for numerical computation, visualization, and programming.</p>
+<pre class=" ">$ module load MATLAB<br />$ matlab</pre>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab">Matlab<span class="internal-link"></span> page</a>.</p>
+<h2 class=" ">Octave</h2>
+<p>GNU Octave is a high-level interpreted language, primarily intended for numerical computations. The Octave language is quite similar to Matlab so that most programs are easily portable.</p>
+<pre class=" ">$ module load Octave<br />$ octave</pre>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/numerical-languages/octave">Octave page</a>.</p>
+<h2 class=" ">R</h2>
+<p>The R is an interpreted language and environment for statistical computing and graphics.</p>
+<pre class=" ">$ module load R<br />$ R</pre>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/numerical-languages/r">R page</a>.</p>
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+++ b/docs.it4i.cz/salomon/software/numerical-languages/introduction.md
@@ -0,0 +1,33 @@
+Numerical languages
+===================
+Interpreted languages for numerical computations and analysis
+
+Introduction
+------------
+This section contains a collection of high-level interpreted languages,
+primarily intended for numerical computations.
+Matlab
+------
+MATLAB^®^ is a high-level language and interactive environment for
+numerical computation, visualization, and programming.
+ $ module load MATLAB
+ $ matlab
+Read more at the [Matlab<span class="internal-link"></span>
+page](https://docs.it4i.cz/salomon/software/numerical-languages/matlab).
+Octave
+------
+GNU Octave is a high-level interpreted language, primarily intended for
+numerical computations. The Octave language is quite similar to Matlab
+so that most programs are easily portable.
+ $ module load Octave
+ $ octave
+Read more at the [Octave
+page](https://docs.it4i.cz/salomon/software/numerical-languages/octave).
+R
+-
+The R is an interpreted language and environment for statistical
+computing and graphics.
+ $ module load R
+ $ R
+Read more at the [R
+page](https://docs.it4i.cz/salomon/software/numerical-languages/r).
diff --git a/salomon/software/numerical-languages/matlab.html b/docs.it4i.cz/salomon/software/numerical-languages/matlab.html
old mode 100755
new mode 100644
similarity index 74%
rename from salomon/software/numerical-languages/matlab.html
rename to docs.it4i.cz/salomon/software/numerical-languages/matlab.html
index 083970202a3bca80ff72c48ea1bef53c0329481e..c6770fc8c6e2a9fa0a8ae854f277404e04c468f6
--- a/salomon/software/numerical-languages/matlab.html
+++ b/docs.it4i.cz/salomon/software/numerical-languages/matlab.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/numerical-languages/matlab by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:55 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Matlab — IT4I Docs</title>
- <link rel="canonical" href="matlab.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="matlab.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="matlab.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../numerical-languages.html">Numerical languages</a>
+ <a href="https://docs.it4i.cz/salomon/software/numerical-languages">Numerical languages</a>
<span class="breadcrumbSeparator">
/
@@ -262,8 +259,8 @@
<p>By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use</p>
<pre class=" ">$ module avail MATLAB</pre>
<p>If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.</p>
-<p>If you require the Matlab GUI, please follow the general informations about <a target="_self" title="" class="internal-link" href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html">running graphical applications</a>.</p>
-<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a target="_self" title="" class="internal-link" href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html">here</a>) is recommended.</p>
+<p>If you require the Matlab GUI, please follow the general informations about <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">running graphical applications</a>.</p>
+<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">here</a>) is recommended.</p>
<p>To run Matlab with GUI, use</p>
<pre class=" ">$ matlab</pre>
<p>To run Matlab in text mode, without the Matlab Desktop GUI environment, use</p>
@@ -279,7 +276,7 @@
<p class=" ">/apps/all/MATLAB/2015b-EDU/SalomonPBSPro.settings</p>
<p class=" ">With the new mode, MATLAB itself launches the workers via PBS, so you can either use interactive mode or a batch mode on one node, but the actual parallel processing will be done in a separate job started by MATLAB itself. Alternatively, you can use "local" mode to run parallel code on just a single node.</p>
<h3 class=" ">Parallel Matlab interactive session</h3>
-<p>Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a target="_self" title="" class="internal-link" href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html">this page</a>.</p>
+<p>Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">this page</a>.</p>
<pre class=" ">$ xhost +<br />$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00 \<br />-l feature__matlab__MATLAB=1 </pre>
<p>This qsub command example shows how to run Matlab on a single node.</p>
<p>The second part of the command shows how to request all necessary licenses. In this case 1 Matlab-EDU license and 48 Distributed Computing Engines licenses.</p>
@@ -357,9 +354,9 @@ whos % T and W are both distributed arrays here.
% shut down parallel pool
delete(pool)</pre>
<h3 class=" ">Non-interactive Session and Licenses</h3>
-<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a target="_self" title="" class="internal-link" href="../../../anselm-cluster-documentation/software/isv_licenses.html">look here</a>.</p>
+<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">look here</a>.</p>
<p class="exclamation">The licensing feature of PBS is currently disabled.</p>
-<p>In case of non-interactive session please read the <a target="_self" title="" class="internal-link" href="../../../anselm-cluster-documentation/software/isv_licenses.html">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
+<p>In case of non-interactive session please read the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
<h3 class=" ">Matlab Distributed Computing Engines start up time</h3>
<p>Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:</p>
<table class="plain">
@@ -472,7 +469,7 @@ delete(pool)</pre>
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -488,7 +485,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -504,7 +501,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -520,7 +517,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -536,7 +533,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -552,7 +549,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -568,7 +565,7 @@ delete(pool)</pre>
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -584,7 +581,7 @@ delete(pool)</pre>
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -600,7 +597,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -616,7 +613,7 @@ delete(pool)</pre>
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -632,7 +629,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -648,7 +645,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -664,10 +661,10 @@ delete(pool)</pre>
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -683,7 +680,7 @@ delete(pool)</pre>
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -699,7 +696,7 @@ delete(pool)</pre>
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -715,7 +712,7 @@ delete(pool)</pre>
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -731,7 +728,7 @@ delete(pool)</pre>
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -747,7 +744,7 @@ delete(pool)</pre>
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -763,7 +760,7 @@ delete(pool)</pre>
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -779,7 +776,7 @@ delete(pool)</pre>
- <a title="Interpreted languages for numerical computations" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -795,7 +792,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="matlab.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab">
<span>Matlab</span>
</a>
@@ -811,7 +808,7 @@ delete(pool)</pre>
- <a title="" class="state-published contenttype-document" href="octave.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/numerical-languages/octave">
<span>Octave</span>
</a>
@@ -827,7 +824,7 @@ delete(pool)</pre>
- <a title="" class="state-published contenttype-document" href="r.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/numerical-languages/r">
<span>R</span>
</a>
@@ -852,7 +849,7 @@ delete(pool)</pre>
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -868,7 +865,7 @@ delete(pool)</pre>
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -884,7 +881,7 @@ delete(pool)</pre>
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -900,7 +897,7 @@ delete(pool)</pre>
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -925,7 +922,7 @@ delete(pool)</pre>
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -950,7 +947,7 @@ delete(pool)</pre>
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -966,7 +963,7 @@ delete(pool)</pre>
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -982,7 +979,7 @@ delete(pool)</pre>
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -998,7 +995,7 @@ delete(pool)</pre>
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -1037,14 +1034,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1066,12 +1063,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1087,7 +1084,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/numerical-languages/matlab by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:56 GMT -->
</html>
diff --git a/salomon/software/numerical-languages/matlab.md b/docs.it4i.cz/salomon/software/numerical-languages/matlab.md
similarity index 72%
rename from salomon/software/numerical-languages/matlab.md
rename to docs.it4i.cz/salomon/software/numerical-languages/matlab.md
index 3447c3932d49e75486b74610a8e02f96b29d1cd2..9b0f238bbfbc8a754ca300b05bf5b6f41366e098 100644
--- a/salomon/software/numerical-languages/matlab.md
+++ b/docs.it4i.cz/salomon/software/numerical-languages/matlab.md
@@ -1,10 +1,10 @@
+Matlab
======
-
-
+
Introduction
------------
Matlab is available in versions R2015a and R2015b. There are always two
-variants of the release
+variants of the release:
- Non commercial or so called EDU variant, which can be used for
common research and educational purposes.
- Commercial or so called COM variant, which can used also for
@@ -23,11 +23,11 @@ can use Matlab directly on the login nodes. But for all computations use
Matlab on the compute nodes via PBS Pro scheduler.
If you require the Matlab GUI, please follow the general informations
about [running graphical
-applications](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+applications](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc).
Matlab GUI is quite slow using the X forwarding built in the PBS (qsub
-X), so using X11 display redirection either via SSH or directly by
xauth (please see the "GUI Applications on Compute Nodes over VNC" part
-[here](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html))
+[here](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc))
is recommended.
To run Matlab with GUI, use
$ matlab
@@ -36,22 +36,22 @@ use
$ matlab -nodesktop -nosplash
plots, images, etc... will be still available.
[]()Running parallel Matlab using Distributed Computing Toolbox / Engine
-------------------------------------------------------------------------
+---
Distributed toolbox is available only for the EDU variant
The MPIEXEC mode available in previous versions is no longer available
in MATLAB 2015. Also, the programming interface has changed. Refer
to [Release
-Notes](http//www.mathworks.com/help/distcomp/release-notes.html#buanp9e-1).
+Notes](http://www.mathworks.com/help/distcomp/release-notes.html#buanp9e-1).
Delete previously used file mpiLibConf.m, we have observed crashes when
using Intel MPI.
To use Distributed Computing, you first need to setup a parallel
profile. We have provided the profile for you, you can either import it
-in MATLAB command line
+in MATLAB command line:
>> parallel.importProfile('/apps/all/MATLAB/2015b-EDU/SalomonPBSPro.settings')
ans =
SalomonPBSProÂ
Or in the GUI, go to tab HOME -> Parallel -> Manage Cluster
-Profiles..., click Import and navigate to
+Profiles..., click Import and navigate to :
/apps/all/MATLAB/2015b-EDU/SalomonPBSPro.settings
With the new mode, MATLAB itself launches the workers via PBS, so you
can either use interactive mode or a batch mode on one node, but the
@@ -62,16 +62,16 @@ code on just a single node.
Following example shows how to start interactive session with support
for Matlab GUI. For more information about GUI based applications on
Anselm see [this
-page](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+page](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc).
$ xhost +
- $ qsub -I -v DISPLAY=$(uname -n)$(echo $DISPLAY | cut -d '' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=003000
+ $ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00
-l feature__matlab__MATLAB=1
This qsub command example shows how to run Matlab on a single node.
The second part of the command shows how to request all necessary
licenses. In this case 1 Matlab-EDU license and 48 Distributed Computing
Engines licenses.
Once the access to compute nodes is granted by PBS, user can load
-following modules and start MatlabÂ
+following modules and start Matlab:Â
r1i0n17$ module load MATLAB/2015a-EDU
r1i0n17$ matlab &
### []()Parallel Matlab batch job in Local mode
@@ -81,7 +81,7 @@ execute one matlab worker instance per allocated core.
#!/bin/bash
#PBS -A PROJECT ID
#PBS -q qprod
- #PBS -l select=1ncpus=24mpiprocs=24ompthreads=1
+ #PBS -l select=1:ncpus=24:mpiprocs=24:ompthreads=1
# change to shared scratch directory
SCR=/scratch/work/user/$USER/$PBS_JOBID
mkdir -p $SCR ; cd $SCR || exit
@@ -107,7 +107,7 @@ script before Distributed Computing Toolbox is started.
cluster = parcluster('local')
This script creates scheduler object "cluster" of type "local" that
starts workers locally.Â
-Please note Every Matlab script that needs to initialize/use matlabpool
+Please noteEvery Matlab script that needs to initialize/use matlabpool
has to contain these three lines prior to calling parpool(sched, ...)
function.Â
The last step is to start matlabpool with "cluster" object and correct
@@ -127,7 +127,7 @@ local mode is shown here.Â
n=2000;
W = rand(n,n);
W = distributed(W);
- x = (1n)';
+ x = (1:n)';
x = distributed(x);
spmd
[~, name] = system('hostname')
@@ -147,16 +147,16 @@ This mode uses PBS scheduler to launch the parallel pool. It uses the
SalomonPBSPro profile that needs to be imported to Cluster Manager, as
mentioned before. This methodod uses MATLAB's PBS Scheduler interface -
it spawns the workers in a separate job submitted by MATLAB using qsub.
-This is an example of m-script using PBS mode
+This is an example of m-script using PBS mode:
cluster = parcluster('SalomonPBSPro');
set(cluster, 'SubmitArguments', '-A OPEN-0-0');
- set(cluster, 'ResourceTemplate', '-q qprod -l select=10ncpus=24');
+ set(cluster, 'ResourceTemplate', '-q qprod -l select=10:ncpus=24');
set(cluster, 'NumWorkers', 240);
pool = parpool(cluster,240);
n=2000;
W = rand(n,n);
W = distributed(W);
- x = (1n)';
+ x = (1:n)';
x = distributed(x);
spmd
[~, name] = system('hostname')
@@ -167,7 +167,7 @@ This is an example of m-script using PBS mode
% shut down parallel pool
delete(pool)
Note that we first construct a cluster object using the imported
-profile, then set some important options, namely SubmitArguments,
+profile, then set some important options, namely SubmitArguments,
where you need to specify accounting id, and ResourceTemplate, where you
need to specify number of nodes to run the job.Â
You can start this script using batch mode the same way as in Local mode
@@ -184,7 +184,7 @@ Please note that this method is experimental.
For this method, you need to use SalomonDirect profile, import it
using [the same way as
SalomonPBSPro](#running-parallel-matlab-using-distributed-computing-toolbox---engine)Â
-This is an example of m-script using direct mode
+This is an example of m-script using direct mode:
parallel.importProfile('/apps/all/MATLAB/2015b-EDU/SalomonDirect.settings')
cluster = parcluster('SalomonDirect');
set(cluster, 'NumWorkers', 48);
@@ -192,7 +192,7 @@ This is an example of m-script using direct mode
n=2000;
W = rand(n,n);
W = distributed(W);
- x = (1n)';
+ x = (1:n)';
x = distributed(x);
spmd
[~, name] = system('hostname')
@@ -208,15 +208,15 @@ appropriate license features with the PBS Pro scheduler, at least the "
-l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More
information about how to check the license features states and how to
request them with PBS Pro, please [look
-here](../../../anselm-cluster-documentation/software/isv_licenses.html).
+here](https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses).
The licensing feature of PBS is currently disabled.
In case of non-interactive session please read the [following
-information](../../../anselm-cluster-documentation/software/isv_licenses.html)
+information](https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses)
on how to modify the qsub command to test for available licenses prior
getting the resource allocation.
### Matlab Distributed Computing Engines start up time
Starting Matlab workers is an expensive process that requires certain
-amount of time. For your information please see the following table
+amount of time. For your information please see the following table:
compute nodes number of workers start-up time[s]
--------------- ------------------- --------------------
16 384 831
@@ -229,70 +229,20 @@ UV2000 machine available in queue "qfat" can be used for MATLAB
computations. This is a SMP NUMA machine with large amount of RAM, which
can be beneficial for certain types of MATLAB jobs. CPU cores are
allocated in chunks of 8 for this machine.
-You can use MATLAB on UV2000 in two parallel modes
+You can use MATLAB on UV2000 in two parallel modes :
### Threaded mode
Since this is a SMP machine, you can completely avoid using Parallel
Toolbox and use only MATLAB's threading. MATLAB will automatically
-detect the number of cores you have allocated and will setÂ
-class="monospace">maxNumCompThreads accordingly and certain
-operations, such as fft, , eig, svd,
+detect the number of cores you have allocated and will set <span
+class="monospace">maxNumCompThreads </span>accordingly and certain
+operations, such as <span class="monospace">fft, , eig, svd</span>,
etc. will be automatically run in threads. The advantage of this mode is
-that you don't need to modify your existing sequential codes.
+that you don't need to modify your existing sequential codes.<span
class="monospace">
+</span>
### Local cluster mode
You can also use Parallel Toolbox on UV2000. Use l[ocal cluster
mode](#parallel-matlab-batch-job-in-local-mode),
"SalomonPBSPro" profile will not work.
Â
Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
diff --git a/salomon/software/numerical-languages/octave.html b/docs.it4i.cz/salomon/software/numerical-languages/octave.html
old mode 100755
new mode 100644
similarity index 68%
rename from salomon/software/numerical-languages/octave.html
rename to docs.it4i.cz/salomon/software/numerical-languages/octave.html
index ee7dfd963fa9647201866a1062fb95f99cbd4e2f..03b8a00f766ef8df6903d50e4d1c3a3487271b0f
--- a/salomon/software/numerical-languages/octave.html
+++ b/docs.it4i.cz/salomon/software/numerical-languages/octave.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/numerical-languages/octave by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:04 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Octave — IT4I Docs</title>
- <link rel="canonical" href="octave.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/numerical-languages/octave" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="octave.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/numerical-languages/octave#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="octave.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/numerical-languages/octave#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../numerical-languages.html">Numerical languages</a>
+ <a href="https://docs.it4i.cz/salomon/software/numerical-languages">Numerical languages</a>
<span class="breadcrumbSeparator">
/
@@ -269,7 +266,7 @@
<pre class=" ">$ octave</pre>
<p>To run octave in batch mode, write an octave script, then write a bash jobscript and execute via the qsub command. By default, octave will use 16 threads when running MKL kernels.</p>
<pre class=" ">#!/bin/bash<br /><br /># change to local scratch directory<br />mkdir -p /scratch/work/user/$USER/$PBS_JOBID<br />cd /scratch/work/user/$USER/$PBS_JOBID || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/octcode.m .<br /><br /># load octave module<br />module load Octave<br /><br /># execute the calculation<br />octave -q --eval octcode > output.out<br /><br /># copy output file to home<br />cp output.out $PBS_O_WORKDIR/.<br /><br />#exit<br />exit</pre>
-<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs are in octcode.m file, outputs in output.out file. See the single node jobscript example in the <a target="_self" title="" class="internal-link" href="../../resource-allocation-and-job-execution.html">Job execution section</a>.</p>
+<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs are in octcode.m file, outputs in output.out file. See the single node jobscript example in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">Job execution section</a>.</p>
<p class="hiddenForView">The octave c compiler mkoctfile calls the GNU gcc 4.8.1 for compiling native c code. This is very useful for running native c subroutines in octave environment.</p>
<p class="hiddenForView">$ mkoctfile -v</p>
<p class="hiddenForView">Octave may use MPI for interprocess communication<br />This functionality is currently not supported on the cluster cluster. In case you require the octave interface to MPI, please contact our <a class="external-link" href="https://support.it4i.cz/rt/" target="_self" title="">cluster support</a>.</p>
@@ -348,7 +345,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -364,7 +361,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -380,7 +377,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -396,7 +393,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -412,7 +409,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -428,7 +425,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -444,7 +441,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -460,7 +457,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -476,7 +473,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -492,7 +489,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -508,7 +505,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -524,7 +521,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -540,10 +537,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -559,7 +556,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -575,7 +572,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -591,7 +588,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -607,7 +604,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -623,7 +620,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -639,7 +636,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -655,7 +652,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -671,7 +668,7 @@
- <a title="" class="state-published contenttype-document" href="matlab.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab">
<span>Matlab</span>
</a>
@@ -687,7 +684,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="octave.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/numerical-languages/octave">
<span>Octave</span>
</a>
@@ -703,7 +700,7 @@
- <a title="" class="state-published contenttype-document" href="r.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/numerical-languages/r">
<span>R</span>
</a>
@@ -728,7 +725,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -744,7 +741,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -760,7 +757,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -776,7 +773,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -801,7 +798,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -826,7 +823,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -842,7 +839,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -858,7 +855,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -874,7 +871,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -913,14 +910,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -942,12 +939,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -963,7 +960,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/numerical-languages/octave by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:04 GMT -->
</html>
diff --git a/salomon/software/numerical-languages/octave.md b/docs.it4i.cz/salomon/software/numerical-languages/octave.md
similarity index 51%
rename from salomon/software/numerical-languages/octave.md
rename to docs.it4i.cz/salomon/software/numerical-languages/octave.md
index ad32a1702619ef9f02e2c3425965e9dffde561a2..bdcf76803f143fe5cea2267a3d8190f9d75885a9 100644
--- a/salomon/software/numerical-languages/octave.md
+++ b/docs.it4i.cz/salomon/software/numerical-languages/octave.md
@@ -1,6 +1,6 @@
+Octave
======
-
-
+
GNU Octave is a high-level interpreted language, primarily intended for
numerical computations. It provides capabilities for the numerical
solution of linear and nonlinear problems, and for performing other
@@ -9,7 +9,7 @@ for data visualization and manipulation. Octave is normally used through
its interactive command line interface, but it can also be used to write
non-interactive programs. The Octave language is quite similar to Matlab
so that most programs are easily portable. Read more on
-****
+<http://www.gnu.org/software/octave/>****
**
**Two versions of octave are available on the cluster, via module
Status Version module
@@ -24,7 +24,7 @@ calculation kernels without any penalty. By default, octave would
parallelize to 24 threads. You may control the threads by setting the
OMP_NUM_THREADS environment variable.
To run octave interactively, log in with ssh -X parameter for X11
-forwarding. Run octave
+forwarding. Run octave:
$ octave
To run octave in batch mode, write an octave script, then write a bash
jobscript and execute via the qsub command. By default, octave will use
@@ -47,7 +47,7 @@ This script may be submitted directly to the PBS workload manager via
the qsub command. The inputs are in octcode.m file, outputs in
output.out file. See the single node jobscript example in the [Job
execution
-section](../../resource-allocation-and-job-execution.html).
+section](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution).
The octave c compiler mkoctfile calls the GNU gcc 4.8.1 for compiling
native c code. This is very useful for running native c subroutines in
octave environment.
@@ -55,55 +55,4 @@ $ mkoctfile -v
Octave may use MPI for interprocess communication
This functionality is currently not supported on the cluster cluster. In
case you require the octave interface to MPI, please contact our
-[cluster support](https//support.it4i.cz/rt/).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
+[cluster support](https://support.it4i.cz/rt/).
diff --git a/salomon/software/numerical-languages/parallel.pdf b/docs.it4i.cz/salomon/software/numerical-languages/package-parallel-vignette
old mode 100755
new mode 100644
similarity index 100%
rename from salomon/software/numerical-languages/parallel.pdf
rename to docs.it4i.cz/salomon/software/numerical-languages/package-parallel-vignette
diff --git a/salomon/software/numerical-languages/r.html b/docs.it4i.cz/salomon/software/numerical-languages/r.html
old mode 100755
new mode 100644
similarity index 76%
rename from salomon/software/numerical-languages/r.html
rename to docs.it4i.cz/salomon/software/numerical-languages/r.html
index 7eb7febc867e79f05dcdc9d12b4103358863c828..d37ee7c2060a148af79550a29ed9cf6f086e1f82
--- a/salomon/software/numerical-languages/r.html
+++ b/docs.it4i.cz/salomon/software/numerical-languages/r.html
@@ -10,45 +10,42 @@
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<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/numerical-languages/r" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
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<title>R — IT4I Docs</title>
- <link rel="canonical" href="r.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/numerical-languages/r" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
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@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="r.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/numerical-languages/r#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="r.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/numerical-languages/r#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../numerical-languages.html">Numerical languages</a>
+ <a href="https://docs.it4i.cz/salomon/software/numerical-languages">Numerical languages</a>
<span class="breadcrumbSeparator">
/
@@ -285,7 +282,7 @@
<p>To run R in batch mode, write an R script, then write a bash jobscript and execute via the qsub command. By default, R will use 24 threads when running MKL kernels.</p>
<p>Example jobscript:</p>
<pre class=" ">#!/bin/bash<br /><br /># change to local scratch directory<br />cd /lscratch/$PBS_JOBID || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/rscript.R .<br /><br /># load R module<br />module load R<br /><br /># execute the calculation<br />R CMD BATCH rscript.R routput.out<br /><br /># copy output file to home<br />cp routput.out $PBS_O_WORKDIR/.<br /><br />#exit<br />exit</pre>
-<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs are in rscript.R file, outputs in routput.out file. See the single node jobscript example in the <a target="_self" title="" class="internal-link" href="../../resource-allocation-and-job-execution/job-submission-and-execution.html">Job execution section</a>.</p>
+<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs are in rscript.R file, outputs in routput.out file. See the single node jobscript example in the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">Job execution section</a>.</p>
<h2 class=" ">Parallel R</h2>
<p>Parallel execution of R may be achieved in many ways. One approach is the implied parallelization due to linked libraries or specially enabled functions, as <a class="anchor-link" href="#interactive-execution" target="_self" title="">described above</a>. In the following sections, we focus on explicit parallelization, where parallel constructs are directly stated within the R script.</p>
<h2 class=" "><a name="package-parallel"></a>Package parallel</h2>
@@ -294,7 +291,7 @@
<pre class=" ">$ R<br />> library(parallel)</pre>
<p class=" ">More information and examples may be obtained directly by reading the documentation available in R</p>
<pre class=" ">> ?parallel<br />> library(help = "parallel")<br />> <span class="internal-link">vignette("parallel")</span></pre>
-<p class=" ">Download the package <a target="_self" title="" class="internal-link" href="parallel.pdf">parallell</a> vignette.</p>
+<p class=" ">Download the package <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/numerical-languages/package-parallel-vignette">parallell</a> vignette.</p>
<p class=" ">The forking is the most simple to use. Forking family of functions provide parallelized, drop in replacement for the serial apply() family of functions.</p>
<p class="callout">Forking via package parallel provides functionality similar to OpenMP construct<br />#omp parallel for <br /><br />Only cores of single node can be utilized this way!</p>
<p class=" ">Forking example:</p>
@@ -304,7 +301,7 @@
<p>Every evaluation of the integrad function runs in parallel on different process.</p>
<h2 class=" ">Package Rmpi</h2>
<p class="callout">package Rmpi provides an interface (wrapper) to MPI APIs.</p>
-<p>It also provides interactive R slave environment. On the cluster, Rmpi provides interface to the <a target="_self" title="" class="internal-link" href="../mpi-1/Running_OpenMPI.html">OpenMPI</a>.</p>
+<p>It also provides interactive R slave environment. On the cluster, Rmpi provides interface to the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI">OpenMPI</a>.</p>
<p>Read more on Rmpi at <a class="external-link" href="http://cran.r-project.org/web/packages/Rmpi/" target="_self" title="">http://cran.r-project.org/web/packages/Rmpi/</a>, reference manual is available at <a class="external-link" href="http://cran.r-project.org/web/packages/Rmpi/Rmpi.pdf" target="_self" title="">http://cran.r-project.org/web/packages/Rmpi/Rmpi.pdf</a></p>
<p>When using package Rmpi, both openmpi and R modules must be loaded</p>
<pre class=" ">$ module load OpenMPI<br />$ module load R</pre>
@@ -337,13 +334,13 @@ Note that this method uses MPI_Comm_spawn (Dynamic process feature of MPI-2) to
<p>The R parallel jobs are executed via the PBS queue system exactly as any other parallel jobs. User must create an appropriate jobscript and submit via the <strong>qsub</strong></p>
<p>Example jobscript for <a class="anchor-link" href="#static-rmpi" target="_self" title="">static Rmpi</a> parallel R execution, running 1 process per core:</p>
<pre class=" ">#!/bin/bash<br />#PBS -q qprod<br />#PBS -N Rjob<br />#PBS -l select=100:ncpus=24:mpiprocs=24:ompthreads=1<br /><br /># change to scratch directory<span class="pln"><br />SCRDIR</span><span class="pun">=/</span><span class="pln">scratch</span><span class="pun">/</span><span class="pln">work/user/$USER</span><span class="pun">/</span><span class="pln">myjob</span><br /><span class="pln">cd $SCRDIR </span><span class="pun">||</span><span class="pln"> exit</span><br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/rscript.R .<br /><br /># load R and openmpi module<br />module load R<br />module load OpenMPI<br /><br /># execute the calculation<br />mpiexec -bycore -bind-to-core R --slave --no-save --no-restore -f rscript.R<br /><br /># copy output file to home<br />cp routput.out $PBS_O_WORKDIR/.<br /><br />#exit<br />exit</pre>
-For more information about jobscripts and MPI execution refer to the <a target="_self" title="" class="internal-link" href="../../resource-allocation-and-job-execution/job-submission-and-execution.html">Job submission</a> and general <a target="_self" title="" class="internal-link" href="../mpi-1.html">MPI</a> sections.</div>
+For more information about jobscripts and MPI execution refer to the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">Job submission</a> and general <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/mpi-1">MPI</a> sections.</div>
<div></div>
<div>
<h2>Xeon Phi Offload</h2>
<p>By leveraging MKL, R can accelerate certain computations, most notably linear algebra operations on the Xeon Phi accelerator by using Automated Offload. To use MKL Automated Offload, you need to first set this environment variable before R execution :</p>
<pre>$ export MKL_MIC_ENABLE=1</pre>
-<p class=" "><a target="_self" title="" class="internal-link" href="../intel-xeon-phi.html">Read more about automatic offload</a></p>
+<p class=" "><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">Read more about automatic offload</a></p>
</div>
</div>
@@ -421,7 +418,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -437,7 +434,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -453,7 +450,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -469,7 +466,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -485,7 +482,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -501,7 +498,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -517,7 +514,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -533,7 +530,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -549,7 +546,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -565,7 +562,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -581,7 +578,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -597,7 +594,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -613,10 +610,10 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -632,7 +629,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -648,7 +645,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -664,7 +661,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -680,7 +677,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -696,7 +693,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -712,7 +709,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -728,7 +725,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="Interpreted languages for numerical computations" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -744,7 +741,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published contenttype-document" href="matlab.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab">
<span>Matlab</span>
</a>
@@ -760,7 +757,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published contenttype-document" href="octave.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/numerical-languages/octave">
<span>Octave</span>
</a>
@@ -776,7 +773,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="r.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/numerical-languages/r">
<span>R</span>
</a>
@@ -801,7 +798,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -817,7 +814,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -833,7 +830,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -849,7 +846,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -874,7 +871,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -899,7 +896,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -915,7 +912,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -931,7 +928,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -947,7 +944,7 @@ For more information about jobscripts and MPI execution refer to the <a target="
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -986,14 +983,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -1015,12 +1012,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1036,7 +1033,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/numerical-languages/r by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:04 GMT -->
</html>
diff --git a/salomon/software/numerical-languages/r.md b/docs.it4i.cz/salomon/software/numerical-languages/r.md
similarity index 76%
rename from salomon/software/numerical-languages/r.md
rename to docs.it4i.cz/salomon/software/numerical-languages/r.md
index dda56192396311ee942cb7ebc629e4d5ded71d43..86ab42f4ecf6b6d4cc1a642fd415efd40bf0f6d1 100644
--- a/salomon/software/numerical-languages/r.md
+++ b/docs.it4i.cz/salomon/software/numerical-languages/r.md
@@ -1,6 +1,6 @@
+R
=
-
-
+
Introduction {#parent-fieldname-title}
------------
The R is a language and environment for statistical computing and
@@ -16,7 +16,8 @@ full control.
Another convenience is the ease with which the C code or third party
libraries may be integrated within R.
Extensive support for parallel computing is available within R.
-Read more on ,
+Read more on <http://www.r-project.org/>,
+<http://cran.r-project.org/doc/manuals/r-release/R-lang.html>
Modules
-------
****The R version 3.1.1 is available on the cluster, along with GUI
@@ -36,14 +37,14 @@ parallelize to 24 threads. You may control the threads by setting the
OMP_NUM_THREADS environment variable.
### Interactive execution
To run R interactively, using Rstudio GUI, log in with ssh -X parameter
-for X11 forwarding. Run rstudio
+for X11 forwarding. Run rstudio:
$ module load Rstudio
$ rstudio
### Batch execution
To run R in batch mode, write an R script, then write a bash jobscript
and execute via the qsub command. By default, R will use 24 threads when
running MKL kernels.
-Example jobscript
+Example jobscript:
#!/bin/bash
# change to local scratch directory
cd /lscratch/$PBS_JOBID || exit
@@ -61,7 +62,7 @@ This script may be submitted directly to the PBS workload manager via
the qsub command. The inputs are in rscript.R file, outputs in
routput.out file. See the single node jobscript example in the [Job
execution
-section](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
+section](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution).
Parallel R
----------
Parallel execution of R may be achieved in many ways. One approach is
@@ -74,7 +75,7 @@ parallel constructs are directly stated within the R script.
The package parallel provides support for parallel computation,
including by forking (taken from package multicore), by sockets (taken
from package snow) and random-number generation.
-The package is activated this way
+The package is activated this way:
$ R
> library(parallel)
More information and examples may be obtained directly by reading the
@@ -82,16 +83,17 @@ documentation available in R
> ?parallel
> library(help = "parallel")
> vignette("parallel")
-Download the package [parallell](parallel.pdf) vignette.
+Download the package
+[parallell](https://docs.it4i.cz/salomon/software/numerical-languages/package-parallel-vignette)
+vignette.
The forking is the most simple to use. Forking family of functions
provide parallelized, drop in replacement for the serial apply() family
of functions.
Forking via package parallel provides functionality similar to OpenMP
construct
#omp parallel for
-
Only cores of single node can be utilized this way!
-Forking example
+Forking example:
library(parallel)
#integrand function
f <- function(i,h) {
@@ -103,7 +105,7 @@ Forking example
while (TRUE)
{
#read number of intervals
- cat("Enter the number of intervals (0 quits) ")
+ cat("Enter the number of intervals(0 quits) ")
fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)
if(n<=0) break
#run the calculation
@@ -116,7 +118,7 @@ Forking example
}
The above example is the classic parallel example for calculating the
number π. Note the **detectCores()** and **mclapply()** functions.
-Execute the example as
+Execute the example as:
$ R --slave --no-save --no-restore -f pi3p.R
Every evaluation of the integrad function runs in parallel on different
process.
@@ -125,9 +127,10 @@ Package Rmpi
package Rmpi provides an interface (wrapper) to MPI APIs.
It also provides interactive R slave environment. On the cluster, Rmpi
provides interface to the
-[OpenMPI](../mpi-1/Running_OpenMPI.html).
-Read more on Rmpi at ,
+[OpenMPI](https://docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI).
+Read more on Rmpi at <http://cran.r-project.org/web/packages/Rmpi/>,
reference manual is available at
+<http://cran.r-project.org/web/packages/Rmpi/Rmpi.pdf>
When using package Rmpi, both openmpi and R modules must be loaded
$ module load OpenMPI
$ module load R
@@ -139,7 +142,7 @@ these concepts.
### []()static Rmpi
Static Rmpi programs are executed via mpiexec, as any other MPI
programs. Number of processes is static - given at the launch time.
-Static Rmpi example
+Static Rmpi example:
library(Rmpi)
#integrand function
f <- function(i,h) {
@@ -155,7 +158,7 @@ Static Rmpi example
{
#read number of intervals
if (rank==0) {
- cat("Enter the number of intervals (0 quits) ")
+ cat("Enter the number of intervals(0 quits) ")
fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)
}
#broadcat the intervals
@@ -173,13 +176,13 @@ Static Rmpi example
mpi.quit()
The above is the static MPI example for calculating the number π. Note
the **library(Rmpi)** and **mpi.comm.dup()** function calls.
-Execute the example as
+Execute the example as:
$ mpirun R --slave --no-save --no-restore -f pi3.R
### dynamic Rmpi
Dynamic Rmpi programs are executed by calling the R directly. OpenMPI
module must be still loaded. The R slave processes will be spawned by a
function call within the Rmpi program.
-Dynamic Rmpi example
+Dynamic Rmpi example:
#integrand function
f <- function(i,h) {
x <- h*(i-0.5)
@@ -196,7 +199,7 @@ Dynamic Rmpi example
{
#read number of intervals
if (rank==0) {
- cat("Enter the number of intervals (0 quits) ")
+ cat("Enter the number of intervals(0 quits) ")
fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)
}
#broadcat the intervals
@@ -214,7 +217,7 @@ Dynamic Rmpi example
}
#main
library(Rmpi)
- cat("Enter the number of slaves ")
+ cat("Enter the number of slaves")
fp<-file("stdin"); ns<-scan(fp,nmax=1); close(fp)
mpi.spawn.Rslaves(nslaves=ns)
mpi.bcast.Robj2slave(f)
@@ -226,7 +229,7 @@ The above example is the dynamic MPI example for calculating the number
Ď€. Both master and slave processes carry out the calculation. Note the
**mpi.spawn.Rslaves(), mpi.bcast.Robj2slave()** and the
**mpi.bcast.cmd()** function calls.
-Execute the example as
+Execute the example as:
$ mpirun -np 1 R --slave --no-save --no-restore -f pi3Rslaves.R
Note that this method uses MPI_Comm_spawn (Dynamic process feature of
MPI-2) to start the slave processes - the master process needs to be
@@ -239,7 +242,7 @@ mpi.apply is a specific way of executing Dynamic Rmpi programs.
mpi.apply() family of functions provide MPI parallelized, drop in
replacement for the serial apply() family of functions.
Execution is identical to other dynamic Rmpi programs.
-mpi.apply Rmpi example
+mpi.apply Rmpi example:
#integrand function
f <- function(i,h) {
x <- h*(i-0.5)
@@ -257,7 +260,7 @@ mpi.apply Rmpi example
}
#main
library(Rmpi)
- cat("Enter the number of slaves ")
+ cat("Enter the number of slaves")
fp<-file("stdin"); ns<-scan(fp,nmax=1); close(fp)
mpi.spawn.Rslaves(nslaves=ns)
mpi.bcast.Robj2slave(f)
@@ -265,7 +268,7 @@ mpi.apply Rmpi example
while (TRUE)
{
#read number of intervals
- cat("Enter the number of intervals (0 quits) ")
+ cat("Enter the number of intervals(0 quits) ")
fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)
if(n<=0) break
#run workerpi
@@ -277,15 +280,15 @@ mpi.apply Rmpi example
mpi.quit()
The above is the mpi.apply MPI example for calculating the number π.
Only the slave processes carry out the calculation. Note the
-**mpi.parSapply(), ** function call. The package
+**mpi.parSapply(), ** function call. The package <span
class="anchor-link">parallel
-[example](#package-parallel)[above](#package-parallel)
+[example](#package-parallel)</span>[above](#package-parallel)
may be trivially adapted (for much better performance) to this structure
using the mclapply() in place of mpi.parSapply().
-Execute the example as
+Execute the example as:
$ mpirun -np 1 R --slave --no-save --no-restore -f pi3parSapply.R
Combining parallel and Rmpi
----------------------------
+----
Currently, the two packages can not be combined for hybrid calculations.
Parallel execution
------------------
@@ -293,11 +296,11 @@ The R parallel jobs are executed via the PBS queue system exactly as any
other parallel jobs. User must create an appropriate jobscript and
submit via the **qsub**
Example jobscript for [static Rmpi](#static-rmpi) parallel
-R execution, running 1 process per core
+R execution, running 1 process per core:
#!/bin/bash
#PBS -q qprod
#PBS -N Rjob
- #PBS -l select=100ncpus=24mpiprocs=24ompthreads=1
+ #PBS -l select=100:ncpus=24:mpiprocs=24:ompthreads=1
# change to scratch directory
SCRDIR=/scratch/work/user/$USER/myjob
cd $SCRDIR || exit
@@ -314,65 +317,16 @@ R execution, running 1 process per core
exit
For more information about jobscripts and MPI execution refer to the
[Job
-submission](../../resource-allocation-and-job-execution/job-submission-and-execution.html)
-and general [MPI](../mpi-1.html) sections.
+submission](https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution)
+and general
+[MPI](https://docs.it4i.cz/salomon/software/mpi-1)
+sections.
Xeon Phi Offload
----------------
By leveraging MKL, R can accelerate certain computations, most notably
linear algebra operations on the Xeon Phi accelerator by using Automated
Offload. To use MKL Automated Offload, you need to first set this
-environment variable before R execution
+environment variable before R execution :
$ export MKL_MIC_ENABLE=1
[Read more about automatic
-offload](../intel-xeon-phi.html)
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
+offload](https://docs.it4i.cz/salomon/software/intel-xeon-phi)
diff --git a/salomon/software/operating-system.html b/docs.it4i.cz/salomon/software/operating-system.html
old mode 100755
new mode 100644
similarity index 66%
rename from salomon/software/operating-system.html
rename to docs.it4i.cz/salomon/software/operating-system.html
index 809ad43c87650f1a85491608958b4279730c4200..b5a3a84b144a6079f955c5b758682f321bb8ae40
--- a/salomon/software/operating-system.html
+++ b/docs.it4i.cz/salomon/software/operating-system.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/software/operating-system by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:34 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/operating-system" /><!--[if lt IE 7]></base><![endif]-->
<meta content="The operating system, deployed on Salomon cluster" name="description" />
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Operating System — IT4I Docs</title>
- <link rel="canonical" href="operating-system.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/operating-system" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="operating-system.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/operating-system#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="operating-system.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/operating-system#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -319,7 +316,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -335,7 +332,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -351,7 +348,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -367,7 +364,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -383,7 +380,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -399,7 +396,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -415,7 +412,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -431,7 +428,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -447,7 +444,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -463,7 +460,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -479,7 +476,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -495,7 +492,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -511,10 +508,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -530,7 +527,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -546,7 +543,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -562,7 +559,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -578,7 +575,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -594,7 +591,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -610,7 +607,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -626,7 +623,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -642,7 +639,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -658,7 +655,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -674,7 +671,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -690,7 +687,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="operating-system.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -715,7 +712,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -740,7 +737,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -756,7 +753,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -772,7 +769,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -788,7 +785,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -827,14 +824,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -856,12 +853,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -877,7 +874,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/docs.it4i.cz/salomon/software/operating-system.md b/docs.it4i.cz/salomon/software/operating-system.md
new file mode 100644
index 0000000000000000000000000000000000000000..93d1c728811df217b1224f1f93e11596f651424a
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/operating-system.md
@@ -0,0 +1,8 @@
+Operating System
+================
+The operating system, deployed on Salomon cluster
+
+The operating system on Salomon is Linux - CentOS 6.6.
+<span>The CentOS Linux distribution is a stable, predictable, manageable
+and reproducible platform derived from the sources of Red Hat Enterprise
+Linux (RHEL).</span>
diff --git a/salomon/storage/storage.html b/docs.it4i.cz/salomon/storage.html
old mode 100755
new mode 100644
similarity index 84%
rename from salomon/storage/storage.html
rename to docs.it4i.cz/salomon/storage.html
index 412c0820fef6f229bd7bf31f6bf0e04e210ea586..29a5bef9df4dbc4141ec2cd05cf04b4310825fd0
--- a/salomon/storage/storage.html
+++ b/docs.it4i.cz/salomon/storage.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/storage/storage by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:02 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/storage/storage" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/IEFixes-cachekey-ec9b60024fd235ff2c883b4b54db91cb.css" />
<![endif]-->
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- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/%2b%2bresource%2b%2bit4i.portal.common/exporting.js"></script>
- <script type="text/javascript" src="../../portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Storage — IT4I Docs</title>
- <link rel="canonical" href="../storage.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/storage" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="storage.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/storage#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="storage.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/storage#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -236,7 +233,7 @@
<p class="callout">Use <a class="anchor-link" href="#home" target="_self" title="">HOME</a> for your most valuable data and programs.<br />Use <a class="anchor-link" href="#work" target="_self" title="">WORK</a> for your large project files<br />Use <a class="anchor-link" href="#temp" target="_self" title="">TEMP</a> for large scratch data.</p>
<p class="callout">Do not use for <a class="anchor-link" href="#archiving" target="_self" title="">archiving</a>!</p>
<h2 class=" "><a name="archiving"></a>Archiving</h2>
-<p>Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use <a target="_self" title="" class="internal-link" href="../../anselm-cluster-documentation/storage-1/cesnet-data-storage.html">CESNET storage service</a>, which is available via SSHFS.</p>
+<p>Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage">CESNET storage service</a>, which is available via SSHFS.</p>
<h2 class=" "><a name="shared-filesystems"></a>Shared Filesystems</h2>
<p class=" ">Salomon computer provides two main shared filesystems, the <a class="anchor-link" href="#home-filesystem" target="_self" title=""><span class="anchor-link">HOME filesystem</span></a> and the <a class="anchor-link" href="#scratch-filesystem" target="_self" title="">SCRATCH filesystem</a>. The SCRATCH filesystem is partitioned to <a class="anchor-link" href="#shared-workspaces" target="_self" title="">WORK and TEMP workspaces</a>. The HOME filesystem is realized as a tiered NFSÂ disk storage. The SCRATCH filesystem is realized as a parallel Lustre filesystem. Both shared file systems are accessible via the Infiniband network. Extended ACLs are provided on both HOME/SCRATCH filesystems for the purpose of sharing data with other users using fine-grained control.</p>
<h3 class=" "><a name="home-filesystem"></a><a name="home-filesystem"></a>HOME filesystem</h3>
@@ -268,7 +265,7 @@
</ul>
</div>
<h3 class=" ">Understanding the Lustre Filesystems</h3>
-<p>(source <a class="external-link" href="http://www.nas.nasa.gov/" target="_self" title="">http://www.nas.nasa.gov</a>)</p>
+<p>(source <a class="external-link" href="http://www.nas.nasa.gov" target="_self" title="">http://www.nas.nasa.gov</a>)</p>
<p>A user file on the Lustre filesystem can be divided into multiple chunks (stripes) and stored across a subset of the object storage targets (OSTs) (disks). The stripes are distributed among the OSTs in a round-robin fashion to ensure load balancing.</p>
<p>When a client (a <span class="glossaryItem">compute <span class="glossaryItem">node</span></span> from your job) needs to create or access a file, the client queries the metadata server (<span class="glossaryItem">MDS</span>) and the metadata target (<span class="glossaryItem">MDT</span>) for the layout and location of the <a href="http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping">file's stripes</a>. Once the file is opened and the client obtains the striping information, the <span class="glossaryItem">MDS</span> is no longer involved in the file I/O process. The client interacts directly with the object storage servers (OSSes) and OSTs to perform I/O operations such as locking, disk allocation, storage, and retrieval.</p>
<p>If multiple clients try to read and write the same part of a file at the same time, the Lustre distributed lock manager enforces coherency so that all clients see consistent results.</p>
@@ -325,7 +322,7 @@
<p>Users home directories /home/username reside on HOME filesystem. Accessible capacity is 0.5PB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 250GB per user. <span>If 250GB should prove as insufficient for particular user, please contact</span>Â <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">support</a>, the quota may be lifted upon request.</p>
<p class="callout">The HOME filesystem is intended for preparation, evaluation, processing and storage of data generated by active Projects.</p>
<p>The HOMEÂ should not be used to archive data of past Projects or other unrelated data.</p>
-<p>The files on HOME will not be deleted until end of the <a target="_self" title="" class="internal-link" href="../../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html">users lifecycle</a>.</p>
+<p>The files on HOME will not be deleted until end of the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials">users lifecycle</a>.</p>
<p class=" ">The workspace is backed up, such that it can be restored in case of catasthropic failure resulting in significant data loss. This backup however is not intended to restore old versions of user data or to restore (accidentaly) deleted files. <br /><br /></p>
<table class="listing">
<tbody>
@@ -599,7 +596,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -615,7 +612,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -631,7 +628,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -647,7 +644,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -663,7 +660,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -679,7 +676,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -695,7 +692,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -711,7 +708,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -727,7 +724,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -743,7 +740,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -759,7 +756,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -775,7 +772,7 @@
- <a title="" class="state-published contenttype-document" href="cesnet-data-storage.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/storage/cesnet-data-storage">
<span>CESNET Data Storage</span>
</a>
@@ -800,7 +797,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -816,10 +813,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -835,7 +832,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -860,7 +857,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -876,7 +873,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -892,7 +889,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -908,7 +905,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -947,14 +944,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -976,12 +973,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -997,7 +994,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/storage/storage by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:18:02 GMT -->
</html>
diff --git a/salomon/storage.md b/docs.it4i.cz/salomon/storage.md
similarity index 75%
rename from salomon/storage.md
rename to docs.it4i.cz/salomon/storage.md
index 57fd541a373d80d83e2b3108dedeea9429dc7705..838cb9c58c384a05029c5e3b7e24a6d2a38659c4 100644
--- a/salomon/storage.md
+++ b/docs.it4i.cz/salomon/storage.md
@@ -1,9 +1,13 @@
+Storage
+=======
+
+Introduction
------------
-There are two main shared file systems on Salomon cluster, the [
-class="anchor-link">
-class="anchor-link">HOME](#home) and [
-class="anchor-link">
-class="anchor-link">SCRATCH](#shared-filesystems).
+There are two main shared file systems on Salomon cluster, the [<span
+class="anchor-link"><span
+class="anchor-link">HOME</span></span>](#home) and [<span
+class="anchor-link"><span
+class="anchor-link">SCRATCH</span></span>](#shared-filesystems).
All login and compute nodes may access same data on shared filesystems.
Compute nodes are also equipped with local (non-shared) scratch, ramdisk
and tmp filesystems.
@@ -19,13 +23,13 @@ Do not use for [archiving](#archiving)!
Please don't use shared filesystems as a backup for large amount of data
or long-term archiving mean. The academic staff and students of research
institutions in the Czech Republic can use [CESNET storage
-service](../anselm-cluster-documentation/storage-1/cesnet-data-storage.html),
+service](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage),
which is available via SSHFS.
[]()Shared Filesystems
----------------------
-Salomon computer provides two main shared filesystems, the [
+Salomon computer provides two main shared filesystems, the [<span
class="anchor-link">HOME
-filesystem](#home-filesystem) and the [SCRATCH
+filesystem</span>](#home-filesystem) and the [SCRATCH
filesystem](#scratch-filesystem). The SCRATCH filesystem
is partitioned to [WORK and TEMP
workspaces](#shared-workspaces). The HOME filesystem is
@@ -44,36 +48,37 @@ The architecture of Lustre on Salomon is composed of two metadata
servers (MDS) and six data/object storage servers (OSS). Accessible
capacity is 1.69 PB, shared among all users. The SCRATCH filesystem
hosts the [WORK and TEMP workspaces](#shared-workspaces).
-Configuration of the SCRATCH Lustre storage
-- SCRATCH Lustre object storage
-
+<span class="listitem">Configuration of the SCRATCH Lustre storage
+</span>
+<span class="emphasis"></span><span class="emphasis"></span>
+- <span class="emphasis">SCRATCH Lustre object storage</span>
+ <div class="itemizedlist">
- Disk array SFA12KX
- 540 4TB SAS 7.2krpm disks
- 54 OSTs of 10 disks in RAID6 (8+2)
- 15 hot-spare disks
- 4x 400GB SSD cache
-- SCRATCH Lustre metadata storage
-
+- <span class="emphasis">SCRATCH Lustre metadata storage</span>
+ <div class="itemizedlist">
- Disk array EF3015
- 12 600GB SAS 15krpm disks
### Understanding the Lustre Filesystems
-(source
-[http//www.nas.nasa.gov](http//www.nas.nasa.gov/))
+(source <http://www.nas.nasa.gov>)
A user file on the Lustre filesystem can be divided into multiple chunks
(stripes) and stored across a subset of the object storage targets
(OSTs) (disks). The stripes are distributed among the OSTs in a
round-robin fashion to ensure load balancing.
-When a client (a compute
-class="glossaryItem">node from your job) needs to create
-or access a file, the client queries the metadata server (
-class="glossaryItem">MDS) and the metadata target (
-class="glossaryItem">MDT) for the layout and location of the
+When a client (a <span class="glossaryItem">compute <span
+class="glossaryItem">node</span></span> from your job) needs to create
+or access a file, the client queries the metadata server (<span
+class="glossaryItem">MDS</span>) and the metadata target (<span
+class="glossaryItem">MDT</span>) for the layout and location of the
[file's
-stripes](http//www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping).
+stripes](http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping).
Once the file is opened and the client obtains the striping information,
-the MDS is no longer involved in the
+the <span class="glossaryItem">MDS</span> is no longer involved in the
file I/O process. The client interacts directly with the object storage
servers (OSSes) and OSTs to perform I/O operations such as locking, disk
allocation, storage, and retrieval.
@@ -82,16 +87,16 @@ same time, the Lustre distributed lock manager enforces coherency so
that all clients see consistent results.
There is default stripe configuration for Salomon Lustre filesystems.
However, users can set the following stripe parameters for their own
-directories or files to get optimum I/O performance
-1. stripe_size the size of the chunk in bytes; specify with k, m, or
+directories or files to get optimum I/O performance:
+1. stripe_sizethe size of the chunk in bytes; specify with k, m, or
g to use units of KB, MB, or GB, respectively; the size must be an
even multiple of 65,536 bytes; default is 1MB for all Salomon Lustre
filesystems
2. stripe_count the number of OSTs to stripe across; default is 1 for
Salomon Lustre filesystems one can specify -1 to use all OSTs in
the filesystem.
-3. stripe_offset The index of the
- class="glossaryItem">OST where the first stripe is to be
+3. stripe_offset The index of the <span
+ class="glossaryItem">OST</span> where the first stripe is to be
placed; default is -1 which results in random selection; using a
non-default value is NOT recommended.
Â
@@ -105,15 +110,15 @@ access patterns.Â
$ lfs getstripe dir|filename
$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir|filename
```
-Example
+Example:
``` {.prettyprint .lang-sh}
$ lfs getstripe /scratch/work/user/username
/scratch/work/user/username
-stripe_count 1 stripe_size 1048576 stripe_offset -1
+stripe_count 1 stripe_size 1048576 stripe_offset -1
$ lfs setstripe -c -1 /scratch/work/user/username/
$ lfs getstripe /scratch/work/user/username/
/scratch/work/user/username/
-stripe_count -1 stripe_size 1048576 stripe_offset -1
+stripe_count -1 stripe_size 1048576 stripe_offset -1
```
In this example, we view current stripe setting of the
/scratch/username/ directory. The stripe count is changed to all OSTs,
@@ -148,40 +153,41 @@ part of a file. However, it can be counterproductive in some cases if it
does not match your I/O pattern. The choice of stripe size has no effect
on a single-stripe file.
Read more on
-Disk usage and quota commands
-------------------------------------------
-User quotas on the Lustre file systems (SCRATCH) can be checked
-and reviewed using following command
+<http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html>
+<span>Disk usage and quota commands</span>
+-------------------
+<span>User quotas on the Lustre file systems (SCRATCH) can be checked
+and reviewed using following command:</span>
``` {.prettyprint .lang-sh}
$ lfs quota dir
```
-Example for Lustre SCRATCH directory
+Example for Lustre SCRATCH directory:
``` {.prettyprint .lang-sh}
$ lfs quota /scratch
-Disk quotas for user user001 (uid 1234)
+Disk quotas for user user001 (uid 1234):
Filesystem kbytes quota limit grace files quota limit grace
 /scratch    8    0 100000000000    -    3    0    0    -
-Disk quotas for group user001 (gid 1234)
+Disk quotas for group user001 (gid 1234):
Filesystem kbytes quota limit grace files quota limit grace
/scratch    8    0    0    -    3    0    0    -
```
In this example, we view current quota size limit of 100TB and 8KB
currently used by user001.
HOME directory is mounted via NFS, so a different command must be used
-to obtain quota information
+to obtain quota information:
 $ quota
-Example output
+Example output:
$ quota
- Disk quotas for user vop999 (uid 1025)
+ Disk quotas for user vop999 (uid 1025):
Filesystem blocks quota limit grace files quota limit grace
- home-nfs-ib.salomon.it4i.cz/home
+ home-nfs-ib.salomon.it4i.cz:/home
28 0 250000000 10 0 500000
To have a better understanding of where the space is exactly used, you
can use following command to find out.
``` {.prettyprint .lang-sh}
$ du -hs dir
```
-Example for your HOME directory
+Example for your HOME directory:
``` {.prettyprint .lang-sh}
$ cd /home
$ du -hs * .[a-zA-z0-9]* | grep -E "[0-9]*G|[0-9]*M" | sort -hr
@@ -195,9 +201,8 @@ This will list all directories which are having MegaBytes or GigaBytes
of consumed space in your actual (in this example HOME) directory. List
is sorted in descending order from largest to smallest
files/directories.
-
-To have a better understanding of previous commands, you can read
-manpages.
+<span>To have a better understanding of previous commands, you can read
+manpages.</span>
``` {.prettyprint .lang-sh}
$ man lfs
```
@@ -205,7 +210,7 @@ $ man lfs
$ man du
```
Extended Access Control List (ACL)
-----------------------------------
+-----------
Extended ACLs provide another security mechanism beside the standard
POSIX ACLs which are defined by three entries (for
owner/group/others). Extended ACLs have more than the three basic
@@ -218,53 +223,52 @@ manner. Below, we create a directory and allow a specific user access.
[vop999@login1.salomon ~]$ umask 027
[vop999@login1.salomon ~]$ mkdir test
[vop999@login1.salomon ~]$ ls -ld test
-drwxr-x--- 2 vop999 vop999 4096 Nov 5 1417 test
+drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.salomon ~]$ getfacl test
-# file test
-# owner vop999
-# group vop999
-userrwx
-groupr-x
-other---
-[vop999@login1.salomon ~]$ setfacl -m userjohnsmrwx test
+# filetest
+# ownervop999
+# groupvop999
+user::rwx
+group::r-x
+other::---
+[vop999@login1.salomon ~]$ setfacl -m user:johnsm:rwx test
[vop999@login1.salomon ~]$ ls -ld test
-drwxrwx---+ 2 vop999 vop999 4096 Nov 5 1417 test
+drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.salomon ~]$ getfacl test
-# file test
-# owner vop999
-# group vop999
-userrwx
-userjohnsmrwx
-groupr-x
-maskrwx
-other---
+# filetest
+# ownervop999
+# groupvop999
+user::rwx
+user:johnsm:rwx
+group::r-x
+mask::rwx
+other::---
```
Default ACL mechanism can be used to replace setuid/setgid permissions
on directories. Setting a default ACL on a directory (-d flag to
setfacl) will cause the ACL permissions to be inherited by any newly
created file or subdirectory within the directory. Refer to this page
-for more information on Linux ACL
-[http//www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html ](http//www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html)
+for more information on Linux ACL:
+[http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html ](http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html)
[]()Shared Workspaces
---------------------
### []()[]()HOME
Users home directories /home/username reside on HOME filesystem.
Accessible capacity is 0.5PB, shared among all users. Individual users
are restricted by filesystem usage quotas, set to 250GB per user.
-If 250GB should prove as insufficient for particular user, please
-contact [support](https//support.it4i.cz/rt),
+<span>If 250GB should prove as insufficient for particular user, please
+contact</span>Â [support](https://support.it4i.cz/rt),
the quota may be lifted upon request.
The HOME filesystem is intended for preparation, evaluation, processing
and storage of data generated by active Projects.
The HOMEÂ should not be used to archive data of past Projects or other
unrelated data.
The files on HOME will not be deleted until end of the [users
-lifecycle](../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html).
+lifecycle](https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials).
The workspace is backed up, such that it can be restored in case ofÂ
catasthropic failure resulting in significant data loss. This backup
however is not intended to restore old versions of user data or to
restore (accidentaly) deleted files.
-
HOME workspace
Accesspoint
/home/username
@@ -282,12 +286,11 @@ subdirectories and files in directories **/scratch/work/user/username**
and **/scratch/work/project/projectid. **The /scratch/work/user/username
is private to user, much like the home directory. The
/scratch/work/project/projectid is accessible to all users involved in
-project projectid.
+project projectid. <span></span>
The WORK workspace is intended to store users project data as well as
for high performance access to input and output files. All project data
should be removed once the project is finished. The data on the WORK
workspace are not backed up.
-
Files on the WORK filesystem are **persistent** (not automatically
deleted) throughout duration of the project.
The WORK workspace is hosted on SCRATCH filesystem. The SCRATCH is
@@ -321,18 +324,16 @@ and files on the workspace. Accessible capacity is 1.6P, shared among
all users on TEMP and WORK. Individual users are restricted by
filesystem usage quotas, set to 100TB per user. The purpose of this
quota is to prevent runaway programs from filling the entire filesystem
-and deny service to other users. If 100TB should prove as
+and deny service to other users. <span>If 100TB should prove as
insufficient for particular user, please contact
-[support](https//support.it4i.cz/rt), the quota may be
-lifted upon request.Â
+[support](https://support.it4i.cz/rt), the quota may be
+lifted upon request. </span>
The TEMP workspace is intended for temporary scratch data generated
during the calculation as well as for high performance access to input
and output files. All I/O intensive jobs must use the TEMP workspace as
their working directory.
-
Users are advised to save the necessary data from the TEMP workspace to
HOME or WORK after the calculations and clean up the scratch files.
-
Files on the TEMP filesystem that are **not accessed for more than 90
days** will be automatically **deleted**.
The TEMP workspace is hosted on SCRATCH filesystem. The SCRATCH is
@@ -381,9 +382,9 @@ immediately after the calculation end. Users should take care to save
the output data from within the jobscript.
RAM disk
Mountpoint
-/ramdisk
+<span class="monospace">/ramdisk</span>
Accesspoint
-/ramdisk/$PBS_JOBID
+<span class="monospace">/ramdisk/$PBS_JOBID</span>
Capacity
120 GB
Throughput
@@ -395,30 +396,13 @@ none
**Summary
**
----------
- -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+ -------
Mountpoint Usage Protocol Net Capacity Throughput Limitations Access Services
- ---------------------------------------------- -------------------------------- ------------- -------------- ------------ ------------- ------------------------- -----------------------------
- /home home directory NFS, 2-Tier 0.5 PB 6 GB/s Quota 250GB Compute and login nodes backed up
- /scratch/work large project files Lustre 1.69 PB 30 GB/s Quota Compute and login nodes none
+ --------- ------------- -------------- ------------ ------------- -- ------
+ <span class="monospace">/home</span> home directory NFS, 2-Tier 0.5 PB 6 GB/s Quota 250GB Compute and login nodes backed up
+ <span class="monospace">/scratch/work</span> large project files Lustre 1.69 PB 30 GB/s Quota Compute and login nodes none
1TB
- /scratch/temp job temporary data Lustre 1.69 PB 30 GB/s Quota 100TB Compute and login nodes files older 90 days removed
- /ramdisk job temporary data, node local local 120GB 90 GB/s none Compute nodes purged after job ends
- -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+ <span class="monospace">/scratch/temp</span> job temporary data Lustre 1.69 PB 30 GB/s Quota 100TB Compute and login nodes files older 90 days removed
+ <span class="monospace">/ramdisk</span> job temporary data, node local local 120GB 90 GB/s none Compute nodes purged after job ends
+ -------
Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
-
- - [Hardware
- Overview](hardware-overview-1.html)
diff --git a/salomon/storage/cesnet-data-storage.html b/docs.it4i.cz/salomon/storage/cesnet-data-storage.html
old mode 100755
new mode 100644
similarity index 75%
rename from salomon/storage/cesnet-data-storage.html
rename to docs.it4i.cz/salomon/storage/cesnet-data-storage.html
index a9f6a660c1a740cb50350aa87d5b9478fea86fcb..6ea12b80869a8e1391c955c761062a9a758fb8ce
--- a/salomon/storage/cesnet-data-storage.html
+++ b/docs.it4i.cz/salomon/storage/cesnet-data-storage.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/salomon/storage/cesnet-data-storage by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:18 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/storage/cesnet-data-storage" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>CESNET Data Storage — IT4I Docs</title>
- <link rel="canonical" href="cesnet-data-storage.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/storage/cesnet-data-storage" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="cesnet-data-storage.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/storage/cesnet-data-storage#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="cesnet-data-storage.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/storage/cesnet-data-storage#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../storage.html">Storage</a>
+ <a href="https://docs.it4i.cz/salomon/storage">Storage</a>
<span class="breadcrumbSeparator">
/
@@ -350,7 +347,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -366,7 +363,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -382,7 +379,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -398,7 +395,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -414,7 +411,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -430,7 +427,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -446,7 +443,7 @@
- <a title="" class="state-published contenttype-document" href="../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -462,7 +459,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -478,7 +475,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -494,7 +491,7 @@
- <a title="" class="state-published contenttype-document" href="../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -510,7 +507,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../storage.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -526,7 +523,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="cesnet-data-storage.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/storage/cesnet-data-storage">
<span>CESNET Data Storage</span>
</a>
@@ -551,7 +548,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -567,10 +564,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -586,7 +583,7 @@
- <a title="" class="state-published contenttype-document" href="../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -611,7 +608,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -627,7 +624,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -643,7 +640,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -659,7 +656,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -698,14 +695,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -727,12 +724,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -748,7 +745,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/anselm-cluster-documentation/storage-1/cesnet-data-storage.md b/docs.it4i.cz/salomon/storage/cesnet-data-storage.md
similarity index 68%
rename from anselm-cluster-documentation/storage-1/cesnet-data-storage.md
rename to docs.it4i.cz/salomon/storage/cesnet-data-storage.md
index 7a0aebf6a4911058353b898476041681afb2bc19..51eb708c8ba89f571f846712728ebbb61fbf8ad8 100644
--- a/anselm-cluster-documentation/storage-1/cesnet-data-storage.md
+++ b/docs.it4i.cz/salomon/storage/cesnet-data-storage.md
@@ -1,5 +1,6 @@
-
-
+CESNET Data Storage
+===================
+
Introduction
------------
Do not use shared filesystems at IT4Innovations as a backup for large
@@ -7,40 +8,38 @@ amount of data or long-term archiving purposes.
The IT4Innovations does not provide storage capacity for data archiving.
Academic staff and students of research institutions in the Czech
Republic can use [CESNET Storage
-service](https//du.cesnet.cz/).
+service](https://du.cesnet.cz/).
The CESNET Storage service can be used for research purposes, mainly by
academic staff and students of research institutions in the Czech
Republic.
-
User of data storage CESNET (DU) association can become organizations or
an individual person who is either in the current employment
relationship (employees) or the current study relationship (students) to
a legal entity (organization) that meets the “Principles for access to
CESNET Large infrastructure (Access Policy)”.
-
User may only use data storage CESNET for data transfer and storage
which are associated with activities in science, research, development,
the spread of education, culture and prosperity. In detail see
“Acceptable Use Policy CESNET Large Infrastructure (Acceptable Use
Policy, AUP)”.
The service is documented at
-. For special requirements
+<https://du.cesnet.cz/wiki/doku.php/en/start>. For special requirements
please contact directly CESNET Storage Department via e-mail
-[du-support(at)cesnet.cz](mailtodu-support@cesnet.cz){.email-link}.
+[du-support(at)cesnet.cz](mailto:du-support@cesnet.cz){.email-link}.
The procedure to obtain the CESNET access is quick and trouble-free.
(source
-[https//du.cesnet.cz/](https//du.cesnet.cz/wiki/doku.php/en/start "CESNET Data Storage"))
+[https://du.cesnet.cz/](https://du.cesnet.cz/wiki/doku.php/en/start "CESNET Data Storage"))
CESNET storage access
---------------------
### Understanding Cesnet storage
It is very important to understand the Cesnet storage before uploading
data. Please read
- first.
+<https://du.cesnet.cz/en/navody/home-migrace-plzen/start> first.
Once registered for CESNET Storage, you may [access the
-storage](https//du.cesnet.cz/en/navody/faq/start) in
+storage](https://du.cesnet.cz/en/navody/faq/start) in
number of ways. We recommend the SSHFS and RSYNC methods.
### SSHFS Access
-SSHFS The storage will be mounted like a local hard drive
+SSHFSThe storage will be mounted like a local hard drive
The SSHFSÂ provides a very convenient way to access the CESNET Storage.
The storage will be mounted onto a local directory, exposing the vast
CESNET Storage as if it was a local removable harddrive. Files can be
@@ -49,12 +48,12 @@ First, create the mountpoint
$ mkdir cesnet
Mount the storage. Note that you can choose among the ssh.du1.cesnet.cz
(Plzen), ssh.du2.cesnet.cz (Jihlava), ssh.du3.cesnet.cz (Brno)
-Mount tier1_home **(only 5120M !)**
- $ sshfs username@ssh.du1.cesnet.cz. cesnet/
+Mount tier1_home **(only 5120M !)**:
+ $ sshfs username@ssh.du1.cesnet.cz:. cesnet/
For easy future access from Anselm, install your public key
$ cp .ssh/id_rsa.pub cesnet/.ssh/authorized_keys
-Mount tier1_cache_tape for the Storage VO
- $ sshfs username@ssh.du1.cesnet.cz/cache_tape/VO_storage/home/username cesnet/
+Mount tier1_cache_tape for the Storage VO:
+ $ sshfs username@ssh.du1.cesnet.cz:/cache_tape/VO_storage/home/username cesnet/
View the archive, copy the files and directories in and out
$ ls cesnet/
$ cp -a mydir cesnet/.
@@ -70,7 +69,6 @@ data sent over the network by sending only the differences between the
source files and the existing files in the destination. Rsync is widely
used for backups and mirroring and as an improved copy command for
everyday use.
-
Rsync finds files that need to be transferred using a "quick check"
algorithm (by default) that looks for files that have changed in size or
in last-modified time. Any changes in the other preserved attributes
@@ -78,29 +76,13 @@ in last-modified time. Any changes in the other preserved attributes
the quick check indicates that the file's data does not need to be
updated.
More about Rsync at
+<https://du.cesnet.cz/en/navody/rsync/start#pro_bezne_uzivatele>
Transfer large files to/from Cesnet storage, assuming membership in the
Storage VO
- $ rsync --progress datafile username@ssh.du1.cesnet.czVO_storage-cache_tape/.
- $ rsync --progress username@ssh.du1.cesnet.czVO_storage-cache_tape/datafile .
+ $ rsync --progress datafile username@ssh.du1.cesnet.cz:VO_storage-cache_tape/.
+ $ rsync --progress username@ssh.du1.cesnet.cz:VO_storage-cache_tape/datafile .
Transfer large directories to/from Cesnet storage, assuming membership
in the Storage VO
- $ rsync --progress -av datafolder username@ssh.du1.cesnet.czVO_storage-cache_tape/.
- $ rsync --progress -av username@ssh.du1.cesnet.czVO_storage-cache_tape/datafolder .
+ $ rsync --progress -av datafolder username@ssh.du1.cesnet.cz:VO_storage-cache_tape/.
+ $ rsync --progress -av username@ssh.du1.cesnet.cz:VO_storage-cache_tape/datafolder .
Transfer rates of about 28MB/s can be expected.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
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- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Anselm Cluster
- Documentation](../../anselm-cluster-documentation.html)
diff --git a/salomon/storage.html b/docs.it4i.cz/salomon/storage/storage.html
old mode 100755
new mode 100644
similarity index 84%
rename from salomon/storage.html
rename to docs.it4i.cz/salomon/storage/storage.html
index 6d614e5292f804fe50d743df9aa8a995c7398c22..c7aabb1393b59c013ce2ffd15c5f4409f29687c0
--- a/salomon/storage.html
+++ b/docs.it4i.cz/salomon/storage/storage.html
@@ -10,45 +10,42 @@
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ <base href="https://docs.it4i.cz/salomon/storage/storage" /><!--[if lt IE 7]></base><![endif]-->
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Storage — IT4I Docs</title>
- <link rel="canonical" href="storage.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/storage" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="storage.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/storage/storage#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="storage.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/storage/storage#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../index.html">
- <img src="../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -236,7 +233,7 @@
<p class="callout">Use <a class="anchor-link" href="#home" target="_self" title="">HOME</a> for your most valuable data and programs.<br />Use <a class="anchor-link" href="#work" target="_self" title="">WORK</a> for your large project files<br />Use <a class="anchor-link" href="#temp" target="_self" title="">TEMP</a> for large scratch data.</p>
<p class="callout">Do not use for <a class="anchor-link" href="#archiving" target="_self" title="">archiving</a>!</p>
<h2 class=" "><a name="archiving"></a>Archiving</h2>
-<p>Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use <a target="_self" title="" class="internal-link" href="../anselm-cluster-documentation/storage-1/cesnet-data-storage.html">CESNET storage service</a>, which is available via SSHFS.</p>
+<p>Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage">CESNET storage service</a>, which is available via SSHFS.</p>
<h2 class=" "><a name="shared-filesystems"></a>Shared Filesystems</h2>
<p class=" ">Salomon computer provides two main shared filesystems, the <a class="anchor-link" href="#home-filesystem" target="_self" title=""><span class="anchor-link">HOME filesystem</span></a> and the <a class="anchor-link" href="#scratch-filesystem" target="_self" title="">SCRATCH filesystem</a>. The SCRATCH filesystem is partitioned to <a class="anchor-link" href="#shared-workspaces" target="_self" title="">WORK and TEMP workspaces</a>. The HOME filesystem is realized as a tiered NFSÂ disk storage. The SCRATCH filesystem is realized as a parallel Lustre filesystem. Both shared file systems are accessible via the Infiniband network. Extended ACLs are provided on both HOME/SCRATCH filesystems for the purpose of sharing data with other users using fine-grained control.</p>
<h3 class=" "><a name="home-filesystem"></a><a name="home-filesystem"></a>HOME filesystem</h3>
@@ -268,7 +265,7 @@
</ul>
</div>
<h3 class=" ">Understanding the Lustre Filesystems</h3>
-<p>(source <a class="external-link" href="http://www.nas.nasa.gov/" target="_self" title="">http://www.nas.nasa.gov</a>)</p>
+<p>(source <a class="external-link" href="http://www.nas.nasa.gov" target="_self" title="">http://www.nas.nasa.gov</a>)</p>
<p>A user file on the Lustre filesystem can be divided into multiple chunks (stripes) and stored across a subset of the object storage targets (OSTs) (disks). The stripes are distributed among the OSTs in a round-robin fashion to ensure load balancing.</p>
<p>When a client (a <span class="glossaryItem">compute <span class="glossaryItem">node</span></span> from your job) needs to create or access a file, the client queries the metadata server (<span class="glossaryItem">MDS</span>) and the metadata target (<span class="glossaryItem">MDT</span>) for the layout and location of the <a href="http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping">file's stripes</a>. Once the file is opened and the client obtains the striping information, the <span class="glossaryItem">MDS</span> is no longer involved in the file I/O process. The client interacts directly with the object storage servers (OSSes) and OSTs to perform I/O operations such as locking, disk allocation, storage, and retrieval.</p>
<p>If multiple clients try to read and write the same part of a file at the same time, the Lustre distributed lock manager enforces coherency so that all clients see consistent results.</p>
@@ -325,7 +322,7 @@
<p>Users home directories /home/username reside on HOME filesystem. Accessible capacity is 0.5PB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 250GB per user. <span>If 250GB should prove as insufficient for particular user, please contact</span>Â <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">support</a>, the quota may be lifted upon request.</p>
<p class="callout">The HOME filesystem is intended for preparation, evaluation, processing and storage of data generated by active Projects.</p>
<p>The HOMEÂ should not be used to archive data of past Projects or other unrelated data.</p>
-<p>The files on HOME will not be deleted until end of the <a target="_self" title="" class="internal-link" href="../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html">users lifecycle</a>.</p>
+<p>The files on HOME will not be deleted until end of the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials">users lifecycle</a>.</p>
<p class=" ">The workspace is backed up, such that it can be restored in case of catasthropic failure resulting in significant data loss. This backup however is not intended to restore old versions of user data or to restore (accidentaly) deleted files. <br /><br /></p>
<table class="listing">
<tbody>
@@ -599,7 +596,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -615,7 +612,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -631,7 +628,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -647,7 +644,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -663,7 +660,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -679,7 +676,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -695,7 +692,7 @@
- <a title="" class="state-published contenttype-document" href="environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -711,7 +708,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -727,7 +724,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -743,7 +740,7 @@
- <a title="" class="state-published contenttype-document" href="compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -759,7 +756,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="storage.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -775,7 +772,7 @@
- <a title="" class="state-published contenttype-document" href="storage/cesnet-data-storage.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/storage/cesnet-data-storage">
<span>CESNET Data Storage</span>
</a>
@@ -800,7 +797,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -816,10 +813,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeFolderish contenttype-folder" href="software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -835,7 +832,7 @@
- <a title="" class="state-published contenttype-document" href="prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -860,7 +857,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -876,7 +873,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -892,7 +889,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -908,7 +905,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -947,14 +944,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -976,12 +973,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -997,7 +994,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/salomon/storage by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:45 GMT -->
</html>
diff --git a/salomon/storage/storage.md b/docs.it4i.cz/salomon/storage/storage.md
similarity index 75%
rename from salomon/storage/storage.md
rename to docs.it4i.cz/salomon/storage/storage.md
index 60998f869ae1c8aac4c214f78cc1e64b4292310b..838cb9c58c384a05029c5e3b7e24a6d2a38659c4 100644
--- a/salomon/storage/storage.md
+++ b/docs.it4i.cz/salomon/storage/storage.md
@@ -1,9 +1,13 @@
+Storage
+=======
+
+Introduction
------------
-There are two main shared file systems on Salomon cluster, the [
-class="anchor-link">
-class="anchor-link">HOME](#home) and [
-class="anchor-link">
-class="anchor-link">SCRATCH](#shared-filesystems).
+There are two main shared file systems on Salomon cluster, the [<span
+class="anchor-link"><span
+class="anchor-link">HOME</span></span>](#home) and [<span
+class="anchor-link"><span
+class="anchor-link">SCRATCH</span></span>](#shared-filesystems).
All login and compute nodes may access same data on shared filesystems.
Compute nodes are also equipped with local (non-shared) scratch, ramdisk
and tmp filesystems.
@@ -19,13 +23,13 @@ Do not use for [archiving](#archiving)!
Please don't use shared filesystems as a backup for large amount of data
or long-term archiving mean. The academic staff and students of research
institutions in the Czech Republic can use [CESNET storage
-service](../../anselm-cluster-documentation/storage-1/cesnet-data-storage.html),
+service](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage),
which is available via SSHFS.
[]()Shared Filesystems
----------------------
-Salomon computer provides two main shared filesystems, the [
+Salomon computer provides two main shared filesystems, the [<span
class="anchor-link">HOME
-filesystem](#home-filesystem) and the [SCRATCH
+filesystem</span>](#home-filesystem) and the [SCRATCH
filesystem](#scratch-filesystem). The SCRATCH filesystem
is partitioned to [WORK and TEMP
workspaces](#shared-workspaces). The HOME filesystem is
@@ -44,36 +48,37 @@ The architecture of Lustre on Salomon is composed of two metadata
servers (MDS) and six data/object storage servers (OSS). Accessible
capacity is 1.69 PB, shared among all users. The SCRATCH filesystem
hosts the [WORK and TEMP workspaces](#shared-workspaces).
-Configuration of the SCRATCH Lustre storage
-- SCRATCH Lustre object storage
-
+<span class="listitem">Configuration of the SCRATCH Lustre storage
+</span>
+<span class="emphasis"></span><span class="emphasis"></span>
+- <span class="emphasis">SCRATCH Lustre object storage</span>
+ <div class="itemizedlist">
- Disk array SFA12KX
- 540 4TB SAS 7.2krpm disks
- 54 OSTs of 10 disks in RAID6 (8+2)
- 15 hot-spare disks
- 4x 400GB SSD cache
-- SCRATCH Lustre metadata storage
-
+- <span class="emphasis">SCRATCH Lustre metadata storage</span>
+ <div class="itemizedlist">
- Disk array EF3015
- 12 600GB SAS 15krpm disks
### Understanding the Lustre Filesystems
-(source
-[http//www.nas.nasa.gov](http//www.nas.nasa.gov/))
+(source <http://www.nas.nasa.gov>)
A user file on the Lustre filesystem can be divided into multiple chunks
(stripes) and stored across a subset of the object storage targets
(OSTs) (disks). The stripes are distributed among the OSTs in a
round-robin fashion to ensure load balancing.
-When a client (a compute
-class="glossaryItem">node from your job) needs to create
-or access a file, the client queries the metadata server (
-class="glossaryItem">MDS) and the metadata target (
-class="glossaryItem">MDT) for the layout and location of the
+When a client (a <span class="glossaryItem">compute <span
+class="glossaryItem">node</span></span> from your job) needs to create
+or access a file, the client queries the metadata server (<span
+class="glossaryItem">MDS</span>) and the metadata target (<span
+class="glossaryItem">MDT</span>) for the layout and location of the
[file's
-stripes](http//www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping).
+stripes](http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping).
Once the file is opened and the client obtains the striping information,
-the MDS is no longer involved in the
+the <span class="glossaryItem">MDS</span> is no longer involved in the
file I/O process. The client interacts directly with the object storage
servers (OSSes) and OSTs to perform I/O operations such as locking, disk
allocation, storage, and retrieval.
@@ -82,16 +87,16 @@ same time, the Lustre distributed lock manager enforces coherency so
that all clients see consistent results.
There is default stripe configuration for Salomon Lustre filesystems.
However, users can set the following stripe parameters for their own
-directories or files to get optimum I/O performance
-1. stripe_size the size of the chunk in bytes; specify with k, m, or
+directories or files to get optimum I/O performance:
+1. stripe_sizethe size of the chunk in bytes; specify with k, m, or
g to use units of KB, MB, or GB, respectively; the size must be an
even multiple of 65,536 bytes; default is 1MB for all Salomon Lustre
filesystems
2. stripe_count the number of OSTs to stripe across; default is 1 for
Salomon Lustre filesystems one can specify -1 to use all OSTs in
the filesystem.
-3. stripe_offset The index of the
- class="glossaryItem">OST where the first stripe is to be
+3. stripe_offset The index of the <span
+ class="glossaryItem">OST</span> where the first stripe is to be
placed; default is -1 which results in random selection; using a
non-default value is NOT recommended.
Â
@@ -105,15 +110,15 @@ access patterns.Â
$ lfs getstripe dir|filename
$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir|filename
```
-Example
+Example:
``` {.prettyprint .lang-sh}
$ lfs getstripe /scratch/work/user/username
/scratch/work/user/username
-stripe_count 1 stripe_size 1048576 stripe_offset -1
+stripe_count 1 stripe_size 1048576 stripe_offset -1
$ lfs setstripe -c -1 /scratch/work/user/username/
$ lfs getstripe /scratch/work/user/username/
/scratch/work/user/username/
-stripe_count -1 stripe_size 1048576 stripe_offset -1
+stripe_count -1 stripe_size 1048576 stripe_offset -1
```
In this example, we view current stripe setting of the
/scratch/username/ directory. The stripe count is changed to all OSTs,
@@ -148,40 +153,41 @@ part of a file. However, it can be counterproductive in some cases if it
does not match your I/O pattern. The choice of stripe size has no effect
on a single-stripe file.
Read more on
-Disk usage and quota commands
-------------------------------------------
-User quotas on the Lustre file systems (SCRATCH) can be checked
-and reviewed using following command
+<http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html>
+<span>Disk usage and quota commands</span>
+-------------------
+<span>User quotas on the Lustre file systems (SCRATCH) can be checked
+and reviewed using following command:</span>
``` {.prettyprint .lang-sh}
$ lfs quota dir
```
-Example for Lustre SCRATCH directory
+Example for Lustre SCRATCH directory:
``` {.prettyprint .lang-sh}
$ lfs quota /scratch
-Disk quotas for user user001 (uid 1234)
+Disk quotas for user user001 (uid 1234):
Filesystem kbytes quota limit grace files quota limit grace
 /scratch    8    0 100000000000    -    3    0    0    -
-Disk quotas for group user001 (gid 1234)
+Disk quotas for group user001 (gid 1234):
Filesystem kbytes quota limit grace files quota limit grace
/scratch    8    0    0    -    3    0    0    -
```
In this example, we view current quota size limit of 100TB and 8KB
currently used by user001.
HOME directory is mounted via NFS, so a different command must be used
-to obtain quota information
+to obtain quota information:
 $ quota
-Example output
+Example output:
$ quota
- Disk quotas for user vop999 (uid 1025)
+ Disk quotas for user vop999 (uid 1025):
Filesystem blocks quota limit grace files quota limit grace
- home-nfs-ib.salomon.it4i.cz/home
+ home-nfs-ib.salomon.it4i.cz:/home
28 0 250000000 10 0 500000
To have a better understanding of where the space is exactly used, you
can use following command to find out.
``` {.prettyprint .lang-sh}
$ du -hs dir
```
-Example for your HOME directory
+Example for your HOME directory:
``` {.prettyprint .lang-sh}
$ cd /home
$ du -hs * .[a-zA-z0-9]* | grep -E "[0-9]*G|[0-9]*M" | sort -hr
@@ -195,9 +201,8 @@ This will list all directories which are having MegaBytes or GigaBytes
of consumed space in your actual (in this example HOME) directory. List
is sorted in descending order from largest to smallest
files/directories.
-
-To have a better understanding of previous commands, you can read
-manpages.
+<span>To have a better understanding of previous commands, you can read
+manpages.</span>
``` {.prettyprint .lang-sh}
$ man lfs
```
@@ -205,7 +210,7 @@ $ man lfs
$ man du
```
Extended Access Control List (ACL)
-----------------------------------
+-----------
Extended ACLs provide another security mechanism beside the standard
POSIX ACLs which are defined by three entries (for
owner/group/others). Extended ACLs have more than the three basic
@@ -218,53 +223,52 @@ manner. Below, we create a directory and allow a specific user access.
[vop999@login1.salomon ~]$ umask 027
[vop999@login1.salomon ~]$ mkdir test
[vop999@login1.salomon ~]$ ls -ld test
-drwxr-x--- 2 vop999 vop999 4096 Nov 5 1417 test
+drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.salomon ~]$ getfacl test
-# file test
-# owner vop999
-# group vop999
-userrwx
-groupr-x
-other---
-[vop999@login1.salomon ~]$ setfacl -m userjohnsmrwx test
+# filetest
+# ownervop999
+# groupvop999
+user::rwx
+group::r-x
+other::---
+[vop999@login1.salomon ~]$ setfacl -m user:johnsm:rwx test
[vop999@login1.salomon ~]$ ls -ld test
-drwxrwx---+ 2 vop999 vop999 4096 Nov 5 1417 test
+drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.salomon ~]$ getfacl test
-# file test
-# owner vop999
-# group vop999
-userrwx
-userjohnsmrwx
-groupr-x
-maskrwx
-other---
+# filetest
+# ownervop999
+# groupvop999
+user::rwx
+user:johnsm:rwx
+group::r-x
+mask::rwx
+other::---
```
Default ACL mechanism can be used to replace setuid/setgid permissions
on directories. Setting a default ACL on a directory (-d flag to
setfacl) will cause the ACL permissions to be inherited by any newly
created file or subdirectory within the directory. Refer to this page
-for more information on Linux ACL
-[http//www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html ](http//www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html)
+for more information on Linux ACL:
+[http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html ](http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html)
[]()Shared Workspaces
---------------------
### []()[]()HOME
Users home directories /home/username reside on HOME filesystem.
Accessible capacity is 0.5PB, shared among all users. Individual users
are restricted by filesystem usage quotas, set to 250GB per user.
-If 250GB should prove as insufficient for particular user, please
-contact [support](https//support.it4i.cz/rt),
+<span>If 250GB should prove as insufficient for particular user, please
+contact</span>Â [support](https://support.it4i.cz/rt),
the quota may be lifted upon request.
The HOME filesystem is intended for preparation, evaluation, processing
and storage of data generated by active Projects.
The HOMEÂ should not be used to archive data of past Projects or other
unrelated data.
The files on HOME will not be deleted until end of the [users
-lifecycle](../../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html).
+lifecycle](https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials).
The workspace is backed up, such that it can be restored in case ofÂ
catasthropic failure resulting in significant data loss. This backup
however is not intended to restore old versions of user data or to
restore (accidentaly) deleted files.
-
HOME workspace
Accesspoint
/home/username
@@ -282,12 +286,11 @@ subdirectories and files in directories **/scratch/work/user/username**
and **/scratch/work/project/projectid. **The /scratch/work/user/username
is private to user, much like the home directory. The
/scratch/work/project/projectid is accessible to all users involved in
-project projectid.
+project projectid. <span></span>
The WORK workspace is intended to store users project data as well as
for high performance access to input and output files. All project data
should be removed once the project is finished. The data on the WORK
workspace are not backed up.
-
Files on the WORK filesystem are **persistent** (not automatically
deleted) throughout duration of the project.
The WORK workspace is hosted on SCRATCH filesystem. The SCRATCH is
@@ -321,18 +324,16 @@ and files on the workspace. Accessible capacity is 1.6P, shared among
all users on TEMP and WORK. Individual users are restricted by
filesystem usage quotas, set to 100TB per user. The purpose of this
quota is to prevent runaway programs from filling the entire filesystem
-and deny service to other users. If 100TB should prove as
+and deny service to other users. <span>If 100TB should prove as
insufficient for particular user, please contact
-[support](https//support.it4i.cz/rt), the quota may be
-lifted upon request.Â
+[support](https://support.it4i.cz/rt), the quota may be
+lifted upon request. </span>
The TEMP workspace is intended for temporary scratch data generated
during the calculation as well as for high performance access to input
and output files. All I/O intensive jobs must use the TEMP workspace as
their working directory.
-
Users are advised to save the necessary data from the TEMP workspace to
HOME or WORK after the calculations and clean up the scratch files.
-
Files on the TEMP filesystem that are **not accessed for more than 90
days** will be automatically **deleted**.
The TEMP workspace is hosted on SCRATCH filesystem. The SCRATCH is
@@ -381,9 +382,9 @@ immediately after the calculation end. Users should take care to save
the output data from within the jobscript.
RAM disk
Mountpoint
-/ramdisk
+<span class="monospace">/ramdisk</span>
Accesspoint
-/ramdisk/$PBS_JOBID
+<span class="monospace">/ramdisk/$PBS_JOBID</span>
Capacity
120 GB
Throughput
@@ -395,30 +396,13 @@ none
**Summary
**
----------
- -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+ -------
Mountpoint Usage Protocol Net Capacity Throughput Limitations Access Services
- ---------------------------------------------- -------------------------------- ------------- -------------- ------------ ------------- ------------------------- -----------------------------
- /home home directory NFS, 2-Tier 0.5 PB 6 GB/s Quota 250GB Compute and login nodes backed up
- /scratch/work large project files Lustre 1.69 PB 30 GB/s Quota Compute and login nodes none
+ --------- ------------- -------------- ------------ ------------- -- ------
+ <span class="monospace">/home</span> home directory NFS, 2-Tier 0.5 PB 6 GB/s Quota 250GB Compute and login nodes backed up
+ <span class="monospace">/scratch/work</span> large project files Lustre 1.69 PB 30 GB/s Quota Compute and login nodes none
1TB
- /scratch/temp job temporary data Lustre 1.69 PB 30 GB/s Quota 100TB Compute and login nodes files older 90 days removed
- /ramdisk job temporary data, node local local 120GB 90 GB/s none Compute nodes purged after job ends
- -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+ <span class="monospace">/scratch/temp</span> job temporary data Lustre 1.69 PB 30 GB/s Quota 100TB Compute and login nodes files older 90 days removed
+ <span class="monospace">/ramdisk</span> job temporary data, node local local 120GB 90 GB/s none Compute nodes purged after job ends
+ -------
Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
diff --git a/salomon/uv-2000/@@images/04ce7514-8d27-4cdb-bf0f-45d875c75df0.jpg b/docs.it4i.cz/salomon/uv-2000/@@images/04ce7514-8d27-4cdb-bf0f-45d875c75df0.jpeg
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old mode 100755
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diff --git a/docs.it4i.cz/sitemap.html b/docs.it4i.cz/sitemap.html
new file mode 100644
index 0000000000000000000000000000000000000000..ff50cff2f9b5d12f5085316f019cb164ee5599ef
--- /dev/null
+++ b/docs.it4i.cz/sitemap.html
@@ -0,0 +1,1212 @@
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+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials">
+
+ <span>Obtaining Login Credentials</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="FAQ about certificates in general" href="https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq">
+
+ <span>Certificates FAQ</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters">
+
+ <span>Accessing the Clusters</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer">
+
+ <span>Shell access and data transfer</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface">
+
+ <span>Graphical User Interface</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
+
+ <span>Salomon Cluster Documentation</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel2">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
+
+ <span>Hardware Overview</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
+
+ <span>Accessing the Cluster</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access">
+
+ <span>Shell access and data transfer</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface">
+
+ <span>Graphical User Interface</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/vpn-access">
+
+ <span>VPN Access</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections">
+
+ <span>Outgoing connections</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
+
+ <span>Environment and Modules</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
+
+ <span>List of Available Modules</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
+
+ <span>Resource Allocation and Job Execution</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy">
+
+ <span>Resources Allocation Policy</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution">
+
+ <span>Job submission and execution</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority">
+
+ <span>Job scheduling</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing">
+
+ <span>Capacity computing</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
+
+ <span>Compute Nodes</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
+
+ <span>Storage</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/storage/cesnet-data-storage">
+
+ <span>CESNET Data Storage</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
+
+ <span>Network</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube">
+
+ <span>7D Enhanced Hypercube</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology">
+
+ <span>IB single-plane topology</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="In this section we provide overview of installed software and its usage.
+
+
+" href="https://docs.it4i.cz/salomon/software">
+
+ <span>Software</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
+
+ <span>ANSYS</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
+
+ <span>COMSOL</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
+
+ <span>Debuggers and profilers</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
+
+ <span>Chemistry, Physics and Materials science</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
+
+ <span>Intel Parallel studio</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
+
+ <span>MPI</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
+
+ <span>Numerical languages</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
+
+ <span>Compilers</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
+
+ <span>Intel Xeon Phi</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
+
+ <span>Java</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
+
+ <span>Operating System</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
+
+ <span>PRACE User Support</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
+
+ <span>Anselm Cluster Documentation</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel2">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview">
+
+ <span>Hardware Overview</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster">
+
+ <span>Accessing the Cluster</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access">
+
+ <span>Shell access and data transfer</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-link" title="" href="/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface">
+
+ <span>Graphical User Interface</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access">
+
+ <span>VPN Access</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections">
+
+ <span>Outgoing connections</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules">
+
+ <span>Environment and Modules</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution">
+
+ <span>Resource Allocation and Job Execution</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy">
+
+ <span>Resources Allocation Policy</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution">
+
+ <span>Job submission and execution</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority">
+
+ <span>Job scheduling</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing">
+
+ <span>Capacity computing</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes">
+
+ <span>Compute Nodes</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1">
+
+ <span>Storage</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage">
+
+ <span>CESNET Data Storage</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/network">
+
+ <span>Network</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="In this section we provide overview of installed software and its usage.
+
+
+" href="https://docs.it4i.cz/anselm-cluster-documentation/software">
+
+ <span>Software</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/anselm-cluster-documentation/software/ansys">
+
+ <span>ANSYS</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol">
+
+ <span>COMSOL</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers">
+
+ <span>Debuggers and profilers</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/anselm-cluster-documentation/software/chemistry">
+
+ <span>Chemistry and Materials science</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite">
+
+ <span>Intel Parallel studio</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1">
+
+ <span>MPI</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="Libraries for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries">
+
+ <span>Numerical Libraries</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages">
+
+ <span>Numerical languages</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization">
+
+ <span>Virtualization</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/anselm-cluster-documentation/software/compilers">
+
+ <span>Compilers</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi">
+
+ <span>Intel Xeon Phi</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="A guide to managing Independent Software Vendor licences" href="https://docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses">
+
+ <span>ISV Licenses</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="Java on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/java">
+
+ <span>Java</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="A guide to nVidia CUDA programming and GPU usage" href="https://docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda">
+
+ <span>nVidia CUDA</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1">
+
+ <span>OMICS Master</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="A free, open source CFD software package" href="https://docs.it4i.cz/anselm-cluster-documentation/software/openfoam">
+
+ <span>OpenFOAM</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="The operating system, deployed on ANSELM" href="https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system">
+
+ <span>Operating System</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a class="state-published contenttype-document" title="An open-source, multi-platform data analysis and visualization application " href="https://docs.it4i.cz/anselm-cluster-documentation/software/paraview">
+
+ <span>ParaView</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
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old mode 100755
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<title>VPN - Connection fail in Win 8.1 — IT4I Docs</title>
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+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
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<div class="cell width-full position-0">
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<p class="hiddenStructure">
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- <a accesskey="6" href="vpn-connection-fail-in-win-8.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/vpn-connection-fail-in-win-8.1#portal-globalnav">PĹ™ejĂt na navigaci</a>
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</form>
<div id="portal-advanced-search" class="hiddenStructure">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
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<li>Click 'Test Program'. This will open the program.</li>
<li>Close</li>
</ul>
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<span>What's New</span>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="salomon.html">
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- <a title="" class="state-published contenttype-document" href="links.html">
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<span>Links</span>
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- <a title="" class="state-published contenttype-collection" href="changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
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- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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- <a title="Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS patch" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="vpn-connection-fail-in-win-8.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS patch" href="https://docs.it4i.cz/vpn-connection-fail-in-win-8.1">
<span>VPN - Connection fail in Win 8.1</span>
</a>
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
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})();
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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diff --git a/docs.it4i.cz/vpn-connection-fail-in-win-8.1.md b/docs.it4i.cz/vpn-connection-fail-in-win-8.1.md
new file mode 100644
index 0000000000000000000000000000000000000000..874989a59c88f9e3594913018943922262aa04ba
--- /dev/null
+++ b/docs.it4i.cz/vpn-connection-fail-in-win-8.1.md
@@ -0,0 +1,21 @@
+VPN - Connection fail in Win 8.1
+================================
+Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS patch
+AnyConnect users on Windows 8.1 will receive a "Failed to initialize
+connection subsystem" error after installing the Windows 8.1 02/10/15
+security patch. This OS defect introduced with the 02/10/15 patch update
+will also impact WIndows 7 users with IE11. Windows Server
+2008/2012 are also impacted by this defect, but neither is a supported
+OS for AnyConnect.
+**Workaround:**
+- Close the Cisco AnyConnect Window and the taskbar mini-icon
+- Right click vpnui.exe in the 'Cisco AnyConnect Secure Mobility
+ Client' folder. (C:Program Files (x86)CiscoCisco AnyConnect
+ Secure Mobility
+- Client)
+- Click on the 'Run compatibility troubleshooter' button
+- Choose 'Try recommended settings'
+- The wizard suggests Windows 8 compatibility.
+- Click 'Test Program'. This will open the program.
+- Close
+
diff --git a/vpnuiV.png b/docs.it4i.cz/vpnuiV.png
old mode 100755
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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- <link rel="stylesheet" type="text/css" href="portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<title>News — IT4I Docs</title>
- <link rel="canonical" href="whats-new.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/whats-new" />
- <link rel="shortcut icon" type="image/x-icon" href="favicon.ico" />
- <link rel="apple-touch-icon" href="touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="whats-new.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/whats-new#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="whats-new.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/whats-new#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
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<div id="portal-advanced-search" class="hiddenStructure">
- <a href="%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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- <img src="logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
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<td class="listing-body-Title">
- <a href="whats-new/news-feed/matlab-2015b.html" title="MATLAB 2015b">MATLAB 2015b</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/matlab-2015b" title="MATLAB 2015b">MATLAB 2015b</a>
</td>
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<td class="listing-body-Title">
- <a href="whats-new/news-feed/vampir-installed.html" title="Vampir installed">Vampir installed</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/vampir-installed" title="Vampir installed">Vampir installed</a>
</td>
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<td class="listing-body-Title">
- <a href="whats-new/news-feed/allinea-tools-updated-to-6-0.html" title="Allinea Tools updated to 6.0.6">Allinea Tools updated to 6.0.6</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/allinea-tools-updated-to-6-0.6" title="Allinea Tools updated to 6.0.6">Allinea Tools updated to 6.0.6</a>
</td>
@@ -314,7 +311,7 @@
<td class="listing-body-Title">
- <a href="whats-new/news-feed/intel-vtune-amplifier-support-for-xeon-phi-on-salomon.html" title="Intel VTune Amplifier support for Xeon Phi on Salomon">Intel VTune Amplifier support for Xeon Phi on Salomon</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/intel-vtune-amplifier-support-for-xeon-phi-on-salomon" title="Intel VTune Amplifier support for Xeon Phi on Salomon">Intel VTune Amplifier support for Xeon Phi on Salomon</a>
</td>
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<td class="listing-body-Title">
- <a href="whats-new/news-feed/new-method-to-execute-parallel-matlab-jobs.html" title="New method to execute parallel MATLAB jobs">New method to execute parallel MATLAB jobs</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/new-method-to-execute-parallel-matlab-jobs" title="New method to execute parallel MATLAB jobs">New method to execute parallel MATLAB jobs</a>
</td>
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<td class="listing-body-Title">
- <a href="whats-new/news-feed/new-versions-of-allinea-forge-and-performance-version.html" title="New versions of Allinea Forge and Performance Reports">New versions of Allinea Forge and Performance Reports</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/new-versions-of-allinea-forge-and-performance-version" title="New versions of Allinea Forge and Performance Reports">New versions of Allinea Forge and Performance Reports</a>
</td>
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<td class="listing-body-Title">
- <a href="whats-new/news-feed/intel-vtune-is-working.html" title="Intel VTune is working">Intel VTune is working</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/intel-vtune-is-working" title="Intel VTune is working">Intel VTune is working</a>
</td>
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<td class="listing-body-Title">
- <a href="whats-new/news-feed/intel-parallel-studio-2016-update-3.html" title="Intel Parallel Studio 2016 update 3">Intel Parallel Studio 2016 update 3</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/intel-parallel-studio-2016-update-3" title="Intel Parallel Studio 2016 update 3">Intel Parallel Studio 2016 update 3</a>
</td>
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<td class="listing-body-Title">
- <a href="whats-new/news-feed/ansys-17-0-installed.html" title="ANSYS 17.0 Installed">ANSYS 17.0 Installed</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/ansys-17-0-installed" title="ANSYS 17.0 Installed">ANSYS 17.0 Installed</a>
</td>
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<td class="listing-body-Title">
- <a href="whats-new/news-feed/allinea-forge-6.html" title="Allinea Forge 6.0">Allinea Forge 6.0</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/allinea-forge-6.0" title="Allinea Forge 6.0">Allinea Forge 6.0</a>
</td>
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<td class="listing-body-Title">
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+ <a href="https://docs.it4i.cz/whats-new/news-feed/issue-with-intel-mpi-4-1-1-on-salomon" title="Issue with Intel MPI 4.1.1 on Salomon">Issue with Intel MPI 4.1.1 on Salomon</a>
</td>
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<td class="listing-body-Title">
- <a href="whats-new/news-feed/new-modules-for-parallel-programming-in-modern-fortran-course.html" title="New modules for Parallel programming in modern Fortran course">New modules for Parallel programming in modern Fortran course</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/new-modules-for-parallel-programming-in-modern-fortran-course" title="New modules for Parallel programming in modern Fortran course">New modules for Parallel programming in modern Fortran course</a>
</td>
@@ -530,7 +527,7 @@
<td class="listing-body-Title">
- <a href="whats-new/news-feed/octave-updated-to-4-0-1-on-anselm.html" title="Octave updated to 4.0.1 on Anselm">Octave updated to 4.0.1 on Anselm</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/octave-updated-to-4-0-1-on-anselm" title="Octave updated to 4.0.1 on Anselm">Octave updated to 4.0.1 on Anselm</a>
</td>
@@ -554,7 +551,7 @@
<td class="listing-body-Title">
- <a href="whats-new/news-feed/allinea-forge-5-1-installed-on-anselm.html" title="Allinea Forge 5.1 installed on Anselm">Allinea Forge 5.1 installed on Anselm</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/allinea-forge-5-1-installed-on-anselm" title="Allinea Forge 5.1 installed on Anselm">Allinea Forge 5.1 installed on Anselm</a>
</td>
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<td class="listing-body-Title">
- <a href="whats-new/news-feed/cuda-7-5-is-now-installed-on-anselm.html" title="Cuda 7.5 is now installed on Anselm">Cuda 7.5 is now installed on Anselm</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/cuda-7-5-is-now-installed-on-anselm" title="Cuda 7.5 is now installed on Anselm">Cuda 7.5 is now installed on Anselm</a>
</td>
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<td class="listing-body-Title">
- <a href="salomon/software/intel-suite/index.html" title="Added basic documentation for Intel Advisor and Intel Inspector">Added basic documentation for Intel Advisor and Intel Inspector</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/added-basic-documentation-for-intel-advisor-and-intel-inspector" title="Added basic documentation for Intel Advisor and Intel Inspector">Added basic documentation for Intel Advisor and Intel Inspector</a>
</td>
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<td class="listing-body-Title">
- <a href="whats-new/news-feed/anselm-downtime-has-been-extended-to-feb-26th.html" title="Anselm downtime has been extended to Feb 26th.">Anselm downtime has been extended to Feb 26th.</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/anselm-downtime-has-been-extended-to-feb-26th" title="Anselm downtime has been extended to Feb 26th.">Anselm downtime has been extended to Feb 26th.</a>
</td>
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<td class="listing-body-Title">
- <a href="salomon/software/debuggers/allinea-ddt.html" title="Allinea Forge documentation updated">Allinea Forge documentation updated</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/allinea-forge-documentation-updated" title="Allinea Forge documentation updated">Allinea Forge documentation updated</a>
</td>
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<td class="listing-body-Title">
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+ <a href="https://docs.it4i.cz/whats-new/news-feed/new-bioinformatic-tools-installed-fastqc-0-11-3-gatk-3-5-java-1-7-0_79-picard-2-1-0-samtools-1-3-foss-2015g-snpeff-4-1_g-trimmomatic-0-35-java-1-7.0_79" title="New bioinformatic tools installed: FastQC/0.11.3, GATK/3.5-Java-1.7.0_79, picard/2.1.0, SAMtools/1.3-foss-2015g, SnpEff/4.1_G, Trimmomatic/0.35-Java-1.7.0_79">New bioinformatic tools installed: FastQC/0.11.3, GATK/3.5-Java-1.7.0_79, picard/2.1.0, SAMtools/1.3-foss-2015g, SnpEff/4.1_G, Trimmomatic/0.35-Java-1.7.0_79</a>
</td>
@@ -698,7 +695,7 @@
<td class="listing-body-Title">
- <a href="whats-new/news-feed/salomon-pbs-changes.html" title="Salomon PBS changes">Salomon PBS changes</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/salomon-pbs-changes" title="Salomon PBS changes">Salomon PBS changes</a>
</td>
@@ -722,7 +719,7 @@
<td class="listing-body-Title">
- <a href="salomon/resource-allocation-and-job-execution/capacity.zip" title="Capacity computing updated for Salomon">Capacity computing updated for Salomon</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/capacity-computing-updated-for-salomon" title="Capacity computing updated for Salomon">Capacity computing updated for Salomon</a>
</td>
@@ -746,7 +743,7 @@
<td class="listing-body-Title">
- <a href="whats-new/news-feed/mono-4-2-2-and-mpi-net-1-2-on-salomon.html" title="Mono 4.2.2 and MPI.NET 1.2 on Salomon">Mono 4.2.2 and MPI.NET 1.2 on Salomon</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/mono-4-2-2-and-mpi-net-1-2-on-salomon" title="Mono 4.2.2 and MPI.NET 1.2 on Salomon">Mono 4.2.2 and MPI.NET 1.2 on Salomon</a>
</td>
@@ -813,7 +810,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
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- <a title="Full history of important announcements related to IT4I infrastructure, planned downtimes, outages etc." class="state-published contenttype-document" href="whats-new/downtimes_history.html">
+ <a class="state-published contenttype-document" title="Full history of important announcements related to IT4I infrastructure, planned downtimes, outages etc." href="https://docs.it4i.cz/whats-new/downtimes_history">
<span>History of Downtimes</span>
</a>
@@ -870,7 +867,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -886,7 +883,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -902,7 +899,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
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- <a title="" class="state-published contenttype-document" href="links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -934,7 +931,7 @@
- <a title="" class="state-published contenttype-collection" href="changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -950,7 +947,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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diff --git a/docs.it4i.cz/whats-new.md b/docs.it4i.cz/whats-new.md
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/whats-new/downtimes_history.html b/docs.it4i.cz/whats-new/downtimes_history.html
old mode 100755
new mode 100644
similarity index 87%
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index fd31bc9805d69ef2b47a5729b1a69d42fa0c6110..9f9c11a8da2ec6c2347a8246e60429090b146e85
--- a/whats-new/downtimes_history.html
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<table class="listing">
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<td>
<b>Heartbleed bug</b>
<p><div class="plain" id="parent-fieldname-text">
- <p>Dear users of the Anselm cluster,<br /> <br /> A serious bug in the OpenSSL library, known as the "Heartbleed bug" has been recently discovered. <span>We would like to ensure you that IT4I has taken all necessary steps to fix the OpenSSL library on all the systems.</span><br /> The bug in OpenSSL library affected many sites worldwide for nearly two years. At this moment, there is no evidence that any abuse of data took place at IT4I.<br /> In order to ensure the security and integrity of IT4I systems, all users will be issued new login credentials, including password and ssh keys.<br /> <span>For more informations about the Heartbleed bug, please see: </span><a class="moz-txt-link-freetext external-link" href="../heartbleed-bug.html" target="_self" title="">https://docs.it4i.cz/heartbleed-bug</a><br /> <br />Thank you for your understanding.<br /> IT4Innovations team</p>
+ <p>Dear users of the Anselm cluster,<br /> <br /> A serious bug in the OpenSSL library, known as the "Heartbleed bug" has been recently discovered. <span>We would like to ensure you that IT4I has taken all necessary steps to fix the OpenSSL library on all the systems.</span><br /> The bug in OpenSSL library affected many sites worldwide for nearly two years. At this moment, there is no evidence that any abuse of data took place at IT4I.<br /> In order to ensure the security and integrity of IT4I systems, all users will be issued new login credentials, including password and ssh keys.<br /> <span>For more informations about the Heartbleed bug, please see: </span><a class="moz-txt-link-freetext external-link" href="https://docs.it4i.cz/heartbleed-bug" target="_self" title="">https://docs.it4i.cz/heartbleed-bug</a><br /> <br />Thank you for your understanding.<br /> IT4Innovations team</p>
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<span>History of Downtimes</span>
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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diff --git a/docs.it4i.cz/whats-new/downtimes_history.md b/docs.it4i.cz/whats-new/downtimes_history.md
new file mode 100644
index 0000000000000000000000000000000000000000..332d2f066a48f04f9c81fe50faf38b29fd465f6e
--- /dev/null
+++ b/docs.it4i.cz/whats-new/downtimes_history.md
@@ -0,0 +1,449 @@
+History of Downtimes
+====================
+Full history of important announcements related to IT4I infrastructure,
+planned downtimes, outages etc.
+<table>
+<colgroup>
+<col width="50%" />
+<col width="50%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="left">Date and time</th>
+<th align="left">Title and description</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="left">2016-06-29 13:50:00</td>
+<td align="left"><strong>Salomon cluster maintenance outage prolonged</strong>
+<p></p>
+<p>Important! Salomon cluster maintenance outage will be prolonged till 2016-06-29 20:00 CEST.</p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2016-06-16 00:00:00</td>
+<td align="left"><strong>Salomon planned downtime</strong>
+<p></p>
+<p>There's a planned maintenance window from 2016-06-28 09:00 till 2016-06-29 20:00 CEST.</p>
+<p>Thank you for understanding,<br />
+the IT4Innovations team</p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2016-05-26 10:31:44</td>
+<td align="left"><strong>Salomon planned downtime</strong>
+<p></p>
+<p>There's a planned maintenance window from 2016-06-08 09:00 till 2016-06-09 09:00 CEST.</p>
+<p>Thank you for understanding,<br />
+the IT4Innovations team</p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2016-04-27 15:57:28</td>
+<td align="left"><strong>Salomon cluster maintenance outage prolonged</strong>
+<p></p>
+<p>Important! Salomon cluster maintenance outage will be prolonged till 2016-04-28 14:00 CEST</p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2016-04-19 08:20:00</td>
+<td align="left"><strong>Salomon cluster maintenance outage</strong>
+<p></p>
+<p>From 2016-04-26 09:00 till  2016-04-27 14:00 CEST will be maintenance outage for Salomon. We are going to reinstall compute nodes operating system to the latest CentOS 6.7.</p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2016-03-31 19:03:25</td>
+<td align="left"><strong>Failure on Salomon Cooling System</strong>
+<p></p>
+<p>We have very serious issue with Salomon cooling system since 2016-03-31 10:00. We are working to resolve the issue.</p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2016-03-31 18:59:04</td>
+<td align="left"><strong>Salomon Back in Production</strong>
+<p></p>
+<p>As of 2016-03-31 19:30 CET, the Salomon is back in production. The outage was caused by an issue in cooling system.</p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2016-03-30 15:57:57</td>
+<td align="left"><strong>PBS malfunction</strong>
+<p></p>
+<p>We've had several issues with PBS scheduler since 2016-03-30 13:00 CEST. We are still working on it.</p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2016-03-26 09:52:41</td>
+<td align="left"><strong>Salomon back to production</strong>
+<p></p>
+<p>We have recovered all the issues with the Salomon cluster.</p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2016-03-26 09:51:16</td>
+<td align="left"><strong>Failure on Salomon Cooling Infrastructure</strong>
+<p></p>
+<p>We had an issue with the cooling infra of Salomon. This issue led to InfiniBand and storage outage. We are working to resolve the issue.</p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2016-03-14 14:57:51</td>
+<td align="left"><strong>Infrastructure Maintenance</strong>
+<p></p>
+<p>The Salomon supercomputer will be down for the maintenance from 2016-03-22 10:00 CEST to 2016-03-22 17:00 CEST.</p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2016-02-24 12:30:00</td>
+<td align="left"><strong>Anselm Upgrade</strong>
+<p></p>
+<p>The Anselm supercomputer will be down for the updates from 2016-02-01 to 2016-02-29.</p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2016-02-23 08:45:45</td>
+<td align="left"><strong>Anselm Upgrade</strong>
+<p></p>
+<p>The Anselm supercomputer will be down for the updates from 2016-02-01 to 2016-02-29.</p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2016-02-14 08:07:46</td>
+<td align="left"><strong>Failure on Salomon Infiniband Network</strong>
+<p></p>
+<p>We have very serious issue with Salomon Infiniband network since 2016-02-11 10:18. We are working to resolve the issue as quickly as possible and apologize for any inconvenience.</p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2016-02-04 11:53:30</td>
+<td align="left"><strong>Short network outage</strong>
+<p></p>
+<p>We need to apply some changes in network devices settings which may cause short network outage for Anselm Login nodes. This work will start around 6 am 2016-01-26.</p>
+<p>Thanks for your understanding.</p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2016-02-04 11:52:37</td>
+<td align="left"><strong>Salomon Upgrade</strong>
+<p></p>
+<p>The Salomon supercomputer will be down for the updates from 2016-02-16 09:00 CEST to 2016-02-16 13:00 CEST.</p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2016-02-04 11:52:25</td>
+<td align="left"><strong>Salomon Upgrade</strong>
+<p></p>
+<p>The Salomon supercomputer will be down for the updates from 2016-02-16 09:00 CEST to 2016-02-16 13:00 CEST.</p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2015-11-26 08:11:25</td>
+<td align="left"><strong>/home downtime</strong>
+<p></p>
+<p>Dear HPC users<br />
+<br />
+There's a /home downtime on the Salomon supercomputer planned for 25th November. The reason is a maintenance of the underlying CXFS filesystem. Your jobs will be scheduled with respect to this maintenance window.<br />
+<br />
+Thank you for understanding,<br />
+the IT4I team</p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2015-11-24 09:10:15</td>
+<td align="left"><strong>The /home filesystem was down</strong>
+<p></p>
+<p><span>On 23.11.2015, 13:55 - 14:55, the /home filesystem was down due to acute technical problems.</span><br />
+<span>We apologize for inconvenience.</span></p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2015-09-04 16:14:12</td>
+<td align="left"><strong>SCRATCH downtime</strong>
+<p></p>
+<p>Dear IT4I users<br />
+<br />
+Salomon's SCRATCH will *not* be accessible on Thursday (10th September 2015) from 13:00 till 18:00 CEST.<br />
+<br />
+Thank you for understanding,<br />
+the IT4Innovations team</p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2015-08-27 00:00:00</td>
+<td align="left"><strong>Today's SCRATCH downtime</strong>
+<p></p>
+<p>Dear IT4I users<br />
+<br />
+We are sorry for today's (27th August) inaccessibility of SCRATCH filesystem due to a broken service which normally provides mapping for user/group IDs (UIDs/GIDs). The issue has been fixed. No data were lost.<br />
+<br />
+Thank you for understanding,<br />
+the IT4Innovations team</p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2015-08-12 00:00:00</td>
+<td align="left"><strong>Unplanned downtime</strong>
+<p></p>
+<p>Dear Salomon users,<br />
+<br />
+there was an unplanned downtime of the non-accelerated nodes. At this moment, systems are booting and we are revising consequences. Temporarily inaccessible SCRATCH filesystem is one of them.<br />
+<br />
+We're sorry for the inconvenience,<br />
+the IT4I team</p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2015-08-06 00:00:00</td>
+<td align="left"><strong>SCRATCH downtime</strong>
+<p></p>
+<p>Dear IT4I users<br />
+<br />
+Salomon's SCRATCH will not be accessible tomorrow (7th August 2015) from 08:30 till 11:00 CEST.<br />
+<br />
+Thank you for understanding,<br />
+the IT4Innovations team</p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2014-11-14 10:27:51</td>
+<td align="left"><strong>Unplanned PBS Downtime</strong>
+<p></p>
+<p>Dear Anselm users,<br />
+<br />
+we apologize for the unavailability of our PBS scheduler during the last weekend. However, running jobs shouldn't have been affected at that time.<br />
+<br />
+Thank you for understanding,<br />
+Anselm Admins</p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2014-11-14 10:27:50</td>
+<td align="left"><strong>Login1 troubles</strong>
+<p></p>
+<p>Login1 had a short unplanned downtime. Sorry for the troubles.</p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2014-10-14 20:30:00</td>
+<td align="left"><strong>Unexpected power failure</strong>
+<p></p>
+<p><span>Dear Anselm users,</span></p>
+<p><span><br />
+</span></p>
+<p><span>on Tuesday 14th approximately at 17:20 CEST we encountered power failure during service operation on backup diesel generator. The system shut down. Additional checks after the shutdown took more time than what would expect.</span><span><span> The system was back on-line with all services approximately at 21:00 CEST.</span> We are very sorry for any troubles, this matter may caused you. If some of your jobs ended in incorrect state, please feel free to reclaim your core hours.</span></p>
+<p><span><br />
+</span></p>
+<p><span>Thank you for understanding, <br />
+Anselm Administrators</span></p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2014-07-17 13:50:00</td>
+<td align="left"><strong>Login2(!) downtime</strong>
+<p></p>
+<p>Dear Anselm users,<br />
+<br />
+there's an upgrade planned on Friday, 18th July from 13:00 till 16:00 CEST. Please, take in mind that login2.anselm.it4i.cz will be unavailable at the given time-frame. We are sorry for the inconvenience.<br />
+<br />
+Thank you for understanding,<br />
+Anselm Admins</p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2014-07-16 13:11:34</td>
+<td align="left"><strong>Login1 downtime</strong>
+<p></p>
+<p>Dear Anselm users,<br />
+<br />
+there's an upgrade planned on Thursday, 17th July from 13:00 till 16:00 CEST. Please, take in mind that login1.anselm.it4i.cz will be unavailable at the given time-frame. We are sorry for the inconvenience.<br />
+<br />
+Thank you for understanding,<br />
+Anselm Admins</p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2014-06-18 10:51:56</td>
+<td align="left"><strong>Login2 downtime</strong>
+<p></p>
+<p>Dear Anselm users,<br />
+<br />
+there's an upgrade planned on Wednesday, 18th June from 11:20 till 14:20 CEST. Please, take in mind that login2.anselm.it4i.cz will be unavailable at the given time-frame. We are sorry for the inconvenience.<br />
+<br />
+Thank you for understanding,<br />
+Anselm Admins</p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2014-05-22 00:00:00</td>
+<td align="left"><strong>Outage</strong>
+<p></p>
+<p>Dear Anselm users.<br />
+<br />
+As of today (20140523 10:45) we had an unmanaged outage of a few nodes. Affected nodes were cn[117-126,193-195].<br />
+<br />
+Sorry for the inconveniences,<br />
+Anselm admins</p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2014-04-11 11:30:00</td>
+<td align="left"><strong>Heartbleed bug</strong>
+<p></p>
+<p>Dear users of the Anselm cluster,<br />
+<br />
+A serious bug in the OpenSSL library, known as the "Heartbleed bug" has been recently discovered. <span>We would like to ensure you that IT4I has taken all necessary steps to fix the OpenSSL library on all the systems.</span><br />
+The bug in OpenSSL library affected many sites worldwide for nearly two years. At this moment, there is no evidence that any abuse of data took place at IT4I.<br />
+In order to ensure the security and integrity of IT4I systems, all users will be issued new login credentials, including password and ssh keys.<br />
+<span>For more informations about the Heartbleed bug, please see</span><a href="https://docs.it4i.cz/heartbleed-bug" class="uri" class="moz-txt-link-freetext external-link">https://docs.it4i.cz/heartbleed-bug</a><br />
+<br />
+Thank you for your understanding.<br />
+IT4Innovations team</p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2014-04-02 13:05:00</td>
+<td align="left"><strong>Scheduler is Down</strong>
+<p></p>
+<p>We are sorry for the current scheduler issues which are caused by an inconsistency of the internal PBS database. Thus it's not possible to interact with the scheduler now. In addition, some jobs may be affected and some job outputs may not be retrieved at this moment.</p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2014-03-26 15:50:00</td>
+<td align="left"><strong>Temporary Scratch Mount on Login1</strong>
+<p></p>
+<p>Because of the Lustre issues (mentioned in previous announcements) there's a temporary mount point for Scratch filesystem on login1 node. Please, follow this path to access your data:</p>
+<p>/scratch_nfs/</p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2014-03-26 13:10:00</td>
+<td align="left"><strong>Both Login Nodes Inaccessible</strong>
+<p></p>
+<p>We are sorry for the inaccessibility of both login nodes. We are co-operating with our supplier and trying hard to solve this problem as soon as possible.</p>
+<p>Thank you for understanding.</p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2014-03-25 22:05:00</td>
+<td align="left"><strong>Login1(!) Not Responding</strong>
+<p></p>
+<p>Currently, if you're having trouble while accessing Anselm, please use address login2.anselm.it4i.cz instead of anselm.it4i.cz. There's a Lustre issue with the login1 node, which causes it to not respond.</p>
+<p>We'll let you know by MOTD when login1 comes back online.</p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2013-12-03 00:00:00</td>
+<td align="left"><strong>Planned Downtime</strong>
+<p></p>
+<p>On 17th December 08:00 to 18:00 CET Anselm will be down for maintenance. Power supply upgrade will take place, as well as system maintenance and software updates.<br />
+<br />
+Prior to the period:<br />
+- Jobs will be scheduled for running with a respect to the downtime.<br />
+<br />
+During the period:<br />
+- No Anselm HPC service will be available.<br />
+- Following web applications will not be accessibleRequest Tracker, Anselm cluster documentation, Anselm Allocation.<br />
+- Submitting tickets through the e-mail address <script type="text/javascript">
+<!--
+h='';a='@';n='support%5Bat%5Dit4i.cz';e=n+a+h;
+document.write('<a h'+'ref'+'="ma'+'ilto'+':'+e+'" clas'+'s="em' + 'ail">'+'support[at]it4i.cz'+'</'+'a'+'>');
+// -->
+</script><noscript>support[at]it4i.cz (support%5Bat%5Dit4i.cz at )</noscript> will be delayed.<br />
+<br />
+After the period:<br />
+- All service will be brought back to normal.<br />
+- Jobs in a 'Q' state will be scheduled for running.<br />
+<br />
+We are sorry for the inconvenience.</p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2013-10-14 00:00:00</td>
+<td align="left"><strong>Cooling system unstable</strong>
+<p></p>
+<p>Dear Anselm users,<br />
+<br />
+there was an unplanned downtime due to severe issues with the cold doors today. We are trying hard to bring all services up. We assume that we will finish the maintenance at about 13:30 CEST.<br />
+<br />
+Thank you for understanding.<br />
+<br />
+Sincerely yours,<br />
+Anselm admins</p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2013-09-17 15:50:00</td>
+<td align="left"><strong>A Fair Amount of Nodes Down</strong>
+<p></p>
+<p>Dear Anselm users,<br />
+<br />
+We had an outage on the Anselm Cluster. A fair amount of the nodes was unavailable to production.<br />
+<br />
+Consider terminated job resubmission.<br />
+<br />
+We are sorry for the troubles,<br />
+Anselm admins</p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2013-08-23 15:25:00</td>
+<td align="left"><strong>Infiniband Maintenance Window</strong>
+<p></p>
+<p>Dear Anselm users,<br />
+<br />
+We would like to inform you about a planned Infiniband maintenance window, on Wednesday, 28th August from 09:00 till 16:30 CEST.<br />
+No Anselm service will be available during this outage.<br />
+<br />
+New batch jobs will not be scheduled for running during this time. Consider altering the job walltime, to achieve job execution prior to the downtime (See Job Submission in the Anselm Documentation).<br />
+<br />
+Sincerely yours,<br />
+Anselm Admins</p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2013-08-14 17:10:00</td>
+<td align="left"><strong>Planned Upgrade / Scheduler Downtime</strong>
+<p></p>
+<p>Dear Anselm users,<br />
+<br />
+there's an upgrade planned on Thursday, 15th August from 18:00 till 22:00 CEST. Please, take in mind that PBS scheduler won't accept your jobs at the given timeframe. We are sorry for the inconvenience.<br />
+<br />
+Thank you for understanding,<br />
+Anselm Admins</p>
+</td>
+</tr>
+<tr class="odd">
+<td align="left">2013-07-16 13:45:00</td>
+<td align="left"><strong>Anselm Cluster Upgrade - July 23rd</strong>
+<p></p>
+<p>Dear Anselm users.<br />
+<br />
+We would like to inform you that Anselm cluster will be unavailable due to upgrades on Tuesday, July 23rd from 07:00 to 20:00 CEST.<br />
+<br />
+Sorry for the inconvenience,<br />
+Anselm admins<br />
+<br />
+--<br />
+<br />
+Anselm cluster documentation can be found at:<br />
+<a href="http://support.it4i.cz/docs/anselm-cluster-documentation/" class="uri" class="external-link">http://support.it4i.cz/docs/anselm-cluster-documentation/</a></p>
+</td>
+</tr>
+<tr class="even">
+<td align="left">2013-06-27 09:35:00</td>
+<td align="left"><strong>SSH Password Authentication</strong>
+<p></p>
+<p>Dear Anselm users.<br />
+<br />
+If you are experiencing some troubles when using SSH PasswordAuthentication on the client side, please switch to PubkeyAuthentication instead.<br />
+<br />
+We are trying hard to resolve this issue.<br />
+<br />
+Sincerely yours,<br />
+Anselm admins</p>
+</td>
+</tr>
+</tbody>
+</table>
diff --git a/whats-new/news-feed.html b/docs.it4i.cz/whats-new/news-feed.1.html
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new mode 100644
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rename to docs.it4i.cz/whats-new/news-feed.1.html
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--- a/whats-new/news-feed.html
+++ b/docs.it4i.cz/whats-new/news-feed.1.html
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- <link rel="stylesheet" type="text/css" href="../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
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<title>News — IT4I Docs</title>
- <link rel="canonical" href="news-feed.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/whats-new/news-feed" />
- <link rel="shortcut icon" type="image/x-icon" href="../favicon.ico" />
- <link rel="apple-touch-icon" href="../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
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@@ -63,14 +60,14 @@
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- <link rel="alternate" href="news-feed/rss.xml" title="News - RSS 2.0" type="application/rss+xml" />
+ <link rel="alternate" href="https://docs.it4i.cz/whats-new/news-feed/rss.xml" title="News - RSS 2.0" type="application/rss+xml" />
- <link rel="alternate" href="news-feed/RSS" title="News - RSS 1.0" type="application/rss+xml" />
+ <link rel="alternate" href="https://docs.it4i.cz/whats-new/news-feed/RSS" title="News - RSS 1.0" type="application/rss+xml" />
- <link rel="search" href="../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
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<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="news-feed.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/whats-new/news-feed#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="news-feed.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/whats-new/news-feed#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
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+ <a href="https://docs.it4i.cz">Ăšvod</a>
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<span id="breadcrumbs-1" dir="ltr">
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+ <a href="https://docs.it4i.cz/whats-new">What's New</a>
<span class="breadcrumbSeparator">
/
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<span class="summary">
- <a href="news-feed/issue-with-intel-mpi-4-1-1-on-salomon.html" class="contenttype-news-item state-published url">Issue with Intel MPI 4.1.1 on Salomon</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed/issue-with-intel-mpi-4-1-1-on-salomon" class="contenttype-news-item state-published url">Issue with Intel MPI 4.1.1 on Salomon</a>
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<span class="summary">
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<span class="summary">
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+ <a href="https://docs.it4i.cz/whats-new/news-feed/new-method-to-execute-parallel-matlab-jobs" class="contenttype-news-item state-published url">New method to execute parallel MATLAB jobs</a>
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+ <a href="https://docs.it4i.cz/whats-new/news-feed/intel-vtune-amplifier-support-for-xeon-phi-on-salomon" class="contenttype-news-item state-published url">Intel VTune Amplifier support for Xeon Phi on Salomon</a>
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@@ -574,7 +571,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -590,7 +587,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -606,7 +603,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -622,7 +619,7 @@
- <a title="" class="state-published contenttype-document" href="../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -638,7 +635,7 @@
- <a title="" class="state-published contenttype-collection" href="../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -654,7 +651,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
@@ -693,14 +690,14 @@ var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -722,12 +719,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -743,8 +740,6 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
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</html>
diff --git a/docs.it4i.cz/whats-new/news-feed.1.md b/docs.it4i.cz/whats-new/news-feed.1.md
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/whats-new/news-feed/RSS b/docs.it4i.cz/whats-new/news-feed/RSS
old mode 100755
new mode 100644
similarity index 98%
rename from whats-new/news-feed/RSS
rename to docs.it4i.cz/whats-new/news-feed/RSS
index 6e08afe97c06384db43871164d48dd2b790dd76f..191230242e773625c87a9324d95d1857b1503b41
--- a/whats-new/news-feed/RSS
+++ b/docs.it4i.cz/whats-new/news-feed/RSS
@@ -12,9 +12,6 @@
<items>
<rdf:Seq>
- <rdf:li rdf:resource="https://docs.it4i.cz/whats-new/news-feed/matlab-2015b"/>
-
-
<rdf:li rdf:resource="https://docs.it4i.cz/whats-new/news-feed/issue-with-intel-mpi-4-1-1-on-salomon"/>
@@ -32,41 +29,15 @@
<rdf:li rdf:resource="https://docs.it4i.cz/whats-new/news-feed/vampir-installed"/>
+
+ <rdf:li rdf:resource="https://docs.it4i.cz/whats-new/news-feed/matlab-2015b"/>
+
</rdf:Seq>
</items>
</channel>
- <item rdf:about="https://docs.it4i.cz/whats-new/news-feed/matlab-2015b">
- <title>MATLAB 2015b</title>
- <link>https://docs.it4i.cz/whats-new/news-feed/matlab-2015b</link>
- <description></description>
- <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/">
- <![CDATA[
-
-
-
-
-
-
-
- <div id="parent-fieldname-text" class="plain">
- <p>MATLAB 2015b has been installed on Anselm and Salomon. Modules are named MATLAB/2015b-COM and MATLAB/2015b-EDU. Release notes:Â http://www.mathworks.com/help/matlab/release-notes.html#R2015b</p>
- </div>
-
-
-
- ]]>
- </content:encoded>
- <dc:publisher>No publisher</dc:publisher>
-
- <dc:rights></dc:rights>
- <dc:date>2016-07-13T13:40:00Z</dc:date>
- <dc:type>News Item</dc:type>
- </item>
-
-
<item rdf:about="https://docs.it4i.cz/whats-new/news-feed/issue-with-intel-mpi-4-1-1-on-salomon">
<title>Issue with Intel MPI 4.1.1 on Salomon</title>
<link>https://docs.it4i.cz/whats-new/news-feed/issue-with-intel-mpi-4-1-1-on-salomon</link>
@@ -141,7 +112,7 @@
<div id="parent-fieldname-text" class="plain">
- <p>We have implemented a new way to run parallel MATLAB jobs. Unlike the previously documented method, it does not submit a separate new job to run the workers, all is done within a single job. Read about it here:Â <a target="_self" title="" class="external-link" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6">https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6</a></p>
+ <p>We have implemented a new way to run parallel MATLAB jobs. Unlike the previously documented method, it does not submit a separate new job to run the workers, all is done within a single job. Read about it here:Â <a title="" class="external-link" target="_self" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6">https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6</a></p>
</div>
@@ -243,5 +214,34 @@
</item>
+ <item rdf:about="https://docs.it4i.cz/whats-new/news-feed/matlab-2015b">
+ <title>MATLAB 2015b</title>
+ <link>https://docs.it4i.cz/whats-new/news-feed/matlab-2015b</link>
+ <description></description>
+ <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/">
+ <![CDATA[
+
+
+
+
+
+
+
+ <div id="parent-fieldname-text" class="plain">
+ <p>MATLAB 2015b has been installed on Anselm and Salomon. Modules are named MATLAB/2015b-COM and MATLAB/2015b-EDU. Release notes:Â http://www.mathworks.com/help/matlab/release-notes.html#R2015b</p>
+ </div>
+
+
+
+ ]]>
+ </content:encoded>
+ <dc:publisher>No publisher</dc:publisher>
+
+ <dc:rights></dc:rights>
+ <dc:date>2016-07-13T13:40:00Z</dc:date>
+ <dc:type>News Item</dc:type>
+ </item>
+
+
</rdf:RDF>
diff --git a/salomon/software/intel-suite/index.html b/docs.it4i.cz/whats-new/news-feed/added-basic-documentation-for-intel-advisor-and-intel-inspector.html
old mode 100755
new mode 100644
similarity index 65%
rename from salomon/software/intel-suite/index.html
rename to docs.it4i.cz/whats-new/news-feed/added-basic-documentation-for-intel-advisor-and-intel-inspector.html
index 2cdf92a76a4521353f9176d2ae7ae972ffb44fba..5e80175e7ba5d969a1b679a0d525fa53e4b7a7ca
--- a/salomon/software/intel-suite/index.html
+++ b/docs.it4i.cz/whats-new/news-feed/added-basic-documentation-for-intel-advisor-and-intel-inspector.html
@@ -10,45 +10,42 @@
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-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction" /><!--[if lt IE 7]></base><![endif]-->
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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<title>Intel Parallel Studio — IT4I Docs</title>
- <link rel="canonical" href="../intel-suite.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/intel-suite" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="index.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/intel-suite/#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="index.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/intel-suite/#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../../index.html">
- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -273,24 +270,24 @@
<h2 class=" ">Intel compilers</h2>
<p>The Intel compilers version 131.3 are available, via module iccifort/2013.5.192-GCC-4.8.3. The compilers include the icc C and C++ compiler and the ifort fortran 77/90/95 compiler.</p>
<pre class=" ">$ module load intel<br />$ icc -v<br />$ ifort -v</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="intel-compilers.html">Intel Compilers</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-compilers">Intel Compilers</a> page.</p>
<h2 class=" ">Intel debugger</h2>
<p class="exclamation">IDB is no longer available since Parallel Studio 2015.</p>
-<p>Â The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a target="_self" title="" class="internal-link" href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html">X display</a> for running the GUI.</p>
+<p>Â The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">X display</a> for running the GUI.</p>
<pre class=" ">$ module load intel<br />$ idb</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="intel-debugger.html">Intel Debugger</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger">Intel Debugger</a> page.</p>
<h2 class=" ">Intel Math Kernel Library</h2>
<p>Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, extensively threaded and optimized for maximum performance. Intel MKL unites and provides these basic components: BLAS, LAPACK, ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and many more.</p>
<pre class=" ">$ module load imkl</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="intel-mkl.html">Intel MKL</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-mkl">Intel MKL</a> page.</p>
<h2 class=" ">Intel Integrated Performance Primitives</h2>
<p>Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is available, via module ipp. The IPP is a library of highly optimized algorithmic building blocks for media and data applications. This includes signal, image and frame processing algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many more.</p>
<pre class=" ">$ module load ipp</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="intel-integrated-performance-primitives.html">Intel IPP</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives">Intel IPP</a> page.</p>
<h2 class=" ">Intel Threading Building Blocks</h2>
<p>Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. It is designed to promote scalable data parallel programming. Additionally, it fully supports nested parallelism, so you can build larger parallel components from smaller parallel components. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner.</p>
<pre class=" ">$ module load tbb</pre>
-<p>Read more at the <a target="_self" title="" class="internal-link" href="intel-tbb.html">Intel TBB</a> page.</p>
+<p>Read more at the <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb">Intel TBB</a> page.</p>
</div>
@@ -366,7 +363,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -382,7 +379,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -398,7 +395,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -414,7 +411,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -430,7 +427,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -446,7 +443,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -462,7 +459,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -478,7 +475,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -494,7 +491,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -510,7 +507,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
@@ -526,7 +523,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -542,7 +539,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -558,10 +555,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -577,7 +574,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -593,7 +590,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -609,7 +606,7 @@
- <a title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -625,7 +622,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -641,7 +638,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -657,7 +654,7 @@
- <a title="" class="state-published contenttype-document" href="intel-compilers.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-compilers">
<span>Intel Compilers</span>
</a>
@@ -673,7 +670,7 @@
- <a title="" class="state-published contenttype-document" href="intel-debugger.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger">
<span>Intel Debugger</span>
</a>
@@ -689,7 +686,7 @@
- <a title="" class="state-published contenttype-document" href="intel-mkl.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-mkl">
<span>Intel MKL</span>
</a>
@@ -705,7 +702,7 @@
- <a title="" class="state-published contenttype-document" href="intel-integrated-performance-primitives.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives">
<span>Intel IPP</span>
</a>
@@ -721,7 +718,7 @@
- <a title="" class="state-published contenttype-document" href="intel-tbb.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb">
<span>Intel TBB</span>
</a>
@@ -737,7 +734,7 @@
- <a title="" class="state-published contenttype-document" href="intel-trace-analyzer-and-collector.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector">
<span>Intel Trace Analyzer and Collector</span>
</a>
@@ -753,7 +750,7 @@
- <a title="" class="state-published contenttype-document" href="intel-advisor.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-advisor">
<span>Intel Advisor</span>
</a>
@@ -769,7 +766,7 @@
- <a title="" class="state-published contenttype-document" href="intel-inspector.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/intel-suite/intel-inspector">
<span>Intel Inspector</span>
</a>
@@ -794,7 +791,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -810,7 +807,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -826,7 +823,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -842,7 +839,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -858,7 +855,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -874,7 +871,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -899,7 +896,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -924,7 +921,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -940,7 +937,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -956,7 +953,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -972,7 +969,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
-var u="http://extranet.it4i.cz/piwik/";
+var u="//extranet.it4i.cz/piwik/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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@@ -1040,12 +1037,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -1061,7 +1058,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
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</html>
diff --git a/docs.it4i.cz/whats-new/news-feed/added-basic-documentation-for-intel-advisor-and-intel-inspector.md b/docs.it4i.cz/whats-new/news-feed/added-basic-documentation-for-intel-advisor-and-intel-inspector.md
new file mode 100644
index 0000000000000000000000000000000000000000..01daba67ed047a3ccdd229242906476624a594da
--- /dev/null
+++ b/docs.it4i.cz/whats-new/news-feed/added-basic-documentation-for-intel-advisor-and-intel-inspector.md
@@ -0,0 +1,77 @@
+Intel Parallel Studio
+=====================
+
+The Salomon cluster provides following elements of the Intel Parallel
+Studio XE
+ Intel Parallel Studio XE
+ ---
+ Intel Compilers
+ Intel Debugger
+ Intel MKL Library
+ Intel Integrated Performance Primitives Library
+ Intel Threading Building Blocks Library
+ Intel Trace Analyzer and Collector
+ Intel Advisor
+ Intel Inspector
+Intel compilers
+---------------
+The Intel compilers version 131.3 are available, via module
+iccifort/2013.5.192-GCC-4.8.3. The compilers include the icc C and C++
+compiler and the ifort fortran 77/90/95 compiler.
+ $ module load intel
+ $ icc -v
+ $ ifort -v
+Read more at the [Intel
+Compilers](https://docs.it4i.cz/salomon/software/intel-suite/intel-compilers)
+page.
+Intel debugger
+--------------
+IDB is no longer available since Parallel Studio 2015.
+Â The intel debugger version 13.0 is available, via module intel. The
+debugger works for applications compiled with C and C++ compiler and the
+ifort fortran 77/90/95 compiler. The debugger provides java GUI
+environment. Use [X
+display](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc)
+for running the GUI.
+ $ module load intel
+ $ idb
+Read more at the [Intel
+Debugger](https://docs.it4i.cz/salomon/software/intel-suite/intel-debugger)
+page.
+Intel Math Kernel Library
+--
+Intel Math Kernel Library (Intel MKL) is a library of math kernel
+subroutines, extensively threaded and optimized for maximum performance.
+Intel MKL unites and provides these basic componentsBLAS, LAPACK,
+ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and
+many more.
+ $ module load imkl
+Read more at the [Intel
+MKL](https://docs.it4i.cz/salomon/software/intel-suite/intel-mkl)
+page.
+Intel Integrated Performance Primitives
+----------------
+Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX
+is available, via module ipp. The IPP is a library of highly optimized
+algorithmic building blocks for media and data applications. This
+includes signal, image and frame processing algorithms, such as FFT,
+FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many
+more.
+ $ module load ipp
+Read more at the [Intel
+IPP](https://docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives)
+page.
+Intel Threading Building Blocks
+--------
+Intel Threading Building Blocks (Intel TBB) is a library that supports
+scalable parallel programming using standard ISO C++ code. It does not
+require special languages or compilers. It is designed to promote
+scalable data parallel programming. Additionally, it fully supports
+nested parallelism, so you can build larger parallel components from
+smaller parallel components. To use the library, you specify tasks, not
+threads, and let the library map tasks onto threads in an efficient
+manner.
+ $ module load tbb
+Read more at the [Intel
+TBB](https://docs.it4i.cz/salomon/software/intel-suite/intel-tbb)
+page.
diff --git a/whats-new/news-feed/allinea-forge-5-1-installed-on-anselm.html b/docs.it4i.cz/whats-new/news-feed/allinea-forge-5-1-installed-on-anselm.html
old mode 100755
new mode 100644
similarity index 68%
rename from whats-new/news-feed/allinea-forge-5-1-installed-on-anselm.html
rename to docs.it4i.cz/whats-new/news-feed/allinea-forge-5-1-installed-on-anselm.html
index d36f73e74a5c2706d3bfb424b3cba7a08aedffb9..7c03c391b24b7239fb836c2f3e0c4a6defa18dc2
--- a/whats-new/news-feed/allinea-forge-5-1-installed-on-anselm.html
+++ b/docs.it4i.cz/whats-new/news-feed/allinea-forge-5-1-installed-on-anselm.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/whats-new/news-feed/allinea-forge-5-1-installed-on-anselm by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:57 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/whats-new/news-feed/allinea-forge-5-1-installed-on-anselm" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
+ <link rel="stylesheet" type="text/css" media="screen" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <style type="text/css" media="screen">@import url(https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourcecioppino.twothumbs.stylesheetstwothumbs-cachekey-a07097acfdb29ca21e76e2372e673858.css);</style>
+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceplone.app.jquery-cachekey-c2d21aafabd41e32e7d82e9e4e57f6d1.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/collective.js.jqueryui.custom.min-cachekey-d6da9ac77d181fb49c1976e00c066a74.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourcedropdown-menu-cachekey-b132c7c9cab5eb4d3c541e47271da509.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Allinea Forge 5.1 installed on Anselm — IT4I Docs</title>
- <link rel="canonical" href="allinea-forge-5-1-installed-on-anselm.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/whats-new/news-feed/allinea-forge-5-1-installed-on-anselm" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="allinea-forge-5-1-installed-on-anselm.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/whats-new/news-feed/allinea-forge-5-1-installed-on-anselm#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="allinea-forge-5-1-installed-on-anselm.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/whats-new/news-feed/allinea-forge-5-1-installed-on-anselm#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../whats-new.html">What's New</a>
+ <a href="https://docs.it4i.cz/whats-new">What's New</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
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<dt class="portletHeader hiddenStructure">
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<span>Get Started with IT4Innovations</span>
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<span>Anselm Cluster Documentation</span>
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</a>
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<span>Changelog</span>
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<div id="portal-footer">
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- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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diff --git a/docs.it4i.cz/whats-new/news-feed/allinea-forge-5-1-installed-on-anselm.md b/docs.it4i.cz/whats-new/news-feed/allinea-forge-5-1-installed-on-anselm.md
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old mode 100755
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<title>Allinea Forge 6.0 — IT4I Docs</title>
- <link rel="canonical" href="allinea-forge-6.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/whats-new/news-feed/allinea-forge-6.0" />
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<div id="portal-header">
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- <a accesskey="6" href="allinea-forge-6.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/whats-new/news-feed/allinea-forge-6.0#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<div id="portal-advanced-search" class="hiddenStructure">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
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<span id="breadcrumbs-1" dir="ltr">
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<span id="breadcrumbs-2" dir="ltr">
- <a href="../news-feed.html">News</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed">News</a>
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<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
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</a>
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<span>History of Downtimes</span>
</a>
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<span>News</span>
</a>
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<span>Anselm Cluster Documentation</span>
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<span>Links</span>
</a>
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<span>Changelog</span>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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diff --git a/docs.it4i.cz/whats-new/news-feed/allinea-forge-6.0.md b/docs.it4i.cz/whats-new/news-feed/allinea-forge-6.0.md
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<title>Allinea Forge (DDT,MAP) — IT4I Docs</title>
- <link rel="canonical" href="allinea-ddt.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt" />
- <link rel="shortcut icon" type="image/x-icon" href="../../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
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@@ -64,7 +61,7 @@
- <link rel="search" href="../../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="allinea-ddt.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="allinea-ddt.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
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- <img src="../../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
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@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../../salomon.html">Salomon Cluster Documentation</a>
+ <a href="https://docs.it4i.cz/salomon">Salomon Cluster Documentation</a>
<span class="breadcrumbSeparator">
/
@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../../software.html">Software</a>
+ <a href="https://docs.it4i.cz/salomon/software">Software</a>
<span class="breadcrumbSeparator">
/
@@ -173,7 +170,7 @@
</span>
<span id="breadcrumbs-3" dir="ltr">
- <a href="../debuggers.html">Debuggers and profilers</a>
+ <a href="https://docs.it4i.cz/salomon/software/debuggers">Debuggers and profilers</a>
<span class="breadcrumbSeparator">
/
@@ -277,16 +274,16 @@
<p class="callout"><strong>-g</strong> : Generates extra debugging information usable by GDB. -g3 includes even more debugging information. This option is available for GNU and INTEL C/C++ and Fortran compilers.<br /><br /><strong>-O0</strong> : Suppress all optimizations.</p>
<p>Â </p>
<h2 class=" ">Direct starting a Job with Forge</h2>
-<p class=" ">Be sure to log in with an <a target="_self" title="" class="internal-link" href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html"><span class="internal-link">X window forwarding</span> enabled</a>. This could mean using the -X in the ssh: Â </p>
+<p class=" ">Be sure to log in with an <a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc"><span class="internal-link">X window forwarding</span> enabled</a>. This could mean using the -X in the ssh: Â </p>
<pre class=" ">$ ssh -X username@clustername.it4i.cz </pre>
-<p class=" ">Other options is to access login node using VNC. Please see the detailed information on <span class="internal-link"><a target="_self" title="" class="internal-link" href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html">how to <span class="internal-link">use graphic user interface on the clusters</span></a></span><span class="internal-link"></span>.</p>
+<p class=" ">Other options is to access login node using VNC. Please see the detailed information on <span class="internal-link"><a title="" class="internal-link" target="_self" href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc">how to <span class="internal-link">use graphic user interface on the clusters</span></a></span><span class="internal-link"></span>.</p>
<p class=" ">From the login node an interactive session <strong>with X windows forwarding</strong> (-X option) can be started by following command:Â </p>
<pre class=" ">$ qsub -I -X -A NONE-0-0 -q qexp -lselect=1:ncpus=24:mpiprocs=24,walltime=01:00:00Â </pre>
<p class=" ">Then launch the debugger with the ddt command followed by the name of the executable to debug:</p>
<pre class=" ">$ ddt test_debug</pre>
<p class="exclamation">Forge now has common GUI for both DDT and MAP. In interactive mode, you can launch Forge using <span class="monospace">forge, ddt or map, </span>the latter two will just launch forge and swith to the respective tab in the common GUI.</p>
<p class=" ">A<span style="text-align: start; "> submission window that appears have a prefilled path to the executable to debug. You can select the number of MPI processors and/or OpenMP threads on which to run and press run. Command line arguments to a program can be entered to the</span> "Arguments<span class="Apple-converted-space">" </span><span style="text-align: start; ">box.</span></p>
-<p class=" "><a target="_blank" title="" class="internal-link" href="ddt1.png"><img width="451" height="513" alt="" class="image-inline" title="" src="ddt1.png" /></a>Â </p>
+<p class=" "><a title="" class="internal-link" target="_blank" href="https://docs.it4i.cz/salomon/software/debuggers/ddt1.png"><img class="image-inline" src="https://docs.it4i.cz/salomon/software/debuggers/ddt1.png" alt="" width="451" title="" height="513" /></a>Â </p>
<p class=" ">To start the debugging directly without the submission window, user can specify the debugging and execution parameters from the command line. For example the number of MPI processes is set by option "-np 4". Skipping the dialog is done by "-start" option. To see the list of the "ddt" command line parameters, run "ddt --help". Â </p>
<pre class=" ">ddt -start -np 4 ./hello_debug_impi</pre>
<p class=" ">All of the above text also applies for MAP, just replace ddt command with map.</p>
@@ -295,7 +292,7 @@
<p>To use Reverse connect, use a jobscript that you would normally use to launch your application, just prepend ddt/map --connect to your application:</p>
<pre>map --connect mpirun -np 24 ./mpi-test<br />ddt --connect mpirun -np 24 ./mpi-test</pre>
<p>Launch Forge GUI on login node and submit the job using qsub. When the job starts running, Forge will ask you to accept the connection:</p>
-<p><img title="Allinea Reverse Connect" class="image-inline" alt="Allinea Reverse Connect" src="Snmekobrazovky20160211v14.27.45.png/%40%40images/3550e4ae-2eab-4571-8387-11a112dd6ca8.png" /></p>
+<p><img alt="Allinea Reverse Connect" class="image-inline" title="Allinea Reverse Connect" src="https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160211v14.27.45.png/@@images/3550e4ae-2eab-4571-8387-11a112dd6ca8.png" /></p>
<p>After accepting the request, you can start remote profiling/debugging.</p>
<h2 class=" ">Xeon Phi</h2>
<p>Forge allows debugging and profiling of both offload and native mode Xeon Phi programs.</p>
@@ -398,7 +395,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
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@@ -414,7 +411,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../whats-new.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../../salomon.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../hardware-overview-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/hardware-overview-1">
<span>Hardware Overview</span>
</a>
@@ -478,7 +475,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../accessing-the-cluster/shell-and-data-access.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/accessing-the-cluster">
<span>Accessing the Cluster</span>
</a>
@@ -494,7 +491,7 @@
- <a title="" class="state-published contenttype-document" href="../../environment-and-modules.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/environment-and-modules">
<span>Environment and Modules</span>
</a>
@@ -510,7 +507,7 @@
- <a title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document" href="../../list_of_modules.html">
+ <a class="state-published contenttype-document" title="List of Available Modules on Salomon Cluster" href="https://docs.it4i.cz/salomon/list_of_modules">
<span>List of Available Modules</span>
</a>
@@ -526,7 +523,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../resource-allocation-and-job-execution.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/resource-allocation-and-job-execution">
<span>Resource Allocation and Job Execution</span>
</a>
@@ -542,7 +539,7 @@
- <a title="" class="state-published contenttype-document" href="../../compute-nodes.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/compute-nodes">
<span>Compute Nodes</span>
</a>
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- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../storage.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/storage">
<span>Storage</span>
</a>
@@ -574,7 +571,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../network-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon/network-1">
<span>Network</span>
</a>
@@ -590,10 +587,10 @@
- <a title="In this section we provide overview of installed software and its usage.
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="In this section we provide overview of installed software and its usage.
-" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../software.html">
+" href="https://docs.it4i.cz/salomon/software">
<span>Software</span>
</a>
@@ -609,7 +606,7 @@
- <a title="An engineering simulation software " class="state-published navTreeFolderish contenttype-folder" href="../ansys.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="An engineering simulation software " href="https://docs.it4i.cz/salomon/software/ansys">
<span>ANSYS</span>
</a>
@@ -625,7 +622,7 @@
- <a title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder" href="../comsol.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title=" A finite element analysis, solver and Simulation software" href="https://docs.it4i.cz/salomon/software/comsol">
<span>COMSOL</span>
</a>
@@ -641,7 +638,7 @@
- <a title="A collection of development tools" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../debuggers.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="A collection of development tools" href="https://docs.it4i.cz/salomon/software/debuggers">
<span>Debuggers and profilers</span>
</a>
@@ -657,7 +654,7 @@
- <a title="" class="state-published contenttype-document" href="aislinn.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/aislinn">
<span>Aislinn</span>
</a>
@@ -673,7 +670,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" href="allinea-ddt.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-ddt">
<span>Allinea Forge (DDT,MAP)</span>
</a>
@@ -689,7 +686,7 @@
- <a title="quick application profiling" class="state-published contenttype-document" href="allinea-performance-reports.html">
+ <a class="state-published contenttype-document" title="quick application profiling" href="https://docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports">
<span>Allinea Performance Reports</span>
</a>
@@ -705,7 +702,7 @@
- <a title="" class="state-published contenttype-document" href="intel-vtune-amplifier.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier">
<span>Intel VTune Amplifier XE</span>
</a>
@@ -721,7 +718,7 @@
- <a title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " class="state-published contenttype-document" href="total-view.html">
+ <a class="state-published contenttype-document" title="TotalView is a GUI-based source code multi-process, multi-thread debugger. " href="https://docs.it4i.cz/salomon/software/debuggers/total-view">
<span>Total View</span>
</a>
@@ -737,7 +734,7 @@
- <a title="Valgrind is a tool for memory debugging and profiling." class="state-published contenttype-document" href="valgrind.html">
+ <a class="state-published contenttype-document" title="Valgrind is a tool for memory debugging and profiling." href="https://docs.it4i.cz/salomon/software/debuggers/valgrind">
<span>Valgrind</span>
</a>
@@ -753,7 +750,7 @@
- <a title="" class="state-published contenttype-document" href="vampir.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/software/debuggers/vampir">
<span>Vampir</span>
</a>
@@ -778,7 +775,7 @@
- <a title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder" href="../chemistry.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Tools for computational chemistry." href="https://docs.it4i.cz/salomon/software/chemistry">
<span>Chemistry, Physics and Materials science</span>
</a>
@@ -794,7 +791,7 @@
- <a title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder" href="../intel-suite.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="The Intel Parallel Studio XE" href="https://docs.it4i.cz/salomon/software/intel-suite">
<span>Intel Parallel studio</span>
</a>
@@ -810,7 +807,7 @@
- <a title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder" href="../mpi-1.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Message Passing Interface libraries on ANSELM" href="https://docs.it4i.cz/salomon/software/mpi-1">
<span>MPI</span>
</a>
@@ -826,7 +823,7 @@
- <a title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder" href="../numerical-languages.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="Interpreted languages for numerical computations" href="https://docs.it4i.cz/salomon/software/numerical-languages">
<span>Numerical languages</span>
</a>
@@ -842,7 +839,7 @@
- <a title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document" href="../compilers.html">
+ <a class="state-published contenttype-document" title="Available compilers, including GNU, INTEL and UPC compilers" href="https://docs.it4i.cz/salomon/software/compilers">
<span>Compilers</span>
</a>
@@ -858,7 +855,7 @@
- <a title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document" href="../intel-xeon-phi.html">
+ <a class="state-published contenttype-document" title="A guide to Intel Xeon Phi usage" href="https://docs.it4i.cz/salomon/software/intel-xeon-phi">
<span>Intel Xeon Phi</span>
</a>
@@ -874,7 +871,7 @@
- <a title="Java on the cluster" class="state-published contenttype-document" href="../java.html">
+ <a class="state-published contenttype-document" title="Java on the cluster" href="https://docs.it4i.cz/salomon/software/java">
<span>Java</span>
</a>
@@ -890,7 +887,7 @@
- <a title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document" href="../operating-system.html">
+ <a class="state-published contenttype-document" title="The operating system, deployed on Salomon cluster" href="https://docs.it4i.cz/salomon/software/operating-system">
<span>Operating System</span>
</a>
@@ -915,7 +912,7 @@
- <a title="" class="state-published contenttype-document" href="../../prace.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/salomon/prace">
<span>PRACE User Support</span>
</a>
@@ -940,7 +937,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -956,7 +953,7 @@
- <a title="" class="state-published contenttype-document" href="../../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -972,7 +969,7 @@
- <a title="" class="state-published contenttype-collection" href="../../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -988,7 +985,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
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})();
</script>
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@@ -1056,12 +1053,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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@@ -1077,7 +1074,5 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
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-
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diff --git a/salomon/software/debuggers/allinea-ddt.md b/docs.it4i.cz/whats-new/news-feed/allinea-forge-documentation-updated.md
similarity index 50%
rename from salomon/software/debuggers/allinea-ddt.md
rename to docs.it4i.cz/whats-new/news-feed/allinea-forge-documentation-updated.md
index 77e8240c479a4d74db566bd56aff70cffc24125f..c48c182fe3c2c928d01951b9581cbe278b4196ff 100644
--- a/salomon/software/debuggers/allinea-ddt.md
+++ b/docs.it4i.cz/whats-new/news-feed/allinea-forge-documentation-updated.md
@@ -1,6 +1,6 @@
+Allinea Forge (DDT,MAP)
=======================
-
-
+
Allinea Forge consist of two tools - debugger DDT and profiler MAP.
Allinea DDT, is a commercial debugger primarily for debugging parallel
MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel
@@ -12,66 +12,65 @@ implementation.
Allinea MAP is a profiler for C/C++/Fortran HPC codes. It is designed
for profiling parallel code, which uses pthreads, OpenMP or MPI.
License and Limitations for the clusters Users
-----------------------------------------------
On the clusters users can debug OpenMP or MPI code that runs up to 64
parallel processes. In case of debugging GPU or Xeon Phi accelerated
-codes the limit is 8 accelerators. These limitation means that
+codes the limit is 8 accelerators. These limitation means that:
- 1 user can debug up 64 processes, or
- 32 users can debug 2 processes, etc.
-In case of debugging on accelerators
+In case of debugging on accelerators:
- 1 user can debug on up to 8 accelerators, orÂ
- 8 users can debug on single accelerator.Â
Compiling Code to run with Forge
---------------------------------
+---------
### Modules
-Load all necessary modules to compile the code. For exampleÂ
+Load all necessary modules to compile the code. For example:Â
$ module load intel
$ module load impi ... or ... module load OpenMPI
-Load the Allinea DDT module
+Load the Allinea DDT module:
$ module load Forge
-Compile the code
-``` {.code-basic style="text-align start; "}
+Compile the code:
+``` {.code-basic style="text-alignstart; "}
$ mpicc -g -O0 -o test_debug test.c
$ mpif90 -g -O0 -o test_debug test.f
```
### Compiler flags
-Before debugging, you need to compile your code with theses flags
-**-g** Generates extra debugging information usable by GDB. -g3
+Before debugging, you need to compile your code with theses flags:
+**-g** Generates extra debugging information usable by GDB. -g3
includes even more debugging information. This option is available for
GNU and INTEL C/C++ and Fortran compilers.
-
-**-O0** Suppress all optimizations.
+**-O0** Suppress all optimizations.
Â
Direct starting a Job with Forge
---------------------------------
-Be sure to log in with an [X window
-forwarding
-enabled](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
-This could mean using the -X in the ssh Â
+---------
+Be sure to log in with an [<span class="internal-link">X window
+forwarding</span>
+enabled](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc).
+This could mean using the -X in the sshÂ
$ ssh -X username@clustername.it4i.cz
Other options is to access login node using VNC. Please see the detailed
-information on [how to
+information on <span class="internal-link">[how to <span
class="internal-link">use graphic user interface on the
-clusters](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
-class="internal-link">.
+clusters</span>](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc)</span><span
+class="internal-link"></span>.
From the login node an interactive session **with X windows forwarding**
-(-X option) can be started by following commandÂ
- $ qsub -I -X -A NONE-0-0 -q qexp -lselect=1ncpus=24mpiprocs=24,walltime=010000Â
+(-X option) can be started by following command:Â
+ $ qsub -I -X -A NONE-0-0 -q qexp -lselect=1:ncpus=24:mpiprocs=24,walltime=01:00:00Â
Then launch the debugger with the ddt command followed by the name of
-the executable to debug
+the executable to debug:
$ ddt test_debug
Forge now has common GUI for both DDT and MAP. In interactive mode, you
-can launch Forge using forge, ddt or map,
-the latter two will just launch forge and swith to the respective
+can launch Forge using <span class="monospace">forge, ddt or map,
+</span>the latter two will just launch forge and swith to the respective
tab in the common GUI.
-A submission window that appears have
+A<span style="text-alignstart; "> submission window that appears have
a prefilled path to the executable to debug. You can select the number
of MPI processors and/or OpenMP threads on which to run and press run.
-Command line arguments to a program can be entered to the
-"Arguments"
-style="text-align start; ">box.
-[{.image-inline width="451"
-height="513"}](ddt1.png)Â
+Command line arguments to a program can be entered to the</span>
+"Arguments<span class="Apple-converted-space">" </span><span
+style="text-alignstart; ">box.</span>
+[{.image-inline
+width="451"
+height="513"}](https://docs.it4i.cz/salomon/software/debuggers/ddt1.png)Â
To start the debugging directly without the submission window, user can
specify the debugging and execution parameters from the command line.
For example the number of MPI processes is set by option "-np 4".
@@ -88,13 +87,13 @@ reserved - DDT/MAP is launched as a server in the job which then
connects to a running instance of your GUI.
To use Reverse connect, use a jobscript that you would normally use to
launch your application, just prepend ddt/map --connect to your
-application
+application:
map --connect mpirun -np 24 ./mpi-test
ddt --connect mpirun -np 24 ./mpi-test
Launch Forge GUI on login node and submit the job using qsub. When the
-job starts running, Forge will ask you to accept the connection
+job starts running, Forge will ask you to accept the connection:
+Connect](https://docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160211v14.27.45.png/@@images/3550e4ae-2eab-4571-8387-11a112dd6ca8.png "Allinea Reverse Connect")
After accepting the request, you can start remote profiling/debugging.
Xeon Phi
--------
@@ -102,7 +101,7 @@ Forge allows debugging and profiling of both offload and native mode
Xeon Phi programs.
### Offload mode
It is recommended to set the following environment values on the offload
-host
+host:
export MYO_WATCHDOG_MONITOR=-1 # To make sure the host process isn't killed when we enter a debugging session
export AMPLXE_COI_DEBUG_SUPPORT=true # To make sure that debugging symbols are accessible on the host and the card
unset OFFLOAD_MAIN # To make sure allinea DDT can attach to offloaded codes
@@ -111,105 +110,41 @@ connect also works.)
### Native mode
Native mode programs can be profiled/debugged using the remote launch
feature. First, you need to create a script that will setup the
-environment on the Phi card. An example
+environment on the Phi card. An example:
#!/bin/bash
# adjust PATH and LD_LIBRARY_PATH according to the toolchain/libraries your app is using.
- export PATH=/apps/all/impi/5.0.3.048-iccifort-2015.3.187/mic/bin$PATH
- export LD_LIBRARY_PATH=/apps/all/impi/5.0.3.048-iccifort-2015.3.187/mic/lib/apps/all/ifort/2015.3.187/lib/mic/apps/all/icc/2015.3.187/lib/mic$LD_LIBRARY_PATH
+ export PATH=/apps/all/impi/5.0.3.048-iccifort-2015.3.187/mic/bin:$PATH
+ export LD_LIBRARY_PATH=/apps/all/impi/5.0.3.048-iccifort-2015.3.187/mic/lib:/apps/all/ifort/2015.3.187/lib/mic:/apps/all/icc/2015.3.187/lib/mic:$LD_LIBRARY_PATH
export MIC_OMP_NUM_THREADS=60
export MYO_WATCHDOG_MONITOR=-1
export AMPLXE_COI_DEBUG_SUPPORT=true
unset OFFLOAD_MAIN
export I_MPI_MIC=1
-Save the script in eg. ~/remote-mic.sh.
-Now, start an interactive graphical session on a node with
-accelerator
- $ qsub â€IX â€q qexp â€l select=1ncpus=24accelerator=True
-Launch Forge
+Save the script in eg.<span class="monospace"> ~/remote-mic.sh.
+</span>Now, start an interactive graphical session on a node with
+accelerator:
+ $ qsub â€IX â€q qexp â€l select=1:ncpus=24:accelerator=True
+Launch Forge :
$ module load Forge
$ forge&
Now click on the remote launch drop-down list, select "Configure..." and
-Add a new remote connection with the following parameters
-
-Connection name mic0
-Hostname mic0
-Remote Installation Directory /apps/all/Forge/5.1-43967/
-Remote script ~/remote-mic.sh
+Add a new remote connection with the following parameters:
+Connection namemic0
+Hostnamemic0
+Remote Installation Directory:Â /apps/all/Forge/5.1-43967/
+Remote script~/remote-mic.sh
You can click Test Remote Launch to verify the configuration. After you
save the remote launch configuration and select it in the dropdown list,
you can use the Run button in the main windows to remotely launch your
program on mic0.
Documentation
-------------
-Users can find original User Guide after loading the Forge moduleÂ
+Users can find original User Guide after loading the Forge module:Â
$EBROOTFORGE/doc/userguide-forge.pdf
Â
Â
-Â [1] Discipline, Magic, Inspiration and Science Best Practice
+Â [1] Discipline, Magic, Inspiration and ScienceBest Practice
Debugging with Allinea DDT, Workshop conducted at LLNL by Allinea on May
10, 2013,
-[link](https//computing.llnl.gov/tutorials/allineaDDT/index.html)
+[link](https://computing.llnl.gov/tutorials/allineaDDT/index.html)
Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
- .navTreeFolderish
- .contenttype-folder}
- - [Aislinn](aislinn.html)
-
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
- - [Intel VTune Amplifier
- XE](intel-vtune-amplifier.html)
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
diff --git a/whats-new/news-feed/allinea-tools-updated-to-6-0.html b/docs.it4i.cz/whats-new/news-feed/allinea-tools-updated-to-6-0.6.html
old mode 100755
new mode 100644
similarity index 68%
rename from whats-new/news-feed/allinea-tools-updated-to-6-0.html
rename to docs.it4i.cz/whats-new/news-feed/allinea-tools-updated-to-6-0.6.html
index 2e3caca48fb6501426605b3433161f5a21348e6a..b06f571445b115252a6e1e99c9bf34fd401e06ca
--- a/whats-new/news-feed/allinea-tools-updated-to-6-0.html
+++ b/docs.it4i.cz/whats-new/news-feed/allinea-tools-updated-to-6-0.6.html
@@ -10,45 +10,42 @@
-
-<!-- Mirrored from docs.it4i.cz/whats-new/news-feed/allinea-tools-updated-to-6-0.6 by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:17:07 GMT -->
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- <base /><!--[if lt IE 7]></base><![endif]-->
+ <base href="https://docs.it4i.cz/whats-new/news-feed/allinea-tools-updated-to-6-0.6" /><!--[if lt IE 7]></base><![endif]-->
- <link rel="stylesheet" type="text/css" media="screen" href="../../portal_css/Sunburst%20Theme/reset-cachekey-e265a1e68e2103b05918ef661c168cdb.css" />
- <link rel="stylesheet" type="text/css" href="../../portal_css/Sunburst%20Theme/base-cachekey-f42567a9b3d7b2318db6477cef6d2d1b.css" />
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+ <link rel="stylesheet" type="text/css" href="https://docs.it4i.cz/portal_css/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-5939d0a22955a2f783ae949901e3df21.css" />
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Allinea Tools updated to 6.0.6 — IT4I Docs</title>
- <link rel="canonical" href="allinea-tools-updated-to-6-0.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/whats-new/news-feed/allinea-tools-updated-to-6-0.6" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="allinea-tools-updated-to-6-0.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/whats-new/news-feed/allinea-tools-updated-to-6-0.6#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="allinea-tools-updated-to-6-0.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/whats-new/news-feed/allinea-tools-updated-to-6-0.6#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
@@ -145,7 +142,7 @@
<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
/
@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../whats-new.html">What's New</a>
+ <a href="https://docs.it4i.cz/whats-new">What's New</a>
<span class="breadcrumbSeparator">
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@@ -163,7 +160,7 @@
</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../news-feed.html">News</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed">News</a>
<span class="breadcrumbSeparator">
/
@@ -286,7 +283,7 @@
<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
@@ -302,7 +299,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -318,7 +315,7 @@
- <a title="Full history of important announcements related to IT4I infrastructure, planned downtimes, outages etc." class="state-published contenttype-document" href="../downtimes_history.html">
+ <a class="state-published contenttype-document" title="Full history of important announcements related to IT4I infrastructure, planned downtimes, outages etc." href="https://docs.it4i.cz/whats-new/downtimes_history">
<span>History of Downtimes</span>
</a>
@@ -334,7 +331,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../news-feed.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new/news-feed">
<span>News</span>
</a>
@@ -350,7 +347,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-news-item" href="allinea-tools-updated-to-6-0.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-news-item" title="" href="https://docs.it4i.cz/whats-new/news-feed/allinea-tools-updated-to-6-0.6">
<span>Allinea Tools updated to 6.0.6</span>
</a>
@@ -384,7 +381,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
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<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
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<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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<title>Anselm downtime has been extended to Feb 26th. — IT4I Docs</title>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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<title>ANSYS 17.0 Installed — IT4I Docs</title>
- <link rel="canonical" href="ansys-17-0-installed.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/whats-new/news-feed/ansys-17-0-installed" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="ansys-17-0-installed.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/whats-new/news-feed/ansys-17-0-installed#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="ansys-17-0-installed.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/whats-new/news-feed/ansys-17-0-installed#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
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</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
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- <img src="../../logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
+ <img src="https://docs.it4i.cz/logo.png" alt="IT4I Docs" title="IT4I Docs" height="73" width="565" /></a>
</div>
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
<span class="breadcrumbSeparator">
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@@ -153,7 +150,7 @@
</span>
<span id="breadcrumbs-1" dir="ltr">
- <a href="../../whats-new.html">What's New</a>
+ <a href="https://docs.it4i.cz/whats-new">What's New</a>
<span class="breadcrumbSeparator">
/
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</span>
<span id="breadcrumbs-2" dir="ltr">
- <a href="../news-feed.html">News</a>
+ <a href="https://docs.it4i.cz/whats-new/news-feed">News</a>
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<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
+ <a href="https://docs.it4i.cz/sitemap" class="tile">Navigace</a>
<span class="portletTopRight"></span>
</dt>
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- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../../whats-new.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new">
<span>What's New</span>
</a>
@@ -318,7 +315,7 @@
- <a title="Full history of important announcements related to IT4I infrastructure, planned downtimes, outages etc." class="state-published contenttype-document" href="../downtimes_history.html">
+ <a class="state-published contenttype-document" title="Full history of important announcements related to IT4I infrastructure, planned downtimes, outages etc." href="https://docs.it4i.cz/whats-new/downtimes_history">
<span>History of Downtimes</span>
</a>
@@ -334,7 +331,7 @@
- <a title="" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" href="../news-feed.html">
+ <a class="state-published navTreeItemInPath navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/whats-new/news-feed">
<span>News</span>
</a>
@@ -350,7 +347,7 @@
- <a title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-news-item" href="ansys-17-0-installed.html">
+ <a class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-news-item" title="" href="https://docs.it4i.cz/whats-new/news-feed/ansys-17-0-installed">
<span>ANSYS 17.0 Installed</span>
</a>
@@ -384,7 +381,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../get-started-with-it4innovations.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/get-started-with-it4innovations">
<span>Get Started with IT4Innovations</span>
</a>
@@ -400,7 +397,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../salomon.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/salomon">
<span>Salomon Cluster Documentation</span>
</a>
@@ -416,7 +413,7 @@
- <a title="" class="state-published navTreeFolderish contenttype-folder" href="../../anselm-cluster-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="" href="https://docs.it4i.cz/anselm-cluster-documentation">
<span>Anselm Cluster Documentation</span>
</a>
@@ -432,7 +429,7 @@
- <a title="" class="state-published contenttype-document" href="../../links.html">
+ <a class="state-published contenttype-document" title="" href="https://docs.it4i.cz/links">
<span>Links</span>
</a>
@@ -448,7 +445,7 @@
- <a title="" class="state-published contenttype-collection" href="../../changelog.html">
+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
<span>Changelog</span>
</a>
@@ -464,7 +461,7 @@
- <a title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder" href="../../pbspro-documentation.html">
+ <a class="state-published navTreeFolderish contenttype-folder" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" href="https://docs.it4i.cz/pbspro-documentation">
<span>PBSPro Documentation</span>
</a>
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_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', 5]);
var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
})();
</script>
-<noscript><p><img src="http://extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
+<noscript><p><img src="//extranet.it4i.cz/piwik/piwik.php?idsite=5" style="border:0;" alt="" /></p></noscript>
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<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
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</div>
</body>
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</html>
diff --git a/docs.it4i.cz/whats-new/news-feed/ansys-17-0-installed.md b/docs.it4i.cz/whats-new/news-feed/ansys-17-0-installed.md
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/whats-new/news-feed/atom.xml b/docs.it4i.cz/whats-new/news-feed/atom.xml
old mode 100755
new mode 100644
similarity index 98%
rename from whats-new/news-feed/atom.xml
rename to docs.it4i.cz/whats-new/news-feed/atom.xml
index e307253d68a66ab69b582574268555dd97c8717b..e8b1a33e0cf723dde67d2f1a748480d0d5a516a4
--- a/whats-new/news-feed/atom.xml
+++ b/docs.it4i.cz/whats-new/news-feed/atom.xml
@@ -14,45 +14,6 @@
- <entry>
- <title>MATLAB 2015b</title>
- <link rel="alternate" type="text/html" href="https://docs.it4i.cz/whats-new/news-feed/matlab-2015b"/>
-
- <id>urn:syndication:9b996ea95ba04f218d1eff951249ac50</id>
-
- <content type="xhtml" xml:base="https://docs.it4i.cz/whats-new/news-feed" xml:lang="cs" xml:space="preserve">
- <div xmlns="http://www.w3.org/1999/xhtml">
-
-
-
-
-
-
-
- <div id="parent-fieldname-text" class="plain">
- <p>MATLAB 2015b has been installed on Anselm and Salomon. Modules are named MATLAB/2015b-COM and MATLAB/2015b-EDU. Release notes:Â http://www.mathworks.com/help/matlab/release-notes.html#R2015b</p>
- </div>
-
-
-
- </div>
- </content>
-
- <author>
-
- <name>sta545</name>
-
- </author>
-
- <published>2016-07-13T15:40:00+02:00</published>
-
- <updated>2016-07-13T15:38:48+02:00</updated>
-
-
- </entry>
-
-
-
<entry>
<title>Issue with Intel MPI 4.1.1 on Salomon</title>
<link rel="alternate" type="text/html" href="https://docs.it4i.cz/whats-new/news-feed/issue-with-intel-mpi-4-1-1-on-salomon"/>
@@ -149,7 +110,7 @@
<div id="parent-fieldname-text" class="plain">
- <p>We have implemented a new way to run parallel MATLAB jobs. Unlike the previously documented method, it does not submit a separate new job to run the workers, all is done within a single job. Read about it here:Â <a target="_self" title="" class="external-link" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6">https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6</a></p>
+ <p>We have implemented a new way to run parallel MATLAB jobs. Unlike the previously documented method, it does not submit a separate new job to run the workers, all is done within a single job. Read about it here:Â <a title="" class="external-link" target="_self" href="https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6">https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6</a></p>
</div>
@@ -288,5 +249,44 @@
</entry>
+
+ <entry>
+ <title>MATLAB 2015b</title>
+ <link rel="alternate" type="text/html" href="https://docs.it4i.cz/whats-new/news-feed/matlab-2015b"/>
+
+ <id>urn:syndication:9b996ea95ba04f218d1eff951249ac50</id>
+
+ <content type="xhtml" xml:base="https://docs.it4i.cz/whats-new/news-feed" xml:lang="cs" xml:space="preserve">
+ <div xmlns="http://www.w3.org/1999/xhtml">
+
+
+
+
+
+
+
+ <div id="parent-fieldname-text" class="plain">
+ <p>MATLAB 2015b has been installed on Anselm and Salomon. Modules are named MATLAB/2015b-COM and MATLAB/2015b-EDU. Release notes:Â http://www.mathworks.com/help/matlab/release-notes.html#R2015b</p>
+ </div>
+
+
+
+ </div>
+ </content>
+
+ <author>
+
+ <name>sta545</name>
+
+ </author>
+
+ <published>2016-07-13T15:40:00+02:00</published>
+
+ <updated>2016-07-13T15:38:48+02:00</updated>
+
+
+ </entry>
+
+
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diff --git a/salomon/resource-allocation-and-job-execution/capacity.zip b/docs.it4i.cz/whats-new/news-feed/capacity-computing-updated-for-salomon
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rename to docs.it4i.cz/whats-new/news-feed/capacity-computing-updated-for-salomon
diff --git a/whats-new/news-feed/cuda-7-5-is-now-installed-on-anselm.html b/docs.it4i.cz/whats-new/news-feed/cuda-7-5-is-now-installed-on-anselm.html
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new mode 100644
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rename from whats-new/news-feed/cuda-7-5-is-now-installed-on-anselm.html
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+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/++resource++it4i.portal.common/exporting.js"></script>
+ <script type="text/javascript" src="https://docs.it4i.cz/portal_javascripts/Sunburst%20Theme/resourceit4i.portal.commonjquery.dataTables.min-cachekey-58659b8d76594989f3faa967a94e5541.js"></script>
<title>Cuda 7.5 is now installed on Anselm — IT4I Docs</title>
- <link rel="canonical" href="cuda-7-5-is-now-installed-on-anselm.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/whats-new/news-feed/cuda-7-5-is-now-installed-on-anselm" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
- <link rel="apple-touch-icon" href="../../touch_icon.png" />
+ <link rel="shortcut icon" type="image/x-icon" href="https://docs.it4i.cz/favicon.ico" />
+ <link rel="apple-touch-icon" href="https://docs.it4i.cz/touch_icon.png" />
<script type="text/javascript">
@@ -64,7 +61,7 @@
- <link rel="search" href="../../%40%40search.html" title="Prohledejte portál" />
+ <link rel="search" href="https://docs.it4i.cz/@@search" title="Prohledejte portál" />
@@ -87,9 +84,9 @@
<div class="cell width-full position-0">
<div id="portal-header">
<p class="hiddenStructure">
- <a accesskey="2" href="cuda-7-5-is-now-installed-on-anselm.html#content">PĹ™ejĂt na obsah</a> |
+ <a accesskey="2" href="https://docs.it4i.cz/whats-new/news-feed/cuda-7-5-is-now-installed-on-anselm#content">PĹ™ejĂt na obsah</a> |
- <a accesskey="6" href="cuda-7-5-is-now-installed-on-anselm.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/whats-new/news-feed/cuda-7-5-is-now-installed-on-anselm#portal-globalnav">PĹ™ejĂt na navigaci</a>
</p>
<div id="portal-personaltools-wrapper">
@@ -125,13 +122,13 @@
</form>
<div id="portal-advanced-search" class="hiddenStructure">
- <a href="../../%40%40search.html" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
+ <a href="https://docs.it4i.cz/@@search" accesskey="5">PokroÄŤilĂ© vyhledávánĂ...</a>
</div>
</div>
-<a id="portal-logo" title="IT4I Docs" accesskey="1" href="../../index.html">
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<title>Intel VTune Amplifier support for Xeon Phi on Salomon — IT4I Docs</title>
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<title>Intel VTune is working — IT4I Docs</title>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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rename to docs.it4i.cz/whats-new/news-feed/new-bioinformatic-tools-installed-fastqc-0-11-3-gatk-3-5-java-1-7-0_79-picard-2-1-0-samtools-1-3-foss-2015g-snpeff-4-1_g-trimmomatic-0-35-java-1-7.0_79.html
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<title>New bioinformatic tools installed: FastQC/0.11.3, GATK/3.5-Java-1.7.0_79, picard/2.1.0, SAMtools/1.3-foss-2015g, SnpEff/4.1_G, Trimmomatic/0.35-Java-1.7.0_79 — IT4I Docs</title>
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+ <link rel="canonical" href="https://docs.it4i.cz/whats-new/news-feed/new-bioinformatic-tools-installed-fastqc-0-11-3-gatk-3-5-java-1-7-0_79-picard-2-1-0-samtools-1-3-foss-2015g-snpeff-4-1_g-trimmomatic-0-35-java-1-7.0_79" />
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
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<span id="breadcrumbs-1" dir="ltr">
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<span id="breadcrumbs-2" dir="ltr">
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<dt class="portletHeader hiddenStructure">
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<span>New bioinformatic tools installed: FastQC/0.11.3, GATK/3.5-Java-1.7.0_79, picard/2.1.0, SAMtools/1.3-foss-2015g, SnpEff/4.1_G, Trimmomatic/0.35-Java-1.7.0_79</span>
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<span>Get Started with IT4Innovations</span>
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<span>Salomon Cluster Documentation</span>
</a>
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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<title>New method to execute parallel MATLAB jobs — IT4I Docs</title>
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- <p>We have implemented a new way to run parallel MATLAB jobs. Unlike the previously documented method, it does not submit a separate new job to run the workers, all is done within a single job. Read about it here:Â <a target="_self" title="" class="external-link" href="../../salomon/software/numerical-languages/matlab.html#section-6">https://docs.it4i.cz/salomon/software/numerical-languages/matlab#section-6</a></p>
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diff --git a/docs.it4i.cz/whats-new/news-feed/new-method-to-execute-parallel-matlab-jobs.md b/docs.it4i.cz/whats-new/news-feed/new-method-to-execute-parallel-matlab-jobs.md
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<title>New modules for Parallel programming in modern Fortran course — IT4I Docs</title>
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- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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<title>New versions of Allinea Forge and Performance Reports — IT4I Docs</title>
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- <a accesskey="6" href="new-versions-of-allinea-forge-and-performance-version.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/whats-new/news-feed/new-versions-of-allinea-forge-and-performance-version#portal-globalnav">PĹ™ejĂt na navigaci</a>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
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<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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<title>Octave updated to 4.0.1 on Anselm — IT4I Docs</title>
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+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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diff --git a/docs.it4i.cz/whats-new/news-feed/octave-updated-to-4-0-1-on-anselm.md b/docs.it4i.cz/whats-new/news-feed/octave-updated-to-4-0-1-on-anselm.md
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<title>Salomon PBS changes — IT4I Docs</title>
- <link rel="canonical" href="salomon-pbs-changes.html" />
+ <link rel="canonical" href="https://docs.it4i.cz/whats-new/news-feed/salomon-pbs-changes" />
- <link rel="shortcut icon" type="image/x-icon" href="../../favicon.ico" />
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- <a accesskey="6" href="salomon-pbs-changes.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<div id="portal-advanced-search" class="hiddenStructure">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
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<span>News</span>
</a>
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<span>Salomon PBS changes</span>
</a>
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</a>
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<span>Anselm Cluster Documentation</span>
</a>
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<span>Links</span>
</a>
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<span>Changelog</span>
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<span>PBSPro Documentation</span>
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<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
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- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
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diff --git a/docs.it4i.cz/whats-new/news-feed/salomon-pbs-changes.md b/docs.it4i.cz/whats-new/news-feed/salomon-pbs-changes.md
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<title>Vampir installed — IT4I Docs</title>
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<div id="portal-header">
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- <a accesskey="6" href="vampir-installed.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+ <a accesskey="6" href="https://docs.it4i.cz/whats-new/news-feed/vampir-installed#portal-globalnav">PĹ™ejĂt na navigaci</a>
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<div id="portal-advanced-search" class="hiddenStructure">
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+<a id="portal-logo" title="IT4I Docs" accesskey="1" href="https://docs.it4i.cz">
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<span id="breadcrumbs-you-are-here">NacházĂte se zde:</span>
<span id="breadcrumbs-home">
- <a href="../../index.html">Ăšvod</a>
+ <a href="https://docs.it4i.cz">Ăšvod</a>
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<span id="breadcrumbs-1" dir="ltr">
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<span id="breadcrumbs-2" dir="ltr">
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+ <a href="https://docs.it4i.cz/whats-new/news-feed">News</a>
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<dt class="portletHeader hiddenStructure">
<span class="portletTopLeft"></span>
- <a href="../../sitemap.html" class="tile">Navigace</a>
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</a>
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<span>History of Downtimes</span>
</a>
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<span>News</span>
</a>
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<span>Anselm Cluster Documentation</span>
</a>
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<span>Links</span>
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+ <a class="state-published contenttype-collection" title="" href="https://docs.it4i.cz/changelog">
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<!-- End Piwik Code -->
<!-- nagios_check_http_expect_string -->
@@ -532,12 +529,12 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
<div id="portal-footer">
<p>
<a href="http://www.it4i.cz/?lang=en">IT4Innovations</a>
- <a href="../../anselm-cluster-documentation.html">Dokumentace pro Anselm</a>
- <a href="https://events.it4i.cz/">Events</a>
- <a href="https://extranet.it4i.cz/">Extranet</a>
+ <a href="https://docs.it4i.cz/anselm">Dokumentace pro Anselm</a>
+ <a href="https://events.it4i.cz">Events</a>
+ <a href="https://extranet.it4i.cz">Extranet</a>
<a href="http://prace.it4i.cz/">HPC & PRACE</a>
<a href="http://study.it4i.cz/">HPC Study</a>
- <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="https://docs.it4i.cz/salomon">Dokumentace pro Salomon</a>
<a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
<a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
</p>
@@ -553,8 +550,6 @@ g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.pare
</div>
</body>
-
-<!-- Mirrored from docs.it4i.cz/whats-new/news-feed/vampir-installed by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:16:57 GMT -->
</html>
diff --git a/docs.it4i.cz/whats-new/news-feed/vampir-installed.md b/docs.it4i.cz/whats-new/news-feed/vampir-installed.md
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/filter.txt b/filter.txt
index f9a2d24a6a5d29170cdf28ea0ae093d816d8cd86..c8050f2e678937d45fb404999b904322664b9d8a 100644
--- a/filter.txt
+++ b/filter.txt
@@ -1,29 +1,8 @@
-{#parent-fieldname-title .documentFirstHeading}
-Obsah
-:
+ {#parent-fieldname-title .documentFirstHeading}
{.internal-link}
-{.image-inline}
-{.external-link}
{.anchor-link}
+{.external-link}
+{.image-inline}
{.prettyprint .lang-sh .prettyprinted}
-{.tile}
-{.state-published
-.navTreeFolderish .contenttype-folder}
-{.state-published .navTreeItemInPath .navTreeFolderish .contenttype-folder}
-{.state-published .contenttype-document}
-{.state-published .navTreeItemInPath .navTreeFolderish .contenttype-folder}
-{.state-published .navTreeCurrentItem .navTreeCurrentNode .contenttype-document}
-{.state-published .contenttype-document}
-{.state-published .navTreeFolderish .contenttype-folder}
-{#tlspu_cookiepolicy_title}
-.navTreeItemInPath
-.contenttype-document}
-.navTreeItemInPath
-.navTreeCurrentItem .navTreeCurrentNode .contenttype-document}
-.contenttype-document}
-.contenttype-collection}
-<span
-class="portletBottomRight">
-.navTreeCurrentItem
-.navTreeCurrentNode
-.navTreeCurrentItem
+-----------------------
+Obsah
diff --git a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.md b/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.md
deleted file mode 100644
index 8be8fe328642ca2b1b0f41ffd39b34833df190e9..0000000000000000000000000000000000000000
--- a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.md
+++ /dev/null
@@ -1,28 +0,0 @@
-========================
-
-
-X Window System
----------------
-The X Window system is a principal way to get GUI access to the
-clusters.
-Read more about configuring [**X Window
-System**](graphical-user-interface/x-window-system/x-window-and-vnc.html).
-VNC
----
-The **Virtual Network Computing** (**VNC**) is a graphical
-class="link-external">[desktop
-sharing](http//en.wikipedia.org/wiki/Desktop_sharing "Desktop sharing")
-system that uses the [Remote Frame Buffer
-protocol
-(RFB)](http//en.wikipedia.org/wiki/RFB_protocol "RFB protocol")
-to remotely control another
-class="link-external">[computer](http//en.wikipedia.org/wiki/Computer "Computer").
-Read more about configuring
-**[VNC](graphical-user-interface/vnc.html)**.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
diff --git a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md b/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md
deleted file mode 100644
index f90e112f20682d83ced254786304fbf268d091dd..0000000000000000000000000000000000000000
--- a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md
+++ /dev/null
@@ -1,209 +0,0 @@
-
-VNC
-===
-
-
-The **Virtual Network Computing** (**VNC**) is a graphical [desktop
-sharing](http//en.wikipedia.org/wiki/Desktop_sharing "Desktop sharing")
-system that uses the [Remote Frame Buffer protocol
-(RFB)](http//en.wikipedia.org/wiki/RFB_protocol "RFB protocol") to
-remotely control another
-[computer](http//en.wikipedia.org/wiki/Computer "Computer"). It
-transmits the
-[keyboard](http//en.wikipedia.org/wiki/Computer_keyboard "Computer keyboard")
-and
-[mouse](http//en.wikipedia.org/wiki/Computer_mouse "Computer mouse"){.mw-redirect}
-events from one computer to another, relaying the graphical
-[screen](http//en.wikipedia.org/wiki/Computer_screen "Computer screen"){.mw-redirect}
-updates back in the other direction, over a
-[network](http//en.wikipedia.org/wiki/Computer_network "Computer network").^[[1]](http//en.wikipedia.org/wiki/Virtual_Network_Computing#cite_note-1)^
-The recommended clients are
-[TightVNC](http//www.tightvnc.com/) or
-[TigerVNC](http//sourceforge.net/apps/mediawiki/tigervnc/index.php?title=Main_Page)
-(free, open source, available for almost any platform).
-Create VNC password
--------------------
-Local VNC password should be set before the first login. Do use a strong
-password.
-```
-[username@login2 ~]$ vncpasswd
-Password
-Verify
-```
-Start vncserver
----------------
-To access VNC a local vncserver must be started first and also a tunnel
-using SSH port forwarding must be established.
-[See below](#linux-example-of-creating-a-tunnel) for the
-details on SSH tunnels. In this example we use port 61.
-You can find ports which are already occupied. Here you can see that
-ports "/usr/bin/Xvnc 79" and "
-class="pln">/usr/bin/Xvnc 60" are occupied.
-```
-[username@login2 ~]$ ps aux | grep Xvnc
-username   5971 0.0 0.0 201072 92564 ?       SN  Sep22  419 /usr/bin/Xvnc 79 -desktop login279 (username) -auth /home/gre196/.Xauthority -geometry 1024x768 -rfbwait 30000 -rfbauth /home/username/.vnc/passwd -rfbport 5979 -fp catalogue/etc/X11/fontpath.d -pn
-username   10296 0.0 0.0 131772 21076 pts/29  SN  1301  001 /usr/bin/Xvnc 60 -desktop login261 (username) -auth /home/username/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/jir13/.vnc/passwd -rfbport 5960 -fp catalogue/etc/X11/fontpath.d -pn
-.....
-```
-Choose free port e.g. 61 and start your VNC server
-```
-[username@login2 ~]$ vncserver 61 -geometry 1600x900 -depth 16
-New 'login21 (username)' desktop is login21
-Starting applications specified in /home/username/.vnc/xstartup
-Log file is /home/username/.vnc/login21.log
-```
-Check if VNC server is started on the port (in this example 61)
-```
-[username@login2 .vnc]$ vncserver -list
-TigerVNC server sessions
-X DISPLAY #Â Â Â Â PROCESS ID
-61Â Â Â Â Â Â Â Â Â Â Â Â Â 18437
-```
-Another command
-```
-[username@login2 .vnc]$ Â ps aux | grep Xvnc
-username   10296 0.0 0.0 131772 21076 pts/29  SN  1301  001 /usr/bin/Xvnc 61 -desktop login261 (username) -auth /home/jir13/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/username/.vnc/passwd -rfbport 5961 -fp catalogue/etc/X11/fontpath.d -pn
-```
-To access the VNC server you have to create a tunnel between the login
-node using TCP **port 5961** and your machine using a free TCP port (for
-simplicity the very same, in this case).
-The tunnel must point to the same login node where you launched the VNC
-server, eg. login2. If you use just cluster-name.it4i.cz, the tunnel
-might point to a different node due to DNS round robin.
-### []()[]()Linux/Mac OS example of creating a tunnel
-At your machine, create the tunnel
-```
-local $Â ssh -TN -f username@login2.cluster-name.it4i.cz -L 5961localhost5961
-```
-Issue the following command to check the tunnel is established (please
-note the PID 2022 in the last column, you'll need it for closing the
-tunnel)
-```
-local $ netstat -natp | grep 5961
-(Not all processes could be identified, non-owned process info
-Â will not be shown, you would have to be root to see it all.)
-tcp       0     0 127.0.0.15961         0.0.0.0*              LISTEN     2022/ssh      Â
-tcp6Â Â Â Â Â Â 0Â Â Â Â Â 0 15961Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â *Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â LISTENÂ Â Â Â Â 2022/ssh
-```
-Or on Mac OS use this command
-``` {.prettyprint .lang-sh}
-local-mac $ lsof -n -i4TCP5961 | grep LISTEN
-ssh 75890 sta545 7u IPv4 0xfb062b5c15a56a3b 0t0 TCP 127.0.0.15961 (LISTEN)
-```
-Connect with the VNC client
-```
-local $ vncviewer 127.0.0.15961
-```
-In this example, we connect to VNC server on port 5961, via the ssh
-tunnel. The connection is encrypted and secured. The VNC server
-listening on port 5961 provides screen of 1600x900 pixels.
-You have to destroy the SSH tunnel which is still running at the
-background after you finish the work. Use the following command (PID
-2022 in this case, see the netstat command above)
-```
-kill 2022
-```
-### Windows example of creating a tunnel
-Use PuTTY to log in on cluster.
-Start vncserver using command vncserver described above.
-Search for the localhost and port number (in this case
-127.0.0.15961).**
-**
-```
-[username@login2 .vnc]$ netstat -tanp | grep Xvnc
-(Not all processes could be identified, non-owned process info
-Â will not be shown, you would have to be root to see it all.)
-tcp       0     0 127.0.0.15961             0.0.0.0*                  LISTEN     24031/Xvnc
-```
-On the PuTTY Configuration screen go to Connection->SSH->Tunnels
-to set up the tunnel.
-Fill the Source port and Destination fields. **Do not forget to click
-the Add button**.
-
-[](vnc/2015-10-02_135100cV.png)
-Run the VNC client of your choice, select VNC server 127.0.0.1, port
-5961 and connect using VNC password.
-### Example of starting TigerVNC viewer
-
-In this example, we connect to VNC server on port 5961, via the ssh
-tunnel, using TigerVNC viewer. The connection is encrypted and secured.
-The VNC server listening on port 5961 provides screen of 1600x900
-pixels.
-### Example of starting TightVNC Viewer
-Use your VNC password to log using TightVNC Viewer and start a Gnome
-Session on the login node.
-[****](vnc/2015-10-02_135128cV.png)
-Gnome session
--------------
-You should see after the successful login.
-[](../../gnome_screen.html)
-### **Disable your Gnome session screensaver
-**
-Open Screensaver preferences dialog
-[](../../../salomon/salomon-gdm.png)
-Uncheck both options below the slider
-[](vnc/gdm-disable-screensaver-acV.png)
-### Kill screensaver if locked screen
-If the screen gets locked you have to kill the screensaver. Do not to
-forget to disable the screensaver then.
-```
-[username@login2 .vnc]$ ps aux | grep screen
-username    1503 0.0 0.0 103244  892 pts/4   S+  1437  000 grep screen
-username    24316 0.0 0.0 270564 3528 ?       Ss  1412  000 gnome-screensaver
-[username@login2 .vnc]$ kill 24316
-```
-### Kill vncserver after finished work
-You should kill your VNC server using command
-```
-[username@login2 .vnc]$ vncserver -kill 61
-Killing Xvnc process ID 7074
-Xvnc process ID 7074 already killed
-```
-Or this way
-```
-[username@login2 .vnc]$Â pkill vnc
-```
-GUI applications on compute nodes over VNC
-------------------------------------------
-The very [same methods as described
-above](x-window-and-vnc.html#gui-applications-on-compute-nodes),
-may be used to run the GUI applications on compute nodes. However, for
-**maximum performance**, proceed following these steps
-Open a Terminal (Applications -> System Tools -> Terminal). Run
-all the next commands in the terminal.
-
-[](vnc/2015-10-07_121839acV.png)
-Allow incoming X11 graphics from the compute nodes at the login node
-```
-$ xhost +
-```
-Get an interactive session on a compute node (for more detailed info
-[look
-here](../../../anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.html)).
-Use the **-v DISPLAY** option to propagate the DISPLAY on the compute
-node. In this example, we want a complete node (24 cores in this
-example) from the production queue
-```
-$ qsub -I -v DISPLAY=$(uname -n)$(echo $DISPLAY | cut -d '' -f 2) -A PROJECT_ID -q qprod -l select=1ncpus=24
-```
-Test that the DISPLAY redirection into your VNC session works, by
-running a X11 application (e. g. XTerm) on the assigned compute node
-```
-$ xterm
-```
-Example described above
-[](vnc/2015-10-07_120255acV.png)
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
diff --git a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/TightVNC_login.png/@@images/e53354d8-a2e8-4947-92b3-dd107d498408.png b/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/TightVNC_login.png/@@images/e53354d8-a2e8-4947-92b3-dd107d498408.png
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diff --git a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding.md b/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding.md
deleted file mode 100644
index f5634052d2bbba425d1f81f973fa61e8ab8cabfe..0000000000000000000000000000000000000000
--- a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding.md
+++ /dev/null
@@ -1,55 +0,0 @@
-class="breadcrumbSeparator"> / id="breadcrumbs-5"
-dir="ltr"> Cygwin and X11
-forwarding
-Info
-
-Cygwin and X11 forwarding
-=========================
-### If no able to forward X11 using PuTTY to CygwinX
-``` {.prettyprint .lang-sh}
-[usename@login1.anselm ~]$ gnome-session &
-[1] 23691
-[usename@login1.anselm ~]$ PuTTY X11 proxy unable to connect to forwarded X server Network error Connection refused
-PuTTY X11 proxy unable to connect to forwarded X server Network error Connection refused
-** (gnome-session23691) WARNING ** Cannot open display
-```
-Â
-1. Locate and modify
- Cygwin shortcut that
- uses
- class="Apple-converted-space">Â [startxwin](http//x.cygwin.com/docs/man1/startxwin.1.html)
- locate
- Ccygwin64binXWin.exe
-
- style="text-align left; float none; ">
- style="text-align left; float none; ">change it
- to
- C*cygwin64binXWin.exe -listen tcp*
-
- 
-
-
- style="text-align left; float none; ">
-2.
- style="text-align left; float none; ">Check Putty settings
- Enable X11
- forwarding
- style="text-align left; float none; ">
- class="Apple-converted-space">
-
- [](cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.html)
-
-Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../sitemap.html)
- - [What's
- New](../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../get-started-with-it4innovations.html)
-
diff --git a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.md b/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.md
deleted file mode 100644
index b5b39245c347e3be9f7e69da357c47311722898f..0000000000000000000000000000000000000000
--- a/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.md
+++ /dev/null
@@ -1,55 +0,0 @@
-class="breadcrumbSeparator"> / id="breadcrumbs-5"
-dir="ltr"> Cygwin and X11
-forwarding
-Info
-
-Cygwin and X11 forwarding
-=========================
-### If no able to forward X11 using PuTTY to CygwinX
-``` {.prettyprint .lang-sh}
-[usename@login1.anselm ~]$ gnome-session &
-[1] 23691
-[usename@login1.anselm ~]$ PuTTY X11 proxy unable to connect to forwarded X server Network error Connection refused
-PuTTY X11 proxy unable to connect to forwarded X server Network error Connection refused
-** (gnome-session23691) WARNING ** Cannot open display
-```
-Â
-1. Locate and modify
- Cygwin shortcut that
- uses
- class="Apple-converted-space">Â [startxwin](http//x.cygwin.com/docs/man1/startxwin.1.html)
- locate
- Ccygwin64binXWin.exe
-
- style="text-align left; float none; ">
- style="text-align left; float none; ">change it
- to
- C*cygwin64binXWin.exe -listen tcp*
-
- 
-
-
- style="text-align left; float none; ">
-2.
- style="text-align left; float none; ">Check Putty settings
- Enable X11
- forwarding
- style="text-align left; float none; ">
- class="Apple-converted-space">
-
- [](cygwin-and-x11-forwarding.html)
-
-Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../../sitemap.html)
- - [What's
- New](../../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../../get-started-with-it4innovations.html)
-
diff --git a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer.md b/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer.md
deleted file mode 100644
index f26c8aa5db49136738692c7e655fb10182ce8308..0000000000000000000000000000000000000000
--- a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer.md
+++ /dev/null
@@ -1,21 +0,0 @@
-======================
-The IT4Innovations clusters are accessed by SSH protocol via login
-nodes.
-Read more on [Accessing the Salomon
-Cluste](../../salomon/accessing-the-cluster/shell-and-data-access.html)r
-or [Accessing the Anselm
-Cluster](../../anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access.html)
-pages.
-### PuTTY
-On **Windows**, use [PuTTY ssh
-client](shell-access-and-data-transfer/putty/putty.html).
-### SSH keys {#parent-fieldname-title}
-Read more about [SSH keys
-management](shell-access-and-data-transfer/ssh-keys.html).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
diff --git a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md b/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md
deleted file mode 100644
index b8feffa503d51a9d119b1de49536822527be72da..0000000000000000000000000000000000000000
--- a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md
+++ /dev/null
@@ -1,90 +0,0 @@
-Info
-
-PuTTY
-=====
-
-
-PuTTY - before we start SSH connection {#putty---before-we-start-ssh-connection style="text-align start; "}
----------------------------------------------------------------------------------
-### Windows PuTTY Installer
-We recommned you to download "**A Windows installer for everything
-except PuTTYtel**" with ***Pageant*** (SSH authentication agent) and
-**PuTTYgen** (PuTTY key generator) which is available
-[here](http//www.chiark.greenend.org.uk/~sgtatham/putty/download.html).
-After installation you can proceed directly
-to private keys authentication using
-["Putty"](#putty).
-"Change Password for Existing Private Key" is optional.
-"Generate a New Public/Private key pair" is intended for users without
-Public/Private key in the initial email containing login credentials.
-"Pageant" is optional.
-### PuTTYgen
-PuTTYgen is the PuTTY key generator. Read more how to load in an
-existing private key and change your passphrase or generate a new
-public/private key pair using
-[PuTTYgen](putty/puttygen.html) if needed.
-### Pageant SSH agent
-[Pageant](putty/pageant.html) holds your private key in
-memory without needing to retype a passphrase on every login. We
-recommend its usage.
-[]()PuTTY - how to connect to the IT4Innovations cluster
---------------------------------------------------------
-- Run PuTTY
-- Enter Host name and Save session fields with [Login
- address](../../../salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html)
- and browse Connection - > SSH -> Auth menu.
- The *Host Name* input may be in the format
- **"username@clustername.it4i.cz"** so you don't have to type your
- login each time.
- In this example we will connect to the Salomon cluster using
- Â **"salomon.it4i.cz"**.
-
- [](putty/PuTTY_host_SalomonV.png)
-Â
-- Category -> Connection - > SSH -> Auth
- Select Attempt authentication using Pageant.
- Select Allow agent forwarding.
- Browse and select your [private key](ssh-keys.html)
- file.
-
- [](putty/PuTTY_keyV.png)
-
-- Return to Session page and Save selected configuration with *Save*
- button.
-
- [](putty/PuTTY_save_SalomonV.png)
-
-- Now you can log in using *Open* button.
-
- [](putty/PuTTY_open_SalomonV.png)
-
-- Enter your username if the *Host Name* input is not in the format
- "username@salomon.it4i.cz".
-
-- Enter passphrase for selected [private
- key](ssh-keys.html) file if Pageant ****SSH
- authentication agent is not used.
-
-Another PuTTY Settings
-----------------------
-- Category -> Windows -> Translation -> Remote character set
- and select **UTF-8**.
-- Category -> Terminal -> Features and select **Disable
- application keypad mode** (enable numpad)
-- Save your configuration on Session page in to Default Settings with
- *Save* button .
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Applying for
- Resources](../../applying-for-resources.html)
diff --git a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/20150312_143443.png/@@images/29ff0f89-8203-4777-9a00-c068d3188fd0.png b/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/20150312_143443.png/@@images/29ff0f89-8203-4777-9a00-c068d3188fd0.png
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diff --git a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant.md b/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant.md
deleted file mode 100644
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--- a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant.md
+++ /dev/null
@@ -1,35 +0,0 @@
-
-id="breadcrumbs-current">Pageant SSH agent
-Info
-
-Pageant SSH agent
-=================
-
-
-Pageant holds your private key in memory without needing to retype a
-passphrase on every login.
-- Run Pageant.
-- On Pageant Key List press *Add key* and select your private
- key (id_rsa.ppk).
-- Enter your passphrase.
-- Now you have your private key in memory without needing to retype a
- passphrase on every login.
-
- [](PageantV.png)
-Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../sitemap.html)
- - [What's
- New](../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../get-started-with-it4innovations.html)
-
- - [Applying for
- Resources](../../../applying-for-resources.html)
-
diff --git a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.md b/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.md
deleted file mode 100644
index b69a293901837608d84b2fad139f95593a69e344..0000000000000000000000000000000000000000
--- a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.md
+++ /dev/null
@@ -1,90 +0,0 @@
-Info
-
-PuTTY
-=====
-
-
-PuTTY - before we start SSH connection {#putty---before-we-start-ssh-connection style="text-align start; "}
----------------------------------------------------------------------------------
-### Windows PuTTY Installer
-We recommned you to download "**A Windows installer for everything
-except PuTTYtel**" with ***Pageant*** (SSH authentication agent) and
-**PuTTYgen** (PuTTY key generator) which is available
-[here](http//www.chiark.greenend.org.uk/~sgtatham/putty/download.html).
-After installation you can proceed directly
-to private keys authentication using
-["Putty"](#putty).
-"Change Password for Existing Private Key" is optional.
-"Generate a New Public/Private key pair" is intended for users without
-Public/Private key in the initial email containing login credentials.
-"Pageant" is optional.
-### PuTTYgen
-PuTTYgen is the PuTTY key generator. Read more how to load in an
-existing private key and change your passphrase or generate a new
-public/private key pair using [PuTTYgen](puttygen.html)
-if needed.
-### Pageant SSH agent
-[Pageant](pageant.html) holds your private key in memory
-without needing to retype a passphrase on every login. We recommend its
-usage.
-[]()PuTTY - how to connect to the IT4Innovations cluster
---------------------------------------------------------
-- Run PuTTY
-- Enter Host name and Save session fields with [Login
- address](../../../../salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html)
- and browse Connection - > SSH -> Auth menu.
- The *Host Name* input may be in the format
- **"username@clustername.it4i.cz"** so you don't have to type your
- login each time.
- In this example we will connect to the Salomon cluster using
- Â **"salomon.it4i.cz"**.
-
- [](PuTTY_host_SalomonV.png)
-Â
-- Category -> Connection - > SSH -> Auth
- Select Attempt authentication using Pageant.
- Select Allow agent forwarding.
- Browse and select your [private
- key](../ssh-keys.html) file.
-
- [](PuTTY_keyV.png)
-
-- Return to Session page and Save selected configuration with *Save*
- button.
-
- [](PuTTY_save_SalomonV.png)
-
-- Now you can log in using *Open* button.
-
- [](PuTTY_open_SalomonV.png)
-
-- Enter your username if the *Host Name* input is not in the format
- "username@salomon.it4i.cz".
-
-- Enter passphrase for selected [private
- key](../ssh-keys.html) file if Pageant ****SSH
- authentication agent is not used.
-
-Another PuTTY Settings
-----------------------
-- Category -> Windows -> Translation -> Remote character set
- and select **UTF-8**.
-- Category -> Terminal -> Features and select **Disable
- application keypad mode** (enable numpad)
-- Save your configuration on Session page in to Default Settings with
- *Save* button .
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../sitemap.html)
- - [What's
- New](../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../get-started-with-it4innovations.html)
-
- - [Applying for
- Resources](../../../applying-for-resources.html)
diff --git a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.md b/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.md
deleted file mode 100644
index 597312d6838a71851f7abd12f1b5d199bb11ea62..0000000000000000000000000000000000000000
--- a/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.md
+++ /dev/null
@@ -1,81 +0,0 @@
-
-id="breadcrumbs-current">PuTTY key generator
-Info
-
-PuTTY key generator
-===================
-
-
-PuTTYgen is the PuTTY key generator. You can load in an existing private
-key and change your passphrase or generate a new public/private key
-pair.
-### Change Password for Existing Private Key
-You can change the password of your SSH key with "PuTTY Key Generator".
-Make sure to backup the key.
-- Load your [private key](../ssh-keys.html) file with
- *Load* button.
-- Enter your current passphrase.
-- Change key passphrase.
-- Confirm key passphrase.
-- Save your private key with *Save private key* button.
-
- [](PuttyKeygeneratorV.png)
-Â
-### Generate a New Public/Private key pair
-You can generate an additional public/private key pair and insert public
-key into authorized_keys file for authentication with your own private
-key.
-- Start with *Generate* button.
-
- [](PuttyKeygenerator_001V.png)
-
-- Generate some randomness.
-
- [](PuttyKeygenerator_002V.png)
-
-- Wait.
-
- [](2015-03-12_143443V.png)
-
-- Enter a *comment* for your key using formatÂ
- 'username@organization.example.com'.
- Enter key passphrase.
- Confirm key passphrase.
- Save your new private key `in "*.ppk" `format with *Save private
- key* button.
-
- [](PuttyKeygenerator_004V.png)
-
-- Save the public key with *Save public key* button.
- You can copy public key out of the â€Public key for pasting into
- authorized_keys file’ box.
-
- [](PuttyKeygenerator_005V.png)
-
-- Export private key in OpenSSH format "id_rsa" using Conversion
- -> Export OpenSSH key
-
- [](PuttyKeygenerator_006V.png)
-
-- Now you can insert additional public key into authorized_keys file
- for authentication with your own private key.
- You must log in using ssh key received after registration. Then
- proceed to [How to add your own
- key](../ssh-keys.html).
-
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../sitemap.html)
- - [What's
- New](../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../get-started-with-it4innovations.html)
-
- - [Applying for
- Resources](../../../applying-for-resources.html)
-
diff --git a/get-started-with-it4innovations/obtaining-login-credentials.md b/get-started-with-it4innovations/obtaining-login-credentials.md
deleted file mode 100644
index 20db9bafa276876e942f971f2b0d5f058aaf56e4..0000000000000000000000000000000000000000
--- a/get-started-with-it4innovations/obtaining-login-credentials.md
+++ /dev/null
@@ -1,8 +0,0 @@
-----------------------------------------------------------------------------------------------------------
-[Obtaining Login Credentials -
-VĂce...](obtaining-login-credentials/obtaining-login-credentials.html)
-[Certificates FAQ](obtaining-login-credentials/certificates-faq.html){.summary .url} {#certificates-faq .tileHeadline}
-------------------------------------------------------------------------------------
-FAQ about certificates in general
-[Certificates FAQ -
-VĂce...](obtaining-login-credentials/certificates-faq.html)
diff --git a/get-started-with-it4innovations/obtaining-login-credentials/filtr.txt b/get-started-with-it4innovations/obtaining-login-credentials/filtr.txt
deleted file mode 100644
index c28b99b45bfe41f6e4b291f866e95397ce6bc8ed..0000000000000000000000000000000000000000
--- a/get-started-with-it4innovations/obtaining-login-credentials/filtr.txt
+++ /dev/null
@@ -1,32 +0,0 @@
-{#parent-fieldname-title .documentFirstHeading}
-Obsah
-:
-{.internal-link}
-{.image-inline}
-{.external-link}
-{.anchor-link}
-{.prettyprint .lang-sh .prettyprinted}
-{.tile}
-{.state-published
-.navTreeFolderish .contenttype-folder}
-{.state-published .navTreeItemInPath .navTreeFolderish .contenttype-folder}
-{.state-published .contenttype-document}
-{.state-published .navTreeItemInPath .navTreeFolderish .contenttype-folder}
-{.state-published .navTreeCurrentItem .navTreeCurrentNode .contenttype-document}
-{.state-published .contenttype-document}
-{.state-published .navTreeFolderish .contenttype-folder}
-{#tlspu_cookiepolicy_title}
-.navTreeItemInPath
-.contenttype-document}
-.navTreeItemInPath
-.navTreeCurrentItem .navTreeCurrentNode .contenttype-document}
-.contenttype-document}
-.contenttype-collection}
-<span
-class="portletBottomRight">
-.navTreeCurrentItem
-.navTreeCurrentNode
-.navTreeCurrentItem
-
-
-
diff --git a/get-started-with-it4innovations/obtaining-login-credentials/test.sh b/get-started-with-it4innovations/obtaining-login-credentials/test.sh
deleted file mode 100755
index 437e448ef777547bd88eb9e22122ebc274820596..0000000000000000000000000000000000000000
--- a/get-started-with-it4innovations/obtaining-login-credentials/test.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/bin/sh
-
-cat obtaining-login-credentials.md > test.md
-
-cat filtr.txt |
-while read i;
-do
- echo "$i";
- cat test.md | sed -e 's/'"$i"'//g' | sed -e 's/\\//g' > testTMP.md;
- cat testTMP.md > test.md;
-done
-
-rm testTMP.md
-
-
-
diff --git a/html_md.sh b/html_md.sh
index 3a0f4fc06fc8bd4854dd8808fe25812f6183e43a..5c80c21ad50dd5bafb0f1b5feeb2cf1ef1892516 100755
--- a/html_md.sh
+++ b/html_md.sh
@@ -1,45 +1,86 @@
#!/bin/sh
-### .html -> .md, filtering ###
-# parameters -d ... delete all .md files
-# files: html_md.sh, filter.txt
-# run in .
-### version 1.0
+#wget --mirror --convert-links --adjust-extension --page-requisites --no-parent https://docs.it4i.cz
+
if [ "$1" = "-d" ]; then
# delete all .md files
- rm -rf info;
+ if [ "$2" = "-html" ]; then
+ # delete all .html files
+ find . -name "*.ht*" |
+ while read i;
+ do
+ rm "$i";
+ echo "$i deleted";
+ done
+ fi
+ if [ "$2" = "-md" ]; then
+ # delete all .md files
+ find . -name "*.md" |
+ while read i;
+ do
+ rm "$i";
+ echo "$i deleted";
+ done
+ fi
+else
+ # delete all .md files
find . -name "*.md" |
while read i;
do
rm "$i";
-
echo "$i deleted";
done
-else
- mkdir info
+
+ # create folder info
+ mkdir info;
+
+ find . -name "*.png" |
+ while read i;
+ do
+ echo "$i" >> ./info/list_png.txt;
+ done
+
+ find . -name "*.jpg" |
+ while read i;
+ do
+ echo "$i" >> ./info/list_jpg.txt;
+ done
+
+
+ # html -> md
find . -name "*.ht*" |
while read i;
do
- # converted .html to .md
- pandoc -f html -t markdown+pipe_tables-grid_tables "$i" -o "${i%.*}TMP.md";
+ # filtering html
echo "$i";
+ echo "\t\tfiltering html files...";
+
+ HEAD=$(cat "$i" | grep -n -m1 '<h1' |cut -f1 -d: | tr --delete '\n')
+ END=$(cat "$i" | grep -n -m1 '<!-- <div tal:content=' |cut -f1 -d: | tr --delete '\n')
+ LAST=$(cat "$i" | wc -l | tr --delete '\n')
+ DOWN=$((LAST-END+2))
+
+ cat "$i" | sed '1,'"$((HEAD-1))"'d' | sed -n -e :a -e '1,'"$DOWN"'!{P;N;D;};N;ba' > "${i%.*}TMP.html"
+
+ # converted .html to .md
echo "\t\t.html -> .md"
+ pandoc -f html -t markdown+pipe_tables-grid_tables "${i%.*}TMP.html" -o "${i%.*}.md";
+ rm "${i%.*}TMP.html";
+
# folder info, file strukture, list of all files and his addres into folders
- echo "${i%.*}" >> ./info/strukture;
- # remove html tags, empty lines, first 21 lines and last 59 lines
- cat "${i%.*}TMP.md" | sed -e 's/<[^>]*>//g' | sed '/^$/d' | sed '1,21d' | sed -n -e :a -e '1,58!{P;N;D;};N;ba'> "${i%.*}.md";
- echo "\t\tfiltering...";
+ echo "${i%.*}" >> ./info/files_md.txt;
+
# text filtering of html, css, ..
+ echo "\t\tfiltering text..."
cat filter.txt |
while read y;
do
# search and delete according with filter
- cat "${i%.*}.md" | sed -e 's/'"$y"'//g' | sed -e 's/\\//g' > "${i%.*}TMP.md";
+ cat "${i%.*}.md" | sed -e 's/'"$y"'//g' | sed -e 's/\\//g' | sed -e 's/: //g' | sed -e 's/<\/div>//g' | sed '/^<div/d' | sed '/^$/d' > "${i%.*}TMP.md";
cat "${i%.*}TMP.md" > "${i%.*}.md";
done
-
# delete temporary files
rm "${i%.*}TMP.md";
done
diff --git a/index.html b/index.html
deleted file mode 100755
index 646ed9c336c321b4b518c79bd0beaf2f58c08494..0000000000000000000000000000000000000000
--- a/index.html
+++ /dev/null
@@ -1,15 +0,0 @@
-<HTML>
-<!-- Created by HTTrack Website Copier/3.48-21 [XR&CO'2014] -->
-
-<!-- Mirrored from docs.it4i.cz/ by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:15:42 GMT -->
-<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8" /><!-- /Added by HTTrack -->
-<HEAD>
-<META HTTP-EQUIV="Content-Type" CONTENT="text/html;charset=UTF-8"><META HTTP-EQUIV="Refresh" CONTENT="0; URL=get-started-with-it4innovations.html"><TITLE>Page has moved</TITLE>
-</HEAD>
-<BODY>
-<A HREF="get-started-with-it4innovations.html"><h3>Click here...</h3></A>
-</BODY>
-<!-- Created by HTTrack Website Copier/3.48-21 [XR&CO'2014] -->
-
-<!-- Mirrored from docs.it4i.cz/ by HTTrack Website Copier/3.x [XR&CO'2014], Wed, 13 Jul 2016 18:15:42 GMT -->
-</HTML>
diff --git a/info/files_md.txt b/info/files_md.txt
new file mode 100644
index 0000000000000000000000000000000000000000..85d02eef7edf1eb302d89bc3d9483274690e7766
--- /dev/null
+++ b/info/files_md.txt
@@ -0,0 +1,552 @@
+./docs.it4i.cz/whats-new
+./docs.it4i.cz/salomon
+./docs.it4i.cz/whats-new/downtimes_history
+./docs.it4i.cz/whats-new/news-feed.1
+./docs.it4i.cz/whats-new/news-feed/salomon-pbs-changes
+./docs.it4i.cz/whats-new/news-feed/new-method-to-execute-parallel-matlab-jobs
+./docs.it4i.cz/whats-new/news-feed/new-versions-of-allinea-forge-and-performance-version
+./docs.it4i.cz/whats-new/news-feed/new-bioinformatic-tools-installed-fastqc-0-11-3-gatk-3-5-java-1-7-0_79-picard-2-1-0-samtools-1-3-foss-2015g-snpeff-4-1_g-trimmomatic-0-35-java-1-7.0_79
+./docs.it4i.cz/whats-new/news-feed/new-modules-for-parallel-programming-in-modern-fortran-course
+./docs.it4i.cz/whats-new/news-feed/allinea-forge-5-1-installed-on-anselm
+./docs.it4i.cz/whats-new/news-feed/intel-vtune-is-working
+./docs.it4i.cz/whats-new/news-feed/vampir-installed
+./docs.it4i.cz/whats-new/news-feed/issue-with-intel-mpi-4-1-1-on-salomon
+./docs.it4i.cz/whats-new/news-feed/added-basic-documentation-for-intel-advisor-and-intel-inspector
+./docs.it4i.cz/whats-new/news-feed/ansys-17-0-installed
+./docs.it4i.cz/whats-new/news-feed/allinea-forge-documentation-updated
+./docs.it4i.cz/whats-new/news-feed/intel-vtune-amplifier-support-for-xeon-phi-on-salomon
+./docs.it4i.cz/whats-new/news-feed/anselm-downtime-has-been-extended-to-feb-26th
+./docs.it4i.cz/whats-new/news-feed/octave-updated-to-4-0-1-on-anselm
+./docs.it4i.cz/whats-new/news-feed/allinea-tools-updated-to-6-0.6
+./docs.it4i.cz/whats-new/news-feed/mono-4-2-2-and-mpi-net-1-2-on-salomon
+./docs.it4i.cz/whats-new/news-feed/allinea-forge-6.0
+./docs.it4i.cz/whats-new/news-feed/cuda-7-5-is-now-installed-on-anselm
+./docs.it4i.cz/whats-new/news-feed/intel-parallel-studio-2016-update-3
+./docs.it4i.cz/whats-new/news-feed/matlab-2015b
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/vnc
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.1
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.1
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/accessing-the-clusters
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface
+./docs.it4i.cz/get-started-with-it4innovations/changelog
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters
+./docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq
+./docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials
+./docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials
+./docs.it4i.cz/get-started-with-it4innovations/applying-for-resources
+./docs.it4i.cz/get-started-with-it4innovations/introduction
+./docs.it4i.cz/salomon/hardware-overview-1.1
+./docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority
+./docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy
+./docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution
+./docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction
+./docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing
+./docs.it4i.cz/salomon/storage
+./docs.it4i.cz/salomon/compute-nodes
+./docs.it4i.cz/salomon/resource-allocation-and-job-execution
+./docs.it4i.cz/salomon/network-1
+./docs.it4i.cz/salomon/prace
+./docs.it4i.cz/salomon/network-1/IB single-plane topology - Accelerated nodes.pdf/view
+./docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB single-plane topology - ICEX Mcell.pdf/view
+./docs.it4i.cz/salomon/network-1/ib-single-plane-topology/schematic-representation-of-the-salomon-cluster-ib-single-plain-topology-hypercube-dimension-0
+./docs.it4i.cz/salomon/network-1/ib-single-plane-topology
+./docs.it4i.cz/salomon/network-1/network
+./docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube
+./docs.it4i.cz/salomon/accessing-the-cluster/vpn-access
+./docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc
+./docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access
+./docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections
+./docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface
+./docs.it4i.cz/salomon/software/debuggers/summary
+./docs.it4i.cz/salomon/software/debuggers/valgrind
+./docs.it4i.cz/salomon/software/debuggers/total-view
+./docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports
+./docs.it4i.cz/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56
+./docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier
+./docs.it4i.cz/salomon/software/debuggers/score-p
+./docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/image_view_fullscreen
+./docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/view
+./docs.it4i.cz/salomon/software/debuggers/aislinn
+./docs.it4i.cz/salomon/software/debuggers/vampir
+./docs.it4i.cz/salomon/software/mpi-1
+./docs.it4i.cz/salomon/software/numerical-languages/r
+./docs.it4i.cz/salomon/software/numerical-languages/octave
+./docs.it4i.cz/salomon/software/numerical-languages/matlab
+./docs.it4i.cz/salomon/software/numerical-languages/introduction
+./docs.it4i.cz/salomon/software/mpi-1/mpi
+./docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python
+./docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI
+./docs.it4i.cz/salomon/software/intel-suite
+./docs.it4i.cz/salomon/software/operating-system
+./docs.it4i.cz/salomon/software/numerical-languages.1
+./docs.it4i.cz/salomon/software/java
+./docs.it4i.cz/salomon/software/chemistry/nwchem
+./docs.it4i.cz/salomon/software/chemistry/phono3py-input
+./docs.it4i.cz/salomon/software/chemistry/phono3py-input/KPOINTS/view
+./docs.it4i.cz/salomon/software/chemistry/phono3py-input/POTCAR/view
+./docs.it4i.cz/salomon/software/chemistry/phono3py-input/gofree-cond1.sh/view
+./docs.it4i.cz/salomon/software/chemistry/phono3py-input/INCAR/view
+./docs.it4i.cz/salomon/software/chemistry/phono3py-input/prepare.sh/view
+./docs.it4i.cz/salomon/software/chemistry/phono3py-input/submit.sh/view
+./docs.it4i.cz/salomon/software/chemistry/phono3py-input/poscar-si/view
+./docs.it4i.cz/salomon/software/chemistry/phono3py-input/run.sh/view
+./docs.it4i.cz/salomon/software/chemistry/molpro
+./docs.it4i.cz/salomon/software/chemistry/phono3py
+./docs.it4i.cz/salomon/software/chemistry
+./docs.it4i.cz/salomon/software/compilers
+./docs.it4i.cz/salomon/software/ansys
+./docs.it4i.cz/salomon/software/intel-suite/intel-inspector
+./docs.it4i.cz/salomon/software/intel-suite/intel-compilers
+./docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector
+./docs.it4i.cz/salomon/software/intel-suite/intel-tbb
+./docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction
+./docs.it4i.cz/salomon/software/intel-suite/intel-debugger
+./docs.it4i.cz/salomon/software/intel-suite/intel-mkl
+./docs.it4i.cz/salomon/software/intel-suite/intel-advisor
+./docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives
+./docs.it4i.cz/salomon/software/comsol
+./docs.it4i.cz/salomon/software/comsol/comsol-multiphysics
+./docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions
+./docs.it4i.cz/salomon/software/isv_licenses
+./docs.it4i.cz/salomon/software/ansys/ls-dyna-pbs-file/view
+./docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view
+./docs.it4i.cz/salomon/software/ansys/ansys-cfx-pbs-file/view
+./docs.it4i.cz/salomon/software/ansys/licensing
+./docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/view
+./docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view
+./docs.it4i.cz/salomon/software/ansys/ansys-fluent
+./docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl
+./docs.it4i.cz/salomon/software/ansys/setting-license-preferences
+./docs.it4i.cz/salomon/software/ansys/workbench
+./docs.it4i.cz/salomon/software/ansys/ansys-cfx
+./docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl
+./docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna
+./docs.it4i.cz/salomon/software/debuggers.1
+./docs.it4i.cz/salomon/software/intel-xeon-phi
+./docs.it4i.cz/salomon/accessing-the-cluster
+./docs.it4i.cz/salomon/storage/storage
+./docs.it4i.cz/salomon/storage/cesnet-data-storage
+./docs.it4i.cz/salomon/list_of_modules
+./docs.it4i.cz/salomon/index
+./docs.it4i.cz/salomon/introduction
+./docs.it4i.cz/salomon/hardware-overview-1/hardware-overview
+./docs.it4i.cz/salomon/software
+./docs.it4i.cz/salomon/environment-and-modules
+./docs.it4i.cz/sitemap
+./docs.it4i.cz/heartbleed-bug
+./docs.it4i.cz/vpn-connection-fail-in-win-8.1
+./docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority
+./docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy
+./docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution
+./docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction
+./docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing
+./docs.it4i.cz/anselm-cluster-documentation/remote-visualization
+./docs.it4i.cz/anselm-cluster-documentation/storage
+./docs.it4i.cz/anselm-cluster-documentation/compute-nodes
+./docs.it4i.cz/anselm-cluster-documentation/software.1
+./docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution
+./docs.it4i.cz/anselm-cluster-documentation/hardware-overview
+./docs.it4i.cz/anselm-cluster-documentation/storage-1/storage
+./docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage
+./docs.it4i.cz/anselm-cluster-documentation/prace
+./docs.it4i.cz/anselm-cluster-documentation/network
+./docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access
+./docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc
+./docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access
+./docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections
+./docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1
+./docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries
+./docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary
+./docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind
+./docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view
+./docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports
+./docs.it4i.cz/anselm-cluster-documentation/software/debuggers/mympiprog_32p_2014-10-15_16-56
+./docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier
+./docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p
+./docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt
+./docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube
+./docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi
+./docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor
+./docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca
+./docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir
+./docs.it4i.cz/anselm-cluster-documentation/software/mpi-1
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diff --git a/info/strukture b/info/strukture
deleted file mode 100644
index ab66eab09f07f6490bdbfe96358a69cca60d6865..0000000000000000000000000000000000000000
--- a/info/strukture
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@@ -1,258 +0,0 @@
-./whats-new
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-
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-
-
-/* - ++resource++it4i.portal.common/base.css - */
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-/*
- *
- * base.css
- * IT4I Portal-wide base CSS library
- *
- */
-
-body {
- /* background if any */
- background: url('../../background.png');
- min-height: 100%;
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-}
-
-/* wow effect */
-a {
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-div#portal-columns {
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-/* official colours */
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-}
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-div#portal-columns a:hover {
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-ul#portal-globalnav {
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-ul#portal-globalnav li a:after {
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-/* portal footer */
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- text-align: right;
-}
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-#portal-footer {
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-/*
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-*/
-
-/* Vim sunburst theme by David Leibovic */
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-pre .pun, code .pun { color: #fff; } /* punctuation - white */
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-
-/*
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-
-}
-
-
-/* - ploneCustom.css - */
-@media all {
-/* https://docs.it4i.cz/portal_css/ploneCustom.css?original=1 */
-/* */
-/* */
-/* */
-/* */
-/* */
-/* */
-
-}
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-/* - custom.css - */
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-body {
- font-size: 110%;
-}
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-h1 {
- color: #000;
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-h2, h3 {
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- margin-bottom: 0.6em;
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-#portal-header {
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-#portal-column-content {
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- border-collapse: collapse;
-}
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-#big-picture-of-cluster td {
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-#big-picture-of-cluster {
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diff --git a/salomon.md b/salomon.md
deleted file mode 100644
index 4c3f6205be50e8962fcc96712d1d7bff9d2dabfc..0000000000000000000000000000000000000000
--- a/salomon.md
+++ /dev/null
@@ -1,32 +0,0 @@
-cores, at least 128GB RAM. Nodes are interconnected by 7D Enhanced
-hypercube Infiniband network and equipped with Intel Xeon E5-2680v3
-processors. The Salomon cluster consists of 576 nodes without
-accelerators and 432 nodes equipped with Intel Xeon Phi MIC
-accelerators. Read more in [Hardware
-Overview](salomon/hardware-overview-1/hardware-overview.html).
-The cluster runs CentOS Linux [
-class="WYSIWYG_LINK">](http//www.bull.com/bullx-logiciels/systeme-exploitation.html)
-class="internal-link">operating system, which is compatible with
-the RedHat [
-class="WYSIWYG_LINK">Linux
-family.](http//upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
-**Water-cooled Compute Nodes With MIC Accelerator**
-[](salomon/salomon_1.jpg)
-
-**Tape Library T950B**
-
-
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](sitemap.html)
- - [What's New](whats-new.html)
-
- - [Get Started with
- IT4Innovations](get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](salomon.html)
diff --git a/salomon/accessing-the-cluster/vpn-access.md b/salomon/accessing-the-cluster/vpn-access.md
deleted file mode 100644
index 9b4db7eadf810cb3e90a0fb08dcf1fb105e6cb01..0000000000000000000000000000000000000000
--- a/salomon/accessing-the-cluster/vpn-access.md
+++ /dev/null
@@ -1,104 +0,0 @@
-
-Accessing IT4Innovations internal resources via VPN
----------------------------------------------------
-For using resources and licenses which are located at IT4Innovations
-local network, it is necessary to VPN connect to this network.
-We use Cisco AnyConnect Secure Mobility Client, which is supported on
-the following operating systems
-- Windows XP
-- Windows Vista
-- Windows 7
-- Windows 8
-- Linux
-- MacOS
-It is impossible to connect to VPN from other operating systems.
-VPN client installation
-------------------------------------
-You can install VPN client from web interface after successful login
-with LDAP credentials on address
-[](../vpn_web_login.png)
-According to the Java settings after login, the client either
-automatically installs, or downloads installation file for your
-operating system. It is necessary to allow start of installation tool
-for automatic installation.
-[](../vpn_web_login_2.png)
-[](../vpn_web_install_2.png)[](../vpn_web_install_3.png)
-After successful installation, VPN connection will be established and
-you can use available resources from IT4I network.
-[](../vpn_web_install_4.png)
-If your Java setting doesn't allow automatic installation, you can
-download installation file and install VPN client manually.
-[](../vpn_web_download.png)
-After you click on the link, download of installation file will start.
-[](../vpn_web_download_2.png)
-After successful download of installation file, you have to execute this
-tool with administrator's rights and install VPN client manually.
-Working with VPN client
------------------------
-You can use graphical user interface or command line interface to run
-VPN client on all supported operating systems. We suggest using GUI.
-
-Before the first login to VPN, you have to fill
-URLÂ **https//vpn.it4i.cz/user** into the text field.
-[](../vpn_contacting_https_cluster.png)
-After you click on the Connect button, you must fill your login
-credentials.
-[](../vpn_contacting_https.png)
-After a successful login, the client will minimize to the system tray.
-If everything works, you can see a lock in the Cisco tray icon.
-[](../../anselm-cluster-documentation/anyconnect%20icon.jpg)
-If you right-click on this icon, you will see a context menu in which
-you can control the VPN connection.
-[](../../anselm-cluster-documentation/anyconnect-contextmenu.jpg)
-When you connect to the VPN for the first time, the client downloads the
-profile and creates a new item "IT4I cluster" in the connection list.
-For subsequent connections, it is not necessary to re-enter the URL
-address, but just select the corresponding item.
-[](../vpn_contacting.png)
-Then AnyConnect automatically proceeds like in the case of first logon.
-[](../vpn_login.png)
-After a successful logon, you can see a green circle with a tick mark on
-the lock icon.
-[](../vpn_successfull_connection.png)
-For disconnecting, right-click on the AnyConnect client icon in the
-system tray and select **VPN Disconnect**.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](shell-and-data-access.html)
-
- - [Shell access and data
- transfer](shell-and-data-access.html)
-
- - [Graphical User
- Interface](../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html)
diff --git a/salomon/cn_m_cell/@@images/ced0a5ef-b233-4f4f-9391-092abeb378d3.jpg b/salomon/cn_m_cell/@@images/ced0a5ef-b233-4f4f-9391-092abeb378d3.jpg
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index 3784f17a062231fc16caf668db88f8a556852a91..0000000000000000000000000000000000000000
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diff --git a/salomon/cn_mic-1/@@images/b4318449-6c9a-4acf-b53c-3c7ad0998655.jpg b/salomon/cn_mic-1/@@images/b4318449-6c9a-4acf-b53c-3c7ad0998655.jpg
deleted file mode 100755
index c4adf3414d1a0903aa1dcf11ebea5c2d917941f6..0000000000000000000000000000000000000000
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diff --git a/salomon/cn_mic/@@images/08b13efa-248a-4ece-949b-f66c165cecad.jpg b/salomon/cn_mic/@@images/08b13efa-248a-4ece-949b-f66c165cecad.jpg
deleted file mode 100755
index ed40318b854318493771ae71f6629ebef2eb911f..0000000000000000000000000000000000000000
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diff --git a/salomon/compute-nodes.md b/salomon/compute-nodes.md
deleted file mode 100644
index 9181ee7f651a317f2d847da485a87140f85fc612..0000000000000000000000000000000000000000
--- a/salomon/compute-nodes.md
+++ /dev/null
@@ -1,158 +0,0 @@
--------------------
-Salomon is cluster of x86-64 Intel based nodes. The cluster contains two
-types of compute nodes of the same processor type and memory size.
-Compute nodes with MIC accelerator**** contains two Intel Xeon Phi 7120P
-accelerators.
-[More about schematic representation of the Salomon cluster compute
-nodes IB
-topology](network-1/ib-single-plane-topology.html).
-### **Compute Nodes Without Accelerator**
-- codename "grafton"
-- 576Â nodes
--
- 13Â 824 cores in total
-
--
- two Intel Xeon E5-2680v3, 12-core, 2.5GHz processors per node
-
--
- 128 GB of physical memory per node
-
-[](cn_m_cell.jpg)
-### **Compute Nodes With MIC Accelerator**
-- codename "perrin"
-- 432Â nodes
--
- 10Â 368Â cores in total
-
--
- two Intel Xeon E5-2680v3, 12-core, 2.5GHz processors per node
-
--
- 128 GB of physical memory per node
-
--
- MIC accelerator 2x Intel Xeon Phi 7120P per node, 61-cores, 16GB per
- accelerator
-
-[](cn_mic_1.jpg)
-[](https//www.sgi.com/products/servers/rackable/1u_intel.html#v3 "(source Silicon Graphics International Corp.)")[{.image-inline
-width="87" height="122"}](cn_mic_2.jpg)
-### UV 2000
-- codename "UV2000"
-- 1 node
--
- 112 cores in total
-
--
- 14x Intel Xeon E5-4627v2, 8-core, 3.3GHz processors, in 14 NUMA
- nodes
-
--
- 3328 GB of physical memory per node
-
--
- 1x NVIDIA GM200 (GeForce GTX TITAN X), 12GB RAM
-
-
-### Compute Nodes Summary********
-Node type
-Count
-Memory
-Cores
-Nodes without accelerator
-576
-128GB
-24 @ 2.5Ghz
-Nodes with MIC accelerator
-432
-128GB
-32GB
-24 @ 2.5Ghz
-61 @ 1.238GHz
-UV2000 SMP node
-1
-3328GB
-112 @ 3.3GHz
-Processor Architecture
-----------------------
-Salomon is equipped with Intel Xeon processors Intel Xeon E5-2680v3.
-Processors support Advanced Vector Extensions 2.0 (AVX2) 256-bit
-instruction set.
-### Intel Xeon E5-2680v3 Processor
-- 12-core
-- speed 2.5 GHz, up toÂ
- style="text-align start; float none; ">3.3 GHz using Turbo
- Boost Technology
-- peak performance 19.2 Gflop/s per
- core
-- caches
-
- - Intel® Smart
- Cache 30
- MB
-
-- memory bandwidth at the level of the processor
- style="text-align start; float none; ">68 GB/s
-### MIC Accelerator Intel Xeon Phi 7120PÂ Processor
-- 61-core
-- speed 1.238
- GHz, up toÂ
- style="text-align start; float none; ">1.333 GHz using
- Turbo Boost Technology
-- peak performance 18.4 Gflop/s per
- core
-- caches
-
- - L2 30.5
- MB
-
-- memory bandwidth at the level of the processor
- style="text-align start; float none; ">352 GB/s
-Â
-Memory Architecture
--------------------
-Memory is equally distributed across all CPUs and cores for optimal
-performance. Memory is composed of memory modules of the same size and
-evenly distributed across all memory controllers and memory channels.
-### Compute Node Without Accelerator
-- 2 sockets
-- Memory Controllers are integrated into processors.
-
- - 8Â DDR4 DIMMS per node
- - 4Â DDR4 DIMMS per CPU
- - 1Â DDR4 DIMMS per channel
-
-- Populated memory 8x 16GB DDR4 DIMM 2133MHz
-### Compute Node With MIC Accelerator
-2 sockets
-Memory Controllers are integrated into processors.
-- 8Â DDR4 DIMMS per node
-- 4Â DDR4 DIMMS per CPU
-- 1Â DDR4 DIMMS per channel
-Populated memory 8x 16GB DDR4 DIMM 2133MHz
-MIC Accelerator Intel Xeon Phi 7120P Processor
-- 2 sockets
-- Memory Controllers are are connected via an
- Interprocessor Network (IPN) ring.
-
- - 16 GDDR5 DIMMS per node
- - 8Â GDDR5 DIMMS per CPU
- - 2Â GDDR5 DIMMS per channel
-
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
diff --git a/salomon/copy_of_vpn_web_install_3.png/@@images/9c34e8ad-64b1-4e1d-af3a-13c7a18fbca4.png b/salomon/copy_of_vpn_web_install_3.png/@@images/9c34e8ad-64b1-4e1d-af3a-13c7a18fbca4.png
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diff --git a/salomon/index.md b/salomon/index.md
deleted file mode 100644
index 842dd5041a046ffc03b3da6c23ead2315563ef3f..0000000000000000000000000000000000000000
--- a/salomon/index.md
+++ /dev/null
@@ -1,32 +0,0 @@
-cores, at least 128GB RAM. Nodes are interconnected by 7D Enhanced
-hypercube Infiniband network and equipped with Intel Xeon E5-2680v3
-processors. The Salomon cluster consists of 576 nodes without
-accelerators and 432 nodes equipped with Intel Xeon Phi MIC
-accelerators. Read more in [Hardware
-Overview](hardware-overview-1/hardware-overview.html).
-The cluster runs CentOS Linux [
-class="WYSIWYG_LINK">](http//www.bull.com/bullx-logiciels/systeme-exploitation.html)
-class="internal-link">operating system, which is compatible with
-the RedHat [
-class="WYSIWYG_LINK">Linux
-family.](http//upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
-**Water-cooled Compute Nodes With MIC Accelerator**
-[](salomon_1.jpg)
-
-**Tape Library T950B**
-
-
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
diff --git a/salomon/introduction.md b/salomon/introduction.md
deleted file mode 100644
index 842dd5041a046ffc03b3da6c23ead2315563ef3f..0000000000000000000000000000000000000000
--- a/salomon/introduction.md
+++ /dev/null
@@ -1,32 +0,0 @@
-cores, at least 128GB RAM. Nodes are interconnected by 7D Enhanced
-hypercube Infiniband network and equipped with Intel Xeon E5-2680v3
-processors. The Salomon cluster consists of 576 nodes without
-accelerators and 432 nodes equipped with Intel Xeon Phi MIC
-accelerators. Read more in [Hardware
-Overview](hardware-overview-1/hardware-overview.html).
-The cluster runs CentOS Linux [
-class="WYSIWYG_LINK">](http//www.bull.com/bullx-logiciels/systeme-exploitation.html)
-class="internal-link">operating system, which is compatible with
-the RedHat [
-class="WYSIWYG_LINK">Linux
-family.](http//upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
-**Water-cooled Compute Nodes With MIC Accelerator**
-[](salomon_1.jpg)
-
-**Tape Library T950B**
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-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
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- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
diff --git a/salomon/list_of_modules.md b/salomon/list_of_modules.md
deleted file mode 100644
index 2033a84389d6a886189291727a45bbcd0b7ccd93..0000000000000000000000000000000000000000
--- a/salomon/list_of_modules.md
+++ /dev/null
@@ -1,1664 +0,0 @@
-----------
-- [base](#base)
-- [bio](#bio)
-- [cae](#cae)
-- [chem](#chem)
-- [compiler](#compiler)
-- [data](#data)
-- [debugger](#debugger)
-- [devel](#devel)
-- [geo](#geo)
-- [lang](#lang)
-- [lib](#lib)
-- [math](#math)
-- [mpi](#mpi)
-- [numlib](#numlib)
-- [perf](#perf)
-- [phys](#phys)
-- [system](#system)
-- [toolchain](#toolchain)
-- [tools](#tools)
-- [vis](#vis)
-[base](#categories "Go to list of categories..."){.tooltip}
------------------------------------------------------------
-Module
-Description
-Available versions
-EasyBuild
-http//hpcugent.github.com/easybuild/
-EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.
-2.1.1
-2.2.0
-2.3.0
-Python
-http//python.org/
-Python is a programming language that lets you work more quickly and integrate your systems more effectively.
-3.4.3-intel-2015b
-[bio](#categories "Go to list of categories..."){.tooltip}
-----------------------------------------------------------
-Module
-Description
-Available versions
-Amber
-http//ambermd.org
-A set of molecular mechanical force fields for the simulation of biomolecules
-14
-BCFtools
-http//www.htslib.org/
-Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
-1.3-foss-2015g
-BWA
-http//bio-bwa.sourceforge.net/
-Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
-0.7.5a-foss-2015g
-FastQC
-http//www.bioinformatics.babraham.ac.uk/projects/fastqc/
-FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.
-0.11.3
-GATK
-http//www.broadinstitute.org/gatk/
-The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
-2.6-5-Java-1.7.0_79
-3.5-Java-1.7.0_79
-GROMACS
-http//www.gromacs.org
-GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
-4.6.7-foss-2015g-hybrid-single-PLUMED
-5.0.4-foss-2015e-hybrid-single-PLUMED
-5.0.4-foss-2015g-hybrid-single
-5.0.4-foss-2015g-hybrid-single-PLUMED
-5.0.4-ictce-7.3.5-hybrid-single
-HTSlib
-http//www.htslib.org/
-A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
-1.3-foss-2015g
-PLUMED
-http//www.plumed-code.org
-PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
-2.1.3-foss-2015g
-RELION
-http//www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
-RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).
-1.3-intel-2015b
-SAMtools
-http//www.htslib.org/
-SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
-1.3-foss-2015g
-SnpEff
-http//snpeff.sourceforge.net/
-Genetic variant annotation and effect prediction toolbox.
-4.1_G
-Trimmomatic
-http//www.usadellab.org/cms/?page=trimmomatic
-Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
-0.35-Java-1.7.0_79
-almost
-http//www-almost.ch.cam.ac.uk/site
-all atom molecular simulation toolkit - is a fast and flexible molecular modeling environment that provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations.
-2.1.0-foss-2015b
-2.1.0-foss-2015g
-2.1.0-intel-2015b
-picard
-http//sourceforge.net/projects/picard
-A set of tools (in Java) for working with next generation sequencing data in the BAM format.
-1.119
-2.1.0
-[cae](#categories "Go to list of categories..."){.tooltip}
-----------------------------------------------------------
-Module
-Description
-Available versions
-ANSYS
-16.1
-17.0
-Adams
-2013.2
-COMSOL
-51-COM
-51-EDU
-Digimat
-5.0.1-COM
-5.0.1-EDU
-FreeFem++
-http//www.freefem.org
-FreeFem++ is a partial differential equation solver. It has its own language. freefem scripts can solve multiphysics non linear systems in 2D and 3D. Problems involving PDE (2d, 3d) from several branches of physics such as fluid-structure interactions require interpolations of data on several meshes and their manipulation within one program. FreeFem++ includes a fast 2^d-tree-based interpolation algorithm and a language for the manipulation of data on multiple meshes (as a follow up of bamg (now a part of FreeFem++ ). FreeFem++ is written in C++ and the FreeFem++ language is a C++ idiom. It runs on Macs, Windows, Unix machines. FreeFem++ replaces the older freefem and freefem+.
-3.45-intel-2015b
-HyperWorks
-13.0
-Marc
-2013.1.0
-OpenFOAM
-http//www.openfoam.com/
-OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.
-2.2.2-intel-2015b
-2.3.0-intel-2015b
-3.0.0-intel-2016.01
-[chem](#categories "Go to list of categories..."){.tooltip}
------------------------------------------------------------
-Module
-Description
-Available versions
-ABINIT
-http//www.abinit.org/
-Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.
-7.10.1-foss-2015b
-7.10.1-intel-2015b
-CP2K
-http//www.cp2k.org/
-CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.
-2.6.0-intel-2015b
-LAMMPS
-http//lammps.sandia.gov
-LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. Has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.
-28Jun14-intel-2015b
-Libint
-https//sourceforge.net/p/libint/
-Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.
-1.1.4-foss-2015b
-1.1.4-gompi-2015b
-1.1.4-intel-2015b
-Molpro
-2010.1-patch-57-intel2015b
-NAMD
-http//www.ks.uiuc.edu/Research/namd/
-NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
-2.9-mpi
-NWChem
-http//www.nwchem-sw.org
-NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity.
-6.3.revision2-2013-10-17-Python-2.7.8
-6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.8
-S4MPLE
-http//infochim.u-strasbg.fr/spip.php?rubrique152
-S4MPLE (Sampler For Multiple Protein-Ligand Entities) is a flexible molecular modeling tool, supporting empirical force field-driven conformational sampling and geometry optimization heuristics using a hybrid genetic algorithm (GA).
-1.0.0
-libctl
-http//ab-initio.mit.edu/libctl
-libctl is a free Guile-based library implementing flexible control files for scientific simulations.
-3.2.2-intel-2015b
-libxc
-http//www.tddft.org/programs/octopus/wiki/index.php/Libxc
-Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.
-2.2.0-foss-2015b
-2.2.0-gompi-2015b
-2.2.1-intel-2015b
-[compiler](#categories "Go to list of categories..."){.tooltip}
----------------------------------------------------------------
-Module
-Description
-Available versions
-BerkeleyUPC
-http//upc.lbl.gov
-The goal of the Berkeley UPC compiler group is to develop a portable, high performance implementation of UPC for large-scale multiprocessors, PC clusters, and clusters of shared memory multiprocessors.
-2.16.2-gompi-2015b
-Clang
-http//clang.llvm.org/
-C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.
-3.7.0-GNU-5.1.0-2.25
-GCC
-http//gcc.gnu.org/
-The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
-4.4.7-system
-4.7.4
-4.8.3
-4.9.2-binutils-2.25
-4.9.3
-4.9.3-2.25
-4.9.3-binutils-2.25
-5.1.0-binutils-2.25
-5.2.0
-5.3.0-2.25
-5.3.0-2.26
-5.3.0-binutils-2.25
-5.3.1-snapshot-20160419-2.25
-GCCcore
-http//gcc.gnu.org/
-The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
-4.9.3
-5.3.0
-5.3.1-snapshot-20160419
-LLVM
-http//llvm.org/
-The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator.
-3.7.1-foss-2015g
-OpenCoarrays
-http//www.opencoarrays.org/
-A transport layer for coarray Fortran compilers.
-1.4.0-GCC-5.3.0-2.25
-1.4.0-GCC-5.3.1-snapshot-20160419-2.25
-PGI
-15.7
-icc
-http//software.intel.com/en-us/intel-compilers/
-C and C++ compiler from Intel
-2013.5.192
-2013.5.192-GCC-4.8.3
-2015.3.187
-2015.3.187-GNU-4.9.3-2.25
-2015.3.187-GNU-5.1.0-2.25
-2016.0.109-GCC-4.9.3
-2016.1.150
-2016.1.150-GCC-4.9.3
-2016.1.150-GCC-4.9.3-2.25
-2016.3.210-GCC-5.3.0-2.26
-ifort
-http//software.intel.com/en-us/intel-compilers/
-Fortran compiler from Intel
-2013.5.192
-2013.5.192-GCC-4.8.3
-2015.3.187
-2015.3.187-GNU-4.9.3-2.25
-2015.3.187-GNU-5.1.0-2.25
-2016.0.109-GCC-4.9.3
-2016.1.150
-2016.1.150-GCC-4.9.3
-2016.1.150-GCC-4.9.3-2.25
-2016.3.210-GCC-5.3.0-2.26
-[data](#categories "Go to list of categories..."){.tooltip}
------------------------------------------------------------
-Module
-Description
-Available versions
-GDAL
-http//www.gdal.org/
-GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.
-1.9.2-foss-2015g
-2.0.1-foss-2015b
-2.1.0-GNU-5.1.0-2.25
-2.1.0-GNU-5.1.0-2.25-intel-2015b
-2.1.0-foss-2015g
-2.1.0-intel-2015b
-HDF5
-http//www.hdfgroup.org/HDF5/
-HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.
-1.10.0-patch1-intel-2016.01-mic
-1.8.13-foss-2015g
-1.8.13-intel-2015b
-1.8.13-intel-2015b-no-mpi
-1.8.13-intel-2016.01
-1.8.14-ictce-7.3.5-serial
-1.8.15-patch1-foss-2015b
-1.8.16-foss-2015g
-1.8.16-intel-2015b
-1.8.16-intel-2015b-threadsafe
-h5py
-http//www.h5py.org/
-HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.
-2.4.0-ictce-7.3.5-Python-2.7.9-serial
-netCDF
-http//www.unidata.ucar.edu/software/netcdf/
-NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
-4.3.2-foss-2015g
-4.3.2-intel-2015b
-4.3.2-intel-2016.01
-4.3.3.1-foss-2015b
-netCDF-Fortran
-http//www.unidata.ucar.edu/software/netcdf/
-NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
-4.4.0-intel-2016.01
-[debugger](#categories "Go to list of categories..."){.tooltip}
----------------------------------------------------------------
-Module
-Description
-Available versions
-DDT
-4.2
-5.0.1
-Forge
-http//www.allinea.com/products/develop-allinea-forge
-Allinea Forge is the complete toolsuite for software development - with everything needed to debug, profile, optimize, edit and build C, C++ and FORTRAN applications on Linux for high performance - from single threads through to complex parallel HPC codes with MPI, OpenMP, threads or CUDA.
-5.1-43967
-6.0.5
-6.0.6
-PerformanceReports
-http//www.allinea.com/products/allinea-performance-reports
-Allinea Performance Reports are the most effective way to characterize and understand the performance of HPC application runs. One single-page HTML report elegantly answers a range of vital questions for any HPC site. - Is this application well-optimized for the system and the processors it is running on? - Does it benefit from running at this scale? - Are there I/O, networking or threading bottlenecks affecting performance? - Which hardware, software or configuration changes can we make to improve performance further. - How much energy did this application use?
-5.1-43967
-6.0.6
-TotalView
-8.15.4-6-linux-x86-64
-Valgrind
-http//valgrind.org/downloads/
-Valgrind Debugging and profiling tools
-3.11.0-foss-2015b
-3.11.0-intel-2015b
-aislinn
-20160105-Python-2.7.9-gompi-2015e
-[devel](#categories "Go to list of categories..."){.tooltip}
-------------------------------------------------------------
-Module
-Description
-Available versions
-Autoconf
-http//www.gnu.org/software/autoconf/
-Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.
-2.69
-2.69-GCC-4.9.3-2.25
-2.69-GNU-4.9.3-2.25
-2.69-GNU-5.1.0-2.25
-2.69-foss-2015g
-2.69-intel-2015b
-2.69-intel-2016.01
-Automake
-http//www.gnu.org/software/automake/automake.html
-Automake GNU Standards-compliant Makefile generator
-1.15
-1.15-GCC-4.9.3-2.25
-1.15-GNU-4.9.3-2.25
-1.15-GNU-5.1.0-2.25
-1.15-foss-2015g
-1.15-intel-2015b
-1.15-intel-2016.01
-Autotools
-http//autotools.io
-This bundle collect the standard GNU build tools Autoconf, Automake and libtool
-20150215
-20150215-GCC-4.9.3-2.25
-20150215-GNU-4.9.3-2.25
-20150215-GNU-5.1.0-2.25
-20150215-intel-2015b
-20150215-intel-2016.01
-Boost
-http//www.boost.org/
-Boost provides free peer-reviewed portable C++ source libraries.
-1.58.0-Python-2.7.9
-1.58.0-foss-2015g-Python-2.7.9
-1.58.0-gompi-2015e-Python-2.7.9
-1.58.0-ictce-7.3.5-Python-2.7.9
-1.58.0-intel-2015b-Python-2.7.9
-1.58.0-intel-2016.01-Python-2.7.9
-1.59.0-intel-2015b-Python-2.7.11
-1.59.0-intel-2016.01
-1.60.0-foss-2015g-Python-2.7.9
-CMake
-http//www.cmake.org
-CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
-3.0.0-foss-2015g
-3.0.0-ictce-7.3.5
-3.0.0-intel-2015b
-3.0.0-intel-2016.01
-3.3.1-GCC-5.3.0-2.25
-3.3.1-GCC-5.3.1-snapshot-20160419-2.25
-3.3.1-GNU-4.9.3-2.25
-3.3.1-GNU-5.1.0-2.25
-3.3.1-foss-2015g
-3.3.1-intel-2016.01
-3.3.2-GNU-4.9.3-2.25
-3.3.2-intel-2016.01
-3.4.1-GCCcore-4.9.3
-3.4.1-foss-2015b
-3.4.1-intel-2015b
-3.5.2
-Doxygen
-http//www.doxygen.org
-Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.
-1.8.10-foss-2015b
-1.8.11
-1.8.7-foss-2015g
-1.8.7-intel-2015b
-1.8.7-intel-2016.01
-JUnit
-http//sourceforge.net/projects/junit
-A programmer-oriented testing framework for Java.
-4.11-Java-1.7.0_79
-M4
-http//www.gnu.org/software/m4/m4.html
-GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.
-1.4.16-foss-2015g
-1.4.16-intel-2015b
-1.4.17
-1.4.17-GCC-4.9.3-2.25
-1.4.17-GCC-4.9.3-binutils-2.25
-1.4.17-GCC-5.1.0-binutils-2.25
-1.4.17-GCCcore-4.9.3
-1.4.17-GCCcore-5.3.0
-1.4.17-GCCcore-5.3.1-snapshot-20160419
-1.4.17-GNU-4.9.3-2.25
-1.4.17-GNU-5.1.0-2.25
-1.4.17-foss-2015b
-1.4.17-foss-2015g
-1.4.17-intel-2015b
-1.4.17-intel-2016.01
-Maven
-http//maven.apache.org/index.html
-Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information.
-3.3.9
-PCRE
-http//www.pcre.org/
-The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
-8.36-foss-2015g
-8.36-intel-2015b
-8.36-intel-2016.01
-8.37
-8.37-foss-2015g
-Qt
-http//qt-project.org/
-Qt is a comprehensive cross-platform C++ application framework.
-4.8.6-foss-2015g
-SCons
-http//www.scons.org/
-SCons is a software construction tool.
-2.3.6-Python-2.7.9
-2.3.6-foss-2015g-Python-2.7.9
-SQLite
-http//www.sqlite.org/
-SQLite SQL Database Engine in a C Library
-3.10.1-foss-2015g
-3.8.10.2-GCC-4.9.3-2.25
-3.8.10.2-GNU-4.9.3-2.25
-3.8.8.1
-3.8.8.1-GNU-5.1.0-2.25
-3.8.8.1-foss-2015b
-3.8.8.1-foss-2015g
-3.8.8.1-gompi-2015e
-3.8.8.1-ictce-7.3.5
-3.8.8.1-intel-2015b
-3.8.8.1-intel-2016.01
-3.9.2-foss-2015g
-3.9.2-intel-2015b
-3.9.2-intel-2016.01
-SWIG
-http//www.swig.org/
-SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
-2.0.12-Python-2.7.9
-2.0.12-intel-2015b-Python-2.7.9
-3.0.7-Python-2.7.9
-Spark
-http//spark.apache.org
-Spark is Hadoop MapReduce done in memory
-1.5.2
-ant
-http//ant.apache.org/
-Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.
-1.9.3-Java-1.7.0_79
-fontsproto
-http//www.freedesktop.org/wiki/Software/xlibs
-X11 font extension wire protocol
-2.1.3-foss-2015g
-glproto
-http//www.freedesktop.org/wiki/Software/xlibs
-X protocol and ancillary headers
-1.4.16-foss-2015g
-gperf
-http//www.gnu.org/software/gperf/
-GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.
-3.0.4-foss-2015g
-guile
-http//www.gnu.org/software/guile
-Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system.
-1.8.8-foss-2015b
-1.8.8-foss-2015g
-1.8.8-intel-2015b
-libSM
-http//www.freedesktop.org/wiki/Software/xlibs
-X11 Session Management library, which allows for applications to both manage sessions, and make use of session managers to save and restore their state for later use.
-1.2.2
-1.2.2-foss-2015g
-1.2.2-intel-2015b
-make
-http//www.gnu.org/software/make/make.html
-make-3.82 GNU version of make utility
-3.82
-3.82-intel-2015b
-makedepend
-http//www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html
-The makedepend package contains a C-preprocessor like utility to determine build-time dependencies.
-1.0.4-foss-2015g
-ncurses
-http//www.gnu.org/software/ncurses/
-The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.
-5.9
-5.9-GCC-5.3.0-2.25
-5.9-GCC-5.3.1-snapshot-20160419-2.25
-5.9-GNU-4.9.3-2.25
-5.9-GNU-5.1.0-2.25
-5.9-foss-2015b
-5.9-foss-2015g
-5.9-gompi-2015e
-5.9-ictce-5.5.0
-5.9-ictce-7.3.5
-5.9-intel-2015b
-5.9-intel-2016.01
-6.0
-6.0-GCCcore-4.9.3
-6.0-foss-2015b
-6.0-foss-2015g
-6.0-intel-2016.01
-pkg-config
-http//www.freedesktop.org/wiki/Software/pkg-config/
-pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries).
-0.27.1
-0.27.1-foss-2015b
-0.27.1-foss-2015g
-0.27.1-intel-2015b
-python-meep
-https//code.launchpad.net/python-meep
-Python wrapper for the Meep FDTD solver.
-1.4.2-intel-2015b-Python-2.7.9-Meep-1.3
-renderproto
-http//www.freedesktop.org/wiki/Software/xlibs
-Xrender protocol and ancillary headers
-0.11-intel-2015b
-xbitmaps
-http//www.freedesktop.org/wiki/Software/xlibs
-provides bitmaps for x
-1.1.1
-1.1.1-foss-2015g
-1.1.1-intel-2015b
-xcb-proto
-http//xcb.freedesktop.org/
-The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.
-1.10-Python-2.7.8
-1.11-foss-2015g-Python-2.7.9
-1.11-intel-2015b-Python-2.7.9
-xextproto
-http//www.freedesktop.org/wiki/Software/xlibs
-XExtProto protocol headers.
-7.3.0
-7.3.0-foss-2015g
-7.3.0-intel-2015b
-xineramaproto
-http//www.freedesktop.org/wiki/Software/xlibs
-X protocol and ancillary headers for xinerama
-1.2.1-intel-2015b
-xorg-macros
-http//cgit.freedesktop.org/xorg/util/macros
-X.org macros utilities.
-1.17-foss-2015g
-xproto
-http//www.freedesktop.org/wiki/Software/xlibs
-X protocol and ancillary headers
-7.0.26
-7.0.26-foss-2015g
-7.0.26-intel-2015b
-xtrans
-http//www.freedesktop.org/wiki/Software/xlibs
-xtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet.
-1.3.4-intel-2015b
-1.3.5
-1.3.5-foss-2015g
-1.3.5-intel-2015b
-[geo](#categories "Go to list of categories..."){.tooltip}
-----------------------------------------------------------
-Module
-Description
-Available versions
-DCW
-http//gmt.soest.hawaii.edu/projects/gmt
-country polygons for GMT
-1.1.2
-GMT
-http//gmt.soest.hawaii.edu/
-GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools.
-5.2.1-foss-2015g
-PROJ_4
-http//proj.osgeo.org
-PROJ.4 - Cartographic Projections Library originally written by Gerald Evenden then of the USGS.
-4.9.2-foss-2015g
-[lang](#categories "Go to list of categories..."){.tooltip}
------------------------------------------------------------
-Module
-Description
-Available versions
-Bison
-http//www.gnu.org/software/bison
-Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.
-2.5-intel-2015b
-2.7-GNU-5.1.0-2.25
-2.7-foss-2015b
-2.7-foss-2015g
-2.7-intel-2015b
-3.0.2
-3.0.2-foss-2015g
-3.0.2-intel-2015b
-3.0.2-intel-2016.01
-3.0.4
-3.0.4-GCC-4.9.3-binutils-2.25
-3.0.4-GCC-5.1.0-binutils-2.25
-3.0.4-GCCcore-4.9.3
-3.0.4-GCCcore-5.3.0
-3.0.4-GCCcore-5.3.1-snapshot-20160419
-3.0.4-foss-2015b
-3.0.4-intel-2016.01
-Java
-http//java.com/
-Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
-1.7.0_79
-1.8.0_51
-1.8.0_72
-Mono
-http//www.mono-project.com
-Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.
-3.12.1
-3.12.1-GCC-4.4.7-system
-4.0.3.20-GNU-5.1.0-2.25
-4.2.2.10-intel-2016.01
-NASM
-http//www.nasm.us/
-NASM General-purpose x86 assembler
-2.11.05
-2.11.05-foss-2015b
-2.11.05-foss-2015g
-2.11.05-intel-2015b
-2.11.06-intel-2015b
-2.11.08-foss-2015b
-OpenCL-builder
-https//software.intel.com/en-us/intel-opencl
-OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software. This is builder (formerly runtime) package.
-2015
-OpenCL-runtime
-https//software.intel.com/en-us/intel-opencl
-OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software.
-15.1
-Perl
-http//www.perl.org/
-Larry Wall's Practical Extraction and Report Language
-5.16.3-intel-2015b
-5.20.2-GNU-4.9.3-2.25-bare
-5.20.2-bare
-Python
-http//python.org/
-Python is a programming language that lets you work more quickly and integrate your systems more effectively.
-2.7.10-GCC-4.9.3-2.25-bare
-2.7.10-GNU-4.9.3-2.25-bare
-2.7.11-intel-2015b
-2.7.8-intel-2015b
-2.7.8-intel-2016.01
-2.7.9-GNU-5.1.0-2.25
-2.7.9-foss-2015b
-2.7.9-foss-2015g
-2.7.9-gompi-2015e
-2.7.9-ictce-7.3.5
-2.7.9-intel-2015b
-2.7.9-intel-2016.01
-3.5.1-intel-2016.01
-R
-http//www.r-project.org/
-R is a free software environment for statistical computing and graphics.
-3.1.1-intel-2015b
-3.2.3-foss-2015b
-3.2.3-intel-2016.01
-Racket
-http//racket-lang.org
-Racket is a full-spectrum programming language. It goes beyond Lisp and Scheme with dialects that support objects, types, laziness, and more.
-6.1.1-GNU-5.1.0-2.25
-Ruby
-https//www.ruby-lang.org
-Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.
-2.1.5-intel-2015b
-SIP
-http//www.riverbankcomputing.com/software/sip/
-SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.
-4.16.4-foss-2015g-Python-2.7.9
-4.17-foss-2015g-Python-2.7.9
-SnuCL
-http//snucl.snu.ac.kr
-An OpenCL Framework for Heterogeneous Clusters
-1.3.3-gompi-2015e
-Tcl
-http//www.tcl.tk/
-Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.
-8.5.12-intel-2015b
-8.6.3
-8.6.3-GNU-5.1.0-2.25
-8.6.3-foss-2015b
-8.6.3-foss-2015g
-8.6.3-gompi-2015e
-8.6.3-ictce-7.3.5
-8.6.3-intel-2015b
-8.6.3-intel-2016.01
-8.6.4
-8.6.4-GCC-4.9.3-2.25
-8.6.4-GNU-4.9.3-2.25
-8.6.4-foss-2015b
-8.6.4-foss-2015g
-8.6.4-intel-2015b
-8.6.4-intel-2016.01
-byacc
-http//invisible-island.net/byacc/byacc.html
-Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular compiler.
-20120526-foss-2015b
-20120526-foss-2015g
-20120526-intel-2015b
-flex
-http//flex.sourceforge.net/
-Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.
-2.5.35-intel-2015b
-2.5.37-intel-2015b
-2.5.38-GCC-4.8.3
-2.5.39
-2.5.39-GCC-4.9.3-binutils-2.25
-2.5.39-GCC-5.1.0-binutils-2.25
-2.5.39-GCCcore-4.9.3
-2.5.39-GCCcore-5.3.0
-2.5.39-GCCcore-5.3.1-snapshot-20160419
-2.5.39-foss-2015b
-2.5.39-foss-2015g
-2.5.39-intel-2015b
-2.5.39-intel-2016.01
-2.6.0
-2.6.0-GCCcore-5.3.0
-libgdiplus
-https//github.com/mono/libgdiplus
-An Open Source implementation of the GDI+ API.
-3.12-GCC-4.4.7-system
-3.12-GNU-5.1.0-2.25
-3.12-intel-2016.01
-[lib](#categories "Go to list of categories..."){.tooltip}
-----------------------------------------------------------
-Module
-Description
-Available versions
-FOX
-http//fox-toolkit.org
-FOX is a C++ based Toolkit for developing Graphical User Interfaces easily and effectively. It offers a wide, and growing, collection of Controls, and provides state of the art facilities such as drag and drop, selection, as well as OpenGL widgets for 3D graphical manipulation.
-1.6.51-foss-2015g
-LibTIFF
-http//www.remotesensing.org/libtiff/
-tiff Library and tools for reading and writing TIFF data files
-4.0.3-intel-2015b
-OpenCoarrays
-http//www.opencoarrays.org
-OpenCoarrays is an open-source software project for developing, porting and tuning transport layers that support coarray Fortran compilers.
-1.0.0-GNU-5.1.0-2.25
-1.0.1-GNU-5.1.0-2.25
-PROJ
-http//trac.osgeo.org/proj/
-Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
-4.8.0-foss-2015b
-QCA
-http//delta.affinix.com/qca/
-QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers
-2.1.0-foss-2015g
-QGIS
-http//www.qgis.org
-A Free and Open Source Geographic Information System
-2.12.3-foss-2015g
-Qwt
-http//qwt.sourceforge.net/index.html
-The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Beside a framework for 2D plots it provides scales, sliders, dials, compasses, thermometers, wheels and knobs to control or display values, arrays, or ranges of type double.
-6.1.2-foss-2015g
-SpatiaLite
-https//www.gaia-gis.it/fossil/libspatialite/index
-SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities.
-4.3.0a-foss-2015g
-libMesh
-http//libmesh.github.io/
-The libMesh library provides a framework for the numerical simulation of partial differential equations using arbitrary unstructured discretizations on serial and parallel platforms. A major goal of the library is to provide support for adaptive mesh refinement (AMR) computations in parallel while allowing a research scientist to focus on the physics they are modeling.
-0.9.5-intel-2016.01
-libdrm
-http//dri.freedesktop.org
-Direct Rendering Manager runtime library.
-2.4.27-foss-2015g
-libffi
-http//sourceware.org/libffi/
-The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.
-3.0.13-foss-2015b
-3.0.13-foss-2015g
-3.0.13-intel-2015b
-3.1-GNU-5.1.0-2.25
-3.1-foss-2015b
-3.1-intel-2015b
-3.1-intel-2016.01
-libfontenc
-http//www.freedesktop.org/wiki/Software/xlibs/
-X11 font encoding library
-1.1.3-foss-2015g
-libjpeg-turbo
-http//sourceforge.net/libjpeg-turbo/
-libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.
-1.3.1-foss-2015b
-1.3.1-intel-2015b
-1.4.0
-1.4.0-foss-2015g
-1.4.0-intel-2015b
-1.4.1-foss-2015b
-libmatheval
-http//www.gnu.org/software/libmatheval/
-GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.
-1.1.8-foss-2015b
-1.1.8-foss-2015g
-1.1.8-intel-2015b
-libpng
-http//www.libpng.org/pub/png/libpng.html
-libpng is the official PNG reference library
-1.6.12
-1.6.12-foss-2015b
-1.6.12-foss-2015g
-1.6.12-intel-2015b
-1.6.12-intel-2016.01
-1.6.17-foss-2015b
-1.6.21-foss-2015b
-1.6.21-foss-2015g
-1.6.9-ictce-5.5.0
-1.6.9-intel-2015b
-libpthread-stubs
-http//xcb.freedesktop.org/
-The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.
-0.3
-0.3-foss-2015g
-0.3-intel-2015b
-libreadline
-http//cnswww.cns.cwru.edu/php/chet/readline/rltop.html
-The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
-6.2-ictce-5.5.0
-6.2-intel-2015b
-6.3
-6.3-GCCcore-4.9.3
-6.3-GNU-4.9.3-2.25
-6.3-GNU-5.1.0-2.25
-6.3-foss-2015b
-6.3-foss-2015g
-6.3-gompi-2015e
-6.3-ictce-7.3.5
-6.3-intel-2015b
-6.3-intel-2016.01
-libtool
-http//www.gnu.org/software/libtool
-GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.
-2.4.2-foss-2015b
-2.4.2-foss-2015g
-2.4.2-intel-2015b
-2.4.6
-2.4.6-GCC-4.9.3-2.25
-2.4.6-GNU-4.9.3-2.25
-2.4.6-GNU-5.1.0-2.25
-2.4.6-foss-2015g
-2.4.6-intel-2015b
-2.4.6-intel-2016.01
-libunistring
-http//www.gnu.org/software/libunistring/
-This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.
-0.9.3-foss-2015b
-0.9.3-foss-2015g
-0.9.3-intel-2015b
-libxcb
-http//xcb.freedesktop.org/
-The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.
-1.10-Python-2.7.8
-1.11-foss-2015g-Python-2.7.9
-1.11-intel-2015b-Python-2.7.9
-libxml2
-http//xmlsoft.org/
-Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).
-2.9.2-GCC-4.9.3-2.25
-2.9.2-GNU-4.9.3-2.25
-2.9.2-GNU-5.1.0-2.25
-2.9.2-foss-2015b
-2.9.2-foss-2015g
-2.9.2-foss-2015g-Python-2.7.9
-2.9.2-gompi-2015e
-2.9.2-ictce-7.3.5
-2.9.2-intel-2015b
-spatialindex
-https//libspatialindex.github.io/index.html
-The purpose of this library is to provide * An extensible framework that will support robust spatial indexing methods. * Support for sophisticated spatial queries. Range, point location, nearest neighbor and k-nearest neighbor as well as parametric queries (defined by spatial constraints) should be easy to deploy and run. * Easy to use interfaces for inserting, deleting and updating information.
-1.8.5-foss-2015g
-tbb
-http//software.intel.com/en-us/articles/intel-tbb/
-Intel Threading Building Blocks 4.0 (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms.
-4.3.5.187
-4.4.2.152
-zlib
-http//www.zlib.net/
-zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.
-1.2.7-foss-2015b
-1.2.7-ictce-5.5.0
-1.2.7-intel-2015b
-1.2.8
-1.2.8-GCC-4.9.3-2.25
-1.2.8-GCC-4.9.3-binutils-2.25
-1.2.8-GCC-5.1.0-binutils-2.25
-1.2.8-GCCcore-4.9.3
-1.2.8-GCCcore-5.3.0
-1.2.8-GCCcore-5.3.1-snapshot-20160419
-1.2.8-GNU-4.9.3-2.25
-1.2.8-GNU-5.1.0-2.25
-1.2.8-GNU-5.1.0-2.25-intel-2015b
-1.2.8-foss-2015b
-1.2.8-foss-2015g
-1.2.8-gompi-2015e
-1.2.8-ictce-7.3.5
-1.2.8-intel-2015b
-1.2.8-intel-2016.01
-[math](#categories "Go to list of categories..."){.tooltip}
------------------------------------------------------------
-Module
-Description
-Available versions
-FIAT
-https//bitbucket.org/fenics-project/fiat
-The FInite element Automatic Tabulator FIAT supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.
-1.6.0-intel-2015b-Python-2.7.11
-1.6.0-intel-2015b-Python-2.7.9
-1.6.0-intel-2016.01-Python-2.7.9
-GEOS
-http//trac.osgeo.org/geos
-GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)
-3.5.0-foss-2015g
-GMP
-http//gmplib.org/
-GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
-5.0.5-foss-2015b
-5.0.5-foss-2015g
-5.0.5-intel-2015b
-6.0.0a-GNU-4.9.3-2.25
-6.0.0a-GNU-5.1.0-2.25
-6.0.0a-foss-2015b
-6.1.0-GCC-4.9.3-2.25
-6.1.0-intel-2015b
-6.1.0-intel-2016.01
-Harminv
-http//ab-initio.mit.edu/wiki/index.php/Harminv
-Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.
-1.4-intel-2015b
-ISL
-http//isl.gforge.inria.fr/
-isl is a library for manipulating sets and relations of integer points bounded by linear constraints.
-0.14-GNU-5.1.0-2.25
-0.15-GCC-4.9.3-2.25
-0.15-GNU-4.9.3-2.25
-METIS
-http//glaros.dtc.umn.edu/gkhome/metis/metis/overview
-METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.
-5.1.0-intel-2015b
-5.1.0-intel-2016.01
-5.1.0-intel-2016.01-32bitIDX
-Octave
-http//www.gnu.org/software/octave/
-GNU Octave is a high-level interpreted language, primarily intended for numerical computations.
-3.8.2-foss-2015g
-3.8.2-intel-2015b
-4.0.0-foss-2015g
-ParMETIS
-http//glaros.dtc.umn.edu/gkhome/metis/parmetis/overview
-ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.
-4.0.3-intel-2015b
-4.0.3-intel-2016.01
-SCOTCH
-http//gforge.inria.fr/projects/scotch/
-Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
-5.1.12b_esmumps-foss-2015b
-6.0.0_esmumps-intel-2015b
-6.0.3-intel-2015b
-6.0.3-intel-2016.01
-6.0.4-intel-2015b
-6.0.4-intel-2016.01
-ScientificPython
-https//sourcesup.cru.fr/projects/scientific-py/
-ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization.
-2.9.4-intel-2015b-Python-2.7.11
-2.9.4-intel-2015b-Python-2.7.9
-2.9.4-intel-2016.01-Python-2.7.9
-numpy
-http//www.numpy.org
-NumPy is the fundamental package for scientific computing with Python. It contains among other things a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.
-1.8.2-intel-2015b-Python-2.7.11
-1.8.2-intel-2015b-Python-2.7.9
-1.8.2-intel-2016.01-Python-2.7.9
-1.9.1-intel-2015b-Python-2.7.9
-sympy
-http//sympy.org/
-SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries.
-0.7.6-intel-2015b-Python-2.7.9
-0.7.6-intel-2016.01-Python-2.7.9
-0.7.6.1-intel-2015b-Python-2.7.11
-[mpi](#categories "Go to list of categories..."){.tooltip}
-----------------------------------------------------------
-Module
-Description
-Available versions
-MPICH
-http//www.mpich.org/
-MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).
-3.2-GCC-5.3.0-2.25
-3.2-GCC-5.3.1-snapshot-20160419-2.25
-MPI_NET
-http//www.osl.iu.edu/research/mpi.net/
-MPI.NET is a high-performance, easy-to-use implementation of the Message Passing Interface (MPI) for Microsoft's .NET environment
-1.2.0-gompi-2015e
-1.2.0-intel-2016.01
-MVAPICH2
-http//mvapich.cse.ohio-state.edu/overview/mvapich2/
-This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH.
-2.1-GCC-4.4.7-system
-2.1-GNU-5.1.0-2.25
-2.1-iccifort-2015.3.187-GNU-5.1.0-2.25
-OpenMPI
-http//www.open-mpi.org/
-The Open MPI Project is an open source MPI-2 implementation.
-1.10.1-GNU-4.9.3-2.25
-1.10.2-GCC-5.3.0-2.26
-1.8.6-GCC-4.4.7-system
-1.8.6-GNU-5.1.0-2.25
-1.8.6-iccifort-2015.3.187-GNU-5.1.0-2.25
-1.8.8-GNU-4.9.3-2.25
-1.8.8-GNU-5.1.0-2.25
-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25
-impi
-http//software.intel.com/en-us/intel-mpi-library/
-The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.
-2017-BETA.ENG
-4.1.1.036-iccifort-2013.5.192
-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3
-5.0.3.048
-5.0.3.048-iccifort-2015.3.187
-5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25
-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3
-5.1.2.150-iccifort-2016.1.150
-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3
-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25
-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26
-mpt
-2.12
-[numlib](#categories "Go to list of categories..."){.tooltip}
--------------------------------------------------------------
-Module
-Description
-Available versions
-FFTW
-http//www.fftw.org
-FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
-2.1.5-gompi-2015b
-2.1.5-iimpi-7.3.5-GNU-5.1.0-2.25
-3.3.4-gompi-2015b
-3.3.4-gompi-2015e
-3.3.4-gompi-2015g
-3.3.4-gompi-2016.04
-3.3.4-intel-2015b
-3.3.4-intel-2016.01
-GSL
-http//www.gnu.org/software/gsl/
-The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.
-1.16-intel-2015b
-Hypre
-https//computation.llnl.gov/casc/linear_solvers/sls_hypre.html
-Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.
-2.10.0b-intel-2015b
-2.10.0b-intel-2016.01
-2.10.1-intel-2015b
-LAPACKE
-http//www.netlib.org/lapack/lapacke.html
-LAPACKE C Interface to LAPACK header files and library
-3.5.0-LAPACK-3.5.0
-OpenBLAS
-http//xianyi.github.com/OpenBLAS/
-OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0
-0.2.14-GNU-5.1.0-2.25-LAPACK-3.5.0
-0.2.14-LAPACK-3.5.0
-0.2.14-gompi-2015e-LAPACK-3.5.0
-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0
-PETSc
-http//www.mcs.anl.gov/petsc
-PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.
-3.6.1-intel-2015b-Python-2.7.9
-3.6.1-intel-2016.01-Python-2.7.9
-3.6.3-intel-2015b-Python-2.7.11
-ScaLAPACK
-http//www.netlib.org/scalapack/
-The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
-2.0.2-OpenBLAS-0.2.14-LAPACK-3.5.0
-2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0
-2.0.2-gompi-2015e-OpenBLAS-0.2.14-LAPACK-3.5.0
-2.0.2-gompi-2015g-OpenBLAS-0.2.14-LAPACK-3.5.0
-2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0
-SuiteSparse
-http//www.cise.ufl.edu/research/sparse/SuiteSparse/
-SuiteSparse is a collection of libraries manipulate sparse matrices.
-4.4.3-intel-2015b-ParMETIS-4.0.3
-4.4.3-intel-2016.01-ParMETIS-4.0.3
-4.4.6-intel-2015b-ParMETIS-4.0.3
-arpack-ng
-http//forge.scilab.org/index.php/p/arpack-ng/
-ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
-3.3.0-intel-2015b
-imkl
-http//software.intel.com/en-us/intel-mkl/
-Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.
-11.0.5.192-iimpi-5.5.0
-11.0.5.192-iimpi-5.5.0-GCC-4.8.3
-11.2.3.187
-11.2.3.187-iimpi-7.3.5
-11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25
-11.2.3.187-iompi-2015.03
-11.3.0.109-iimpi-2016.00-GCC-4.9.3
-11.3.1.150-iimpi-2016.00-GCC-4.9.3
-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25
-11.3.1.150-iimpi-8.3.5
-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26
-[perf](#categories "Go to list of categories..."){.tooltip}
------------------------------------------------------------
-Module
-Description
-Available versions
-Advisor
-https//software.intel.com/intel-advisor-xe
-Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance “dies” - Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain
-2016_update2
-MAP
-4.2
-5.0.1
-OPARI2
-http//www.score-p.org
-OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface.
-1.1.4-intel-2015b
-OTF2
-http//www.score-p.org
-The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library. It will become the new standard trace format for Scalasca, Vampir, and Tau and is open for other tools.
-1.4-intel-2015b
-PAPI
-http//icl.cs.utk.edu/projects/papi/
-PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack.
-5.4.0-intel-2015b
-PerfReports
-5.0.1
-Vampir
-http//www.vampir.eu
-The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.
-8.5.0
-ipp
-http//software.intel.com/en-us/articles/intel-ipp/
-Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms.
-9.0.1.150
-perfboost
-1.0
-perfcatcher
-1.0
-perfsuite
-1a5.3
-[phys](#categories "Go to list of categories..."){.tooltip}
------------------------------------------------------------
-Module
-Description
-Available versions
-Meep
-http//ab-initio.mit.edu/wiki/index.php/Meep
-Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems.
-1.3-intel-2015b
-phono3py
-http//phonopy.sourceforge.net/phono3py/index.html
-This software calculates phonon-phonon interaction related properties
-0.9.14-ictce-7.3.5-Python-2.7.9
-[system](#categories "Go to list of categories..."){.tooltip}
--------------------------------------------------------------
-Module
-Description
-Available versions
-hwloc
-http//www.open-mpi.org/projects/hwloc/
-The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.
-1.11.0-GNU-4.9.3-2.25
-1.11.0-GNU-5.1.0-2.25
-1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25
-1.11.2-GCC-4.9.3-2.25
-1.11.3-GCC-5.3.0-2.26
-1.5-GCC-4.4.7-system
-libpciaccess
-http//cgit.freedesktop.org/xorg/lib/libpciaccess/
-Generic PCI access library.
-0.13.1-foss-2015g
-[toolchain](#categories "Go to list of categories..."){.tooltip}
-----------------------------------------------------------------
-Module
-Description
-Available versions
-GNU
-http//www.gnu.org/software/
-Compiler-only toolchain with GCC and binutils.
-4.9.3-2.25
-5.1.0-2.25
-5.1.0-2.25-intel-2015b
-PRACE
-http//www.prace-ri.eu/PRACE-Common-Production
-The PRACE Common Production Environment (PCPE) is a set of software tools and libraries that are planned to be available on all PRACE execution sites. The PCPE also defines a set of environment variables that try to make compilation on all sites as homogeneous and simple as possible.
-20150630-intel-2015b
-foss
-(none)
-GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
-2015b
-2015e
-2015g
-2016.04
-gompi
-(none)
-GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
-2015b
-2015e
-2015g
-2016.04
-iccifort
-http//software.intel.com/en-us/intel-cluster-toolkit-compiler/
-Intel C, C++ and Fortran compilers
-2013.5.192
-2013.5.192-GCC-4.8.3
-2015.3.187
-2015.3.187-GNU-4.9.3-2.25
-2015.3.187-GNU-5.1.0-2.25
-2016.0.109-GCC-4.9.3
-2016.1.150
-2016.1.150-GCC-4.9.3
-2016.1.150-GCC-4.9.3-2.25
-2016.3.210-GCC-5.3.0-2.26
-ictce
-http//software.intel.com/en-us/intel-cluster-toolkit-compiler/
-Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.
-5.5.0
-7.3.5
-8.3.5
-iimpi
-http//software.intel.com/en-us/intel-cluster-toolkit-compiler/
-Intel C/C++ and Fortran compilers, alongside Intel MPI.
-2016.00-GCC-4.9.3
-2016.01-GCC-4.9.3
-2016.01-GCC-4.9.3-2.25
-2016.03-GCC-5.3.0-2.26
-5.5.0
-5.5.0-GCC-4.8.3
-7.3.5
-7.3.5-GNU-5.1.0-2.25
-8.3.5
-intel
-http//software.intel.com/en-us/intel-cluster-toolkit-compiler/
-Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.
-2014.06
-2015b
-2015b-intel-2015b
-2016.00
-2016.01
-2016.03-GCC-5.3
-prace
-http//www.prace-ri.eu/PRACE-Common-Production
-**** PRACE Common Production Environment (PCPE) **** Initialisation of the PRACE common production environment. This allows you to assume that the following tools/libraries are available by default in your PATH/environment. * Fortran, C, C++ Compilers * MPI * BLAS, LAPACK, BLACS, ScaLAPACK * FFTW * HDF5, NetCDF The compiler commands on are * mpif90 - Fortran compiler * mpicc - C compiler * mpicxx - C++ compiler For more information on the PCPE please see the documentation at http//www.prace-ri.eu/PRACE-Common-Production For help using this system, please see Local User Guide available at http//prace-ri.eu/Best-Practice-Guide-Anselm-HTML
-20160107-intel-2016.01
-[tools](#categories "Go to list of categories..."){.tooltip}
-------------------------------------------------------------
-Module
-Description
-Available versions
-APR
-http//apr.apache.org/
-Apache Portable Runtime (APR) libraries.
-1.5.2-foss-2015g
-APR-util
-http//apr.apache.org/
-Apache Portable Runtime (APR) util libraries.
-1.5.4-foss-2015g
-Bash
-http//www.gnu.org/software/bash
-Bash is an sh-compatible command language interpreter that executes commands read from the standard input or from a file. Bash also incorporates useful features from the Korn and C shells (ksh and csh).
-4.2-intel-2015b
-EasyBuild
-http//hpcugent.github.com/easybuild/
-EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.
-2.4.0
-2.5.0
-2.7.0
-2.8.0
-HPL
-http//www.netlib.org/benchmark/hpl/
-HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.
-2.1-foss-2015b
-2.1-intel-2015b
-Inspector
-http//software.intel.com/en-us/intel-inspector-xe
-Intel Inspector XE 2013 is an easy to use memory error checker and thread checker for serial and parallel applications
-2016_update1
-JOE
-http//joe-editor.sourceforge.net
-JOE is a full featured terminal-based screen editor which is distributed under the GNU General Public License (GPL)
-4.2
-MATLAB
-2015a-COM
-2015a-EDU
-MIKE
-http//www.mikepoweredbydhi.com
-MIKE Powered by DHI is a part of DHI, the global organisation dedicated to solving challenges in water environments worldwide.
-2014
-2016
-2016-SP2
-Mercurial
-http//mercurial.selenic.com/
-Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface.
-3.5-Python-2.7.9
-3.7.3-foss-2015g-Python-2.7.9
-QEMU
-http//wiki.qemu.org/Main_Page
-QEMU is a generic and open source machine emulator and virtualizer.
-2.1.2-GCC-4.4.7-system
-2.1.2-GCC-4.4.7-system-VDE2
-SDE
-https//software.intel.com/en-us/articles/intel-software-development-emulator
-Intel Software Development Emulator is a pintool that enables the development of applications using instruction set extensions that are not currently implemented in hardware.
-7.41.0
-Serf
-http//serf.apache.org/
-The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library
-1.3.8-foss-2015g
-Subversion
-http//subversion.apache.org/
-Subversion is an open source version control system.
-1.8.16-foss-2015g
-Szip
-http//www.hdfgroup.org/doc_resource/SZIP/
-Szip compression software, providing lossless compression of scientific data
-2.1-foss-2015b
-2.1-foss-2015g
-2.1-ictce-7.3.5
-2.1-intel-2015b
-2.1-intel-2016.01
-VDE2
-http//vde.sourceforge.net
-VDE is an ethernet compliant virtual network that can be spawned over a set of physical computer over the Internet. VDE is part of virtualsquare project.
-2.3.2-GCC-4.4.7-system
-VTune
-http//software.intel.com/en-us/intel-vtune-amplifier-xe
-Intel VTune Amplifier XE 2016 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.
-2016_update1
-VirtualGL
-http//www.virtualgl.org
-VirtualGL is an open source toolkit that gives any Unix or Linux remote display software the ability to run OpenGL applications with full 3D hardware acceleration.
-2.4.1
-Wine
-https//www.winehq.org
-Wine (originally an acronym for "Wine Is Not an Emulator") is a compatibility layer capable of running Windows applications on several POSIX-compliant operating systems, such as Linux, Mac OSX, & BSD.
-1.7.29-GCC-4.4.7-system
-1.7.29-GNU-5.1.0-2.25
-XZ
-http//tukaani.org/xz/
-xz XZ utilities
-5.2.2-intel-2016.01
-binutils
-http//directory.fsf.org/project/binutils/
-binutils GNU binary utilities
-2.25
-2.25-GCC-4.9.3-binutils-2.25
-2.25-GCC-5.1.0-binutils-2.25
-2.25-GCCcore-4.9.3
-2.25-GCCcore-5.3.0
-2.25-GCCcore-5.3.1-snapshot-20160419
-2.25-foss-2015b
-2.26
-2.26-GCCcore-5.3.0
-bzip2
-http//www.bzip.org/
-bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.
-1.0.6
-1.0.6-GCC-4.9.3-2.25
-1.0.6-GNU-4.9.3-2.25
-1.0.6-GNU-5.1.0-2.25
-1.0.6-foss-2015b
-1.0.6-foss-2015g
-1.0.6-gompi-2015e
-1.0.6-ictce-7.3.5
-1.0.6-intel-2015b
-1.0.6-intel-2016.01
-cURL
-http//curl.haxx.se
-libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.
-7.37.1
-7.37.1-foss-2015g
-7.37.1-intel-2015b
-7.37.1-intel-2016.01
-7.45.0-foss-2015b
-expat
-http//expat.sourceforge.net/
-Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags)
-2.1.0
-2.1.0-foss-2015b
-2.1.0-foss-2015g
-2.1.0-intel-2015b
-git
-http//git-scm.com/
-Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.
-2.8.0
-2.8.0-GNU-4.9.3-2.25
-gzip
-http//www.gnu.org/software/gzip/
-gzip (GNU zip) is a popular data compression program as a replacement for compress
-1.6-foss-2015g
-1.6-intel-2015b
-itac
-http//software.intel.com/en-us/intel-trace-analyzer/
-The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays.
-9.1.2.024
-numactl
-http//oss.sgi.com/projects/libnuma/
-The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.
-2.0.10-GNU-4.9.3-2.25
-2.0.10-GNU-5.1.0-2.25
-2.0.10-iccifort-2015.3.187-GNU-4.9.3-2.25
-2.0.11-GCC-4.9.3-2.25
-2.0.11-GCC-5.3.0-2.26
-2.0.9-GCC-4.4.7-system
-parallel
-http//savannah.gnu.org/projects/parallel/
-parallel Build and execute shell commands in parallel
-20150322-GNU-5.1.0-2.25
-tcsh
-http//www.tcsh.org
-Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax.
-6.18.01-intel-2015b
-turbovnc
-http//www.turbovnc.org
-TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide peak performance for 3D and video workloads.
-1.2.3
-util-linux
-http//www.kernel.org/pub/linux/utils/util-linux
-Set of Linux utilities
-2.26.1
-2.26.1-foss-2015g
-[vis](#categories "Go to list of categories..."){.tooltip}
-----------------------------------------------------------
-Module
-Description
-Available versions
-FLTK
-http//www.fltk.org
-FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.
-1.3.2-intel-2015b
-GLib
-http//www.gtk.org/
-GLib is one of the base libraries of the GTK+ project
-2.40.0-foss-2015g
-2.40.0-intel-2015b
-2.40.0-intel-2016.01
-GPI-2
-http//www.gpi-site.com/gpi2/
-GPI-2 is an API for the development of scalable, asynchronous and fault tolerant parallel applications.
-1.1.1-gompi-2015e
-1.1.1-gompi-2015e-MPI
-JasPer
-http//www.ece.uvic.ca/~frodo/jasper/
-The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
-1.900.1-intel-2015b
-Mesa
-http//www.mesa3d.org/
-Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
-11.0.8-foss-2015g-Python-2.7.9
-OSPRay
-http//www.ospray.org
-A Ray Tracing Based Rendering Engine for High-Fidelity Visualization
-0.9.1
-OpenCV
-http//opencv.org/
-OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products.
-2.4.9-intel-2015b
-3.0.0-intel-2015b
-OpenDX
-http//www.opendx.org
-Open source visualization software package based on IBM's Visualization Data Explorer.
-4.4.4-foss-2015g
-ParaView
-http//www.paraview.org
-ParaView is a scientific parallel visualizer.
-4.3-OSPRay
-5.0.0-binary
-PyQt
-http//www.riverbankcomputing.co.uk/software/pyqt
-PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.
-4.11.3-foss-2015g-Python-2.7.9
-4.11.4-foss-2015g-Python-2.7.9
-SUMO
-http//www.sumo.dlr.de/wiki/Main_Page
-Simulation of Urban MObility (SUMO) is an open source, highly portable, microscopic and continuous road traffic simulation package designed to handle large road networks.
-0.25.0-foss-2015g
-0.26.0-foss-2015g
-Tk
-http//www.tcl.tk/
-Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.
-8.5.12-intel-2015b
-8.6.4-GCC-4.9.3-2.25-no-X11
-8.6.4-GNU-4.9.3-2.25-no-X11
-8.6.4-foss-2015b-no-X11
-8.6.4-foss-2015g-no-X11
-8.6.4-intel-2015b-no-X11
-8.6.4-intel-2016.01-no-X11
-8.6.4-no-X11
-VisIt
-https//wci.llnl.gov/simulation/computer-codes/visit
-VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool
-2.10.0
-cairo
-http//cairographics.org
-Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB
-1.12.18-foss-2015b
-ffmpeg
-https//www.ffmpeg.org/
-A complete, cross-platform solution to record, convert and stream audio and video.
-2.4-foss-2015g
-2.4-intel-2015b
-fixesproto
-http//www.freedesktop.org/wiki/Software/xlibs
-X.org FixesProto protocol headers.
-5.0-foss-2015g
-fontconfig
-http//www.freedesktop.org/software/fontconfig
-Fontconfig is a library designed to provide system-wide font configuration, customization and application access.
-2.11.1-foss-2015b
-2.11.1-intel-2015b
-freetype
-http//freetype.org
-FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.
-2.5.3
-2.5.3-foss-2015b
-2.5.3-foss-2015g
-2.5.3-intel-2015b
-gettext
-http//www.gnu.org/software/gettext/
-GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation
-0.19.2
-0.19.2-GNU-5.1.0-2.25
-0.19.2-foss-2015b
-0.19.2-foss-2015g
-0.19.2-intel-2015b
-0.19.2-intel-2016.01
-0.19.6-foss-2015g
-0.19.6-intel-2016.01
-grace
-http//freecode.com/projects/grace
-Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.
-5.1.25-intel-2015b
-inputproto
-http//www.freedesktop.org/wiki/Software/xlibs
-X.org InputProto protocol headers.
-2.3
-2.3-foss-2015g
-2.3-intel-2015b
-kbproto
-http//www.freedesktop.org/wiki/Software/xlibs
-X.org KBProto protocol headers.
-1.0.6
-1.0.6-foss-2015g
-1.0.6-intel-2015b
-libGLU
-ftp//ftp.freedesktop.org/pub/mesa/glu/
-The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.
-9.0.0-foss-2015g
-libICE
-http//www.freedesktop.org/wiki/Software/xlibs
-X Inter-Client Exchange library for freedesktop.org
-1.0.9
-1.0.9-foss-2015g
-1.0.9-intel-2015b
-libX11
-http//www.freedesktop.org/wiki/Software/xlibs
-X11 client-side library
-1.6.2-Python-2.7.8
-1.6.2-foss-2015g-Python-2.7.9
-1.6.2-intel-2015b-Python-2.7.9
-libXau
-http//www.freedesktop.org/wiki/Software/xlibs
-The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display.
-1.0.8
-1.0.8-foss-2015g
-1.0.8-intel-2015b
-libXdamage
-http//www.freedesktop.org/wiki/Software/xlibs
-X Damage extension library
-1.1.4-foss-2015g-Python-2.7.9
-libXdmcp
-http//www.freedesktop.org/wiki/Software/xlibs
-The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is useful for allowing clients to interact with the X Display Manager.
-1.1.2
-1.1.2-foss-2015g
-1.1.2-intel-2015b
-libXext
-http//www.freedesktop.org/wiki/Software/xlibs
-Common X Extensions library
-1.3.2-Python-2.7.8
-1.3.3-foss-2015g
-1.3.3-foss-2015g-Python-2.7.9
-1.3.3-intel-2015b
-libXfixes
-http//www.freedesktop.org/wiki/Software/xlibs
-X Fixes extension library
-5.0.1-foss-2015g
-libXfont
-http//www.freedesktop.org/wiki/Software/xlibs
-X font libary
-1.5.1-foss-2015g-Python-2.7.9
-libXft
-http//www.freedesktop.org/wiki/Software/xlibs
-X11 client-side library
-2.3.2-intel-2015b
-libXinerama
-http//www.freedesktop.org/wiki/Software/xlibs
-Xinerama multiple monitor library
-1.1.3-intel-2015b
-libXrender
-http//www.freedesktop.org/wiki/Software/xlibs
-X11 client-side library
-0.9.8-intel-2015b
-libXt
-http//www.freedesktop.org/wiki/Software/xlibs
-libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).
-1.1.4-foss-2015g-libX11-1.6.2
-1.1.4-intel-2015b-libX11-1.6.2
-1.1.5-foss-2015g
-motif
-http//motif.ics.com/
-Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix.
-2.3.4-foss-2015g-libX11-1.6.2
-2.3.4-intel-2015b-libX11-1.6.2
-p4vasp
-http//www.p4vasp.at
-p4vasp is a visualization suite for the Vienna Ab-initio Simulation Package (VASP). It contains an extensible GUI framework, that can be used to view material structure, density of states, band-structure and more.
-0.3.29-GNU-4.9.3-2.25
-pixman
-http//www.pixman.org/
-Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.
-0.32.6-foss-2015b
-0.32.6-intel-2015b
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
diff --git a/salomon/network-1.md b/salomon/network-1.md
deleted file mode 100644
index d839c0d1543c1b9ad36f4262332d2f6de3e9bede..0000000000000000000000000000000000000000
--- a/salomon/network-1.md
+++ /dev/null
@@ -1,77 +0,0 @@
-hypercube
-[Infiniband](http//en.wikipedia.org/wiki/InfiniBand)
-network and by Gigabit
-[Ethernet](http//en.wikipedia.org/wiki/Ethernet)
-network. Only
-[Infiniband](http//en.wikipedia.org/wiki/InfiniBand)
-network may be used to transfer user data.
-Infiniband Network
-------------------
-All compute and login nodes of Salomon are interconnected by 7D Enhanced
-hypercube
-[Infiniband](http//en.wikipedia.org/wiki/InfiniBand)
-network (56 Gbps). The network topology is a [7D Enhanced
-hypercube](network-1/7d-enhanced-hypercube.html).
-Read more about schematic representation of the Salomon cluster [IB
-single-plain
-topology](network-1/ib-single-plane-topology.html)
-([hypercube
-dimension](network-1/7d-enhanced-hypercube.html)
-0).[](network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf/view.html){.state-missing-value
-.contenttype-file}
-- -
-The compute nodes may be accessed via the Infiniband network using ib0
-network interface, in address range 10.17.0.0 (mask 255.255.224.0). The
-MPI may be used to establish native Infiniband connection among the
-nodes.
-The network provides **2170MB/s** transfer rates via the TCP connection
-(single stream) and up to **3600MB/s** via native Infiniband protocol.
-Â
-Example
--------
-``` {.prettyprint .lang-sh}
-$ qsub -q qexp -l select=4ncpus=16 -N Name0 ./myjob
-$ qstat -n -u username
- Req'd Req'd Elap
-Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
---------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
-15209.isrv5 username qexp Name0 5530 4 96 -- 0100 R 0000
- r4i1n0/0*24+r4i1n1/0*24+r4i1n2/0*24+r4i1n3/0*24
-```
-In this example, we access the node r4i1n0 by Infiniband network via the
-ib0 interface.
-``` {.prettyprint .lang-sh}
-$ ssh 10.17.35.19
-```
-In this example, we get
-information of the Infiniband network.
-``` {.prettyprint .lang-sh}
-$ ifconfig
-....
-inet addr10.17.35.19....
-....
-$ ip addr show ib0
-....
-inet 10.17.35.19....
-....
-```
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
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- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
-
- - [Hardware
- Overview](hardware-overview-1.html)
-
- - [Accessing the
- Cluster](accessing-the-cluster/shell-and-data-access.html)
diff --git a/salomon/network-1/7D_Enhanced_hypercube.png/@@images/03693a91-beec-4d04-bf11-7d89c20420a6.png b/salomon/network-1/7D_Enhanced_hypercube.png/@@images/03693a91-beec-4d04-bf11-7d89c20420a6.png
deleted file mode 100755
index 77add3c6f6f44a97a2a078d4b0c697bb4b75da81..0000000000000000000000000000000000000000
Binary files a/salomon/network-1/7D_Enhanced_hypercube.png/@@images/03693a91-beec-4d04-bf11-7d89c20420a6.png and /dev/null differ
diff --git a/salomon/network-1/7d-enhanced-hypercube.md b/salomon/network-1/7d-enhanced-hypercube.md
deleted file mode 100644
index 4fe58462a764c04af1057493d7caa2090c2eeb2f..0000000000000000000000000000000000000000
--- a/salomon/network-1/7d-enhanced-hypercube.md
+++ /dev/null
@@ -1,44 +0,0 @@
-dimension.](../resource-allocation-and-job-execution/job-submission-and-execution.html)
-Nodes may be selected via the PBS resource attribute ehc_[1-7]d .
- Hypercube dimension node_group_key
- --------------------- -------------------------------------------
- 1D ehc_1d
- 2D ehc_2d
- 3D ehc_3d
- 4D ehc_4d
- 5D ehc_5d
- 6D ehc_6d
- 7D ehc_7d
-[Schematic representation of the Salomon cluster IB single-plain
-topology represents hypercube
-dimension 0](ib-single-plane-topology.html).
-### 7D Enhanced Hypercube {#d-enhanced-hypercube}
-[](7D_Enhanced_hypercube.png)
-Â
- Node type Count Short name Long name Rack
- -------------------------------------- ------- ------------------ -------------------------- -------
- M-Cell compute nodes w/o accelerator 576 cns1 -cns576 r1i0n0 - r4i7n17 1-4
- compute nodes MIC accelerated 432 cns577 - cns1008 r21u01n577 - r37u31n1008 21-38
-### Â IB Topology
-Â [](Salomon_IB_topology.png)
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
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- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
diff --git a/salomon/network-1/Salomon_IB_topology.png/@@images/93b8536b-60de-438d-ac4d-a33a843c4eb2.png b/salomon/network-1/Salomon_IB_topology.png/@@images/93b8536b-60de-438d-ac4d-a33a843c4eb2.png
deleted file mode 100755
index 78e57c5769dee58dca59e5c26543386a87f78b3d..0000000000000000000000000000000000000000
Binary files a/salomon/network-1/Salomon_IB_topology.png/@@images/93b8536b-60de-438d-ac4d-a33a843c4eb2.png and /dev/null differ
diff --git a/salomon/network-1/ib-single-plane-topology.md b/salomon/network-1/ib-single-plane-topology.md
deleted file mode 100644
index 7a5c1e4b7632dd2741128aca85a5ecfeec8960d9..0000000000000000000000000000000000000000
--- a/salomon/network-1/ib-single-plane-topology.md
+++ /dev/null
@@ -1,60 +0,0 @@
-
-
-A complete M-Cell assembly consists of four compute racks. Each rack
-contains 4x physical IRUs - Independent rack units. Using one dual
-socket node per one blade slot leads to 8 logical IRUs. Each rack
-contains 4x2 SGI ICE X IB Premium Blades.
-The SGI ICE X IB Premium Blade provides the first level of
-interconnection via dual 36-port Mellanox FDR InfiniBand ASIC switch
-with connections as follows
-- 9 ports from each switch chip connect to the unified backplane, to
- connect the 18 compute node slots
-- 3 ports on each chip provide connectivity between the chips
-- 24 ports from each switch chip connect to the external bulkhead, for
- a total of 48
-### **IB single-plane topology - ICEX Mcell**
-Each colour in each physical IRU represents one dual-switch ASIC switch.
-[](ib-single-plane-topology/IB%20single-plane%20topology%20-%20ICEX%20Mcell.pdf)
-Â
-### IB single-plane topology - Accelerated nodes
-Each of the 3 inter-connected D racks are equivalent to one half of
-Mcell rack. 18x D rack with MIC accelerated nodes [r21-r38] are
-equivalent to 3 Mcell racks as shown in a diagram [7D Enhanced
-Hypercube](7d-enhanced-hypercube.html).
-As shown in a diagram [IB
-Topology](Salomon_IB_topology.png)
-- Racks 21, 22, 23, 24, 25, 26 are equivalent to one Mcell rack.
-- Racks 27, 28, 29, 30, 31, 32 are equivalent to one Mcell rack.
-- Racks 33, 34, 35, 36, 37, 38 are equivalent to one Mcell rack.
-[](ib-single-plane-topology/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf)
-Â
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-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [List of Available
- Modules](../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
diff --git a/salomon/network-1/ib-single-plane-topology/IB single-plane topology - Accelerated nodes.pdf/view-2.html b/salomon/network-1/ib-single-plane-topology/IB single-plane topology - Accelerated nodes.pdf/view-2.html
deleted file mode 100755
index 965c7dbee5cac2eaccb88d17669968a4734de2e2..0000000000000000000000000000000000000000
--- a/salomon/network-1/ib-single-plane-topology/IB single-plane topology - Accelerated nodes.pdf/view-2.html
+++ /dev/null
@@ -1,775 +0,0 @@
-
-<!DOCTYPE html>
-
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-
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diff --git a/salomon/network-1/ib-single-plane-topology/IB single-plane topology - Accelerated nodes.pdf/view-2.md b/salomon/network-1/ib-single-plane-topology/IB single-plane topology - Accelerated nodes.pdf/view-2.md
deleted file mode 100644
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--- a/salomon/network-1/ib-single-plane-topology/IB single-plane topology - Accelerated nodes.pdf/view-2.md
+++ /dev/null
@@ -1,38 +0,0 @@
-
-IB single-plane topology - Accelerated nodes.pdf
-================================================
- [ IB single-plane
-topology - Accelerated
-nodes.pdf](at_download/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf)
- — PDF document, 84 KB (86980 bytes)
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diff --git a/salomon/network-1/ib-single-plane-topology/IB single-plane topology - Accelerated nodes.pdf/view.md b/salomon/network-1/ib-single-plane-topology/IB single-plane topology - Accelerated nodes.pdf/view.md
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--- a/salomon/network-1/ib-single-plane-topology/IB single-plane topology - Accelerated nodes.pdf/view.md
+++ /dev/null
@@ -1,38 +0,0 @@
-
-IB single-plane topology - Accelerated nodes.pdf
-================================================
- [ IB single-plane
-topology - Accelerated
-nodes.pdf](at_download/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf)
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diff --git a/salomon/network-1/ib-single-plane-topology/IB single-plane topology - ICEX Mcell.pdf/at_download/IB single-plane topology - ICEX Mcell.pdf b/salomon/network-1/ib-single-plane-topology/IB single-plane topology - ICEX Mcell.pdf/at_download/IB single-plane topology - ICEX Mcell.pdf
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diff --git a/salomon/network-1/ib-single-plane-topology/IB single-plane topology - ICEX Mcell.pdf/view.md b/salomon/network-1/ib-single-plane-topology/IB single-plane topology - ICEX Mcell.pdf/view.md
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--- a/salomon/network-1/ib-single-plane-topology/IB single-plane topology - ICEX Mcell.pdf/view.md
+++ /dev/null
@@ -1,38 +0,0 @@
-
-IB single-plane topology - ICEX Mcell.pdf
-=========================================
- [ IB single-plane
-topology - ICEX
-Mcell.pdf](at_download/IB%20single-plane%20topology%20-%20ICEX%20Mcell.pdf)
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-
- - [List of Available
- Modules](../../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../compute-nodes.html)
diff --git a/salomon/resource-allocation-and-job-execution/introduction.md b/salomon/resource-allocation-and-job-execution/introduction.md
deleted file mode 100644
index db8039035f1b4b5fb8bb3c1ea2b20d577fd5a6fe..0000000000000000000000000000000000000000
--- a/salomon/resource-allocation-and-job-execution/introduction.md
+++ /dev/null
@@ -1,69 +0,0 @@
-To run a [job](job-submission-and-execution.html),
-[computational
-resources](resources-allocation-policy.html) for this
-particular job must be allocated. This is done via the PBS Pro job
-workload manager software, which efficiently distributes workloads
-across the supercomputer. Extensive informations about PBS Pro can be
-found in the [official documentation
-here](../../pbspro-documentation.html), especially in
-the [PBS Pro User's
-Guide](../../pbspro-documentation/PBSProUserGuide12.pdf).
-Resources Allocation Policy
----------------------------
-The resources are allocated to the job in a fairshare fashion, subject
-to constraints set by the queue and resources available to the Project.
-[The Fairshare](job-priority.html) at Salomon ensures
-that individual users may consume approximately equal amount of
-resources per week. The resources are accessible via several queues for
-queueing the jobs. The queues provide prioritized and exclusive access
-to the computational resources. Following queues are available to Anselm
-users
-- **qexp**, the Express queue
-- **qprod**, the Production queue****
-- **qlong**, the Long queue
-- **qmpp**, the Massively parallel queue
-- **qfat**, the queue to access SMP UV2000 machine
-- **qfree,** the Free resource utilization queue
-Check the queue status at
-Read more on the [Resource Allocation
-Policy](resources-allocation-policy.html) page.
-Job submission and execution
-----------------------------
-Use the **qsub** command to submit your jobs.
-The qsub submits the job into the queue. The qsub command creates a
-request to the PBS Job manager for allocation of specified resources.Â
-The **smallest allocation unit is entire node, 24 cores**, with
-exception of the qexp queue. The resources will be allocated when
-available, subject to allocation policies and constraints. **After the
-resources are allocated the jobscript or interactive shell is executed
-on first of the allocated nodes.**
-Read more on the [Job submission and
-execution](job-submission-and-execution.html) page.
-HTML commented section #1 (removed Capacity computing section, this
-will be optimized for Salomon)
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [List of Available
- Modules](../list_of_modules.html "List of Available Modules on Salomon Cluster")
diff --git a/salomon/salomon-2/@@images/25c7db03-5c44-4981-9e19-07c1c23fcf1e.jpg b/salomon/salomon-2/@@images/25c7db03-5c44-4981-9e19-07c1c23fcf1e.jpg
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diff --git a/salomon/software.md b/salomon/software.md
deleted file mode 100644
index d4c479ae56a4e574e7a4ff20ef455e622421bc11..0000000000000000000000000000000000000000
--- a/salomon/software.md
+++ /dev/null
@@ -1,65 +0,0 @@
- [COMSOL](software/comsol.html){.contenttype-folder .state-published .url}
- A finite element analysis, solver and
- Simulation software
- [Debuggers and profilers](software/debuggers.html){.contenttype-folder .state-published .url}
- A collection of development tools
- [Chemistry, Physics and Materials science](software/chemistry.html){.contenttype-folder .state-published .url}
- Tools for computational chemistry.
- [Intel Parallel studio](software/intel-suite.html){.contenttype-folder .state-published .url}
- The Intel Parallel Studio XE
- [MPI](software/mpi-1.html){.contenttype-folder .state-published .url}
- Message Passing Interface libraries on
- ANSELM
- [Numerical languages](software/numerical-languages.html){.contenttype-folder .state-published .url}
- Interpreted languages for numerical
- computations
- [Compilers](software/compilers.html){.contenttype-document .state-published .url}
- Available compilers, including GNU, INTEL
- and UPC compilers
- [Intel Xeon Phi](software/intel-xeon-phi.html){.contenttype-document .state-published .url}
- A guide to Intel Xeon Phi usage
- [Java](software/java.html){.contenttype-document .state-published .url}
- Java on the cluster
- [Operating System](software/operating-system.html){.contenttype-document .state-published .url}
- The operating system, deployed on Salomon
- cluster
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../sitemap.html)
- - [What's New](../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../salomon.html)
-
- - [Hardware
- Overview](hardware-overview-1.html)
-
- - [Accessing the
- Cluster](accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](environment-and-modules.html)
-
- - [List of Available
- Modules](list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](compute-nodes.html)
-
- - [Storage](storage.html)
-
- - [Network](network-1.html)
-
- - [Software](software.html "In this section we provide overview of installed software and its usage.
- ")
-
- - [ANSYS](software/ansys.html "An engineering simulation software ")
-
diff --git a/salomon/software/ansys.md b/salomon/software/ansys.md
deleted file mode 100644
index e23a54e3919bb6092b6f6c98392750b52ea1116d..0000000000000000000000000000000000000000
--- a/salomon/software/ansys.md
+++ /dev/null
@@ -1,104 +0,0 @@
-Channel partner](http//www.ansys.com/)***Â for Czech
-Republic provided all ANSYS licenses for all clusters and supports of
-all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent,
-Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging
-to problem of ANSYS functionality contact
-please [hotline@svsfem.cz](mailtohotline@svsfem.cz?subject=Ostrava%20-%20ANSELM){.email-link}
-The clusters provides as commercial as academic variants. Academic
-variants are distinguished by "**Academic...**" word in the name of
-Â license or by two letter preposition "**aa_**" in the license feature
-name. Change of license is realized on command line respectively
-directly in user's pbs file (see individual products). [More about
-licensing here](ansys/licensing.html)
-To load the latest version of any ANSYS product (Mechanical, Fluent,
-CFX, MAPDL,...) load the module
- $ module load ANSYS
-ANSYS supports interactive regime, but due to assumed solution of
-extremely difficult tasks it is not recommended.
-If user needs to work in interactive regime we recommend to configure
-the RSM service on the client machine which allows to forward the
-solution to the clusters directly from the client's Workbench project
-(see ANSYS RSM service).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [List of Available
- Modules](../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage.html)
-
- - [Network](../network-1.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
-
- - [ANSYS
- MAPDL](ansys/ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](ansys/ansys-cfx.html)
-
- - [ANSYS
- Fluent](ansys/ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](ansys/ansys-ls-dyna.html)
-
- - [Licensing and Available
- Versions](ansys/licensing.html)
-
- - [{width="16" height="16"}
- ANSYS MAPDL PBS
- file](ansys/ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS CFX PBS
- file](ansys/ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS Fluent PBS
- file](ansys/ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS LS-DYNA PBS
- file](ansys/ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- LS-DYNA PBS
- file](ansys/ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [Workbench](ansys/workbench.html)
-
- - [Setting license
- preferences](ansys/setting-license-preferences.html)
-
diff --git a/salomon/software/ansys/Fluent_Licence_1.jpg/@@images/0203aca4-d4f8-4372-ab71-432fcf15df43.jpg b/salomon/software/ansys/Fluent_Licence_1.jpg/@@images/0203aca4-d4f8-4372-ab71-432fcf15df43.jpg
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diff --git a/salomon/software/ansys/Fluent_Licence_4.jpg/@@images/6f6f84e5-5012-42f3-88d6-1ab1c1bfee8f.jpg b/salomon/software/ansys/Fluent_Licence_4.jpg/@@images/6f6f84e5-5012-42f3-88d6-1ab1c1bfee8f.jpg
deleted file mode 100755
index 7a9aa8b06ebf707a5816ea5680ceb1aea0262561..0000000000000000000000000000000000000000
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diff --git a/salomon/software/ansys/ansys-cfx-pbs-file/view.md b/salomon/software/ansys/ansys-cfx-pbs-file/view.md
deleted file mode 100644
index 08eea46ca3e9d586311cb7b92db3522c2673c143..0000000000000000000000000000000000000000
--- a/salomon/software/ansys/ansys-cfx-pbs-file/view.md
+++ /dev/null
@@ -1,87 +0,0 @@
-==================
- [
-cfx.pbs](at_download/cfx.pbs) — shell script, 1
-KB (1036 bytes)
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../sitemap.html)
- - [What's
- New](../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../salomon.html)
-
- - [Hardware
- Overview](../../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../compute-nodes.html)
-
- - [Storage](../../../storage.html)
-
- - [Network](../../../network-1.html)
-
- - [Software](../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](../ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](../ansys-cfx.html)
-
- - [ANSYS
- Fluent](../ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](../ansys-ls-dyna.html)
-
- - [Licensing and Available
- Versions](../licensing.html)
-
- - [{width="16"
- height="16"} ANSYS MAPDL PBS
- file](../ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS CFX PBS
- file](view.html){.state-missing-value
-
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS Fluent PBS
- file](../ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS LS-DYNA PBS
- file](../ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} LS-DYNA PBS
- file](../ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [Workbench](../workbench.html)
-
- - [Setting license
- preferences](../setting-license-preferences.html)
-
diff --git a/salomon/software/ansys/ansys-cfx.md b/salomon/software/ansys/ansys-cfx.md
deleted file mode 100644
index 2f9b884337941e15cecf1a060a3e858e1b9312cf..0000000000000000000000000000000000000000
--- a/salomon/software/ansys/ansys-cfx.md
+++ /dev/null
@@ -1,155 +0,0 @@
-=========
-[ANSYS
-CFX](http//www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+CFX)
-software is a high-performance, general purpose fluid dynamics program
-that has been applied to solve wide-ranging fluid flow problems for over
-20 years. At the heart of ANSYS CFX is its advanced solver technology,
-the key to achieving reliable and accurate solutions quickly and
-robustly. The modern, highly parallelized solver is the foundation for
-an abundant choice of physical models to capture virtually any type of
-phenomena related to fluid flow. The solver and its many physical models
-are wrapped in a modern, intuitive, and flexible GUI and user
-environment, with extensive capabilities for customization and
-automation using session files, scripting and a powerful expression
-language.
-To run ANSYS CFX in batch mode you can utilize/modify the default
-cfx.pbs script and execute it via the qsub command.
- #!/bin/bash
- #PBS -l nodes=2ppn=24
- #PBS -q qprod
- #PBS -N $USER-CFX-Project
- #PBS -A OPEN-0-0
- #! Mail to user when job terminate or abort
- #PBS -m ae
- #!change the working directory (default is home directory)
- #cd (working directory must exists)
- WORK_DIR="/scratch/work/user/$USER"
- cd $WORK_DIR
- echo Running on host `hostname`
- echo Time is `date`
- echo Directory is `pwd`
- echo This jobs runs on the following processors
- echo `cat $PBS_NODEFILE`
- module load ANSYS
- #### Set number of processors per host listing
- procs_per_host=24
- #### Create host list
- hl=""
- for host in `cat $PBS_NODEFILE`
- do
- if [ "$hl" = "" ]
- then hl="$host$procs_per_host"
- else hl="${hl}$host$procs_per_host"
- fi
- done
- echo Machines $hl
- # prevent ANSYS from attempting to use scif0 interface
- export MPI_IC_ORDER="UDAPL"
- #-dev input.def includes the input of CFX analysis in DEF format
- #-P the name of prefered license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial))
- cfx5solve -def input.def -size 4 -size-ni 4x -part-large -start-method "Platform MPI Distributed Parallel" -par-dist $hl -P aa_r
-Header of the pbs file (above) is common and description can be findÂ
-[this
-site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
-SVS FEM recommends to utilize sources by keywords nodes, ppn. These
-keywords allows to address directly the number of nodes (computers) and
-cores (ppn) which will be utilized in the job. Also the rest of code
-assumes such structure of allocated resources.
-Working directory has to be created before sending pbs job into the
-queue. Input file should be in working directory or full path to input
-file has to be specified. Input file has to be defined by common
-CFX def file which is attached to the cfx solver via parameter
--def
-**License**Â should be selected by parameter -P (Big letter **P**).
-Licensed products are the following aa_r
-(ANSYSÂ **Academic**Â Research), ane3fl (ANSYS
-Multiphysics)-**Commercial.**
-[More about licensing here](licensing.html)
-Â We have observed that the -P settings does not always work. Please set
-your [license
-preferences](setting-license-preferences.html) instead.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](ansys-cfx.html)
-
-
- - [ANSYS
- Fluent](ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](ansys-ls-dyna.html)
-
- - [Licensing and Available
- Versions](licensing.html)
-
- - [{width="16" height="16"}
- ANSYS MAPDL PBS
- file](ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS CFX PBS
- file](ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS Fluent PBS
- file](ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS LS-DYNA PBS
- file](ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- LS-DYNA PBS
- file](ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [Workbench](workbench.html)
-
- - [Setting license
- preferences](setting-license-preferences.html)
-
diff --git a/salomon/software/ansys/ansys-fluent-pbs-file/view.md b/salomon/software/ansys/ansys-fluent-pbs-file/view.md
deleted file mode 100644
index 768fb9a9ba65d6e0ff27205366aca0c90a62a4db..0000000000000000000000000000000000000000
--- a/salomon/software/ansys/ansys-fluent-pbs-file/view.md
+++ /dev/null
@@ -1,87 +0,0 @@
-=====================
- [
-fluent.pbs](at_download/fluent.pbs) — shell
-script, 1 KB
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../sitemap.html)
- - [What's
- New](../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../salomon.html)
-
- - [Hardware
- Overview](../../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../compute-nodes.html)
-
- - [Storage](../../../storage.html)
-
- - [Network](../../../network-1.html)
-
- - [Software](../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](../ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](../ansys-cfx.html)
-
- - [ANSYS
- Fluent](../ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](../ansys-ls-dyna.html)
-
- - [Licensing and Available
- Versions](../licensing.html)
-
- - [{width="16"
- height="16"} ANSYS MAPDL PBS
- file](../ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS CFX PBS
- file](../ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS Fluent PBS
- file](view.html){.state-missing-value
-
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS LS-DYNA PBS
- file](../ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} LS-DYNA PBS
- file](../ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [Workbench](../workbench.html)
-
- - [Setting license
- preferences](../setting-license-preferences.html)
-
diff --git a/salomon/software/ansys/ansys-fluent.md b/salomon/software/ansys/ansys-fluent.md
deleted file mode 100644
index fc8c8cebb10093d1513b856e6fbd442cb785f19f..0000000000000000000000000000000000000000
--- a/salomon/software/ansys/ansys-fluent.md
+++ /dev/null
@@ -1,253 +0,0 @@
-============
-[ANSYS
-Fluent](http//www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent)
-software contains the broad physical modeling capabilities needed to
-model flow, turbulence, heat transfer, and reactions for industrial
-applications ranging from air flow over an aircraft wing to combustion
-in a furnace, from bubble columns to oil platforms, from blood flow to
-semiconductor manufacturing, and from clean room design to wastewater
-treatment plants. Special models that give the software the ability to
-model in-cylinder combustion, aeroacoustics, turbomachinery, and
-multiphase systems have served to broaden its reach.
-1. Common way to run Fluent over pbs file
-------------------------------------------------------
-To run ANSYS Fluent in batch mode you can utilize/modify the
-default fluent.pbs script and execute it via the qsub command.
- #!/bin/bash
- #PBS -S /bin/bash
- #PBS -l nodes=2ppn=24
- #PBS -q qprod
- #PBS -N Fluent-Project
- #PBS -A OPEN-0-0
- #! Mail to user when job terminate or abort
- #PBS -m ae
- #!change the working directory (default is home directory)
- #cd (working directory must exists)
- WORK_DIR="/scratch/work/user/$USER"
- cd $WORK_DIR
- echo Running on host `hostname`
- echo Time is `date`
- echo Directory is `pwd`
- echo This jobs runs on the following processors
- echo `cat $PBS_NODEFILE`
- #### Load ansys module so that we find the cfx5solve command
- module load ANSYS
- # Use following line to specify MPI for message-passing instead
- NCORES=`wc -l $PBS_NODEFILE |awk '{print $1}'`
- /apps/cae/ANSYS/16.1/v161/fluent/bin/fluent 3d -t$NCORES -cnf=$PBS_NODEFILE -g -i fluent.jou
-Header of the pbs file (above) is common and description can be find on
-[this
-site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
-[SVS FEM](http//www.svsfem.cz/) recommends to utilize
-sources by keywords nodes, ppn. These keywords allows to address
-directly the number of nodes (computers) and cores (ppn) which will be
-utilized in the job. Also the rest of code assumes such structure of
-allocated resources.
-Working directory has to be created before sending pbs job into the
-queue. Input file should be in working directory or full path to input
-file has to be specified. Input file has to be defined by common Fluent
-journal file which is attached to the Fluent solver via parameter -i
-fluent.jou
-Journal file with definition of the input geometry and boundary
-conditions and defined process of solution has e.g. the following
-structure
- /file/read-case aircraft_2m.cas.gz
- /solve/init
- init
- /solve/iterate
- 10
- /file/write-case-dat aircraft_2m-solution
- /exit yes
-The appropriate dimension of the problem has to be set by
-parameter (2d/3d).Â
-2. Fast way to run Fluent from command line
---------------------------------------------------------
- fluent solver_version [FLUENT_options] -i journal_file -pbs
-This syntax will start the ANSYS FLUENT job under PBS Professional using
-the qsub command in a batch manner. When
-resources are available, PBS Professional will start the job and return
-a job ID, usually in the form of
-class="emphasis">*job_ID.hostname*. This job ID can then be used
-to query, control, or stop the job using standard PBS Professional
-commands, such as qstat or
-class="monospace">qdel. The job will be run out of the current
-working directory, and all output will be written to the file
-class="monospace">fluent.oÂ
-class="emphasis">*job_ID*. Â Â Â Â
-3. Running Fluent via user's config file
-----------------------------------------
-The sample script uses a configuration file called
-class="monospace">pbs_fluent.conf  if no command line arguments
-are present. This configuration file should be present in the directory
-from which the jobs are submitted (which is also the directory in which
-the jobs are executed). The following is an example of what the content
-of pbs_fluent.conf can be
-``` {.screen}
- input="example_small.flin"
- case="Small-1.65m.cas"
- fluent_args="3d -pmyrinet"
- outfile="fluent_test.out"
- mpp="true"
-```
-The following is an explanation of the parameters
-input is the name of the input
-file.
-case is the name of the
-class="monospace">.cas file that the input file will utilize.
-fluent_args are extra ANSYS FLUENT
-arguments. As shown in the previous example, you can specify the
-interconnect by using the -p interconnect
-command. The available interconnects include
-class="monospace">ethernet (the default),
-class="monospace">myrinet,
-infiniband, vendor,
-class="monospace">altix, and
-class="monospace">crayx. The MPI is selected automatically, based
-on the specified interconnect.
-outfile is the name of the file to which
-the standard output will be sent.
-mpp="true" will tell the job script to
-execute the job across multiple processors. Â Â Â Â Â Â Â Â
-To run ANSYS Fluent in batch mode with user's config file you can
-utilize/modify the following script and execute it via the qsub
-command.
-``` {.screen}
-#!/bin/sh
-#PBS -l nodes=2ppn=24
-#PBS -1 qprod
-#PBS -N Fluent-Project
-#PBS -A OPEN-0-0
- cd $PBS_O_WORKDIR
-
- #We assume that if they didn’t specify arguments then they should use the
- #config file if [ "xx${input}${case}${mpp}${fluent_args}zz" = "xxzz" ]; then
- if [ -f pbs_fluent.conf ]; then
- . pbs_fluent.conf
- else
- printf "No command line arguments specified, "
- printf "and no configuration file found. Exiting n"
- fi
- fi
-
- #Augment the ANSYS FLUENT command line arguments case "$mpp" in
- true)
- #MPI job execution scenario
- num_nodes=â€cat $PBS_NODEFILE | sort -u | wc -lâ€
- cpus=â€expr $num_nodes * $NCPUSâ€
- #Default arguments for mpp jobs, these should be changed to suit your
- #needs.
- fluent_args="-t${cpus} $fluent_args -cnf=$PBS_NODEFILE"
- ;;
- *)
- #SMP case
- #Default arguments for smp jobs, should be adjusted to suit your
- #needs.
- fluent_args="-t$NCPUS $fluent_args"
- ;;
- esac
- #Default arguments for all jobs
- fluent_args="-ssh -g -i $input $fluent_args"
- echo "---------- Going to start a fluent job with the following settings
- Input $input
- Case $case
- Output $outfile
- Fluent arguments $fluent_args"
-
- #run the solver
- /apps/cae/ANSYS/16.1/v161/fluent/bin/fluent $fluent_args > $outfile
-```
-It runs the jobs out of the directory from which they are
-submitted (PBS_O_WORKDIR).
-4. Running Fluent in parralel
------------------------------
-[]()Fluent could be run in parallel only under Academic Research
-license. To do so this ANSYS Academic Research license must be placed
-before ANSYS CFD license in user preferences. To make this change
-[anslic_admin utility should be
-run](setting-license-preferences.html).
-Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](ansys-cfx.html)
-
- - [ANSYS
- Fluent](ansys-fluent.html)
-
-
- - [ANSYS
- LS-DYNA](ansys-ls-dyna.html)
-
- - [Licensing and Available
- Versions](licensing.html)
-
- - [{width="16" height="16"}
- ANSYS MAPDL PBS
- file](ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS CFX PBS
- file](ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS Fluent PBS
- file](ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS LS-DYNA PBS
- file](ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- LS-DYNA PBS
- file](ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [Workbench](workbench.html)
-
- - [Setting license
- preferences](setting-license-preferences.html)
-
diff --git a/salomon/software/ansys/ansys-ls-dyna-pbs-file/view.md b/salomon/software/ansys/ansys-ls-dyna-pbs-file/view.md
deleted file mode 100644
index 77c36ff69c9844c80466a33c4333f8e9dee153a5..0000000000000000000000000000000000000000
--- a/salomon/software/ansys/ansys-ls-dyna-pbs-file/view.md
+++ /dev/null
@@ -1,87 +0,0 @@
-======================
- [
-ansysdyna.pbs](at_download/ansysdyna.pbs) —
-shell script, 1 KB
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../sitemap.html)
- - [What's
- New](../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../salomon.html)
-
- - [Hardware
- Overview](../../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../compute-nodes.html)
-
- - [Storage](../../../storage.html)
-
- - [Network](../../../network-1.html)
-
- - [Software](../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](../ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](../ansys-cfx.html)
-
- - [ANSYS
- Fluent](../ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](../ansys-ls-dyna.html)
-
- - [Licensing and Available
- Versions](../licensing.html)
-
- - [{width="16"
- height="16"} ANSYS MAPDL PBS
- file](../ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS CFX PBS
- file](../ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS Fluent PBS
- file](../ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS LS-DYNA PBS
- file](view.html){.state-missing-value
-
- .contenttype-file}
- - [{width="16"
- height="16"} LS-DYNA PBS
- file](../ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [Workbench](../workbench.html)
-
- - [Setting license
- preferences](../setting-license-preferences.html)
-
diff --git a/salomon/software/ansys/ansys-ls-dyna.md b/salomon/software/ansys/ansys-ls-dyna.md
deleted file mode 100644
index f7efe612834852230ae52544302f1efdb2d5720c..0000000000000000000000000000000000000000
--- a/salomon/software/ansys/ansys-ls-dyna.md
+++ /dev/null
@@ -1,154 +0,0 @@
-=============
-[ANSYS
-LS-DYNA](http//www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/Explicit+Dynamics/ANSYS+LS-DYNA)
-software provides convenient and easy-to-use access to the
-technology-rich, time-tested explicit solver without the need to contend
-with the complex input requirements of this sophisticated program.
-Introduced in 1996, ANSYS LS-DYNA capabilities have helped customers in
-numerous industries to resolve highly intricate design
-issues. ANSYS Mechanical users have been able take advantage of
-complex explicit solutions for a long time utilizing the traditional
-ANSYS Parametric Design Language (APDL) environment. These
-explicit capabilities are available to ANSYS Workbench users as well.
-The Workbench platform is a powerful, comprehensive, easy-to-use
-environment for engineering simulation. CAD import from all sources,
-geometry cleanup, automatic meshing, solution, parametric optimization,
-result visualization and comprehensive report generation are all
-available within a single fully interactive modern graphical user
-environment.
-To run ANSYS LS-DYNA in batch mode you can utilize/modify the
-default ansysdyna.pbs script and execute it via the qsub command.
- #!/bin/bash
- #PBS -l nodes=2ppn=24
- #PBS -q qprod
- #PBS -N DYNA-Project
- #PBS -A OPEN-0-0
- #! Mail to user when job terminate or abort
- #PBS -m ae
- #!change the working directory (default is home directory)
- #cd
- WORK_DIR="/scratch/work/user/$USER"
- cd $WORK_DIR
- echo Running on host `hostname`
- echo Time is `date`
- echo Directory is `pwd`
- echo This jobs runs on the following processors
- echo `cat $PBS_NODEFILE`
- module load ANSYS
- #### Set number of processors per node
- procs_per_host=24
- #### Create host list
- hl=""
- for host in `cat $PBS_NODEFILE`
- do
- if [ "$hl" = "" ]
- then hl="$host$procs_per_host"
- else hl="${hl}$host$procs_per_host"
- fi
- done
- echo Machines $hl
- # prevent ANSYS from attempting to use scif0 interface
- export MPI_IC_ORDER="UDAPL"
- lsdyna161 -dis -usessh -machines "$hl" i=input.k
-Header of the pbs file (above) is common and description can be
-find on [this
-site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
-[SVS FEM](http//www.svsfem.cz/) recommends to utilize
-sources by keywords nodes, ppn. These keywords allows to address
-directly the number of nodes (computers) and cores (ppn) which will be
-utilized in the job. Also the rest of code assumes such structure of
-allocated resources.
-Working directory has to be created before sending pbs job into the
-queue. Input file should be in working directory or full path to input
-file has to be specified. Input file has to be defined by common LS-DYNA
-.**k** file which is attached to the ansys solver via parameter i=
-Without setting environment variable MPI_IC_ORDER="UDAPL", ANSYS will
-fail to run on nodes with Xeon Phi accelerator (it will use the virtual
-interface of Phi cards instead of the real InfiniBand interface and MPI
-will fail.
-
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](ansys-cfx.html)
-
- - [ANSYS
- Fluent](ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](ansys-ls-dyna.html)
-
-
- - [Licensing and Available
- Versions](licensing.html)
-
- - [{width="16" height="16"}
- ANSYS MAPDL PBS
- file](ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS CFX PBS
- file](ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS Fluent PBS
- file](ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS LS-DYNA PBS
- file](ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- LS-DYNA PBS
- file](ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [Workbench](workbench.html)
-
- - [Setting license
- preferences](setting-license-preferences.html)
-
diff --git a/salomon/software/ansys/ansys-mapdl-pbs-file/view.md b/salomon/software/ansys/ansys-mapdl-pbs-file/view.md
deleted file mode 100644
index 9db8805e4a5fe5cb3f0d013f3d755dbfe483501d..0000000000000000000000000000000000000000
--- a/salomon/software/ansys/ansys-mapdl-pbs-file/view.md
+++ /dev/null
@@ -1,87 +0,0 @@
-====================
- [
-mapdl.pbs](at_download/mapdl.pbs) — shell
-script, 1 KB (1213 bytes)
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../sitemap.html)
- - [What's
- New](../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../salomon.html)
-
- - [Hardware
- Overview](../../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../compute-nodes.html)
-
- - [Storage](../../../storage.html)
-
- - [Network](../../../network-1.html)
-
- - [Software](../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](../ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](../ansys-cfx.html)
-
- - [ANSYS
- Fluent](../ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](../ansys-ls-dyna.html)
-
- - [Licensing and Available
- Versions](../licensing.html)
-
- - [{width="16"
- height="16"} ANSYS MAPDL PBS
- file](view.html){.state-missing-value
-
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS CFX PBS
- file](../ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS Fluent PBS
- file](../ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS LS-DYNA PBS
- file](../ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} LS-DYNA PBS
- file](../ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [Workbench](../workbench.html)
-
- - [Setting license
- preferences](../setting-license-preferences.html)
-
diff --git a/salomon/software/ansys/ansys-mechanical-apdl.md b/salomon/software/ansys/ansys-mechanical-apdl.md
deleted file mode 100644
index 8b176787a0d196107a3463ecfb491ffa7df48d7c..0000000000000000000000000000000000000000
--- a/salomon/software/ansys/ansys-mechanical-apdl.md
+++ /dev/null
@@ -1,148 +0,0 @@
-===========
-**[ANSYS
-Multiphysics](http//www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics)**
-software offers a comprehensive product solution for both multiphysics
-and single-physics analysis. The product includes structural, thermal,
-fluid and both high- and low-frequency electromagnetic analysis. The
-product also contains solutions for both direct and sequentially coupled
-physics problems including direct coupled-field elements and the ANSYS
-multi-field solver.
-To run ANSYS MAPDL in batch mode you can utilize/modify the
-default mapdl.pbs script and execute it via the qsub command.
- #!/bin/bash
- #PBS -l nodes=2ppn=24
- #PBS -q qprod
- #PBS -N ANSYS-Project
- #PBS -A OPEN-0-0
- #! Mail to user when job terminate or abort
- #PBS -m ae
- #!change the working directory (default is home directory)
- #cd (working directory must exists)
- WORK_DIR="/scratch/work/user/$USER"
- cd $WORK_DIR
- echo Running on host `hostname`
- echo Time is `date`
- echo Directory is `pwd`
- echo This jobs runs on the following processors
- echo `cat $PBS_NODEFILE`
- module load ANSYS/16.1
- #### Set number of processors per host listing
- procs_per_host=24
- #### Create host list
- hl=""
- for host in `cat $PBS_NODEFILE`
- do
- if [ "$hl" = "" ]
- then hl="$host$procs_per_host"
- else hl="${hl}$host$procs_per_host"
- fi
- done
- echo Machines $hl
- # prevent ANSYS from attempting to use scif0 interface
- export MPI_IC_ORDER="UDAPL"
- #-i input.dat includes the input of analysis in APDL format
- #-o file.out is output file from ansys where all text outputs will be redirected
- #-p the name of license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial), aa_r_dy=Academic AUTODYN)
- ansys161 -b -dis -usessh -p aa_r -i input.dat -o file.out -machines "$hl" -dir $WORK_DIR
-Header of the PBS file (above) is common and description can be find on
-[this
-site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
-[SVS FEM](http//www.svsfem.cz/) recommends to utilize
-sources by keywords nodes, ppn. These keywords allows to address
-directly the number of nodes (computers) and cores (ppn) which will be
-utilized in the job. Also the rest of code assumes such structure of
-allocated resources.
-Working directory has to be created before sending pbs job into the
-queue. Input file should be in working directory or full path to input
-file has to be specified. Input file has to be defined by common APDL
-file which is attached to the ansys solver via parameter -i
-**License** should be selected by parameter -p. Licensed products are
-the following aa_r (ANSYS **Academic** Research), ane3fl (ANSYS
-Multiphysics)-**Commercial**, aa_r_dy (ANSYS **Academic**
-AUTODYN)
-[More about licensing here](licensing.html)
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](ansys-mechanical-apdl.html)
-
-
- - [ANSYS
- CFX](ansys-cfx.html)
-
- - [ANSYS
- Fluent](ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](ansys-ls-dyna.html)
-
- - [Licensing and Available
- Versions](licensing.html)
-
- - [{width="16" height="16"}
- ANSYS MAPDL PBS
- file](ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS CFX PBS
- file](ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS Fluent PBS
- file](ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS LS-DYNA PBS
- file](ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- LS-DYNA PBS
- file](ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [Workbench](workbench.html)
-
- - [Setting license
- preferences](setting-license-preferences.html)
-
diff --git a/salomon/software/ansys/licensing.md b/salomon/software/ansys/licensing.md
deleted file mode 100644
index dfa1d46a01cffb01c3ab5dfb7be7cd6902498761..0000000000000000000000000000000000000000
--- a/salomon/software/ansys/licensing.md
+++ /dev/null
@@ -1,117 +0,0 @@
-================================
-ANSYS licence can be used by
------------------------------
-- all persons in the carrying out of the CE IT4Innovations Project (In
- addition to the primary licensee, which is VSB - Technical
- University of Ostrava, users are CE IT4Innovations third parties -
- CE IT4Innovations project partners, particularly the University of
- Ostrava, the Brno University of Technology - Faculty of Informatics,
- the Silesian University in Opava, Institute of Geonics AS CR.)
-- all
- persons who have a valid
- class="hps">license
-- students
- of the Technical University
-ANSYS Academic Research
------------------------
-The licence intended to be used for science and research, publications,
-students’ projects (academic licence).
-ANSYS COM
----------
-The licence intended to be used for science and research, publications,
-students’ projects, commercial research with no commercial use
-restrictions.
-Available Versions
-------------------
-- 16.1
-- 17.0
-License Preferences
--------------------
-Please [see this page to set license
-preferences](setting-license-preferences.html).
-Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](ansys-cfx.html)
-
- - [ANSYS
- Fluent](ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](ansys-ls-dyna.html)
-
- - [Licensing and Available
- Versions](licensing.html)
-
-
- - [{width="16" height="16"}
- ANSYS MAPDL PBS
- file](ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS CFX PBS
- file](ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS Fluent PBS
- file](ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS LS-DYNA PBS
- file](ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- LS-DYNA PBS
- file](ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [Workbench](workbench.html)
-
- - [Setting license
- preferences](setting-license-preferences.html)
-
diff --git a/salomon/software/ansys/ls-dyna-pbs-file/view.md b/salomon/software/ansys/ls-dyna-pbs-file/view.md
deleted file mode 100644
index ebb9b2a86f30351b3626d00755d27cbef8eeee6f..0000000000000000000000000000000000000000
--- a/salomon/software/ansys/ls-dyna-pbs-file/view.md
+++ /dev/null
@@ -1,87 +0,0 @@
-================
- [
-lsdyna.pbs](at_download/lsdyna.pbs) — shell
-script, 1 KB
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../sitemap.html)
- - [What's
- New](../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../salomon.html)
-
- - [Hardware
- Overview](../../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../compute-nodes.html)
-
- - [Storage](../../../storage.html)
-
- - [Network](../../../network-1.html)
-
- - [Software](../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](../ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](../ansys-cfx.html)
-
- - [ANSYS
- Fluent](../ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](../ansys-ls-dyna.html)
-
- - [Licensing and Available
- Versions](../licensing.html)
-
- - [{width="16"
- height="16"} ANSYS MAPDL PBS
- file](../ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS CFX PBS
- file](../ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS Fluent PBS
- file](../ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} ANSYS LS-DYNA PBS
- file](../ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"} LS-DYNA PBS
- file](view.html){.state-missing-value
-
- .contenttype-file}
- - [Workbench](../workbench.html)
-
- - [Setting license
- preferences](../setting-license-preferences.html)
-
diff --git a/salomon/software/ansys/setting-license-preferences.md b/salomon/software/ansys/setting-license-preferences.md
deleted file mode 100644
index 7e2c0cdc3218fcfe539edd39173116ed26acd928..0000000000000000000000000000000000000000
--- a/salomon/software/ansys/setting-license-preferences.md
+++ /dev/null
@@ -1,105 +0,0 @@
-===========================
-Some ANSYS tools allow you to explicitly specify usage of academic or
-commercial licenses in the command line (eg.Â
-class="monospace">ansys161 -p aa_r to select Academic Research
-license). However, we have observed that not all tools obey this option
-and choose commercial license.
-Thus you need to configure preferred license order with ANSLIC_ADMIN.
-Please follow these steps and move Academic Research license to the  top
-or bottom of the list accordingly.
-Launch the ANSLIC_ADMIN utility in a graphical environment
- $ANSYSLIC_DIR/lic_admin/anslic_admin
-ANSLIC_ADMIN Utility will be run
-[](Fluent_Licence_1.jpg)
-[](Fluent_Licence_2.jpg)
-[](Fluent_Licence_3.jpg)
-Â
-ANSYS Academic Research license should be moved up to the top or down to
-the bottom of the list.
-Â
-[](Fluent_Licence_4.jpg)
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](ansys-cfx.html)
-
- - [ANSYS
- Fluent](ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](ansys-ls-dyna.html)
-
- - [Licensing and Available
- Versions](licensing.html)
-
- - [{width="16" height="16"}
- ANSYS MAPDL PBS
- file](ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS CFX PBS
- file](ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS Fluent PBS
- file](ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS LS-DYNA PBS
- file](ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- LS-DYNA PBS
- file](ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [Workbench](workbench.html)
-
- - [Setting license
- preferences](setting-license-preferences.html)
-
-
diff --git a/salomon/software/ansys/workbench.md b/salomon/software/ansys/workbench.md
deleted file mode 100644
index f5440c9968475d241e1505218b08daa42418085b..0000000000000000000000000000000000000000
--- a/salomon/software/ansys/workbench.md
+++ /dev/null
@@ -1,140 +0,0 @@
-=========
-Workbench Batch Mode
---------------------
-It is possible to run Workbench scripts in batch mode. You need to
-configure solvers of individual components to run in parallel mode. Open
-your project in Workbench. Then, for example, in Mechanical, go to Tools
-- Solve Process Settings ..., click Advanced button as shown on the
-screenshot.
-
-Enable Distribute Solution checkbox and enter number of cores (eg. 48 to
-run on two Salomon nodes). If you want the job to run on more then 1
-node, you must also provide a so called MPI appfile. In the Additional
-Command Line Arguments input field, enter
- -mpifile /path/to/my/job/mpifile.txt
-Where /path/to/my/job is the directory where your project is saved. We
-will create the file mpifile.txt programatically later in the batch
-script. For more information, refer to *ANSYS Mechanical APDL Parallel
-Processing* *Guide*.
-Now, save the project and close Workbench. We will use this script to
-launch the job
- #!/bin/bash
- #PBS -l select=2ncpus=24
- #PBS -q qprod
- #PBS -N test9_mpi_2
- #PBS -A OPEN-0-0
- # Mail to user when job terminate or abort
- #PBS -m a
- # change the working directory
- WORK_DIR="$PBS_O_WORKDIR"
- cd $WORK_DIR
- echo Running on host `hostname`
- echo Time is `date`
- echo Directory is `pwd`
- echo This jobs runs on the following nodes
- echo `cat $PBS_NODEFILE`
- module load ANSYS
- #### Set number of processors per host listing
- procs_per_host=24
- #### Create MPI appfile
- echo -n "" > mpifile.txt
- for host in `cat $PBS_NODEFILE`
- do
- echo "-h $host -np $procs_per_host $ANSYS160_DIR/bin/ansysdis161 -dis" >> mpifile.txt
- done
- #-i input.dat includes the input of analysis in APDL format
- #-o file.out is output file from ansys where all text outputs will be redirected
- #-p the name of license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial), aa_r_dy=Academic AUTODYN)
- # prevent using scsif0 interface on accelerated nodes
- export MPI_IC_ORDER="UDAPL"
- # spawn remote process using SSH (default is RSH)
- export MPI_REMSH="/usr/bin/ssh"
- runwb2 -R jou6.wbjn -B -F test9.wbpj
-The solver settings are saved in file solvehandlers.xml, which is not
-located in the project directory. Verify your solved settings when
-uploading a project from your local computer.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
- .navTreeFolderish
- .contenttype-folder}
- - [ANSYS
- MAPDL](ansys-mechanical-apdl.html)
-
- - [ANSYS
- CFX](ansys-cfx.html)
-
- - [ANSYS
- Fluent](ansys-fluent.html)
-
- - [ANSYS
- LS-DYNA](ansys-ls-dyna.html)
-
- - [Licensing and Available
- Versions](licensing.html)
-
- - [{width="16" height="16"}
- ANSYS MAPDL PBS
- file](ansys-mapdl-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS CFX PBS
- file](ansys-cfx-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS Fluent PBS
- file](ansys-fluent-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- ANSYS LS-DYNA PBS
- file](ansys-ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- LS-DYNA PBS
- file](ls-dyna-pbs-file/view.html){.state-missing-value
- .contenttype-file}
- - [Workbench](workbench.html)
-
-
- - [Setting license
- preferences](setting-license-preferences.html)
-
diff --git a/salomon/software/chemistry.md b/salomon/software/chemistry.md
deleted file mode 100644
index dd609e3a80c203737eae6204c924039244daec7f..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry.md
+++ /dev/null
@@ -1,61 +0,0 @@
-Tools for computational chemistry.
- [Molpro](chemistry/molpro.html){.contenttype-document .state-published .url}
- Molpro is a complete system of ab initio
- programs for molecular electronic structure calculations.
- [NWChem](chemistry/nwchem.html){.contenttype-document .state-published .url}
- High-Performance Computational
- Chemistry
- [Phono3py](chemistry/phono3py.html){.contenttype-document .state-published .url}
-
- [Phono3py Input](chemistry/phono3py-input.html){.contenttype-folder .state-published .url}
-
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [List of Available
- Modules](../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage.html)
-
- - [Network](../network-1.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](chemistry.html "Tools for computational chemistry.")
-
-
- - [Molpro](chemistry/molpro.html "Molpro is a complete system of ab initio programs for molecular electronic structure calculations.")
diff --git a/salomon/software/chemistry/molpro.md b/salomon/software/chemistry/molpro.md
deleted file mode 100644
index 1bcdd9520159d9bba3b06eda6a488e0f6aecb11c..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry/molpro.md
+++ /dev/null
@@ -1,121 +0,0 @@
-Molpro
-======
-Molpro is a complete system of ab initio programs for molecular
-electronic structure calculations.
-About Molpro
-------------
-Molpro is a software package used for accurate ab-initio quantum
-chemistry calculations. More information can be found at the [official
-webpage](http//www.molpro.net/).
-License
--------
-Molpro software package is available only to users that have a valid
-license. Please contact support to enable access to Molpro if you have a
-valid license appropriate for running on our cluster (eg. academic
-research group licence, parallel execution).
-To run Molpro, you need to have a valid license token present in
-"$HOME/.molpro/token". You can
-download the token from [Molpro
-website](https//www.molpro.net/licensee/?portal=licensee).
-Installed version
------------------
-Currently on Salomon is installed version 2010.1, patch level 57,
-parallel version compiled with Intel compilers and Intel MPI.
-Compilation parameters are default
- Parameter Value
- ------------------------------------------------- -----------------------------
- max number of atoms 200
- max number of valence orbitals 300
- max number of basis functions 4095
- max number of states per symmmetry 20
- max number of state symmetries 16
- max number of records 200
- max number of primitives maxbfn x [2]
-Â
-Running
--------
-Molpro is compiled for parallel execution using MPI and OpenMP. By
-default, Molpro reads the number of allocated nodes from PBS and
-launches a data server on one node. On the remaining allocated nodes,
-compute processes are launched, one process per node, each with 16
-threads. You can modify this behavior by using -n, -t and helper-server
-options. Please refer to the [Molpro
-documentation](http//www.molpro.net/info/2010.1/doc/manual/node9.html)
-for more details.Â
-The OpenMP parallelization in Molpro is limited and has been observed to
-produce limited scaling. We therefore recommend to use MPI
-parallelization only. This can be achieved by passing option
-class="monospace">mpiprocs=24ompthreads=1 to PBS.
-You are advised to use the -d option to point to a directory in [SCRATCH
-filesystem](../../storage.html). Molpro can produce a
-large amount of temporary data during its run, and it is important that
-these are placed in the fast scratch filesystem.
-### Example jobscript
- #PBS -A IT4I-0-0
- #PBS -q qprod
- #PBS -l select=1ncpus=24mpiprocs=24ompthreads=1
- cd $PBS_O_WORKDIR
- # load Molpro module
- module add Molpro/2010.1-patch-57-intel2015b
- # create a directory in the SCRATCH filesystem
- mkdir -p /scratch/work/user/$USER/$PBS_JOBID
- # copy an example input
- cp /apps/all/Molpro/2010.1-patch57/molprop_2010_1_Linux_x86_64_i8/examples/caffeine_opt_diis.com .
- # run Molpro with default options
- molpro -d /scratch/work/user/$USER/$PBS_JOBID caffeine_opt_diis.com
- # delete scratch directory
- rm -rf /scratch/work/user/$USER/$PBS_JOBIDÂ
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../chemistry.html "Tools for computational chemistry.")
- .navTreeFolderish
- .contenttype-folder}
- - [Molpro](molpro.html "Molpro is a complete system of ab initio programs for molecular electronic structure calculations.")
-
diff --git a/salomon/software/chemistry/nwchem.md b/salomon/software/chemistry/nwchem.md
deleted file mode 100644
index 004b6f3007bdadbf5e675a0e70fafa3c7e910da3..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry/nwchem.md
+++ /dev/null
@@ -1,100 +0,0 @@
-NWChem
-======
-High-Performance Computational Chemistry
-Introduction
--------------------------
-NWChem aims to provide its users with computational chemistry
-tools that are scalable both in their ability to treat large scientific
-computational chemistry problems efficiently, and in their use of
-available parallel computing resources from high-performance parallel
-supercomputers to conventional workstation clusters.
-[Homepage](http//www.nwchem-sw.org/index.php/Main_Page)
-Installed versions
-------------------
-The following versions are currently installed Â
-- NWChem/6.3.revision2-2013-10-17-Python-2.7.8, current release.
- Compiled with Intel compilers, MKL and Intel MPI
- Â
-- NWChem/6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.8
-For a current list of installed versions, execute Â
- module avail NWChem
-The recommend to use version 6.5. Version 6.3 fails on Salomon nodes
-with accelerator, because it attempts to communicate over scif0
-interface. In 6.5 this is avoided by
-setting ARMCI_OPENIB_DEVICE=mlx4_0, this setting is included in the
-module.
-Running
--------
-NWChem is compiled for parallel MPI execution. Normal procedure for MPI
-jobs applies. Sample jobscript
- #PBS -A IT4I-0-0
- #PBS -q qprod
- #PBS -l select=1ncpus=24mpiprocs=24
- cd $PBS_O_WORKDIR
- module add NWChem/6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.8
- mpirun nwchem h2o.nw
-Options
---------------------
-Please refer to [the
-documentation](http//www.nwchem-sw.org/index.php/Release62Top-level)Â and
-in the input file set the following directives
-- MEMORY controls the amount of memory NWChem will use
-- SCRATCH_DIR set this to a directory in [SCRATCH
- filesystem](../../storage.html)Â (or run the
- calculation completely in a scratch directory). For certain
- calculations, it might be advisable to reduce I/O by forcing
- "direct" mode, eg. "scf direct"
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../chemistry.html "Tools for computational chemistry.")
- .navTreeFolderish
- .contenttype-folder}
- - [Molpro](molpro.html "Molpro is a complete system of ab initio programs for molecular electronic structure calculations.")
-
diff --git a/salomon/software/chemistry/phono3py-input.md b/salomon/software/chemistry/phono3py-input.md
deleted file mode 100644
index f337c25a9671b99b2ef00e88f67078630c148a73..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry/phono3py-input.md
+++ /dev/null
@@ -1,103 +0,0 @@
-Phono3py Input
-==============
- {width="16" height="16"} [POSCAR Si](phono3py-input/poscar-si/view.html){.contenttype-file .state-missing-value .url}
- POSCAR
- {width="16" height="16"} [KPOINTS](phono3py-input/KPOINTS/view.html){.contenttype-file .state-missing-value .url}
-
- {width="16" height="16"} [POTCAR](phono3py-input/POTCAR/view.html){.contenttype-file .state-missing-value .url}
-
- {width="16" height="16"} [INCAR](phono3py-input/INCAR/view.html){.contenttype-file .state-missing-value .url}
-
- {width="16" height="16"} [run.sh](phono3py-input/run.sh/view.html){.contenttype-file .state-missing-value .url}
-
- {width="16" height="16"} [submit.sh](phono3py-input/submit.sh/view.html){.contenttype-file .state-missing-value .url}
-
- {width="16" height="16"} [prepare.sh](phono3py-input/prepare.sh/view.html){.contenttype-file .state-missing-value .url}
-
- {width="16" height="16"} [gofree-cond1.sh](phono3py-input/gofree-cond1.sh/view.html){.contenttype-file .state-missing-value .url}
-
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../chemistry.html "Tools for computational chemistry.")
- .navTreeFolderish
- .contenttype-folder}
- - [Molpro](molpro.html "Molpro is a complete system of ab initio programs for molecular electronic structure calculations.")
-
- - [NWChem](nwchem.html "High-Performance Computational Chemistry")
-
- - [Phono3py](phono3py.html "
- ")
- - [Phono3py
- Input](phono3py-input.html)
-
-
- - [{width="16"
- height="16"} POSCAR
- Si](phono3py-input/poscar-si/view.html "POSCAR"){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- KPOINTS](phono3py-input/KPOINTS/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- POTCAR](phono3py-input/POTCAR/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- INCAR](phono3py-input/INCAR/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- run.sh](phono3py-input/run.sh/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16" height="16"}
- submit.sh](phono3py-input/submit.sh/view.html){.state-missing-value
- .contenttype-file}
diff --git a/salomon/software/chemistry/phono3py-input/INCAR/at_download/INCAR b/salomon/software/chemistry/phono3py-input/INCAR/at_download/INCAR
deleted file mode 100755
index 4d2848958e6b7333abdb381bb664e1c389360741..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry/phono3py-input/INCAR/at_download/INCAR
+++ /dev/null
@@ -1,13 +0,0 @@
- PREC = Accurate
- IBRION = -1
- ENCUT = 500
- EDIFF = 1.0e-08
- ISMEAR = 0
- SIGMA = 0.01
- IALGO = 38
- LREAL = .FALSE.
- ADDGRID = .TRUE.
- LWAVE = .FALSE.
- LCHARG = .FALSE.
- NCORE = 8
- KPAR = 8
diff --git a/salomon/software/chemistry/phono3py-input/INCAR/view.md b/salomon/software/chemistry/phono3py-input/INCAR/view.md
deleted file mode 100644
index e76d41d994a8bcb65c6387cbbc723ce9ccff3825..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry/phono3py-input/INCAR/view.md
+++ /dev/null
@@ -1,97 +0,0 @@
-Info
-
-INCAR
-=====
- [
-INCAR](at_download/INCAR) — Octet Stream, 1 KB
-
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../../sitemap.html)
- - [What's
- New](../../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../../salomon.html)
-
- - [Hardware
- Overview](../../../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../../compute-nodes.html)
-
- - [Storage](../../../../storage.html)
-
- - [Network](../../../../network-1.html)
-
- - [Software](../../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../../../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../../../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../../../chemistry.html "Tools for computational chemistry.")
- .navTreeFolderish
- .contenttype-folder}
- - [Molpro](../../molpro.html "Molpro is a complete system of ab initio programs for molecular electronic structure calculations.")
-
- - [NWChem](../../nwchem.html "High-Performance Computational Chemistry")
-
- - [Phono3py](../../phono3py.html "
- ")
- - [Phono3py
- Input](../../phono3py-input.html)
- .navTreeFolderish
- .contenttype-folder}
- - [{width="16"
- height="16"} POSCAR
- Si](../poscar-si/view.html "POSCAR"){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- KPOINTS](../KPOINTS/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- POTCAR](../POTCAR/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- INCAR](view.html){.state-missing-value
-
- .contenttype-file}
- - [{width="16"
- height="16"}
- run.sh](../run.sh/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- submit.sh](../submit.sh/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
diff --git a/salomon/software/chemistry/phono3py-input/KPOINTS/at_download/KPOINTS b/salomon/software/chemistry/phono3py-input/KPOINTS/at_download/KPOINTS
deleted file mode 100755
index cae7400392404a4c9c4e3e7969722ed578825c51..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry/phono3py-input/KPOINTS/at_download/KPOINTS
+++ /dev/null
@@ -1,6 +0,0 @@
-Automatic mesh
-0
-Monkhorst Pack
- 3 3 3
-0.5 0.5 0.5
-
diff --git a/salomon/software/chemistry/phono3py-input/KPOINTS/view.md b/salomon/software/chemistry/phono3py-input/KPOINTS/view.md
deleted file mode 100644
index 3325efbbc9480167847c0f9348d09f78cabe0a82..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry/phono3py-input/KPOINTS/view.md
+++ /dev/null
@@ -1,97 +0,0 @@
-Info
-
-KPOINTS
-=======
- [
-KPOINTS](at_download/KPOINTS) — Octet Stream, 1
-KB
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../../sitemap.html)
- - [What's
- New](../../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../../salomon.html)
-
- - [Hardware
- Overview](../../../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../../compute-nodes.html)
-
- - [Storage](../../../../storage.html)
-
- - [Network](../../../../network-1.html)
-
- - [Software](../../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../../../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../../../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../../../chemistry.html "Tools for computational chemistry.")
- .navTreeFolderish
- .contenttype-folder}
- - [Molpro](../../molpro.html "Molpro is a complete system of ab initio programs for molecular electronic structure calculations.")
-
- - [NWChem](../../nwchem.html "High-Performance Computational Chemistry")
-
- - [Phono3py](../../phono3py.html "
- ")
- - [Phono3py
- Input](../../phono3py-input.html)
- .navTreeFolderish
- .contenttype-folder}
- - [{width="16"
- height="16"} POSCAR
- Si](../poscar-si/view.html "POSCAR"){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- KPOINTS](view.html){.state-missing-value
-
- .contenttype-file}
- - [{width="16"
- height="16"}
- POTCAR](../POTCAR/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- INCAR](../INCAR/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- run.sh](../run.sh/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- submit.sh](../submit.sh/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
diff --git a/salomon/software/chemistry/phono3py-input/POTCAR/at_download/POTCAR b/salomon/software/chemistry/phono3py-input/POTCAR/at_download/POTCAR
deleted file mode 100755
index e69e8a3044c2885f5fc7d2b1e1c90ba7ffef914a..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry/phono3py-input/POTCAR/at_download/POTCAR
+++ /dev/null
@@ -1,2208 +0,0 @@
- PAW_PBE Si 05Jan2001
- 4.00000000000000
- parameters from PSCTR are:
- VRHFIN =Si: s2p2
- LEXCH = PE
- EATOM = 103.0669 eV, 7.5752 Ry
-
- TITEL = PAW_PBE Si 05Jan2001
- LULTRA = F use ultrasoft PP ?
- IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no
- RPACOR = 1.500 partial core radius
- POMASS = 28.085; ZVAL = 4.000 mass and valenz
- RCORE = 1.900 outmost cutoff radius
- RWIGS = 2.480; RWIGS = 1.312 wigner-seitz radius (au A)
- ENMAX = 245.345; ENMIN = 184.009 eV
- ICORE = 2 local potential
- LCOR = T correct aug charges
- LPAW = T paw PP
- EAUG = 322.069
- DEXC = 0.000
- RMAX = 1.950 core radius for proj-oper
- RAUG = 1.300 factor for augmentation sphere
- RDEP = 1.993 radius for radial grids
- RDEPT = 1.837 core radius for aug-charge
-
- Atomic configuration
- 6 entries
- n l j E occ.
- 1 0 0.50 -1785.8828 2.0000
- 2 0 0.50 -139.4969 2.0000
- 2 1 1.50 -95.5546 6.0000
- 3 0 0.50 -10.8127 2.0000
- 3 1 0.50 -4.0811 2.0000
- 3 2 1.50 -4.0817 0.0000
- Description
- l E TYP RCUT TYP RCUT
- 0 -10.8127223 23 1.900
- 0 -7.6451159 23 1.900
- 1 -4.0811372 23 1.900
- 1 2.4879257 23 1.900
- 2 -4.0817478 7 1.900
- Error from kinetic energy argument (eV)
- NDATA = 100
- STEP = 20.000 1.050
- 10.1 9.04 8.56 7.65 7.23 6.44 5.73 5.40
- 4.79 4.25 4.00 3.54 3.13 2.77 2.45 2.16
- 1.91 1.69 1.50 1.24 1.10 0.975 0.812 0.718
- 0.636 0.529 0.440 0.388 0.322 0.266 0.219 0.180
- 0.148 0.121 0.986E-01 0.804E-01 0.614E-01 0.504E-01 0.392E-01 0.328E-01
- 0.265E-01 0.220E-01 0.189E-01 0.166E-01 0.149E-01 0.135E-01 0.123E-01 0.109E-01
- 0.977E-02 0.840E-02 0.707E-02 0.605E-02 0.488E-02 0.387E-02 0.290E-02 0.229E-02
- 0.185E-02 0.152E-02 0.134E-02 0.125E-02 0.121E-02 0.117E-02 0.112E-02 0.102E-02
- 0.915E-03 0.776E-03 0.640E-03 0.524E-03 0.425E-03 0.369E-03 0.331E-03 0.310E-03
- 0.294E-03 0.273E-03 0.242E-03 0.210E-03 0.175E-03 0.146E-03 0.124E-03 0.113E-03
- 0.105E-03 0.973E-04 0.879E-04 0.755E-04 0.633E-04 0.539E-04 0.478E-04 0.438E-04
- 0.404E-04 0.362E-04 0.308E-04 0.264E-04 0.229E-04 0.209E-04 0.192E-04 0.170E-04
- 0.145E-04 0.126E-04 0.112E-04 0.103E-04
-END of PSCTR-controll parameters
- local part
- 98.2657514061040
- 0.84157827E+01 0.84210738E+01 0.84276982E+01 0.84387529E+01 0.84542581E+01
- 0.84742396E+01 0.84987267E+01 0.85277503E+01 0.85613408E+01 0.85995259E+01
- 0.86423293E+01 0.86897698E+01 0.87418601E+01 0.87986073E+01 0.88600119E+01
- 0.89260684E+01 0.89967646E+01 0.90720817E+01 0.91519931E+01 0.92364635E+01
- 0.93254478E+01 0.94188892E+01 0.95167180E+01 0.96188495E+01 0.97251831E+01
- 0.98356006E+01 0.99499656E+01 0.10068122E+02 0.10189896E+02 0.10315092E+02
- 0.10443494E+02 0.10574869E+02 0.10708960E+02 0.10845494E+02 0.10984175E+02
- 0.11124688E+02 0.11266699E+02 0.11409854E+02 0.11553782E+02 0.11698093E+02
- 0.11842379E+02 0.11986220E+02 0.12129179E+02 0.12270807E+02 0.12410647E+02
- 0.12548229E+02 0.12683078E+02 0.12814715E+02 0.12942655E+02 0.13066413E+02
- 0.13185507E+02 0.13299453E+02 0.13407778E+02 0.13510011E+02 0.13605696E+02
- 0.13694386E+02 0.13775649E+02 0.13849071E+02 0.13914257E+02 0.13970832E+02
- 0.14018447E+02 0.14056776E+02 0.14085521E+02 0.14104413E+02 0.14113214E+02
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- 0.13944953E+02 0.13879287E+02 0.13802871E+02 0.13715791E+02 0.13618172E+02
- 0.13510174E+02 0.13391995E+02 0.13263871E+02 0.13126072E+02 0.12978902E+02
- 0.12822701E+02 0.12657837E+02 0.12484712E+02 0.12303752E+02 0.12115414E+02
- 0.11920177E+02 0.11718542E+02 0.11511032E+02 0.11298186E+02 0.11080557E+02
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- 0.11334329E+00 0.11296505E+00 0.11258484E+00 0.11220371E+00 0.11182270E+00
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- 0.94116241E-01 0.93847307E-01 0.93585238E-01 0.93330481E-01 0.93083416E-01
- 0.92844349E-01 0.92613514E-01 0.92391067E-01 0.92177088E-01 0.91971582E-01
- 0.91774473E-01 0.91585615E-01 0.91404784E-01 0.91231686E-01 0.91065960E-01
- 0.90907179E-01 0.90754858E-01 0.90608455E-01 0.90467383E-01 0.90331010E-01
- 0.90198671E-01 0.90069670E-01 0.89943293E-01 0.89818810E-01 0.89695483E-01
- 0.89572578E-01 0.89449363E-01 0.89325125E-01 0.89199170E-01 0.89070830E-01
- 0.88939475E-01 0.88804513E-01 0.88665401E-01 0.88521645E-01 0.88372809E-01
- 0.88218518E-01 0.88058459E-01 0.87892386E-01 0.87720120E-01 0.87541552E-01
- 0.87356640E-01 0.87165411E-01 0.86967963E-01 0.86764459E-01 0.86555125E-01
- 0.86340254E-01 0.86120194E-01 0.85895352E-01 0.85666183E-01 0.85433191E-01
- 0.85196919E-01 0.84957943E-01 0.84716871E-01 0.84474330E-01 0.84230965E-01
- 0.83987427E-01 0.83744375E-01 0.83502460E-01 0.83262325E-01 0.83024599E-01
- 0.82789886E-01 0.82558766E-01 0.82331783E-01 0.82109442E-01 0.81892206E-01
- 0.81680487E-01 0.81474646E-01 0.81274989E-01 0.81081762E-01 0.80895153E-01
- 0.80715285E-01 0.80542223E-01 0.80375965E-01 0.80216452E-01 0.80063558E-01
- 0.79917102E-01 0.79776842E-01 0.79642482E-01 0.79513673E-01 0.79390016E-01
- 0.79271070E-01 0.79156353E-01 0.79045348E-01 0.78937510E-01 0.78832270E-01
- 0.78729044E-01 0.78627233E-01 0.78526236E-01 0.78425450E-01 0.78324279E-01
- 0.78222140E-01 0.78118466E-01 0.78012713E-01 0.77904366E-01 0.77792943E-01
- 0.77678000E-01 0.77559135E-01 0.77435994E-01 0.77308271E-01 0.77175713E-01
- 0.77038121E-01 0.76895353E-01 0.76747321E-01 0.76593998E-01 0.76435410E-01
- 0.76271640E-01 0.76102829E-01 0.75929167E-01 0.75750899E-01 0.75568317E-01
- gradient corrections used for XC
- 5
- core charge-density (partial)
- 0.13681949E+01 0.13676959E+01 0.13662000E+01 0.13637104E+01 0.13602324E+01
- 0.13557734E+01 0.13503428E+01 0.13439523E+01 0.13366153E+01 0.13283472E+01
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- atomic pseudo charge-density
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- 0.15712429E+01 0.15599426E+01 0.14906942E+01 0.13714899E+01 0.12113407E+01
- 0.10198828E+01 0.80699697E+00 0.58245003E+00 0.35557023E+00 0.13496271E+00
- Real Space Part
- -0.87257185E+03 -0.87217325E+03 -0.87097758E+03 -0.86898535E+03 -0.86619740E+03
- -0.86261493E+03 -0.85823952E+03 -0.85307319E+03 -0.84711839E+03 -0.84037811E+03
- -0.83285587E+03 -0.82455582E+03 -0.81548281E+03 -0.80564241E+03 -0.79504105E+03
- -0.78368604E+03 -0.77158570E+03 -0.75874942E+03 -0.74518776E+03 -0.73091251E+03
- -0.71593685E+03 -0.70027535E+03 -0.68394415E+03 -0.66696100E+03 -0.64934533E+03
- -0.63111840E+03 -0.61230331E+03 -0.59292512E+03 -0.57301089E+03 -0.55258976E+03
- -0.53169298E+03 -0.51035396E+03 -0.48860832E+03 -0.46649386E+03 -0.44405060E+03
- -0.42132076E+03 -0.39834870E+03 -0.37518093E+03 -0.35186599E+03 -0.32845440E+03
- -0.30499855E+03 -0.28155254E+03 -0.25817210E+03 -0.23491433E+03 -0.21183758E+03
- -0.18900121E+03 -0.16646531E+03 -0.14429049E+03 -0.12253758E+03 -0.10126731E+03
- -0.80539962E+02 -0.60415079E+02 -0.40951054E+02 -0.22204768E+02 -0.42311995E+01
- 0.12916980E+02 0.29189809E+02 0.44540445E+02 0.58925573E+02 0.72305804E+02
- 0.84646067E+02 0.95915987E+02 0.10609024E+03 0.11514887E+03 0.12307763E+03
- 0.12986821E+03 0.13551849E+03 0.14003271E+03 0.14342163E+03 0.14570263E+03
- 0.14689971E+03 0.14704353E+03 0.14617130E+03 0.14432667E+03 0.14155957E+03
- 0.13792593E+03 0.13348743E+03 0.12831116E+03 0.12246922E+03 0.11603831E+03
- 0.10909924E+03 0.10173648E+03 0.94037578E+02 0.86092680E+02 0.77993902E+02
- 0.69834817E+02 0.61709839E+02 0.53713688E+02 0.45940793E+02 0.38484762E+02
- 0.31437841E+02 0.24890391E+02 0.18930406E+02 0.13643042E+02 0.91101706E+01
- 0.54100403E+01 0.26168332E+01 0.79835325E+00 0.23427012E-01 0.00000000E+00
- Reciprocal Space Part
- -0.36489549E+02 -0.35864156E+02 -0.33998755E+02 -0.30925471E+02 -0.26697153E+02
- -0.21386360E+02 -0.15083959E+02 -0.78973858E+01 0.51413298E-01 0.86282977E+01
- 0.17689472E+02 0.27084188E+02 0.36657552E+02 0.46253383E+02 0.55717063E+02
- 0.64898313E+02 0.73653855E+02 0.81849887E+02 0.89364344E+02 0.96088881E+02
- 0.10193057E+03 0.10681323E+03 0.11067846E+03 0.11348624E+03 0.11521523E+03
- 0.11586261E+03 0.11544365E+03 0.11399089E+03 0.11155304E+03 0.10819353E+03
- 0.10398888E+03 0.99026864E+02 0.93404459E+02 0.87225735E+02 0.80599650E+02
- 0.73637846E+02 0.66452460E+02 0.59154022E+02 0.51849465E+02 0.44640290E+02
- 0.37620922E+02 0.30877278E+02 0.24485577E+02 0.18511398E+02 0.13009009E+02
- 0.80209530E+01 0.35779043E+01 -0.30122499E+00 -0.36089364E+01 -0.63485770E+01
- -0.85335736E+01 -0.10186497E+02 -0.11337984E+02 -0.12025554E+02 -0.12292345E+02
- -0.12185805E+02 -0.11756382E+02 -0.11056219E+02 -0.10137909E+02 -0.90533175E+01
- -0.78525080E+01 -0.65827802E+01 -0.52878430E+01 -0.40071309E+01 -0.27752721E+01
- -0.16217097E+01 -0.57047779E+00 0.35987548E+00 0.11562232E+01 0.18106666E+01
- 0.23202264E+01 0.26864349E+01 0.29148468E+01 0.30144856E+01 0.29972475E+01
- 0.28772789E+01 0.26703472E+01 0.23932227E+01 0.20630867E+01 0.16969795E+01
- 0.13113025E+01 0.92138094E+00 0.54109837E+00 0.18260423E+00 -0.14390035E+00
- -0.43029978E+00 -0.67062595E+00 -0.86104898E+00 -0.99980292E+00 -0.10870535E+01
- -0.11247164E+01 -0.11162365E+01 -0.10663359E+01 -0.98074332E+00 -0.86591280E+00
- -0.72874294E+00 -0.57630417E+00 -0.41558297E+00 -0.25324963E+00 -0.95455204E-01
- Real Space Part
- 0.63319797E+03 0.63291041E+03 0.63204781E+03 0.63061056E+03 0.62859924E+03
- 0.62601473E+03 0.62285817E+03 0.61913101E+03 0.61483503E+03 0.60997237E+03
- 0.60454559E+03 0.59855767E+03 0.59201211E+03 0.58491291E+03 0.57726472E+03
- 0.56907280E+03 0.56034314E+03 0.55108251E+03 0.54129849E+03 0.53099960E+03
- 0.52019530E+03 0.50889609E+03 0.49711358E+03 0.48486054E+03 0.47215095E+03
- 0.45900011E+03 0.44542463E+03 0.43144254E+03 0.41707331E+03 0.40233788E+03
- 0.38725874E+03 0.37185991E+03 0.35616701E+03 0.34020723E+03 0.32400934E+03
- 0.30760369E+03 0.29102220E+03 0.27429832E+03 0.25746694E+03 0.24056440E+03
- 0.22362837E+03 0.20669777E+03 0.18981266E+03 0.17301414E+03 0.15634416E+03
- 0.13984541E+03 0.12356113E+03 0.10753493E+03 0.91810566E+02 0.76431735E+02
- 0.61441833E+02 0.46883707E+02 0.32799393E+02 0.19229849E+02 0.62146659E+01
- -0.62082134E+01 -0.18002788E+02 -0.29135292E+02 -0.39574487E+02 -0.49291950E+02
- -0.58262356E+02 -0.66463744E+02 -0.73877778E+02 -0.80489982E+02 -0.86289957E+02
- -0.91271581E+02 -0.95433167E+02 -0.98777602E+02 -0.10131245E+03 -0.10305002E+03
- -0.10400739E+03 -0.10420642E+03 -0.10367366E+03 -0.10244030E+03 -0.10054203E+03
- -0.98018889E+02 -0.94915012E+02 -0.91278431E+02 -0.87160797E+02 -0.82617056E+02
- -0.77705128E+02 -0.72485556E+02 -0.67021113E+02 -0.61376433E+02 -0.55617588E+02
- -0.49811699E+02 -0.44026502E+02 -0.38329965E+02 -0.32789855E+02 -0.27473361E+02
- -0.22446704E+02 -0.17774762E+02 -0.13520724E+02 -0.97457493E+01 -0.65086493E+01
- -0.38656440E+01 -0.18700414E+01 -0.57059033E+00 -0.16714955E-01 0.00000000E+00
- Non local Part
- 1 2 1.03170241276447
- 2.65859946877321 4.88238126795342 4.88238126795342
- 8.98435195357541
- Reciprocal Space Part
- 0.00000000E+00 0.38861820E+01 0.76566506E+01 0.11198191E+02 0.14402530E+02
- 0.17168669E+02 0.19405054E+02 0.21031535E+02 0.21981079E+02 0.22201184E+02
- 0.21654974E+02 0.20321960E+02 0.18198431E+02 0.15297488E+02 0.11648712E+02
- 0.72974833E+01 0.23039596E+01 -0.32582469E+01 -0.93036735E+01 -0.15736848E+02
- -0.22454324E+02 -0.29346862E+02 -0.36301710E+02 -0.43204929E+02 -0.49943706E+02
- -0.56408622E+02 -0.62495800E+02 -0.68108907E+02 -0.73160964E+02 -0.77575922E+02
- -0.81289979E+02 -0.84252614E+02 -0.86427318E+02 -0.87792019E+02 -0.88339191E+02
- -0.88075654E+02 -0.87022084E+02 -0.85212244E+02 -0.82691957E+02 -0.79517866E+02
- -0.75756000E+02 -0.71480183E+02 -0.66770345E+02 -0.61710747E+02 -0.56388189E+02
- -0.50890222E+02 -0.45303418E+02 -0.39711722E+02 -0.34194931E+02 -0.28827322E+02
- -0.23676453E+02 -0.18802168E+02 -0.14255806E+02 -0.10079632E+02 -0.63064936E+01
- -0.29596904E+01 -0.53068427E-01 0.24086920E+01 0.44295991E+01 0.60217087E+01
- 0.72043400E+01 0.80031754E+01 0.84492707E+01 0.85780039E+01 0.84279913E+01
- 0.80399981E+01 0.74558696E+01 0.67175093E+01 0.58659233E+01 0.49403528E+01
- 0.39775094E+01 0.30109262E+01 0.20704331E+01 0.11817624E+01 0.36628567E+00
- -0.35911990E+00 -0.98208097E+00 -0.14946211E+01 -0.18929483E+01 -0.21771504E+01
- -0.23508116E+01 -0.24205674E+01 -0.23956133E+01 -0.22871843E+01 -0.21080214E+01
- -0.18718417E+01 -0.15928247E+01 -0.12851305E+01 -0.96245910E+00 -0.63766179E+00
- -0.32241090E+00 -0.26933951E-01 0.24018535E+00 0.47213831E+00 0.66395584E+00
- 0.81250966E+00 0.91645487E+00 0.97612004E+00 0.99335246E+00 0.97132649E+00
- Real Space Part
- 0.00000000E+00 -0.22186814E+02 -0.44301839E+02 -0.66273522E+02 -0.88030777E+02
- -0.10950322E+03 -0.13062140E+03 -0.15131703E+03 -0.17152321E+03 -0.19117468E+03
- -0.21020799E+03 -0.22856176E+03 -0.24617690E+03 -0.26299679E+03 -0.27896751E+03
- -0.29403802E+03 -0.30816039E+03 -0.32128994E+03 -0.33338548E+03 -0.34440943E+03
- -0.35432799E+03 -0.36311136E+03 -0.37073379E+03 -0.37717380E+03 -0.38241426E+03
- -0.38644250E+03 -0.38925046E+03 -0.39083470E+03 -0.39119654E+03 -0.39034209E+03
- -0.38828229E+03 -0.38503293E+03 -0.38061467E+03 -0.37505301E+03 -0.36837826E+03
- -0.36062551E+03 -0.35183450E+03 -0.34204958E+03 -0.33131954E+03 -0.31969747E+03
- -0.30724063E+03 -0.29401017E+03 -0.28007097E+03 -0.26549136E+03 -0.25034283E+03
- -0.23469974E+03 -0.21863898E+03 -0.20223959E+03 -0.18558239E+03 -0.16874958E+03
- -0.15182426E+03 -0.13489000E+03 -0.11803038E+03 -0.10132845E+03 -0.84866250E+02
- -0.68724282E+02 -0.52980979E+02 -0.37712173E+02 -0.22990566E+02 -0.88851973E+01
- 0.45390663E+01 0.17222034E+02 0.29108671E+02 0.40149550E+02 0.50301273E+02
- 0.59526856E+02 0.67796071E+02 0.75085739E+02 0.81379975E+02 0.86670373E+02
- 0.90956134E+02 0.94244139E+02 0.96548944E+02 0.97892719E+02 0.98305121E+02
- 0.97823113E+02 0.96490698E+02 0.94358601E+02 0.91483927E+02 0.87929701E+02
- 0.83764422E+02 0.79061549E+02 0.73898935E+02 0.68358280E+02 0.62524490E+02
- 0.56485105E+02 0.50329625E+02 0.44148922E+02 0.38034576E+02 0.32078283E+02
- 0.26371234E+02 0.21003526E+02 0.16063609E+02 0.11637728E+02 0.78094126E+01
- 0.46590409E+01 0.22633368E+01 0.69369210E+00 0.17747648E-01 0.00000000E+00
- Reciprocal Space Part
- 0.00000000E+00 -0.17868362E+01 -0.35144269E+01 -0.51248277E+01 -0.65626676E+01
- -0.77763629E+01 -0.87192468E+01 -0.93505888E+01 -0.96364809E+01 -0.95505728E+01
- -0.90746384E+01 -0.81989629E+01 -0.69225426E+01 -0.52530936E+01 -0.32068705E+01
- -0.80830207E+00 0.19105496E+01 0.49106895E+01 0.81470351E+01 0.11569385E+02
- 0.15123488E+02 0.18752190E+02 0.22396628E+02 0.25997448E+02 0.29496018E+02
- 0.32835608E+02 0.35962514E+02 0.38827099E+02 0.41384736E+02 0.43596618E+02
- 0.45430445E+02 0.46860950E+02 0.47870266E+02 0.48448142E+02 0.48591976E+02
- 0.48306705E+02 0.47604523E+02 0.46504469E+02 0.45031872E+02 0.43217686E+02
- 0.41097721E+02 0.38711805E+02 0.36102874E+02 0.33316045E+02 0.30397658E+02
- 0.27394336E+02 0.24352070E+02 0.21315355E+02 0.18326389E+02 0.15424354E+02
- 0.12644790E+02 0.10019079E+02 0.75740326E+01 0.53316035E+01 0.33087123E+01
- 0.15171909E+01 -0.36159418E-01 -0.13494048E+01 -0.24252171E+01 -0.32705252E+01
- -0.38960921E+01 -0.43160309E+01 -0.45472742E+01 -0.46090120E+01 -0.45221135E+01
- -0.43085463E+01 -0.39908088E+01 -0.35913863E+01 -0.31322454E+01 -0.26343746E+01
- -0.21173800E+01 -0.15991441E+01 -0.10955499E+01 -0.62027500E+00 -0.18465580E+00
- 0.20237976E+00 0.53431322E+00 0.80697500E+00 0.10184279E+01 0.11688016E+01
- 0.12600861E+01 0.12958921E+01 0.12811875E+01 0.12220191E+01 0.11252269E+01
- 0.99816176E+00 0.84841124E+00 0.68354309E+00 0.51087098E+00 0.33724795E+00
- 0.16889148E+00 0.11242749E-01 -0.13113830E+00 -0.25464171E+00 -0.35664077E+00
- -0.43549155E+00 -0.49050126E+00 -0.52186870E+00 -0.53060095E+00 -0.51841055E+00
- Real Space Part
- 0.00000000E+00 0.12161252E+02 0.24283469E+02 0.36327742E+02 0.48255417E+02
- 0.60028220E+02 0.71608383E+02 0.82958767E+02 0.94042991E+02 0.10482555E+03
- 0.11527193E+03 0.12534873E+03 0.13502381E+03 0.14426635E+03 0.15304699E+03
- 0.16133795E+03 0.16911311E+03 0.17634814E+03 0.18302057E+03 0.18910990E+03
- 0.19459770E+03 0.19946767E+03 0.20370573E+03 0.20730009E+03 0.21024135E+03
- 0.21252251E+03 0.21413905E+03 0.21508898E+03 0.21537287E+03 0.21499392E+03
- 0.21395789E+03 0.21227322E+03 0.20995096E+03 0.20700481E+03 0.20345105E+03
- 0.19930856E+03 0.19459875E+03 0.18934552E+03 0.18357519E+03 0.17731641E+03
- 0.17060007E+03 0.16345921E+03 0.15592887E+03 0.14804598E+03 0.13984918E+03
- 0.13137868E+03 0.12267606E+03 0.11378408E+03 0.10474648E+03 0.95607747E+02
- 0.86412883E+02 0.77207157E+02 0.68035844E+02 0.58943963E+02 0.49976000E+02
- 0.41175622E+02 0.32585400E+02 0.24246514E+02 0.16198468E+02 0.84788075E+01
- 0.11228377E+01 -0.58366451E+01 -0.12369614E+02 -0.18449055E+02 -0.24051197E+02
- -0.29155721E+02 -0.33745943E+02 -0.37808973E+02 -0.41335852E+02 -0.44321651E+02
- -0.46765541E+02 -0.48670833E+02 -0.50044982E+02 -0.50899549E+02 -0.51250136E+02
- -0.51116295E+02 -0.50521380E+02 -0.49492378E+02 -0.48059729E+02 -0.46257077E+02
- -0.44121031E+02 -0.41690892E+02 -0.39008342E+02 -0.36117160E+02 -0.33062867E+02
- -0.29892426E+02 -0.26653874E+02 -0.23396010E+02 -0.20168034E+02 -0.17019231E+02
- -0.13998631E+02 -0.11154698E+02 -0.85350264E+01 -0.61860453E+01 -0.41527388E+01
- -0.24784108E+01 -0.12044157E+01 -0.36926989E+00 -0.93979993E-02 0.00000000E+00
- PAW radial sets
- 351 0.989218471734280
-(5E20.12)
- augmentation charges (non sperical)
- -0.118612820244E+00 -0.166184190184E+00 -0.532145144881E-01 -0.101222164724E+00 -0.166184190184E+00
- -0.232848406670E+00 -0.743582353105E-01 -0.141431561143E+00 -0.532145144881E-01 -0.743582353105E-01
- -0.179689550405E-01 -0.343505440708E-01 -0.101222164724E+00 -0.141431561143E+00 -0.343505440708E-01
- -0.655142723317E-01
- uccopancies in atom
- 0.200000000235E+01 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
- 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
- 0.666666668254E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
- 0.000000000000E+00
- grid
- 0.353278105438E-04 0.364765828105E-04 0.376627102856E-04 0.388874076671E-04 0.401519291522E-04
- 0.414575697215E-04 0.428056664648E-04 0.441975999512E-04 0.456347956421E-04 0.471187253514E-04
- 0.486509087530E-04 0.502329149365E-04 0.518663640144E-04 0.535529287814E-04 0.552943364272E-04
- 0.570923703053E-04 0.589488717596E-04 0.608657420098E-04 0.628449440985E-04 0.648885049016E-04
- 0.669985172040E-04 0.691771418426E-04 0.714266099194E-04 0.737492250864E-04 0.761473659044E-04
- 0.786234882792E-04 0.811801279764E-04 0.838199032186E-04 0.865455173661E-04 0.893597616862E-04
- 0.922655182109E-04 0.952657626888E-04 0.983635676325E-04 0.101562105465E-03 0.104864651768E-03
- 0.108274588638E-03 0.111795408149E-03 0.115430715926E-03 0.119184234844E-03 0.123059808833E-03
- 0.127061406819E-03 0.131193126789E-03 0.135459199986E-03 0.139863995240E-03 0.144412023447E-03
- 0.149107942186E-03 0.153956560487E-03 0.158962843759E-03 0.164131918874E-03 0.169469079417E-03
- 0.174979791106E-03 0.180669697392E-03 0.186544625235E-03 0.192610591076E-03 0.198873806993E-03
- 0.205340687067E-03 0.212017853948E-03 0.218912145639E-03 0.226030622496E-03 0.233380574462E-03
- 0.240969528530E-03 0.248805256452E-03 0.256895782699E-03 0.265249392676E-03 0.273874641209E-03
- 0.282780361308E-03 0.291975673207E-03 0.301469993709E-03 0.311273045829E-03 0.321394868748E-03
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- 0.286674509825E-08
- kinetic energy-density
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- 0.317114132527E-06
- mkinetic energy-density pseudized
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- core charge-density (pseudized)
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- 0.286674509825E-08
- pseudo wavefunction
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- 0.162160440109E+00
- ae wavefunction
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- 0.162160440109E+00
- pseudo wavefunction
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- 0.000000000000E+00
- ae wavefunction
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- 0.000000000000E+00
- pseudo wavefunction
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- ae wavefunction
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- pseudo wavefunction
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- 0.000000000000E+00
- End of Dataset
diff --git a/salomon/software/chemistry/phono3py-input/POTCAR/view.md b/salomon/software/chemistry/phono3py-input/POTCAR/view.md
deleted file mode 100644
index 73343c251ff3dcfb425ace0b8b7feea9dd014e74..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry/phono3py-input/POTCAR/view.md
+++ /dev/null
@@ -1,97 +0,0 @@
-Info
-
-POTCAR
-======
- [
-POTCAR](at_download/POTCAR) — Octet Stream, 191
-KB (195673 bytes)
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../../sitemap.html)
- - [What's
- New](../../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../../salomon.html)
-
- - [Hardware
- Overview](../../../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../../compute-nodes.html)
-
- - [Storage](../../../../storage.html)
-
- - [Network](../../../../network-1.html)
-
- - [Software](../../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../../../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../../../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../../../chemistry.html "Tools for computational chemistry.")
- .navTreeFolderish
- .contenttype-folder}
- - [Molpro](../../molpro.html "Molpro is a complete system of ab initio programs for molecular electronic structure calculations.")
-
- - [NWChem](../../nwchem.html "High-Performance Computational Chemistry")
-
- - [Phono3py](../../phono3py.html "
- ")
- - [Phono3py
- Input](../../phono3py-input.html)
- .navTreeFolderish
- .contenttype-folder}
- - [{width="16"
- height="16"} POSCAR
- Si](../poscar-si/view.html "POSCAR"){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- KPOINTS](../KPOINTS/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- POTCAR](view.html){.state-missing-value
-
- .contenttype-file}
- - [{width="16"
- height="16"}
- INCAR](../INCAR/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- run.sh](../run.sh/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- submit.sh](../submit.sh/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
diff --git a/salomon/software/chemistry/phono3py-input/gofree-cond1.sh/at_download/gofree-cond1.sh b/salomon/software/chemistry/phono3py-input/gofree-cond1.sh/at_download/gofree-cond1.sh
deleted file mode 100755
index 8dbf6d276685a7f2275a97e568bc18014c1a31c8..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry/phono3py-input/gofree-cond1.sh/at_download/gofree-cond1.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/bin/bash
-#PBS -A OPEN-6-23
-#PBS -N Si-test1
-#PBS -q qfree
-#PBS -l select=1:ncpus=24:mpiprocs=24:ompthreads=1
-#PBS -l walltime=01:59:59
-##PBS-l mem=6gb
-#PBS -j oe
-#PBS -S /bin/bash
-module purge
-module load phono3py/0.9.14-ictce-7.3.5-Python-2.7.9
-export OMP_NUM_THREADS=1
-export I_MPI_COMPATIBILITY=4
-##export OMP_STACKSIZE=10gb
-##0 1 2 3 4 10 11 12 13 20 21 22 30 31 40 91 92 93 94 101 102 103 111 112 121 182 183 184 192 193 202 273 274 283 364
-cd $PBS_O_WORKDIR
-phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR --sigma 0.1 --br --write_gamma --gp="0 1 3 4 10"
-#phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR --sigma 0.1 --br --write_gamma --gp="11 12 13 20 21"
-#phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR --sigma 0.1 --br --write_gamma --gp="21 22 30 31 40"
-#phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR --sigma 0.1 --br --write_gamma --gp="91 92 93 94 101"
-#phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR --sigma 0.1 --br --write_gamma --gp="102 103 111 112 121"
-#phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR --sigma 0.1 --br --write_gamma --gp="182 183 184 192 193"
-#phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR --sigma 0.1 --br --write_gamma --gp="202 273 274 283 364"
diff --git a/salomon/software/chemistry/phono3py-input/gofree-cond1.sh/view.md b/salomon/software/chemistry/phono3py-input/gofree-cond1.sh/view.md
deleted file mode 100644
index 166738583b39c9115007b481fa5ab1a2dcc078e8..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry/phono3py-input/gofree-cond1.sh/view.md
+++ /dev/null
@@ -1,97 +0,0 @@
-Info
-
-gofree-cond1.sh
-===============
- [
-gofree-cond1.sh](at_download/gofree-cond1.sh) —
-shell script, 1 KB (1286 bytes)
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../../sitemap.html)
- - [What's
- New](../../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../../salomon.html)
-
- - [Hardware
- Overview](../../../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../../compute-nodes.html)
-
- - [Storage](../../../../storage.html)
-
- - [Network](../../../../network-1.html)
-
- - [Software](../../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../../../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../../../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../../../chemistry.html "Tools for computational chemistry.")
- .navTreeFolderish
- .contenttype-folder}
- - [Molpro](../../molpro.html "Molpro is a complete system of ab initio programs for molecular electronic structure calculations.")
-
- - [NWChem](../../nwchem.html "High-Performance Computational Chemistry")
-
- - [Phono3py](../../phono3py.html "
- ")
- - [Phono3py
- Input](../../phono3py-input.html)
- .navTreeFolderish
- .contenttype-folder}
- - [{width="16"
- height="16"} POSCAR
- Si](../poscar-si/view.html "POSCAR"){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- KPOINTS](../KPOINTS/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- POTCAR](../POTCAR/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- INCAR](../INCAR/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- run.sh](../run.sh/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- submit.sh](../submit.sh/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
diff --git a/salomon/software/chemistry/phono3py-input/poscar-si/at_download/POSCAR b/salomon/software/chemistry/phono3py-input/poscar-si/at_download/POSCAR
deleted file mode 100755
index f72a61b992f3348c4260097c12b9bbb2bed40bc3..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry/phono3py-input/poscar-si/at_download/POSCAR
+++ /dev/null
@@ -1,16 +0,0 @@
- Si
- 1.0
- 5.4335600309153529 0.0000000000000000 0.0000000000000000
- 0.0000000000000000 5.4335600309153529 0.0000000000000000
- 0.0000000000000000 0.0000000000000000 5.4335600309153529
- Si
- 8
-Direct
- 0.8750000000000000 0.8750000000000000 0.8750000000000000
- 0.8750000000000000 0.3750000000000000 0.3750000000000000
- 0.3750000000000000 0.8750000000000000 0.3750000000000000
- 0.3750000000000000 0.3750000000000000 0.8750000000000000
- 0.1250000000000000 0.1250000000000000 0.1250000000000000
- 0.1250000000000000 0.6250000000000000 0.6250000000000000
- 0.6250000000000000 0.1250000000000000 0.6250000000000000
- 0.6250000000000000 0.6250000000000000 0.1250000000000000
diff --git a/salomon/software/chemistry/phono3py-input/poscar-si/view.md b/salomon/software/chemistry/phono3py-input/poscar-si/view.md
deleted file mode 100644
index 2271d66bdff7cc6eaf049d8452365014b173456f..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry/phono3py-input/poscar-si/view.md
+++ /dev/null
@@ -1,98 +0,0 @@
-Info
-
-POSCAR Si
-=========
-POSCAR
- [
-POSCAR](at_download/POSCAR) — Octet Stream, 1 KB
-
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../../sitemap.html)
- - [What's
- New](../../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../../salomon.html)
-
- - [Hardware
- Overview](../../../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../../compute-nodes.html)
-
- - [Storage](../../../../storage.html)
-
- - [Network](../../../../network-1.html)
-
- - [Software](../../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../../../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../../../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../../../chemistry.html "Tools for computational chemistry.")
- .navTreeFolderish
- .contenttype-folder}
- - [Molpro](../../molpro.html "Molpro is a complete system of ab initio programs for molecular electronic structure calculations.")
-
- - [NWChem](../../nwchem.html "High-Performance Computational Chemistry")
-
- - [Phono3py](../../phono3py.html "
- ")
- - [Phono3py
- Input](../../phono3py-input.html)
- .navTreeFolderish
- .contenttype-folder}
- - [{width="16"
- height="16"} POSCAR
- Si](view.html "POSCAR"){.state-missing-value
-
- .contenttype-file}
- - [{width="16"
- height="16"}
- KPOINTS](../KPOINTS/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- POTCAR](../POTCAR/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- INCAR](../INCAR/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- run.sh](../run.sh/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- submit.sh](../submit.sh/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
diff --git a/salomon/software/chemistry/phono3py-input/prepare.sh/at_download/prepare.sh b/salomon/software/chemistry/phono3py-input/prepare.sh/at_download/prepare.sh
deleted file mode 100755
index a057dbbadd94d0298e7a4ba19244cb753bea7a9f..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry/phono3py-input/prepare.sh/at_download/prepare.sh
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/bin/bash
-P=`pwd`
-
-# number of displacements
-poc=9
-
- for i in `seq 1 $poc `;
- do
- cd $P
- mkdir disp-0000"$i"
- cd disp-0000"$i"
- cp ../KPOINTS .
- cp ../INCAR .
- cp ../POTCAR .
- cp ../POSCAR-0000"$i" POSCAR
- echo $i
- done
-
-poc=99
-
- for i in `seq 10 $poc `;
- do
- cd $P
- mkdir disp-000"$i"
- cd disp-000"$i"
- cp ../KPOINTS .
- cp ../INCAR .
- cp ../POTCAR .
- cp ../POSCAR-000"$i" POSCAR
- echo $i
- done
-poc=111
-
- for i in `seq 100 $poc `;
- do
- cd $P
- mkdir disp-00"$i"
- cd disp-00"$i"
- cp ../KPOINTS .
- cp ../INCAR .
- cp ../POTCAR .
- cp ../POSCAR-00"$i" POSCAR
- echo $i
- done
diff --git a/salomon/software/chemistry/phono3py-input/prepare.sh/view.md b/salomon/software/chemistry/phono3py-input/prepare.sh/view.md
deleted file mode 100644
index 4eb5dba54d9cb81dbd493ee8d9a6c3011278fce8..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry/phono3py-input/prepare.sh/view.md
+++ /dev/null
@@ -1,97 +0,0 @@
-Info
-
-prepare.sh
-==========
- [
-prepare.sh](at_download/prepare.sh) — shell
-script, 1 KB
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../../sitemap.html)
- - [What's
- New](../../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../../salomon.html)
-
- - [Hardware
- Overview](../../../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../../compute-nodes.html)
-
- - [Storage](../../../../storage.html)
-
- - [Network](../../../../network-1.html)
-
- - [Software](../../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../../../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../../../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../../../chemistry.html "Tools for computational chemistry.")
- .navTreeFolderish
- .contenttype-folder}
- - [Molpro](../../molpro.html "Molpro is a complete system of ab initio programs for molecular electronic structure calculations.")
-
- - [NWChem](../../nwchem.html "High-Performance Computational Chemistry")
-
- - [Phono3py](../../phono3py.html "
- ")
- - [Phono3py
- Input](../../phono3py-input.html)
- .navTreeFolderish
- .contenttype-folder}
- - [{width="16"
- height="16"} POSCAR
- Si](../poscar-si/view.html "POSCAR"){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- KPOINTS](../KPOINTS/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- POTCAR](../POTCAR/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- INCAR](../INCAR/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- run.sh](../run.sh/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- submit.sh](../submit.sh/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
diff --git a/salomon/software/chemistry/phono3py-input/run.sh/at_download/run.sh b/salomon/software/chemistry/phono3py-input/run.sh/at_download/run.sh
deleted file mode 100755
index 63faf63ba41f0f6846c8b59030a64ae9c1415a55..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry/phono3py-input/run.sh/at_download/run.sh
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/bin/bash
-#PBS -A IT4I-9-11
-#PBS -N Si-test
-#PBS -q qprod
-#PBS -l select=8:ncpus=16:mpiprocs=16:ompthreads=1
-#PBS -l walltime=23:59:59
-##PBS-l mem=6gb
-#PBS -j oe
-#PBS -S /bin/bash
-module load impi/4.1.1.036 intel/13.5.192 fftw3-mpi/3.3.3-icc
-export OMP_NUM_THREADS=1
-export I_MPI_COMPATIBILITY=4
-##export OMP_STACKSIZE=10gb
-b=`basename $PBS_O_WORKDIR`
-echo $b >log.vasp
-SCRDIR=/scratch/$USER/$b
-mkdir -p $SCRDIR
-cd $SCRDIR || exit
-
-# copy input file to scratch
-cp $PBS_O_WORKDIR/* .
-
-mpirun ~/bin/vasp5.4.1 > log.exc
-
-# copy output file to home
-cp * $PBS_O_WORKDIR/. && cd ..
-
-rm -rf "$SCRDIR"
-
-#exit
-exit
diff --git a/salomon/software/chemistry/phono3py-input/run.sh/view.md b/salomon/software/chemistry/phono3py-input/run.sh/view.md
deleted file mode 100644
index babeda1953f0d6faad87032e27c64f6e9c498347..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry/phono3py-input/run.sh/view.md
+++ /dev/null
@@ -1,97 +0,0 @@
-Info
-
-run.sh
-======
- [
-run.sh](at_download/run.sh) — shell script, 1 KB
-
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../../sitemap.html)
- - [What's
- New](../../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../../salomon.html)
-
- - [Hardware
- Overview](../../../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../../compute-nodes.html)
-
- - [Storage](../../../../storage.html)
-
- - [Network](../../../../network-1.html)
-
- - [Software](../../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../../../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../../../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../../../chemistry.html "Tools for computational chemistry.")
- .navTreeFolderish
- .contenttype-folder}
- - [Molpro](../../molpro.html "Molpro is a complete system of ab initio programs for molecular electronic structure calculations.")
-
- - [NWChem](../../nwchem.html "High-Performance Computational Chemistry")
-
- - [Phono3py](../../phono3py.html "
- ")
- - [Phono3py
- Input](../../phono3py-input.html)
- .navTreeFolderish
- .contenttype-folder}
- - [{width="16"
- height="16"} POSCAR
- Si](../poscar-si/view.html "POSCAR"){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- KPOINTS](../KPOINTS/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- POTCAR](../POTCAR/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- INCAR](../INCAR/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- run.sh](view.html){.state-missing-value
-
- .contenttype-file}
- - [{width="16"
- height="16"}
- submit.sh](../submit.sh/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
diff --git a/salomon/software/chemistry/phono3py-input/submit.sh/at_download/submit.sh b/salomon/software/chemistry/phono3py-input/submit.sh/at_download/submit.sh
deleted file mode 100755
index 12fa02ecc489a10df486cfd2fc55065c02d4eea4..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry/phono3py-input/submit.sh/at_download/submit.sh
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/bin/bash
-P=`pwd`
-
-# number of displacements
-poc=9
-
- for i in `seq 1 $poc `;
- do
- cd $P
- cd disp-0000"$i"
- cp ../run.sh .
- qsub run.sh
- echo $i
- done
-
-poc=99
-
- for i in `seq 10 $poc `;
- do
- cd $P
- cd disp-000"$i"
- cp ../run.sh .
- qsub run.sh
- echo $i
- done
-poc=111
-
- for i in `seq 100 $poc `;
- do
- cd $P
- cd disp-00"$i"
- cp ../run.sh .
- qsub run.sh
- echo $i
- done
diff --git a/salomon/software/chemistry/phono3py-input/submit.sh/view.md b/salomon/software/chemistry/phono3py-input/submit.sh/view.md
deleted file mode 100644
index f06713b1fbd4dcea8d6b4539bb54f9ada45949bc..0000000000000000000000000000000000000000
--- a/salomon/software/chemistry/phono3py-input/submit.sh/view.md
+++ /dev/null
@@ -1,97 +0,0 @@
-Info
-
-submit.sh
-=========
- [
-submit.sh](at_download/submit.sh) — shell
-script, 1 KB
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../../sitemap.html)
- - [What's
- New](../../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../../salomon.html)
-
- - [Hardware
- Overview](../../../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../../compute-nodes.html)
-
- - [Storage](../../../../storage.html)
-
- - [Network](../../../../network-1.html)
-
- - [Software](../../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../../../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../../../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../../../chemistry.html "Tools for computational chemistry.")
- .navTreeFolderish
- .contenttype-folder}
- - [Molpro](../../molpro.html "Molpro is a complete system of ab initio programs for molecular electronic structure calculations.")
-
- - [NWChem](../../nwchem.html "High-Performance Computational Chemistry")
-
- - [Phono3py](../../phono3py.html "
- ")
- - [Phono3py
- Input](../../phono3py-input.html)
- .navTreeFolderish
- .contenttype-folder}
- - [{width="16"
- height="16"} POSCAR
- Si](../poscar-si/view.html "POSCAR"){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- KPOINTS](../KPOINTS/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- POTCAR](../POTCAR/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- INCAR](../INCAR/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- run.sh](../run.sh/view.html){.state-missing-value
- .contenttype-file}
- - [{width="16"
- height="16"}
- submit.sh](view.html){.state-missing-value
-
- .contenttype-file}
- - [{width="16"
diff --git a/salomon/software/comsol.md b/salomon/software/comsol.md
deleted file mode 100644
index 0b359aa36b429579fc9949bed334b5e6b1f1ede7..0000000000000000000000000000000000000000
--- a/salomon/software/comsol.md
+++ /dev/null
@@ -1,204 +0,0 @@
-
-Introduction
--------------------------
-[COMSOL](http//www.comsol.com/)
-is a powerful environment for modelling and solving various engineering
-and scientific problems based on partial differential equations. COMSOL
-is designed to solve coupled or multiphysics phenomena. For many
-standard engineering problems COMSOL provides add-on products such as
-electrical, mechanical, fluid flow, and chemical
-applications.
-- [Structural Mechanics
- Module](http//www.comsol.com/structural-mechanics-module),
-
-- [Heat Transfer
- Module](http//www.comsol.com/heat-transfer-module),
-
-- [CFD
- Module](http//www.comsol.com/cfd-module),
-
-- [Acoustics
- Module](http//www.comsol.com/acoustics-module),
-
-- and [many
- others](http//www.comsol.com/products)
-COMSOL also allows an
-interface support for
-equation-based modelling of
-partial differential
-equations.
-Execution
-----------------------
-On the clusters COMSOL is available in the latest stable
-version. There are two variants of the release
-- **Non commercial** or so
- called **EDU
- variant**, which can be used for research
- and educational purposes.
-- **Commercial** or so called
- **COM variant**,
- which can used also for commercial activities.
- **COM variant**
- has only subset of features compared to the
- **EDU
- variant** available.
- class="internal-link">
- class="hps">More about
- licensing will be posted here
- soon.
-
-To load the of COMSOL load the module
-``` {.prettyprint .lang-sh}
-$ module load COMSOL/51-EDU
-```
-By default the **EDU
-variant** will be loaded. If user needs other
-version or variant, load the particular version. To obtain the list of
-available versions use
-``` {.prettyprint .lang-sh}
-$ module avail COMSOL
-```
-If user needs to prepare COMSOL jobs in the interactive mode
-it is recommend to use COMSOL on the compute nodes via PBS Pro
-scheduler. In order run the COMSOL Desktop GUI on Windows is recommended
-to use the [Virtual Network Computing
-(VNC)](../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
-``` {.prettyprint .lang-sh}
-$ xhost +
-$ qsub -I -X -A PROJECT_ID -q qprod -l select=1ppn=24
-$ module load COMSOL
-$ comsol
-```
-To run COMSOL in batch mode, without the COMSOL Desktop GUI
-environment, user can utilized the default (comsol.pbs) job script and
-execute it via the qsub command.
-``` {.prettyprint .lang-sh}
-#!/bin/bash
-#PBS -l select=3ppn=24
-#PBS -q qprod
-#PBS -N JOB_NAME
-#PBS -AÂ PROJECT_ID
-cd /scratch/work/user/$USER/ || exit
-echo Time is `date`
-echo Directory is `pwd`
-echo '***PBS_NODEFILE***START*******'
-cat $PBS_NODEFILE
-echo '***PBS_NODEFILE***END*********'
-text_nodes < cat $PBS_NODEFILE
-module load COMSOL
-# module load COMSOL/51-EDU
-ntask=$(wc -l $PBS_NODEFILE)
-comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log
-```
-Working directory has to be created before sending the
-(comsol.pbs) job script into the queue. Input file (name_input_f.mph)
-has to be in working directory or full path to input file has to be
-specified. The appropriate path to the temp directory of the job has to
-be set by command option (-tmpdir).
-LiveLink™* *for MATLAB^®^
--------------------------
-COMSOL is the software package for the numerical solution of
-the partial differential equations. LiveLink for MATLAB allows
-connection to the
-COMSOL^**®**^
-API (Application Programming Interface) with the benefits of the
-programming language and computing environment of the MATLAB.
-LiveLink for MATLAB is available in both
-**EDU** and
-**COM**
-**variant** of the
-COMSOL release. On the clusters 1 commercial
-(**COM**) license
-and the 5 educational
-(**EDU**) licenses
-of LiveLink for MATLAB (please see the [ISV
-Licenses](../../acl_users/credentials_cookie_auth/require_logind8a8.html))
-are available. Following example shows how to start COMSOL model from
-MATLAB via LiveLink in the interactive mode.
-``` {.prettyprint .lang-sh}
-$ xhost +
-$ qsub -I -X -A PROJECT_ID -q qexp -l select=1ppn=24
-$ module load MATLAB
-$ module load COMSOL
-$ comsol server MATLAB
-```
-At the first time to launch the LiveLink for MATLAB
-(client-MATLAB/server-COMSOL connection) the login and password is
-requested and this information is not requested again.
-To run LiveLink for MATLAB in batch mode with
-(comsol_matlab.pbs) job script you can utilize/modify the following
-script and execute it via the qsub command.
-``` {.prettyprint .lang-sh}
-#!/bin/bash
-#PBS -l select=3ppn=24
-#PBS -q qprod
-#PBS -N JOB_NAME
-#PBS -AÂ PROJECT_ID
-cd /scratch/work/user/$USER || exit
-echo Time is `date`
-echo Directory is `pwd`
-echo '***PBS_NODEFILE***START*******'
-cat $PBS_NODEFILE
-echo '***PBS_NODEFILE***END*********'
-text_nodes < cat $PBS_NODEFILE
-module load MATLAB
-module load COMSOL/51-EDU
-ntask=$(wc -l $PBS_NODEFILE)
-comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/work/user/$USER/work &
-cd /apps/cae/COMSOL/51/mli
-matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/work/user/$USER/work; test_job"
-```
-This example shows how to run Livelink for MATLAB with following
-configuration 3 nodes and 16 cores per node. Working directory has to
-be created before submitting (comsol_matlab.pbs) job script into the
-queue. Input file (test_job.m) has to be in working directory or full
-path to input file has to be specified. The Matlab command option (-r
-”mphstart”) created a connection with a COMSOL server using the default
-port number.
-
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [List of Available
- Modules](../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage.html)
-
- - [Network](../network-1.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
-
- - [Licensing and Available
diff --git a/salomon/software/comsol/licensing-and-available-versions.md b/salomon/software/comsol/licensing-and-available-versions.md
deleted file mode 100644
index 58acb492437ff87f476f48137d8834f7791aca39..0000000000000000000000000000000000000000
--- a/salomon/software/comsol/licensing-and-available-versions.md
+++ /dev/null
@@ -1,79 +0,0 @@
-Licensing and Available Versions
-================================
-Comsol licence can be used by
-------------------------------
-- all persons in the carrying out of the CE IT4Innovations Project (In
- addition to the primary licensee, which is VSB - Technical
- University of Ostrava, users are CE IT4Innovations third parties -
- CE IT4Innovations project partners, particularly the University of
- Ostrava, the Brno University of Technology - Faculty of Informatics,
- the Silesian University in Opava, Institute of Geonics AS CR.)
-- all
- persons who have a valid
- class="hps">license
-- students
- of the Technical University
-Comsol EDU Network Licence
---------------------------
-The licence intended to be used for science and research, publications,
-students’ projects, teaching (academic licence).
-Comsol COM Network Licence
---------------------------
-The licence intended to be used for science and research, publications,
-students’ projects, commercial research with no commercial use
-restrictions. E
-class="hps">nables the solution
-class="hps">of at least one job
-class="hps">by one user in one
-class="hps">program start.
-Available Versions
-------------------
-- ver. 51
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
- .navTreeFolderish
- .contenttype-folder}
- - [Licensing and Available
- Versions](licensing-and-available-versions.html)
diff --git a/salomon/software/debuggers.md b/salomon/software/debuggers.md
deleted file mode 100644
index 6b6b6624e0adf3cb6ed87cb23ff82d561581700c..0000000000000000000000000000000000000000
--- a/salomon/software/debuggers.md
+++ /dev/null
@@ -1,124 +0,0 @@
-
-Introduction
-------------
-We provide state of the art programms and tools to develop, profile and
-debug HPC codes at IT4Innovations.
-On these pages, we provide an overview of the profiling and debugging
-tools available on Anslem at IT4I.
-Intel debugger
---------------
-Intel debugger is no longer available since Parallel Studio version 2015
-The intel debugger version 13.0 is available, via module intel. The
-debugger works for applications compiled with C and C++ compiler and the
-ifort fortran 77/90/95 compiler. The debugger provides java GUI
-environment. Use [X
-display](../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
-for running the GUI.
- $ module load intel
- $ idb
-Read more at the [Intel
-Debugger](intel-suite/intel-debugger.html) page.
-Allinea Forge (DDT/MAP)
------------------------
-Allinea DDT, is a commercial debugger primarily for debugging parallel
-MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel
-Xeon Phi accelerators. DDT provides all the standard debugging features
-(stack trace, breakpoints, watches, view variables, threads etc.) for
-every thread running as part of your program, or for every process -
-even if these processes are distributed across a cluster using an MPI
-implementation.
- $ module load Forge
- $ forge
-Read more at the [Allinea
-DDT](debuggers/allinea-ddt.html) page.
-Allinea Performance Reports
----------------------------
-Allinea Performance Reports characterize the performance of HPC
-application runs. After executing your application through the tool, a
-synthetic HTML report is generated automatically, containing information
-about several metrics along with clear behavior statements and hints to
-help you improve the efficiency of your runs. Our license is limited to
-64 MPI processes.
- $ module load PerformanceReports/6.0
- $ perf-report mpirun -n 64 ./my_application argument01 argument02
-Read more at the [Allinea Performance
-Reports](debuggers/allinea-performance-reports.html)
-page.
-RougeWave Totalview
--------------------
-TotalView is a source- and machine-level debugger for multi-process,
-multi-threaded programs. Its wide range of tools provides ways to
-analyze, organize, and test programs, making it easy to isolate and
-identify problems in individual threads and processes in programs of
-great complexity.
- $ module load TotalView/8.15.4-6-linux-x86-64
- $ totalview
-Read more at the [Totalview](debuggers/total-view.html)
-page.
-Vampir trace analyzer
----------------------
-Vampir is a GUI trace analyzer for traces in OTF format.
- $ module load Vampir/8.5.0
- $ vampir
-Read more at the [Vampir](debuggers/vampir.html) page.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [List of Available
- Modules](../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage.html)
-
- - [Network](../network-1.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
-
- - [Aislinn](debuggers/aislinn.html)
-
- - [Allinea
- Forge (DDT,MAP)](debuggers/allinea-ddt.html)
-
- - [Allinea Performance
- Reports](debuggers/allinea-performance-reports.html "quick application profiling")
-
- - [Intel VTune Amplifier
- XE](debuggers/intel-vtune-amplifier.html)
-
- - [Total
- View](debuggers/total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
diff --git a/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/view.md b/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/view.md
deleted file mode 100644
index 1848a0c2339cad9b103c094c778e5b98e2ea354a..0000000000000000000000000000000000000000
--- a/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/view.md
+++ /dev/null
@@ -1,79 +0,0 @@
-=================
-[{width="400"
-height="241"}
-](image_view_fullscreen.html) id="plone-image-details"
-class="discreet visualNoPrint"> Velikost
-obrázku v plné velikosti 202 KB | [
-class="visualNoPrint"> 
-ZobrazenĂ ](image_view_fullscreen.html) [
-class="visualNoPrint"> 
-Stáhnout
-](Snimek%20obrazovky%202016-07-08%20v%2012.33.35.png)
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../../sitemap.html)
- - [What's
- New](../../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../../salomon.html)
-
- - [Hardware
- Overview](../../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../../compute-nodes.html)
-
- - [Storage](../../../storage.html)
-
- - [Network](../../../network-1.html)
-
- - [Software](../../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../../debuggers.html "A collection of development tools")
- .navTreeFolderish
- .contenttype-folder}
- - [Aislinn](../aislinn.html)
-
- - [Allinea
- Forge (DDT,MAP)](../allinea-ddt.html)
-
- - [Allinea Performance
- Reports](../allinea-performance-reports.html "quick application profiling")
-
- - [Intel VTune Amplifier
- XE](../intel-vtune-amplifier.html)
-
- - [Total
- View](../total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
-
- - [Valgrind](../valgrind.html "Valgrind is a tool for memory debugging and profiling.")
-
- - [Vampir](../vampir.html)
-
- - [, use the the perf report wrapper
- $ perf-report mpirun ./mympiprog.x
-The mpi program will run as usual. The perf-report creates two
-additional files, in *.txt and *.html format, containing the
-performance report. Note that demanding MPI
-codes should be run within [the queue
-system](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
-Example
--------
-In this example, we will be profiling the mympiprog.x MPI program, using
-Allinea performance reports. Assume that the code is compiled with intel
-compilers and linked against intel MPI library
-First, we allocate some nodes via the express queue
- $ qsub -q qexp -l select=2ppn=24mpiprocs=24ompthreads=1 -I
- qsub waiting for job 262197.dm2 to start
- qsub job 262197.dm2 ready
-Then we load the modules and run the program the usual way
- $ module load intel impi PerfReports/6.0
- $ mpirun ./mympiprog.x
-Now lets profile the code
- $ perf-report mpirun ./mympiprog.x
-Performance report files
-[mympiprog_32p*.txt](mympiprog_32p_2014-10-15_16-56.txt)
-and
-[mympiprog_32p*.html](mympiprog_32p_2014-10-15_16-56.html)
-were created. We can see that the code is very efficient on MPI and is
-CPU bounded.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
- .navTreeFolderish
- .contenttype-folder}
- - [Aislinn](aislinn.html)
-
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
-
- - [Intel VTune Amplifier
- XE](intel-vtune-amplifier.html)
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
diff --git a/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.md b/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.md
deleted file mode 100644
index 382bda93cf7877a8ac1fdab620de66bc2741fc57..0000000000000000000000000000000000000000
--- a/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.md
+++ /dev/null
@@ -1,10 +0,0 @@
-88.6%
-Time spent running application code. High values are usually good.
-This is high; check the CPU performance section for optimization advice.
-MPI
-11.4%
-Time spent in MPI calls. High values are usually bad.
-This is very low; this code may benefit from increasing the process count.
-I/O
-0.0%
-Time spent in filesystem I/O. High values are usually bad.
diff --git a/salomon/software/debuggers/summary.md b/salomon/software/debuggers/summary.md
deleted file mode 100644
index ffb019ff516a9b3f154ff6e9b637e1f3a0b45b52..0000000000000000000000000000000000000000
--- a/salomon/software/debuggers/summary.md
+++ /dev/null
@@ -1,122 +0,0 @@
-
-Introduction
-------------
-We provide state of the art programms and tools to develop, profile and
-debug HPC codes at IT4Innovations.
-On these pages, we provide an overview of the profiling and debugging
-tools available on Anslem at IT4I.
-Intel debugger
---------------
-Intel debugger is no longer available since Parallel Studio version 2015
-The intel debugger version 13.0 is available, via module intel. The
-debugger works for applications compiled with C and C++ compiler and the
-ifort fortran 77/90/95 compiler. The debugger provides java GUI
-environment. Use [X
-display](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
-for running the GUI.
- $ module load intel
- $ idb
-Read more at the [Intel
-Debugger](../intel-suite/intel-debugger.html) page.
-Allinea Forge (DDT/MAP)
------------------------
-Allinea DDT, is a commercial debugger primarily for debugging parallel
-MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel
-Xeon Phi accelerators. DDT provides all the standard debugging features
-(stack trace, breakpoints, watches, view variables, threads etc.) for
-every thread running as part of your program, or for every process -
-even if these processes are distributed across a cluster using an MPI
-implementation.
- $ module load Forge
- $ forge
-Read more at the [Allinea DDT](allinea-ddt.html) page.
-Allinea Performance Reports
----------------------------
-Allinea Performance Reports characterize the performance of HPC
-application runs. After executing your application through the tool, a
-synthetic HTML report is generated automatically, containing information
-about several metrics along with clear behavior statements and hints to
-help you improve the efficiency of your runs. Our license is limited to
-64 MPI processes.
- $ module load PerformanceReports/6.0
- $ perf-report mpirun -n 64 ./my_application argument01 argument02
-Read more at the [Allinea Performance
-Reports](allinea-performance-reports.html) page.
-RougeWave Totalview
--------------------
-TotalView is a source- and machine-level debugger for multi-process,
-multi-threaded programs. Its wide range of tools provides ways to
-analyze, organize, and test programs, making it easy to isolate and
-identify problems in individual threads and processes in programs of
-great complexity.
- $ module load TotalView/8.15.4-6-linux-x86-64
- $ totalview
-Read more at the [Totalview](total-view.html) page.
-Vampir trace analyzer
----------------------
-Vampir is a GUI trace analyzer for traces in OTF format.
- $ module load Vampir/8.5.0
- $ vampir
-Read more at the [Vampir](vampir.html) page.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
-
- - [Aislinn](aislinn.html)
-
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
- - [Intel VTune Amplifier
- XE](intel-vtune-amplifier.html)
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
diff --git a/salomon/software/debuggers/total-view.md b/salomon/software/debuggers/total-view.md
deleted file mode 100644
index a5b216caefdc47070f33fa7bd401063e98593de0..0000000000000000000000000000000000000000
--- a/salomon/software/debuggers/total-view.md
+++ /dev/null
@@ -1,165 +0,0 @@
-==========
-TotalView is a GUI-based source code multi-process, multi-thread
-debugger.
-License and Limitations for cluster Users
------------------------------------------
-On the cluster users can debug OpenMP or MPI code that runs up to 64
-parallel processes. These limitation means that
-
-Â Â Â 1 user can debug up 64 processes, or
-Â Â Â 32 users can debug 2 processes, etc.
-
-Debugging of GPU accelerated codes is also supported.
-You can check the status of the licenses
-[here](https//extranet.it4i.cz/rsweb/anselm/license/totalview).
-Compiling Code to run with TotalView
-------------------------------------
-### Modules
-Load all necessary modules to compile the code. For example
- module load intel
- module load impi  ... or ... module load OpenMPI/X.X.X-icc
-Load the TotalView module
- module load TotalView/8.15.4-6-linux-x86-64
-Compile the code
- mpicc -g -O0 -o test_debug test.c
- mpif90 -g -O0 -o test_debug test.f
-### Compiler flags
-Before debugging, you need to compile your code with theses flags
-**-g** Generates extra debugging information usable by GDB. -g3
-includes even more debugging information. This option is available for
-GNU and INTEL C/C++ and Fortran compilers.
-
-**-O0** Suppress all optimizations.
-Starting a Job with TotalView
------------------------------
-Be sure to log in with an X window forwarding enabled. This could mean
-using the -X in the sshÂ
- ssh -X username@salomon.it4i.cz
-Other options is to access login node using VNC. Please see the detailed
-information on how to use graphic user interface on Anselm
-[here](resolveuid/11e53ad0d2fd4c5187537f4baeedff33.html#VNC).
-From the login node an interactive session with X windows forwarding (-X
-option) can be started by following command
- qsub -I -X -A NONE-0-0 -q qexp -lselect=1ncpus=24mpiprocs=24,walltime=010000
-Then launch the debugger with the totalview command followed by the name
-of the executable to debug.
-### Debugging a serial code
-To debug a serial code use
- totalview test_debug
-### Debugging a parallel code - option 1
-To debug a parallel code compiled with **OpenMPI** you need
-to setup your TotalView environmentÂ
-**Please note** To be able to run parallel debugging procedure from the
-command line without stopping the debugger in the mpiexec source code
-you have to add the following function to your **~/.tvdrc** file
- proc mpi_auto_run_starter {loaded_id} {
- Â Â Â set starter_programs {mpirun mpiexec orterun}
- Â Â Â set executable_name [TVsymbol get $loaded_id full_pathname]
- Â Â Â set file_component [file tail $executable_name]
- Â Â Â if {[lsearch -exact $starter_programs $file_component] != -1} {
- Â Â Â Â Â Â Â puts "**************************************"
- Â Â Â Â Â Â Â puts "Automatically starting $file_component"
- Â Â Â Â Â Â Â puts "**************************************"
- Â Â Â Â Â Â Â dgo
- Â Â Â }
- }
- # Append this function to TotalView's image load callbacks so that
- # TotalView run this program automatically.
- dlappend TVimage_load_callbacks mpi_auto_run_starter
-The source code of this function can be also found in
- /apps/all/OpenMPI/1.10.1-GNU-4.9.3-2.25/etc/openmpi-totalview.tcl
-You can also add only following line to you ~/.tvdrc file instead of
-the entire function
-
-**source /apps/all/OpenMPI/1.10.1-GNU-4.9.3-2.25/etc/openmpi-totalview.tcl**
-You need to do this step only once. See also [OpenMPI FAQ
-entry](https//www.open-mpi.org/faq/?category=running#run-with-tv)
-Now you can run the parallel debugger using
- mpirun -tv -n 5 ./test_debug
-When following dialog appears click on "Yes"
-[](totalview1.png)
-At this point the main TotalView GUI window will appear and you can
-insert the breakpoints and start debugging
-[](totalview2.png)
-### Debugging a parallel code - option 2
-Other option to start new parallel debugging session from a command line
-is to let TotalView to execute mpirun by itself. In this case user has
-to specify a MPI implementation used to compile the source code.Â
-The following example shows how to start debugging session with Intel
-MPI
- module load intel/2015b-intel-2015b impi/5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25 TotalView/8.15.4-6-linux-x86-64
- totalview -mpi "Intel MPI-Hydra" -np 8 ./hello_debug_impi
-After running previous command you will see the same window as shown in
-the screenshot above.
-More information regarding the command line parameters of the TotalView
-can be found TotalView Reference Guide, Chapter 7 TotalView Command
-Syntax. Â
-Documentation
--------------
-[1] The [TotalView
-documentation](http//www.roguewave.com/support/product-documentation/totalview-family.aspx#totalview)
-web page is a good resource for learning more about some of the advanced
-TotalView features.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
- .navTreeFolderish
- .contenttype-folder}
- - [Aislinn](aislinn.html)
-
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
- - [Intel VTune Amplifier
- XE](intel-vtune-amplifier.html)
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
-
diff --git a/salomon/software/debuggers/totalview1.png/@@images/45a91b6e-7f4d-4084-a5ba-d1ee703adaa1.png b/salomon/software/debuggers/totalview1.png/@@images/45a91b6e-7f4d-4084-a5ba-d1ee703adaa1.png
deleted file mode 100755
index 9c62ff1a4097f9da630f7592d988b967e3ed4ca2..0000000000000000000000000000000000000000
Binary files a/salomon/software/debuggers/totalview1.png/@@images/45a91b6e-7f4d-4084-a5ba-d1ee703adaa1.png and /dev/null differ
diff --git a/salomon/software/debuggers/valgrind.md b/salomon/software/debuggers/valgrind.md
deleted file mode 100644
index 7fdf0e2ffa84dadfc5cc3df0c875ed5c1de1d811..0000000000000000000000000000000000000000
--- a/salomon/software/debuggers/valgrind.md
+++ /dev/null
@@ -1,319 +0,0 @@
-========
-Valgrind is a tool for memory debugging and profiling.
-About Valgrind
---------------
-Valgrind is an open-source tool, used mainly for debuggig memory-related
-problems, such as memory leaks, use of uninitalized memory etc. in C/C++
-applications. The toolchain was however extended over time with more
-functionality, such as debugging of threaded applications, cache
-profiling, not limited only to C/C++.
-Valgind is an extremely useful tool for debugging memory errors such as
-[off-by-one](http//en.wikipedia.org/wiki/Off-by-one_error).
-Valgrind uses a virtual machine and dynamic recompilation of binary
-code, because of that, you can expect that programs being debugged by
-Valgrind run 5-100 times slower.
-The main tools available in Valgrind are
-- **Memcheck**, the original, must used and default tool. Verifies
- memory access in you program and can detect use of unitialized
- memory, out of bounds memory access, memory leaks, double free, etc.
-- **Massif**, a heap profiler.
-- **Hellgrind** and **DRD** can detect race conditions in
- multi-threaded applications.
-- **Cachegrind**, a cache profiler.
-- **Callgrind**, a callgraph analyzer.
-- For a full list and detailed documentation, please refer to the
- [official Valgrind
- documentation](http//valgrind.org/docs/).
-Installed versions
-------------------
-There are two versions of Valgrind available on the cluster.
-- Version 3.8.1, installed by operating system vendor
- in /usr/bin/valgrind.
- This version is available by default, without the need
- to load any module. This version however does not provide additional
- MPI support. Also, it does not support AVX2 instructions,
- **debugging of an AVX2-enabled executable with this version will
- fail**
-- Version 3.11.0 built by ICC with support for Intel MPI,
- available in
- [module](../../environment-and-modules.html)Â
- class="monospace">Valgrind/3.11.0-intel-2015b. After loading
- the module, this version replaces the default valgrind.
-- Version 3.11.0 built by GCC with support for Open MPI, module
- class="monospace">Valgrind/3.11.0-foss-2015b
-Usage
------
-Compile the application which you want to debug as usual. It is
-advisable to add compilation flags -g (to
-add debugging information to the binary so that you will see original
-source code lines in the output) and -O0
-(to disable compiler optimizations).Â
-For example, lets look at this C code, which has two problems
- #include
- void f(void)
- {
- int* x = malloc(10 * sizeof(int));
- x[10] = 0; // problem 1 heap block overrun
- } // problem 2 memory leak -- x not freed
- int main(void)
- {
- f();
- return 0;
- }
-Now, compile it with Intel compiler
- $ module add intel
- $ icc -g valgrind-example.c -o valgrind-exampleÂ
-Now, lets run it with Valgrind. The syntax is
-valgrind [valgrind options] <your program
-binary> [your program options]
-If no Valgrind options are specified, Valgrind defaults to running
-Memcheck tool. Please refer to the Valgrind documentation for a full
-description of command line options.
- $ valgrind ./valgrind-example
- ==12652== Memcheck, a memory error detector
- ==12652== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
- ==12652== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info
- ==12652== Command ./valgrind-example
- ==12652==
- ==12652== Invalid write of size 4
- ==12652== at 0x40053E f (valgrind-example.c6)
- ==12652== by 0x40054E main (valgrind-example.c11)
- ==12652== Address 0x5861068 is 0 bytes after a block of size 40 alloc'd
- ==12652== at 0x4C27AAA malloc (vg_replace_malloc.c291)
- ==12652== by 0x400528 f (valgrind-example.c5)
- ==12652== by 0x40054E main (valgrind-example.c11)
- ==12652==
- ==12652==
- ==12652== HEAP SUMMARY
- ==12652== in use at exit 40 bytes in 1 blocks
- ==12652== total heap usage 1 allocs, 0 frees, 40 bytes allocated
- ==12652==
- ==12652== LEAK SUMMARY
- ==12652== definitely lost 40 bytes in 1 blocks
- ==12652== indirectly lost 0 bytes in 0 blocks
- ==12652== possibly lost 0 bytes in 0 blocks
- ==12652== still reachable 0 bytes in 0 blocks
- ==12652== suppressed 0 bytes in 0 blocks
- ==12652== Rerun with --leak-check=full to see details of leaked memory
- ==12652==
- ==12652== For counts of detected and suppressed errors, rerun with -v
- ==12652== ERROR SUMMARY 1 errors from 1 contexts (suppressed 6 from 6)
-In the output we can see that Valgrind has detected both errors - the
-off-by-one memory access at line 5 and a memory leak of 40 bytes. If we
-want a detailed analysis of the memory leak, we need to run Valgrind
-with --leak-check=full option
- $ valgrind --leak-check=full ./valgrind-example
- ==23856== Memcheck, a memory error detector
- ==23856== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.
- ==23856== Using Valgrind-3.6.0 and LibVEX; rerun with -h for copyright info
- ==23856== Command ./valgrind-example
- ==23856==
- ==23856== Invalid write of size 4
- ==23856== at 0x40067E f (valgrind-example.c6)
- ==23856== by 0x40068E main (valgrind-example.c11)
- ==23856== Address 0x66e7068 is 0 bytes after a block of size 40 alloc'd
- ==23856== at 0x4C26FDE malloc (vg_replace_malloc.c236)
- ==23856== by 0x400668 f (valgrind-example.c5)
- ==23856== by 0x40068E main (valgrind-example.c11)
- ==23856==
- ==23856==
- ==23856== HEAP SUMMARY
- ==23856== in use at exit 40 bytes in 1 blocks
- ==23856== total heap usage 1 allocs, 0 frees, 40 bytes allocated
- ==23856==
- ==23856== 40 bytes in 1 blocks are definitely lost in loss record 1 of 1
- ==23856== at 0x4C26FDE malloc (vg_replace_malloc.c236)
- ==23856== by 0x400668 f (valgrind-example.c5)
- ==23856== by 0x40068E main (valgrind-example.c11)
- ==23856==
- ==23856== LEAK SUMMARY
- ==23856== definitely lost 40 bytes in 1 blocks
- ==23856== indirectly lost 0 bytes in 0 blocks
- ==23856== possibly lost 0 bytes in 0 blocks
- ==23856== still reachable 0 bytes in 0 blocks
- ==23856== suppressed 0 bytes in 0 blocks
- ==23856==
- ==23856== For counts of detected and suppressed errors, rerun with -v
- ==23856== ERROR SUMMARY 2 errors from 2 contexts (suppressed 6 from 6)
-Now we can see that the memory leak is due to the
-class="monospace">malloc() at line 6.
-Usage with MPI
----------------------------
-Although Valgrind is not primarily a parallel debugger, it can be used
-to debug parallel applications as well. When launching your parallel
-applications, prepend the valgrind command. For example
- $ mpirun -np 4 valgrind myapplication
-The default version without MPI support will however report a large
-number of false errors in the MPI library, such as
- ==30166== Conditional jump or move depends on uninitialised value(s)
- ==30166== at 0x4C287E8 strlen (mc_replace_strmem.c282)
- ==30166== by 0x55443BD I_MPI_Processor_model_number (init_interface.c427)
- ==30166== by 0x55439E0 I_MPI_Processor_arch_code (init_interface.c171)
- ==30166== by 0x558D5AE MPID_nem_impi_init_shm_configuration (mpid_nem_impi_extensions.c1091)
- ==30166== by 0x5598F4C MPID_nem_init_ckpt (mpid_nem_init.c566)
- ==30166== by 0x5598B65 MPID_nem_init (mpid_nem_init.c489)
- ==30166== by 0x539BD75 MPIDI_CH3_Init (ch3_init.c64)
- ==30166== by 0x5578743 MPID_Init (mpid_init.c193)
- ==30166== by 0x554650A MPIR_Init_thread (initthread.c539)
- ==30166== by 0x553369F PMPI_Init (init.c195)
- ==30166== by 0x4008BD main (valgrind-example-mpi.c18)
-so it is better to use the MPI-enabled valgrind from module. The MPI
-versions requires library Â
-
-class="monospace">$EBROOTVALGRIND/lib/valgrind/libmpiwrap-amd64-linux.so
-which must be included in the LD_PRELOAD
-environment variable.
-Lets look at this MPI example
- #include
- #include Â
- int main(int argc, char *argv[])
- {
- Â Â Â Â Â int *data = malloc(sizeof(int)*99);
- Â Â Â Â Â MPI_Init(&argc, &argv);
- Â Â Â Â MPI_Bcast(data, 100, MPI_INT, 0, MPI_COMM_WORLD);
- Â Â Â Â Â MPI_Finalize();Â
- Â Â Â Â Â Â Â return 0;
- }
-There are two errors - use of uninitialized memory and invalid length of
-the buffer. Lets debug it with valgrind
- $ module add intel impi
- $ mpiicc -g valgrind-example-mpi.c -o valgrind-example-mpi
- $ module add Valgrind/3.11.0-intel-2015b
- $ mpirun -np 2 -env LD_PRELOAD $EBROOTVALGRIND/lib/valgrind/libmpiwrap-amd64-linux.so valgrind ./valgrind-example-mpi
-Prints this output (note that there is output printed for every
-launched MPI process)
- ==31318== Memcheck, a memory error detector
- ==31318== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
- ==31318== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info
- ==31318== Command ./valgrind-example-mpi
- ==31318==
- ==31319== Memcheck, a memory error detector
- ==31319== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
- ==31319== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info
- ==31319== Command ./valgrind-example-mpi
- ==31319==
- valgrind MPI wrappers 31319 Active for pid 31319
- valgrind MPI wrappers 31319 Try MPIWRAP_DEBUG=help for possible options
- valgrind MPI wrappers 31318 Active for pid 31318
- valgrind MPI wrappers 31318 Try MPIWRAP_DEBUG=help for possible options
- ==31319== Unaddressable byte(s) found during client check request
- ==31319== at 0x4E35974 check_mem_is_addressable_untyped (libmpiwrap.c960)
- ==31319== by 0x4E5D0FE PMPI_Bcast (libmpiwrap.c908)
- ==31319== by 0x400911 main (valgrind-example-mpi.c20)
- ==31319== Address 0x69291cc is 0 bytes after a block of size 396 alloc'd
- ==31319== at 0x4C27AAA malloc (vg_replace_malloc.c291)
- ==31319== by 0x4007BC main (valgrind-example-mpi.c8)
- ==31319==
- ==31318== Uninitialised byte(s) found during client check request
- ==31318== at 0x4E3591D check_mem_is_defined_untyped (libmpiwrap.c952)
- ==31318== by 0x4E5D06D PMPI_Bcast (libmpiwrap.c908)
- ==31318== by 0x400911 main (valgrind-example-mpi.c20)
- ==31318== Address 0x6929040 is 0 bytes inside a block of size 396 alloc'd
- ==31318== at 0x4C27AAA malloc (vg_replace_malloc.c291)
- ==31318== by 0x4007BC main (valgrind-example-mpi.c8)
- ==31318==
- ==31318== Unaddressable byte(s) found during client check request
- ==31318== at 0x4E3591D check_mem_is_defined_untyped (libmpiwrap.c952)
- ==31318== by 0x4E5D06D PMPI_Bcast (libmpiwrap.c908)
- ==31318== by 0x400911 main (valgrind-example-mpi.c20)
- ==31318== Address 0x69291cc is 0 bytes after a block of size 396 alloc'd
- ==31318== at 0x4C27AAA malloc (vg_replace_malloc.c291)
- ==31318== by 0x4007BC main (valgrind-example-mpi.c8)
- ==31318==
- ==31318==
- ==31318== HEAP SUMMARY
- ==31318== in use at exit 3,172 bytes in 67 blocks
- ==31318== total heap usage 191 allocs, 124 frees, 81,203 bytes allocated
- ==31318==
- ==31319==
- ==31319== HEAP SUMMARY
- ==31319== in use at exit 3,172 bytes in 67 blocks
- ==31319== total heap usage 175 allocs, 108 frees, 48,435 bytes allocated
- ==31319==
- ==31318== LEAK SUMMARY
- ==31318== definitely lost 408 bytes in 3 blocks
- ==31318== indirectly lost 256 bytes in 1 blocks
- ==31318== possibly lost 0 bytes in 0 blocks
- ==31318== still reachable 2,508 bytes in 63 blocks
- ==31318== suppressed 0 bytes in 0 blocks
- ==31318== Rerun with --leak-check=full to see details of leaked memory
- ==31318==
- ==31318== For counts of detected and suppressed errors, rerun with -v
- ==31318== Use --track-origins=yes to see where uninitialised values come from
- ==31318== ERROR SUMMARY 2 errors from 2 contexts (suppressed 4 from 4)
- ==31319== LEAK SUMMARY
- ==31319== definitely lost 408 bytes in 3 blocks
- ==31319== indirectly lost 256 bytes in 1 blocks
- ==31319== possibly lost 0 bytes in 0 blocks
- ==31319== still reachable 2,508 bytes in 63 blocks
- ==31319== suppressed 0 bytes in 0 blocks
- ==31319== Rerun with --leak-check=full to see details of leaked memory
- ==31319==
- ==31319== For counts of detected and suppressed errors, rerun with -v
- ==31319== ERROR SUMMARY 1 errors from 1 contexts (suppressed 4 from 4)
-We can see that Valgrind has reported use of unitialised memory on the
-master process (which reads the array to be broadcasted) and use of
-unaddresable memory on both processes.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
- .navTreeFolderish
- .contenttype-folder}
- - [Aislinn](aislinn.html)
-
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
- - [Intel VTune Amplifier
- XE](intel-vtune-amplifier.html)
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
-
diff --git a/salomon/software/debuggers/vampir.md b/salomon/software/debuggers/vampir.md
deleted file mode 100644
index 2e472cd86f9f8b1f23c35d9537de82903da03444..0000000000000000000000000000000000000000
--- a/salomon/software/debuggers/vampir.md
+++ /dev/null
@@ -1,85 +0,0 @@
-======
-Vampir is a commercial trace analysis and visualisation tool. It can
-work with traces in OTF and OTF2 formats. It does not have the
-functionality to collect traces, you need to use a trace collection tool
-(such as
-[Score-P](../../../acl_users/credentials_cookie_auth/require_loginc71d.html))
-first to collect the traces.
-
---------------------------------------------------------------------------------------------------------------------------------------------------
-Installed versions
-------------------
-Version 8.5.0 is currently installed as module
-class="monospace">Vampir/8.5.0
- $ module load Vampir/8.5.0
- $ vampir &
-User manual
------------
-You can find the detailed user manual in PDF format in
-class="monospace">$EBROOTVAMPIR/doc/vampir-manual.pdf
-References
-----------
-1. [https//www.vampir.eu](https//www.vampir.eu/)
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
- .navTreeFolderish
- .contenttype-folder}
- - [Aislinn](aislinn.html)
-
- - [Allinea
- Forge (DDT,MAP)](allinea-ddt.html)
-
- - [Allinea Performance
- Reports](allinea-performance-reports.html "quick application profiling")
-
- - [Intel VTune Amplifier
- XE](intel-vtune-amplifier.html)
-
- - [Total
- View](total-view.html "TotalView is a GUI-based source code multi-process, multi-thread debugger. ")
-
diff --git a/salomon/software/debuggers/vtune-amplifier/@@images/7ca8748b-69ad-4b53-9667-29c2fdaa8913.png b/salomon/software/debuggers/vtune-amplifier/@@images/7ca8748b-69ad-4b53-9667-29c2fdaa8913.png
deleted file mode 100755
index 75ee99d84b87649151f22edad65de021ec348f1c..0000000000000000000000000000000000000000
Binary files a/salomon/software/debuggers/vtune-amplifier/@@images/7ca8748b-69ad-4b53-9667-29c2fdaa8913.png and /dev/null differ
diff --git a/salomon/software/intel-suite.md b/salomon/software/intel-suite.md
deleted file mode 100644
index 2fb7ff8465038ea54ca9376a502110377969328b..0000000000000000000000000000000000000000
--- a/salomon/software/intel-suite.md
+++ /dev/null
@@ -1,138 +0,0 @@
-
-The Salomon cluster provides following elements of the Intel Parallel
-Studio XE
- Intel Parallel Studio XE
- -------------------------------------------------
- Intel Compilers
- Intel Debugger
- Intel MKL Library
- Intel Integrated Performance Primitives Library
- Intel Threading Building Blocks Library
- Intel Trace Analyzer and Collector
- Intel Advisor
- Intel Inspector
-Intel compilers
----------------
-The Intel compilers version 131.3 are available, via module
-iccifort/2013.5.192-GCC-4.8.3. The compilers include the icc C and C++
-compiler and the ifort fortran 77/90/95 compiler.
- $ module load intel
- $ icc -v
- $ ifort -v
-Read more at the [Intel
-Compilers](intel-suite/intel-compilers.html) page.
-Intel debugger
---------------
-IDB is no longer available since Parallel Studio 2015.
-Â The intel debugger version 13.0 is available, via module intel. The
-debugger works for applications compiled with C and C++ compiler and the
-ifort fortran 77/90/95 compiler. The debugger provides java GUI
-environment. Use [X
-display](../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
-for running the GUI.
- $ module load intel
- $ idb
-Read more at the [Intel
-Debugger](intel-suite/intel-debugger.html) page.
-Intel Math Kernel Library
--------------------------
-Intel Math Kernel Library (Intel MKL) is a library of math kernel
-subroutines, extensively threaded and optimized for maximum performance.
-Intel MKL unites and provides these basic components BLAS, LAPACK,
-ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and
-many more.
- $ module load imkl
-Read more at the [Intel MKL](intel-suite/intel-mkl.html)
-page.
-Intel Integrated Performance Primitives
----------------------------------------
-Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX
-is available, via module ipp. The IPP is a library of highly optimized
-algorithmic building blocks for media and data applications. This
-includes signal, image and frame processing algorithms, such as FFT,
-FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many
-more.
- $ module load ipp
-Read more at the [Intel
-IPP](intel-suite/intel-integrated-performance-primitives.html)
-page.
-Intel Threading Building Blocks
--------------------------------
-Intel Threading Building Blocks (Intel TBB) is a library that supports
-scalable parallel programming using standard ISO C++ code. It does not
-require special languages or compilers. It is designed to promote
-scalable data parallel programming. Additionally, it fully supports
-nested parallelism, so you can build larger parallel components from
-smaller parallel components. To use the library, you specify tasks, not
-threads, and let the library map tasks onto threads in an efficient
-manner.
- $ module load tbb
-Read more at the [Intel TBB](intel-suite/intel-tbb.html)
-page.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [List of Available
- Modules](../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage.html)
-
- - [Network](../network-1.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](intel-suite.html "The Intel Parallel Studio XE")
-
-
- - [Intel
- Compilers](intel-suite/intel-compilers.html)
-
- - [Intel
- Debugger](intel-suite/intel-debugger.html)
-
- - [Intel
- MKL](intel-suite/intel-mkl.html)
-
- - [Intel
- IPP](intel-suite/intel-integrated-performance-primitives.html)
-
- - [Intel
diff --git a/salomon/software/intel-suite/index.md b/salomon/software/intel-suite/index.md
deleted file mode 100644
index 00dee759e796521c5a636d557baa437be0debe14..0000000000000000000000000000000000000000
--- a/salomon/software/intel-suite/index.md
+++ /dev/null
@@ -1,136 +0,0 @@
-
-The Salomon cluster provides following elements of the Intel Parallel
-Studio XE
- Intel Parallel Studio XE
- -------------------------------------------------
- Intel Compilers
- Intel Debugger
- Intel MKL Library
- Intel Integrated Performance Primitives Library
- Intel Threading Building Blocks Library
- Intel Trace Analyzer and Collector
- Intel Advisor
- Intel Inspector
-Intel compilers
----------------
-The Intel compilers version 131.3 are available, via module
-iccifort/2013.5.192-GCC-4.8.3. The compilers include the icc C and C++
-compiler and the ifort fortran 77/90/95 compiler.
- $ module load intel
- $ icc -v
- $ ifort -v
-Read more at the [Intel Compilers](intel-compilers.html)
-page.
-Intel debugger
---------------
-IDB is no longer available since Parallel Studio 2015.
-Â The intel debugger version 13.0 is available, via module intel. The
-debugger works for applications compiled with C and C++ compiler and the
-ifort fortran 77/90/95 compiler. The debugger provides java GUI
-environment. Use [X
-display](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
-for running the GUI.
- $ module load intel
- $ idb
-Read more at the [Intel Debugger](intel-debugger.html)
-page.
-Intel Math Kernel Library
--------------------------
-Intel Math Kernel Library (Intel MKL) is a library of math kernel
-subroutines, extensively threaded and optimized for maximum performance.
-Intel MKL unites and provides these basic components BLAS, LAPACK,
-ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and
-many more.
- $ module load imkl
-Read more at the [Intel MKL](intel-mkl.html) page.
-Intel Integrated Performance Primitives
----------------------------------------
-Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX
-is available, via module ipp. The IPP is a library of highly optimized
-algorithmic building blocks for media and data applications. This
-includes signal, image and frame processing algorithms, such as FFT,
-FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many
-more.
- $ module load ipp
-Read more at the [Intel
-IPP](intel-integrated-performance-primitives.html) page.
-Intel Threading Building Blocks
--------------------------------
-Intel Threading Building Blocks (Intel TBB) is a library that supports
-scalable parallel programming using standard ISO C++ code. It does not
-require special languages or compilers. It is designed to promote
-scalable data parallel programming. Additionally, it fully supports
-nested parallelism, so you can build larger parallel components from
-smaller parallel components. To use the library, you specify tasks, not
-threads, and let the library map tasks onto threads in an efficient
-manner.
- $ module load tbb
-Read more at the [Intel TBB](intel-tbb.html) page.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
-
-
- - [Intel
- Compilers](intel-compilers.html)
-
- - [Intel
- Debugger](intel-debugger.html)
-
- - [Intel
- MKL](intel-mkl.html)
-
- - [Intel
- IPP](intel-integrated-performance-primitives.html)
-
- - [Intel
diff --git a/salomon/software/intel-suite/intel-advisor.md b/salomon/software/intel-suite/intel-advisor.md
deleted file mode 100644
index 8815c243c8388d538ecdbd2262c7b6503d24c021..0000000000000000000000000000000000000000
--- a/salomon/software/intel-suite/intel-advisor.md
+++ /dev/null
@@ -1,107 +0,0 @@
-=============
-is tool aiming to assist you in vectorization and threading of your
-code. You can use it to profile your application and identify
-loops, that could benefit from vectorization and/or threading
-parallelism.
-Installed versions
-------------------
-The following versions are currently available on Salomon as modules
- --------------- -----------------------
- **Version** **Module**
- 2016 Update 2 Advisor/2016_update2
- --------------- -----------------------
-Usage
------
-Your program should be compiled with -g switch to include symbol names.
-You should compile with -O2 or higher to see code that is already
-vectorized by the compiler.
-Profiling is possible either directly from the GUI, or from command
-line.
-To profile from GUI, launch Advisor
- $ advixe-gui
-Then select menu File -> New -> Project. Choose a directory to
-save project data to. After clicking OK, Project properties window will
-appear, where you can configure path to your binary, launch arguments,
-working directory etc. After clicking OK, the project is ready.
-In the left pane, you can switch between Vectorization and Threading
-workflows. Each has several possible steps which you can execute by
-clicking Collect button. Alternatively, you can click on Command Line,
-to see the command line required to run the analysis directly from
-command line.
-References
-----------
-1. [Intel® Advisor 2015 Tutorial Find Where to Add Parallelism - C++
- Sample](https//software.intel.com/en-us/advisorxe_2015_tut_lin_c)
-2. [Product
- page](https//software.intel.com/en-us/intel-advisor-xe)
-3. [Documentation](https//software.intel.com/en-us/intel-advisor-2016-user-guide-linux)
-Â
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
- .navTreeFolderish
- .contenttype-folder}
- - [Intel
- Compilers](intel-compilers.html)
-
- - [Intel
- Debugger](intel-debugger.html)
-
- - [Intel
- MKL](intel-mkl.html)
-
- - [Intel
- IPP](intel-integrated-performance-primitives.html)
-
- - [Intel
- TBB](intel-tbb.html)
diff --git a/salomon/software/intel-suite/intel-compilers.md b/salomon/software/intel-suite/intel-compilers.md
deleted file mode 100644
index 2bac5152a683c481a46870b402b1fe7b31f3dda6..0000000000000000000000000000000000000000
--- a/salomon/software/intel-suite/intel-compilers.md
+++ /dev/null
@@ -1,126 +0,0 @@
-===============
-
-
-The Intel compilers in multiple versions are available, via module
-intel. The compilers include the icc C and C++ compiler and the ifort
-fortran 77/90/95 compiler.
- $ module load intel
- $ icc -v
- $ ifort -v
-The intel compilers provide for vectorization of the code, via the AVX2
-instructions and support threading parallelization via OpenMP
-For maximum performance on the Salomon cluster compute nodes, compile
-your programs using the AVX2 instructions, with reporting where the
-vectorization was used. We recommend following compilation options for
-high performance
- $ icc -ipo -O3 -xCORE-AVX2 -qopt-report1 -qopt-report-phase=vec myprog.c mysubroutines.c -o myprog.x
- $ ifort -ipo -O3 -xCORE-AVX2 -qopt-report1 -qopt-report-phase=vec myprog.f mysubroutines.f -o myprog.x
-In this example, we compile the program enabling interprocedural
-optimizations between source files (-ipo), aggresive loop optimizations
-(-O3) and vectorization (-xCORE-AVX2)
-The compiler recognizes the omp, simd, vector and ivdep pragmas for
-OpenMP parallelization and AVX2 vectorization. Enable the OpenMP
-parallelization by the **-openmp** compiler switch.
- $ icc -ipo -O3 -xCORE-AVX2 -qopt-report1 -qopt-report-phase=vec -openmp myprog.c mysubroutines.c -o myprog.x
- $ ifort -ipo -O3 -xCORE-AVX2 -qopt-report1 -qopt-report-phase=vec -openmp myprog.f mysubroutines.f -o myprog.x
-Read more
-atÂ
-Sandy Bridge/Ivy Bridge/Haswell binary compatibility
-----------------------------------------------------
-Anselm nodes are currently equipped with Sandy Bridge CPUs, while
-Salomon compute nodes are equipped with Haswell based architecture. The
-UV1 SMP compute server has Ivy Bridge CPUs, which are equivalent to
-Sandy Bridge (only smaller manufacturing technology). The new
-processors are backward compatible with the Sandy Bridge nodes, so all
-programs that ran on the Sandy Bridge processors, should also run on the
-new Haswell nodes. To get optimal performance out of the
-Haswell processors a program should make use of the
-special AVX2 instructions for this processor. One can do
-this by recompiling codes with the compiler
-flags designated to invoke these instructions. For the
-Intel compiler suite, there are two ways of
-doing this
-- Using compiler flag (both for Fortran and C)
- class="monospace">-xCORE-AVX2. This will create a
- binary with AVX2 instructions, specifically
- for the Haswell processors. Note that the
- executable will not run on Sandy Bridge/Ivy
- Bridge nodes.
-- Using compiler flags (both for Fortran and C)
- class="monospace">-xAVX -axCORE-AVX2. This
- will generate multiple, feature specific auto-dispatch
- code paths for Intel® processors, if there is a
- performance benefit. So this binary will run both on Sandy
- Bridge/Ivy Bridge and Haswell processors. During
- runtime it will be decided which path to follow, dependent on
- which processor you are running on. In general this
- will result in larger binaries.
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
- .navTreeFolderish
- .contenttype-folder}
- - [Intel
- Compilers](intel-compilers.html)
-
-
- - [Intel
- Debugger](intel-debugger.html)
-
- - [Intel
- MKL](intel-mkl.html)
-
- - [Intel
- IPP](intel-integrated-performance-primitives.html)
-
- - [Intel
diff --git a/salomon/software/intel-suite/intel-debugger.md b/salomon/software/intel-suite/intel-debugger.md
deleted file mode 100644
index 4a0e7f088bc9c697f5dd62143c0a38989d722512..0000000000000000000000000000000000000000
--- a/salomon/software/intel-suite/intel-debugger.md
+++ /dev/null
@@ -1,140 +0,0 @@
-==============
-
-
-IDB is no longer available since Intel Parallel Studio 2015
-Debugging serial applications
------------------------------
-The intel debugger version 13.0 is available, via module intel. The
-debugger works for applications compiled with C and C++ compiler and the
-ifort fortran 77/90/95 compiler. The debugger provides java GUI
-environment. Use [X
-display](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
-for running the GUI.
- $ module load intel/2014.06
- $ module load Java
- $ idb
-The debugger may run in text mode. To debug in text mode, use
- $ idbc
-To debug on the compute nodes, module intel must be loaded.
-The GUI on compute nodes may be accessed using the same way as in [the
-GUI
-section](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
-Example
- $ qsub -q qexp -l select=1ncpus=24 -X -I
- qsub waiting for job 19654.srv11 to start
- qsub job 19654.srv11 ready
- $ module load intel
- $ module load Java
- $ icc -O0 -g myprog.c -o myprog.x
- $ idb ./myprog.x
-In this example, we allocate 1 full compute node, compile program
-myprog.c with debugging options -O0 -g and run the idb debugger
-interactively on the myprog.x executable. The GUI access is via X11 port
-forwarding provided by the PBS workload manager.
-Debugging parallel applications
--------------------------------
-Intel debugger is capable of debugging multithreaded and MPI parallel
-programs as well.
-### Small number of MPI ranks
-For debugging small number of MPI ranks, you may execute and debug each
-rank in separate xterm terminal (do not forget the [X
-display](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)).
-Using Intel MPI, this may be done in following way
- $ qsub -q qexp -l select=2ncpus=24 -X -I
- qsub waiting for job 19654.srv11 to start
- qsub job 19655.srv11 ready
- $ module load intel impi
- $ mpirun -ppn 1 -hostfile $PBS_NODEFILE --enable-x xterm -e idbc ./mympiprog.x
-In this example, we allocate 2 full compute node, run xterm on each node
-and start idb debugger in command line mode, debugging two ranks of
-mympiprog.x application. The xterm will pop up for each rank, with idb
-prompt ready. The example is not limited to use of Intel MPI
-### Large number of MPI ranks
-Run the idb debugger from within the MPI debug option. This will cause
-the debugger to bind to all ranks and provide aggregated outputs across
-the ranks, pausing execution automatically just after startup. You may
-then set break points and step the execution manually. Using Intel MPI
- $ qsub -q qexp -l select=2ncpus=24 -X -I
- qsub waiting for job 19654.srv11 to start
- qsub job 19655.srv11 ready
- $ module load intel impi
- $ mpirun -n 48 -idb ./mympiprog.x
-### Debugging multithreaded application
-Run the idb debugger in GUI mode. The menu Parallel contains number of
-tools for debugging multiple threads. One of the most useful tools is
-the **Serialize Execution** tool, which serializes execution of
-concurrent threads for easy orientation and identification of
-concurrency related bugs.
-Further information
--------------------
-Exhaustive manual on idb features and usage is published at Intel
-website,
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
- .navTreeFolderish
- .contenttype-folder}
- - [Intel
- Compilers](intel-compilers.html)
-
- - [Intel
- Debugger](intel-debugger.html)
-
-
- - [Intel
- MKL](intel-mkl.html)
-
- - [Intel
- IPP](intel-integrated-performance-primitives.html)
-
- - [Intel
diff --git a/salomon/software/intel-suite/intel-inspector.md b/salomon/software/intel-suite/intel-inspector.md
deleted file mode 100644
index ea83b50f149c9657952e47ce5ad5e3728b3ebb72..0000000000000000000000000000000000000000
--- a/salomon/software/intel-suite/intel-inspector.md
+++ /dev/null
@@ -1,113 +0,0 @@
-===============
-Intel Inspector is a dynamic memory and threading error checking tool
-for C/C++/Fortran applications. It can detect issues such as memory
-leaks, invalid memory references, uninitalized variables, race
-conditions, deadlocks etc.
-Installed versions
-------------------
-The following versions are currently available on Salomon as modules
- --------------- -------------------------
- **Version** **Module**
- 2016 Update 1 Inspector/2016_update1
- --------------- -------------------------
-Usage
------
-Your program should be compiled with -g switch to include symbol names.
-Optimizations can be turned on.
-Debugging is possible either directly from the GUI, or from command
-line.
-### GUI mode
-To debug from GUI, launch Inspector
- $ inspxe-gui &
-Then select menu File -> New -> Project. Choose a directory to
-save project data to. After clicking OK, Project properties window will
-appear, where you can configure path to your binary, launch arguments,
-working directory etc. After clicking OK, the project is ready.
-In the main pane, you can start a predefined analysis type or define
-your own. Click Start to start the analysis. Alternatively, you can
-click on Command Line, to see the command line required to run the
-analysis directly from command line.
-### Batch mode
-Analysis can be also run from command line in batch mode. Batch mode
-analysis is run with command inspxe-cl.
-To obtain the required parameters, either consult the documentation or
-you can configure the analysis in the GUI and then click "Command Line"
-button in the lower right corner to the respective command line.
-Results obtained from batch mode can be then viewed in the GUI by
-selecting File -> Open -> Result...
-References
-----------
-1. [Product
- page](https//software.intel.com/en-us/intel-inspector-xe)
-2. [Documentation and Release
- Notes](https//software.intel.com/en-us/intel-inspector-xe-support/documentation)
-3. [Tutorials](https//software.intel.com/en-us/articles/inspectorxe-tutorials)
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
- .navTreeFolderish
- .contenttype-folder}
- - [Intel
- Compilers](intel-compilers.html)
-
- - [Intel
- Debugger](intel-debugger.html)
-
- - [Intel
- MKL](intel-mkl.html)
-
- - [Intel
- IPP](intel-integrated-performance-primitives.html)
-
- - [Intel
- TBB](intel-tbb.html)
diff --git a/salomon/software/intel-suite/intel-integrated-performance-primitives.md b/salomon/software/intel-suite/intel-integrated-performance-primitives.md
deleted file mode 100644
index 1f1938db4180aeda6d49d9b2de2b7f0613382e72..0000000000000000000000000000000000000000
--- a/salomon/software/intel-suite/intel-integrated-performance-primitives.md
+++ /dev/null
@@ -1,142 +0,0 @@
-Intel IPP
-=========
-
-
-Intel Integrated Performance Primitives
----------------------------------------
-Intel Integrated Performance Primitives, version 9.0.1, compiled for
-AVX2 vector instructions is available, via module ipp. The IPP is a very
-rich library of highly optimized algorithmic building blocks for media
-and data applications. This includes signal, image and frame processing
-algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough
-transform, Sum, MinMax, as well as cryptographic functions, linear
-algebra functions and many more.
-Check out IPP before implementing own math functions for data
-processing, it is likely already there.
- $ module load ipp
-The module sets up environment variables, required for linking and
-running ipp enabled applications.
-IPP example
------------
- #include "ipp.h"
- #include
- int main(int argc, char* argv[])
- {
- const IppLibraryVersion *lib;
- Ipp64u fm;
- IppStatus status;
- status= ippInit(); //IPP initialization with the best optimization layer
- if( status != ippStsNoErr ) {
- printf("IppInit() Errorn");
- printf("%sn", ippGetStatusString(status) );
- return -1;
- }
- //Get version info
- lib = ippiGetLibVersion();
- printf("%s %sn", lib->Name, lib->Version);
- //Get CPU features enabled with selected library level
- fm=ippGetEnabledCpuFeatures();
- printf("SSE %cn",(fm>>1)&1?'Y''N');
- printf("SSE2 %cn",(fm>>2)&1?'Y''N');
- printf("SSE3 %cn",(fm>>3)&1?'Y''N');
- printf("SSSE3 %cn",(fm>>4)&1?'Y''N');
- printf("SSE41 %cn",(fm>>6)&1?'Y''N');
- printf("SSE42 %cn",(fm>>7)&1?'Y''N');
- printf("AVX %cn",(fm>>8)&1 ?'Y''N');
- printf("AVX2 %cn", (fm>>15)&1 ?'Y''N' );
- printf("----------n");
- printf("OS Enabled AVX %cn", (fm>>9)&1 ?'Y''N');
- printf("AES %cn", (fm>>10)&1?'Y''N');
- printf("CLMUL %cn", (fm>>11)&1?'Y''N');
- printf("RDRAND %cn", (fm>>13)&1?'Y''N');
- printf("F16C %cn", (fm>>14)&1?'Y''N');
- return 0;
- }
-Â Compile above example, using any compiler and the ipp module.
- $ module load intel
- $ module load ipp
- $ icc testipp.c -o testipp.x -lippi -lipps -lippcore
-You will need the ipp module loaded to run the ipp enabled executable.
-This may be avoided, by compiling library search paths into the
-executable
- $ module load intel
- $ module load ipp
- $ icc testipp.c -o testipp.x -Wl,-rpath=$LIBRARY_PATH -lippi -lipps -lippcore
-Code samples and documentation
-------------------------------
-Intel provides number of [Code Samples for
-IPP](https//software.intel.com/en-us/articles/code-samples-for-intel-integrated-performance-primitives-library),
-illustrating use of IPP.
-Read full documentation on IPP [on Intel
-website,](http//software.intel.com/sites/products/search/search.php?q=&x=15&y=6&product=ipp&version=7.1&docos=lin)
-in particular the [IPP Reference
-manual.](http//software.intel.com/sites/products/documentation/doclib/ipp_sa/71/ipp_manual/index.htm)
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
- .navTreeFolderish
- .contenttype-folder}
- - [Intel
- Compilers](intel-compilers.html)
-
- - [Intel
- Debugger](intel-debugger.html)
-
- - [Intel
- MKL](intel-mkl.html)
-
- - [Intel
- IPP](intel-integrated-performance-primitives.html)
-
-
- - [Intel
diff --git a/salomon/software/intel-suite/intel-tbb.md b/salomon/software/intel-suite/intel-tbb.md
deleted file mode 100644
index 8aaccdf2640e86302ff2269a0f51d16b5116b4d2..0000000000000000000000000000000000000000
--- a/salomon/software/intel-suite/intel-tbb.md
+++ /dev/null
@@ -1,106 +0,0 @@
-=========
-
-
-Intel Threading Building Blocks
--------------------------------
-Intel Threading Building Blocks (Intel TBB) is a library that supports
-scalable parallel programming using standard ISO C++ code. It does not
-require special languages or compilers. To use the library, you specify
-tasks, not threads, and let the library map tasks onto threads in an
-efficient manner. The tasks are executed by a runtime scheduler and may
-be offloaded to [MIC
-accelerator](../intel-xeon-phi.html).
-Intel TBB version 4.3.5.187 is available on the cluster.
- $ module load tbb
-The module sets up environment variables, required for linking and
-running tbb enabled applications.
-Link the tbb library, using -ltbb
-Examples
---------
-Number of examples, demonstrating use of TBB and its built-in schedulerÂ
-is available on Anselm, in the $TBB_EXAMPLES directory.
- $ module load intel
- $ module load tbb
- $ cp -a $TBB_EXAMPLES/common $TBB_EXAMPLES/parallel_reduce /tmp/
- $ cd /tmp/parallel_reduce/primes
- $ icc -O2 -DNDEBUG -o primes.x main.cpp primes.cpp -ltbb
- $ ./primes.x
-In this example, we compile, link and run the primes example,
-demonstrating use of parallel task-based reduce in computation of prime
-numbers.
-You will need the tbb module loaded to run the tbb enabled executable.
-This may be avoided, by compiling library search paths into the
-executable.
- $ icc -O2 -o primes.x main.cpp primes.cpp -Wl,-rpath=$LIBRARY_PATH -ltbb
-Further reading
----------------
-Read more on Intel website,
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
- .navTreeFolderish
- .contenttype-folder}
- - [Intel
- Compilers](intel-compilers.html)
-
- - [Intel
- Debugger](intel-debugger.html)
-
- - [Intel
- MKL](intel-mkl.html)
-
- - [Intel
- IPP](intel-integrated-performance-primitives.html)
-
- - [Intel
- TBB](intel-tbb.html)
diff --git a/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md b/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
deleted file mode 100644
index e43e429bec646e494e4abad5e0bb4dc5fc05fb53..0000000000000000000000000000000000000000
--- a/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
+++ /dev/null
@@ -1,108 +0,0 @@
-
-Intel Trace Analyzer and Collector
-==================================
-Intel Trace Analyzer and Collector (ITAC) is a tool to collect and
-graphicaly analyze behaviour of MPI applications. It helps you to
-analyze communication patterns of your application, identify hotspots,
-perform correctnes checking (identify deadlocks, data corruption etc),
-simulate how your application would run on a different interconnect.Â
-ITAC is a offline analysis tool - first you run your application to
-collect a trace file, then you can open the trace in a GUI analyzer to
-view it.
-Installed version
------------------
-Currently on Salomon is version 9.1.2.024 available as moduleÂ
-class="monospace">itac/9.1.2.024
-Collecting traces
------------------
-ITAC can collect traces from applications that are using Intel MPI. To
-generate a trace, simply add -trace option to your mpirun command
- $ module load itac/9.1.2.024
- $ mpirun -trace myapp
-The trace will be saved in file myapp.stf in the current directory.
-Viewing traces
---------------
-To view and analyze the trace, open ITAC GUI in a [graphical
-environment](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
-
- $ module load itac/9.1.2.024
- $ traceanalyzer
-The GUI will launch and you can open the produced *.stf file.
-
-Please refer to Intel documenation about usage of the GUI tool.
-References
-----------
-1. [Getting Started with Intel® Trace Analyzer and
- Collector](https//software.intel.com/en-us/get-started-with-itac-for-linux)
-2. [Intel® Trace Analyzer and Collector -
- Documentation](http//xn--intel%20trace%20analyzer%20and%20collector%20-%20documentation-g6b/)
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
- - [Intel Parallel
- studio](../intel-suite.html "The Intel Parallel Studio XE")
- .navTreeFolderish
- .contenttype-folder}
- - [Intel
- Compilers](intel-compilers.html)
-
- - [Intel
- Debugger](intel-debugger.html)
-
- - [Intel
- MKL](intel-mkl.html)
-
- - [Intel
- IPP](intel-integrated-performance-primitives.html)
-
- - [Intel
- TBB](intel-tbb.html)
diff --git a/salomon/software/java.md b/salomon/software/java.md
deleted file mode 100644
index c01a9766b4573cfe15d3dfdf3317fc6a616b1516..0000000000000000000000000000000000000000
--- a/salomon/software/java.md
+++ /dev/null
@@ -1,63 +0,0 @@
-
-
-Java is available on the cluster. Activate java by loading the Java
-module
- $ module load Java
-Note that the Java module must be loaded on the compute nodes as well,
-in order to run java on compute nodes.
-Check for java version and path
- $ java -version
- $ which java
-With the module loaded, not only the runtime environment (JRE), but also
-the development environment (JDK) with the compiler is available.
- $ javac -version
- $ which javac
-Java applications may use MPI for interprocess communication, in
-conjunction with OpenMPI. Read more
-on .
-This functionality is currently not supported on Anselm cluster. In case
-you require the java interface to MPI, please contact [cluster
-support](https//support.it4i.cz/rt/).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [List of Available
- Modules](../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage.html)
-
- - [Network](../network-1.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
diff --git a/salomon/software/mpi-1/mpi4py-mpi-for-python.md b/salomon/software/mpi-1/mpi4py-mpi-for-python.md
deleted file mode 100644
index 9ccb3c06c5f8d0c68b34772644c21606e32f7414..0000000000000000000000000000000000000000
--- a/salomon/software/mpi-1/mpi4py-mpi-for-python.md
+++ /dev/null
@@ -1,120 +0,0 @@
-=======================
-OpenMPI interface to Python
-
-
-Introduction
-------------
-MPI for Python provides bindings of the Message Passing Interface (MPI)
-standard for the Python programming language, allowing any Python
-program to exploit multiple processors.
-This package is constructed on top of the MPI-1/2 specifications and
-provides an object oriented interface which closely follows MPI-2 C++
-bindings. It supports point-to-point (sends, receives) and collective
-(broadcasts, scatters, gathers) communications of any picklable Python
-object, as well as optimized communications of Python object exposing
-the single-segment buffer interface (NumPy arrays, builtin
-bytes/string/array objects).
-On Anselm MPI4Py is available in standard Python modules.
-Modules
--------
-MPI4Py is build for OpenMPI. Before you start with MPI4Py you need to
-load Python and OpenMPI modules. You can use toolchain, that loads
-Python and OpenMPI at once.
- $ module load Python/2.7.9-foss-2015g
-Execution
----------
-You need to import MPI to your python program. Include the following
-line to the python script
- from mpi4py import MPI
-The MPI4Py enabled python programs [execute as any other
-OpenMPI](Running_OpenMPI.html) code.The simpliest way is
-to run
- $ mpiexec python .py
-For example
- $ mpiexec python hello_world.py
-Examples
---------
-### Hello world!
- from mpi4py import MPI
- comm = MPI.COMM_WORLD
- print "Hello! I'm rank %d from %d running in total..." % (comm.rank, comm.size)
- comm.Barrier() Â # wait for everybody to synchronize
-### Collective Communication with NumPy arrays
- from __future__ import division
- from mpi4py import MPI
- import numpy as np
- comm = MPI.COMM_WORLD
- print("-"*78)
- print(" Running on %d cores" % comm.size)
- print("-"*78)
- comm.Barrier()
- # Prepare a vector of N=5 elements to be broadcasted...
- N = 5
- if comm.rank == 0
- Â Â A = np.arange(N, dtype=np.float64) Â Â # rank 0 has proper data
- else
- Â Â A = np.empty(N, dtype=np.float64) Â Â # all other just an empty array
- # Broadcast A from rank 0 to everybody
- comm.Bcast( [A, MPI.DOUBLE] )
- # Everybody should now have the same...
- print "[%02d] %s" % (comm.rank, A)
-Execute the above code as
- $ qsub -q qexp -l select=4ncpus=24mpiprocs=24ompthreads=1 -I
- $ module load Python/2.7.9-foss-2015g
- $ mpiexec --map-by core --bind-to core python hello_world.py
-In this example, we run MPI4Py enabled code on 4 nodes, 24 cores per
-node (total of 96 processes), each python process is bound to a
-different core.
-More examples and documentation can be found on [MPI for Python
-webpage](https//pythonhosted.org/mpi4py/usrman/index.html).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../../sitemap.html)
- - [What's
- New](../../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../../salomon.html)
-
- - [Hardware
- Overview](../../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../../environment-and-modules.html)
-
- - [List of Available
- Modules](../../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../../compute-nodes.html)
-
- - [Storage](../../storage.html)
-
- - [Network](../../network-1.html)
-
- - [Software](../../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](../ansys.html "An engineering simulation software ")
-
- - [COMSOL](../comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](../debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](../chemistry.html "Tools for computational chemistry.")
-
diff --git a/salomon/software/numerical-languages.md b/salomon/software/numerical-languages.md
deleted file mode 100644
index 4a15fed9a7a3621e25e2596f6a99e649ef751914..0000000000000000000000000000000000000000
--- a/salomon/software/numerical-languages.md
+++ /dev/null
@@ -1,79 +0,0 @@
-
-
-Introduction
-------------
-This section contains a collection of high-level interpreted languages,
-primarily intended for numerical computations.
-Matlab
-------
-MATLAB^®^ is a high-level language and interactive environment for
-numerical computation, visualization, and programming.
- $ module load MATLAB
- $ matlab
-Read more at the [Matlab
-page](numerical-languages/matlab.html).
-Octave
-------
-GNU Octave is a high-level interpreted language, primarily intended for
-numerical computations. The Octave language is quite similar to Matlab
-so that most programs are easily portable.
- $ module load Octave
- $ octave
-Read more at the [Octave
-page](numerical-languages/octave.html).
-R
--
-The R is an interpreted language and environment for statistical
-computing and graphics.
- $ module load R
- $ R
-Read more at the [R page](numerical-languages/r.html).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [List of Available
- Modules](../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage.html)
-
- - [Network](../network-1.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
-
- - [Debuggers and
- profilers](debuggers.html "A collection of development tools")
-
- - [Chemistry, Physics and Materials
- science](chemistry.html "Tools for computational chemistry.")
diff --git a/salomon/software/operating-system.md b/salomon/software/operating-system.md
deleted file mode 100644
index d6d124d97332c6e1d1f78fc5304dbfd4b77c3a5c..0000000000000000000000000000000000000000
--- a/salomon/software/operating-system.md
+++ /dev/null
@@ -1,49 +0,0 @@
-
-
-The operating system on Salomon is Linux - CentOS 6.6.
-The CentOS Linux distribution is a stable, predictable, manageable
-and reproducible platform derived from the sources of Red Hat Enterprise
-Linux (RHEL).
-------------------------------------------------------------------------
-**[Komentáře](#plone-discussions){#plone-discussions-href}**
-<div
-id="portletwrapper-706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e"
-class="portletWrapper"
-data-portlethash="706c6f6e652e6c656674636f6c756d6e0a636f6e746578740a2f646f63730a6e617669676174696f6e">
- [Navigace](../../sitemap.html)
- - [What's New](../../whats-new.html)
-
- - [Get Started with
- IT4Innovations](../../get-started-with-it4innovations.html)
-
- - [Salomon Cluster
- Documentation](../../salomon.html)
-
- - [Hardware
- Overview](../hardware-overview-1.html)
-
- - [Accessing the
- Cluster](../accessing-the-cluster/shell-and-data-access.html)
-
- - [Environment and
- Modules](../environment-and-modules.html)
-
- - [List of Available
- Modules](../list_of_modules.html "List of Available Modules on Salomon Cluster")
-
- - [Resource Allocation and Job
- Execution](../resource-allocation-and-job-execution.html)
-
- - [Compute
- Nodes](../compute-nodes.html)
-
- - [Storage](../storage.html)
-
- - [Network](../network-1.html)
-
- - [Software](../software.html "In this section we provide overview of installed software and its usage.
- ") .navTreeFolderish
- .contenttype-folder}
- - [ANSYS](ansys.html "An engineering simulation software ")
-
- - [COMSOL](comsol.html " A finite element analysis, solver and Simulation software")
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- <span>PBSPro User's Guide</span>
- </a>
-
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diff --git a/sitemap.md b/sitemap.md
deleted file mode 100644
index 36b546f6143b418758bf090abe23da79aa62b036..0000000000000000000000000000000000000000
--- a/sitemap.md
+++ /dev/null
@@ -1,379 +0,0 @@
- [History of
- Downtimes](whats-new/downtimes_history.html "Full history of important announcements related to IT4I infrastructure, planned downtimes, outages etc.")
-
-
--
- [Get Started with
- IT4Innovations](get-started-with-it4innovations.html)
- .contenttype-folder}
-
- -
- [Applying for
- Resources](get-started-with-it4innovations/applying-for-resources.html)
-
-
- -
- [Obtaining Login
- Credentials](get-started-with-it4innovations/obtaining-login-credentials.html)
- .contenttype-folder}
-
- -
- [Obtaining Login
- Credentials](get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html)
-
-
- -
- [Certificates
- FAQ](get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.html "FAQ about certificates in general")
-
-
- -
- [Accessing the
- Clusters](get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer.html)
- .contenttype-folder}
-
- -
- [Shell access and data
- transfer](get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer.html)
- .contenttype-folder}
-
- -
- [Graphical User
- Interface](get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html)
- .contenttype-folder}
-
--
- [Salomon Cluster
- Documentation](salomon.html)
- .contenttype-folder}
-
- -
- [Hardware
- Overview](salomon/hardware-overview-1.html)
- .contenttype-folder}
-
- -
- [Accessing the
- Cluster](salomon/accessing-the-cluster/shell-and-data-access.html)
- .contenttype-folder}
-
- -
- [Shell access and data
- transfer](salomon/accessing-the-cluster/shell-and-data-access.html)
- .contenttype-folder}
-
- -
- [Graphical User
- Interface](get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html)
- .contenttype-folder}
-
- -
- [VPN
- Access](salomon/accessing-the-cluster/vpn-access.html)
-
-
- -
- [Outgoing
- connections](salomon/accessing-the-cluster/outgoing-connections.html)
-
-
- -
- [Environment and
- Modules](salomon/environment-and-modules.html)
-
-
- -
- [List of Available
- Modules](salomon/list_of_modules.html "List of Available Modules on Salomon Cluster")
-
-
- -
- [Resource Allocation and Job
- Execution](salomon/resource-allocation-and-job-execution.html)
- .contenttype-folder}
-
- -
- [Resources Allocation
- Policy](salomon/resource-allocation-and-job-execution/resources-allocation-policy.html)
-
-
- -
- [Job submission and
- execution](salomon/resource-allocation-and-job-execution/job-submission-and-execution.html)
-
-
- -
- [Job
- scheduling](salomon/resource-allocation-and-job-execution/job-priority.html)
-
-
- -
- [Capacity
- computing](salomon/resource-allocation-and-job-execution/capacity-computing.html)
-
-
- -
- [Compute
- Nodes](salomon/compute-nodes.html)
-
-
- -
- [Storage](salomon/storage.html)
- .contenttype-folder}
-
- -
- [CESNET Data
- Storage](salomon/storage/cesnet-data-storage.html)
-
-
- -
- [Network](salomon/network-1.html)
- .contenttype-folder}
-
- -
- [7D Enhanced
- Hypercube](salomon/network-1/7d-enhanced-hypercube.html)
-
-
- -
- [IB single-plane
- topology](salomon/network-1/ib-single-plane-topology.html)
- .contenttype-folder}
-
- -
- [Software](salomon/software.html "In this section we provide overview of installed software and its usage.
- ") .contenttype-folder}
-
- -
- [ANSYS](salomon/software/ansys.html "An engineering simulation software ")
- .contenttype-folder}
-
- -
- [COMSOL](salomon/software/comsol.html " A finite element analysis, solver and Simulation software")
- .contenttype-folder}
-
- -
- [Debuggers and
- profilers](salomon/software/debuggers.html "A collection of development tools")
- .contenttype-folder}
-
- -
- [Chemistry, Physics and Materials
- science](salomon/software/chemistry.html "Tools for computational chemistry.")
- .contenttype-folder}
-
- -
- [Intel Parallel
- studio](salomon/software/intel-suite.html "The Intel Parallel Studio XE")
- .contenttype-folder}
-
- -
- [MPI](salomon/software/mpi-1.html "Message Passing Interface libraries on ANSELM")
- .contenttype-folder}
-
- -
- [Numerical
- languages](salomon/software/numerical-languages.html "Interpreted languages for numerical computations")
- .contenttype-folder}
-
- -
- [Compilers](salomon/software/compilers.html "Available compilers, including GNU, INTEL and UPC compilers")
-
-
- -
- [Intel Xeon
- Phi](salomon/software/intel-xeon-phi.html "A guide to Intel Xeon Phi usage")
-
-
- -
- [Java](salomon/software/java.html "Java on the cluster")
-
-
- -
- [Operating
- System](salomon/software/operating-system.html "The operating system, deployed on Salomon cluster")
-
-
- -
- [PRACE User
- Support](salomon/prace.html)
-
-
--
- [Anselm Cluster
- Documentation](anselm-cluster-documentation.html)
- .contenttype-folder}
-
- -
- [Hardware
- Overview](anselm-cluster-documentation/hardware-overview.html)
-
-
- -
- [Accessing the
- Cluster](anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access.html)
- .contenttype-folder}
-
- -
- [Shell access and data
- transfer](anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access.html)
- .contenttype-folder}
-
- -
- [Graphical User
- Interface](get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html)
- .contenttype-link}
-
- -
- [VPN
- Access](anselm-cluster-documentation/accessing-the-cluster/vpn-access.html)
-
-
- -
- [Outgoing
- connections](anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.html)
-
-
- -
- [Environment and
- Modules](anselm-cluster-documentation/environment-and-modules.html)
-
-
- -
- [Resource Allocation and Job
- Execution](anselm-cluster-documentation/resource-allocation-and-job-execution.html)
- .contenttype-folder}
-
- -
- [Resources Allocation
- Policy](anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.html)
-
-
- -
- [Job submission and
- execution](anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.html)
-
-
- -
- [Job
- scheduling](anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.html)
-
-
- -
- [Capacity
- computing](anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.html)
-
-
- -
- [Compute
- Nodes](anselm-cluster-documentation/compute-nodes.html)
-
-
- -
- [Storage](anselm-cluster-documentation/storage-1.html)
- .contenttype-folder}
-
- -
- [CESNET Data
- Storage](anselm-cluster-documentation/storage-1/cesnet-data-storage.html)
-
-
- -
- [Network](anselm-cluster-documentation/network.html)
-
-
- -
- [Software](anselm-cluster-documentation/software.html "In this section we provide overview of installed software and its usage.
- ") .contenttype-folder}
-
- -
- [ANSYS](anselm-cluster-documentation/software/ansys.html "An engineering simulation software ")
- .contenttype-folder}
-
- -
- [COMSOL](anselm-cluster-documentation/software/comsol.html " A finite element analysis, solver and Simulation software")
- .contenttype-folder}
-
- -
- [Debuggers and
- profilers](anselm-cluster-documentation/software/debuggers.html "A collection of development tools")
- .contenttype-folder}
-
- -
- [Chemistry and Materials
- science](anselm-cluster-documentation/software/chemistry.html "Tools for computational chemistry.")
- .contenttype-folder}
-
- -
- [Intel Parallel
- studio](anselm-cluster-documentation/software/intel-suite.html "The Intel Parallel Studio XE")
- .contenttype-folder}
-
- -
- [MPI](anselm-cluster-documentation/software/mpi-1.html "Message Passing Interface libraries on ANSELM")
- .contenttype-folder}
-
- -
- [Numerical
- Libraries](anselm-cluster-documentation/software/numerical-libraries.html "Libraries for numerical computations")
- .contenttype-folder}
-
- -
- [Numerical
- languages](anselm-cluster-documentation/software/numerical-languages.html "Interpreted languages for numerical computations")
- .contenttype-folder}
-
- -
- [Virtualization](anselm-cluster-documentation/software/virtualization.html)
- .contenttype-folder}
-
- -
- [Compilers](anselm-cluster-documentation/software/compilers.html "Available compilers, including GNU, INTEL and UPC compilers")
-
-
- -
- [Intel Xeon
- Phi](anselm-cluster-documentation/software/intel-xeon-phi.html "A guide to Intel Xeon Phi usage")
-
-
- -
- [ISV
- Licenses](anselm-cluster-documentation/software/isv_licenses.html "A guide to managing Independent Software Vendor licences")
-
-
- -
- [Java](anselm-cluster-documentation/software/java.html "Java on ANSELM")
-
-
- -
- [nVidia
- CUDA](anselm-cluster-documentation/software/nvidia-cuda.html "A guide to nVidia CUDA programming and GPU usage")
-
-
- -
- [OMICS
- Master](anselm-cluster-documentation/software/omics-master-1.html)
- .contenttype-folder}
-
- -
- [OpenFOAM](anselm-cluster-documentation/software/openfoam.html "A free, open source CFD software package")
-
-
- -
- [Operating
- System](anselm-cluster-documentation/software/operating-system.html "The operating system, deployed on ANSELM")
-
-
- -
- [ParaView](anselm-cluster-documentation/software/paraview.html "An open-source, multi-platform data analysis and visualization application ")
-
-
- -
- [GPI-2](anselm-cluster-documentation/software/gpi2.html "A library that implements the GASPI specification")
-
-
- -
- [Remote visualization
- service](anselm-cluster-documentation/remote-visualization.html)
-
-
diff --git a/vpn-connection-fail-in-win-8.md b/vpn-connection-fail-in-win-8.md
deleted file mode 100644
index 77b032f5f45cf0e07cc93e651c77bccafa20fbca..0000000000000000000000000000000000000000
--- a/vpn-connection-fail-in-win-8.md
+++ /dev/null
@@ -1,5 +0,0 @@
-will also impact WIndows 7 users with IE11. Windows Server
-2008/2012 are also impacted by this defect, but neither is a supported
-OS for AnyConnect.
-
-**Workaround**
diff --git a/whats-new.md b/whats-new.md
deleted file mode 100644
index 248fb0a6a7312f3c21aeea654b0b165d0fbcb9ff..0000000000000000000000000000000000000000
--- a/whats-new.md
+++ /dev/null
@@ -1,7 +0,0 @@
- ÄŚtvrtek 30.06.2016 0000 [Intel VTune Amplifier support for Xeon Phi on Salomon](whats-new/news-feed/intel-vtune-amplifier-support-for-xeon-phi-on-salomon.html "Intel VTune Amplifier support for Xeon Phi on Salomon")
- ÄŚtvrtek 23.06.2016 0000 [New method to execute parallel MATLAB jobs](whats-new/news-feed/new-method-to-execute-parallel-matlab-jobs.html "New method to execute parallel MATLAB jobs")
- Středa 08.06.2016 0000 [New versions of Allinea Forge and Performance Reports](whats-new/news-feed/new-versions-of-allinea-forge-and-performance-version.html "New versions of Allinea Forge and Performance Reports")
- Pondělà 06.06.2016 0000 [Intel VTune is working](whats-new/news-feed/intel-vtune-is-working.html "Intel VTune is working")
- ĂšterĂ˝ 31.05.2016 1400 [Intel Parallel Studio 2016 update 3](whats-new/news-feed/intel-parallel-studio-2016-update-3.html "Intel Parallel Studio 2016 update 3")
- ÄŚtvrtek 05.05.2016 1558 [ANSYS 17.0 Installed](whats-new/news-feed/ansys-17-0-installed.html "ANSYS 17.0 Installed")
- Pátek 29.04.2016 1425 [Allinea Forge 6.0](whats-new/news-feed/allinea-forge-6.html "Allinea Forge 6.0")
diff --git a/whats-new/downtimes_history.md b/whats-new/downtimes_history.md
deleted file mode 100644
index 07d50b69022ae1fbbe07bc9f7c249617e2e19311..0000000000000000000000000000000000000000
--- a/whats-new/downtimes_history.md
+++ /dev/null
@@ -1,205 +0,0 @@
-Date and time
-Title and description
-2016-06-29 135000
-Salomon cluster maintenance outage prolonged
-Important! Salomon cluster maintenance outage will be prolonged till 2016-06-29 2000 CEST.
-2016-06-16 000000
-Salomon planned downtime
-There's a planned maintenance window from 2016-06-28 0900 till 2016-06-29 2000 CEST.
-Thank you for understanding,
-the IT4Innovations team
-2016-05-26 103144
-Salomon planned downtime
-There's a planned maintenance window from 2016-06-08 0900 till 2016-06-09 0900 CEST.
-Thank you for understanding,
-the IT4Innovations team
-2016-04-27 155728
-Salomon cluster maintenance outage prolonged
-Important! Salomon cluster maintenance outage will be prolonged till 2016-04-28 1400 CEST
-2016-04-19 082000
-Salomon cluster maintenance outage
-From 2016-04-26 0900 till  2016-04-27 1400 CEST will be maintenance outage for Salomon. We are going to reinstall compute nodes operating system to the latest CentOS 6.7.
-2016-03-31 190325
-Failure on Salomon Cooling System
-We have very serious issue with Salomon cooling system since 2016-03-31 1000. We are working to resolve the issue.
-2016-03-31 185904
-Salomon Back in Production
-As of 2016-03-31 1930 CET, the Salomon is back in production. The outage was caused by an issue in cooling system.
-2016-03-30 155757
-PBS malfunction
-We've had several issues with PBS scheduler since 2016-03-30 1300 CEST. We are still working on it.
-2016-03-26 095241
-Salomon back to production
-We have recovered all the issues with the Salomon cluster.
-2016-03-26 095116
-Failure on Salomon Cooling Infrastructure
-We had an issue with the cooling infra of Salomon. This issue led to InfiniBand and storage outage. We are working to resolve the issue.
-2016-03-14 145751
-Infrastructure Maintenance
-The Salomon supercomputer will be down for the maintenance from 2016-03-22 1000 CEST to 2016-03-22 1700 CEST.
-2016-02-24 123000
-Anselm Upgrade
-The Anselm supercomputer will be down for the updates from 2016-02-01 to 2016-02-29.
-2016-02-23 084545
-Anselm Upgrade
-The Anselm supercomputer will be down for the updates from 2016-02-01 to 2016-02-29.
-2016-02-14 080746
-Failure on Salomon Infiniband Network
-We have very serious issue with Salomon Infiniband network since 2016-02-11 1018. We are working to resolve the issue as quickly as possible and apologize for any inconvenience.
-2016-02-04 115330
-Short network outage
-We need to apply some changes in network devices settings which may cause short network outage for Anselm Login nodes. This work will start around 6 am 2016-01-26.
-Thanks for your understanding.
-2016-02-04 115237
-Salomon Upgrade
-The Salomon supercomputer will be down for the updates from 2016-02-16 0900 CEST to 2016-02-16 1300 CEST.
-2016-02-04 115225
-Salomon Upgrade
-The Salomon supercomputer will be down for the updates from 2016-02-16 0900 CEST to 2016-02-16 1300 CEST.
-2015-11-26 081125
-/home downtime
-Dear HPC users
-There's a /home downtime on the Salomon supercomputer planned for 25th November. The reason is a maintenance of the underlying CXFS filesystem. Your jobs will be scheduled with respect to this maintenance window.
-Thank you for understanding,
-the IT4I team
-2015-11-24 091015
-The /home filesystem was down
-On 23.11.2015, 1355 - 1455, the /home filesystem was down due to acute technical problems.
-We apologize for inconvenience.
-2015-09-04 161412
-SCRATCH downtime
-Dear IT4I users
-Salomon's SCRATCH will *not* be accessible on Thursday (10th September 2015) from 1300 till 1800 CEST.
-Thank you for understanding,
-the IT4Innovations team
-2015-08-27 000000
-Today's SCRATCH downtime
-Dear IT4I users
-We are sorry for today's (27th August) inaccessibility of SCRATCH filesystem due to a broken service which normally provides mapping for user/group IDs (UIDs/GIDs). The issue has been fixed. No data were lost.
-Thank you for understanding,
-the IT4Innovations team
-2015-08-12 000000
-Unplanned downtime
-Dear Salomon users,
-there was an unplanned downtime of the non-accelerated nodes. At this moment, systems are booting and we are revising consequences. Temporarily inaccessible SCRATCH filesystem is one of them.
-We're sorry for the inconvenience,
-the IT4I team
-2015-08-06 000000
-SCRATCH downtime
-Dear IT4I users
-Salomon's SCRATCH will not be accessible tomorrow (7th August 2015) from 0830 till 1100 CEST.
-Thank you for understanding,
-the IT4Innovations team
-2014-11-14 102751
-Unplanned PBS Downtime
-Dear Anselm users,
-we apologize for the unavailability of our PBS scheduler during the last weekend. However, running jobs shouldn't have been affected at that time.
-Thank you for understanding,
-Anselm Admins
-2014-11-14 102750
-Login1 troubles
-Login1 had a short unplanned downtime. Sorry for the troubles.
-2014-10-14 203000
-Unexpected power failure
-Dear Anselm users,
-on Tuesday 14th approximately at 1720 CEST we encountered power failure during service operation on backup diesel generator. The system shut down. Additional checks after the shutdown took more time than what would expect. The system was back on-line with all services approximately at 2100 CEST. We are very sorry for any troubles, this matter may caused you. If some of your jobs ended in incorrect state, please feel free to reclaim your core hours.
-Thank you for understanding,Â
-Anselm Administrators
-2014-07-17 135000
-Login2(!) downtime
-Dear Anselm users,
-there's an upgrade planned on Friday, 18th July from 1300 till 1600 CEST. Please, take in mind that login2.anselm.it4i.cz will be unavailable at the given time-frame. We are sorry for the inconvenience.
-Thank you for understanding,
-Anselm Admins
-2014-07-16 131134
-Login1 downtime
-Dear Anselm users,
-there's an upgrade planned on Thursday, 17th July from 1300 till 1600 CEST. Please, take in mind that login1.anselm.it4i.cz will be unavailable at the given time-frame. We are sorry for the inconvenience.
-Thank you for understanding,
-Anselm Admins
-2014-06-18 105156
-Login2 downtime
-Dear Anselm users,
-there's an upgrade planned on Wednesday, 18th June from 1120 till 1420 CEST. Please, take in mind that login2.anselm.it4i.cz will be unavailable at the given time-frame. We are sorry for the inconvenience.
-Thank you for understanding,
-Anselm Admins
-2014-05-22 000000
-Outage
-Dear Anselm users.
-As of today (20140523 1045) we had an unmanaged outage of a few nodes. Affected nodes were cn[117-126,193-195].
-Sorry for the inconveniences,
-Anselm admins
-2014-04-11 113000
-Heartbleed bug
-Dear users of the Anselm cluster,
-A serious bug in the OpenSSL library, known as the "Heartbleed bug" has been recently discovered. We would like to ensure you that IT4I has taken all necessary steps to fix the OpenSSL library on all the systems.
-The bug in OpenSSL library affected many sites worldwide for nearly two years. At this moment, there is no evidence that any abuse of data took place at IT4I.
-In order to ensure the security and integrity of IT4I systems, all users will be issued new login credentials, including password and ssh keys.
-For more informations about the Heartbleed bug, please see https//docs.it4i.cz/heartbleed-bug
-Thank you for your understanding.
-IT4Innovations team
-2014-04-02 130500
-Scheduler is Down
-We are sorry for the current scheduler issues which are caused by an inconsistency of the internal PBS database. Thus it's not possible to interact with the scheduler now. In addition, some jobs may be affected and some job outputs may not be retrieved at this moment.
-2014-03-26 155000
-Temporary Scratch Mount on Login1
-Because of the Lustre issues (mentioned in previous announcements) there's a temporary mount point for Scratch filesystem on login1 node. Please, follow this path to access your data
-/scratch_nfs/
-2014-03-26 131000
-Both Login Nodes Inaccessible
-We are sorry for the inaccessibility of both login nodes. We are co-operating with our supplier and trying hard to solve this problem as soon as possible.
-Thank you for understanding.
-2014-03-25 220500
-Login1(!) Not Responding
-Currently, if you're having trouble while accessing Anselm, please use address login2.anselm.it4i.cz instead of anselm.it4i.cz. There's a Lustre issue with the login1 node, which causes it to not respond.
-We'll let you know by MOTD when login1 comes back online.
-2013-12-03 000000
-Planned Downtime
-On 17th December 0800 to 1800 CET Anselm will be down for maintenance. Power supply upgrade will take place, as well as system maintenance and software updates.
-Prior to the period
-- Jobs will be scheduled for running with a respect to the downtime.
-During the period
-- No Anselm HPC service will be available.
-- Following web applications will not be accessible Request Tracker, Anselm cluster documentation, Anselm Allocation.
-- Submitting tickets through the e-mail address
-<!--
-h='';a='@';n='support%5Bat%5Dit4i.cz';e=n+a+h;
-document.write(''+'support[at]it4i.cz'+'');
-// -->
-support[at]it4i.cz (support%5Bat%5Dit4i.cz at ) will be delayed.
-After the period
-- All service will be brought back to normal.
-- Jobs in a 'Q' state will be scheduled for running.
-We are sorry for the inconvenience.
-2013-10-14 000000
-Cooling system unstable
-Dear Anselm users,
-there was an unplanned downtime due to severe issues with the cold doors today. We are trying hard to bring all services up. We assume that we will finish the maintenance at about 1330 CEST.
-Thank you for understanding.
-Sincerely yours,
-Anselm admins
-2013-09-17 155000
-A Fair Amount of Nodes Down
-Dear Anselm users,
-We had an outage on the Anselm Cluster. A fair amount of the nodes was unavailable to production.
-Consider terminated job resubmission.
-We are sorry for the troubles,
-Anselm admins
-2013-08-23 152500
-Infiniband Maintenance Window
-Dear Anselm users,
-We would like to inform you about a planned Infiniband maintenance window, on Wednesday, 28th August from 0900 till 1630 CEST.
-No Anselm service will be available during this outage.
-New batch jobs will not be scheduled for running during this time. Consider altering the job walltime, to achieve job execution prior to the downtime (See Job Submission in the Anselm Documentation).
-Sincerely yours,
-Anselm Admins
-2013-08-14 171000
-Planned Upgrade / Scheduler Downtime
-Dear Anselm users,
-there's an upgrade planned on Thursday, 15th August from 1800 till 2200 CEST. Please, take in mind that PBS scheduler won't accept your jobs at the given timeframe. We are sorry for the inconvenience.
-Thank you for understanding,
-Anselm Admins
-2013-07-16 134500
-Anselm Cluster Upgrade - July 23rd
-Dear Anselm users.
-We would like to inform you that Anselm cluster will be unavailable due to upgrades on Tuesday, July 23rd from 0700 to 2000 CEST.
diff --git a/whats-new/news-feed.md b/whats-new/news-feed.md
deleted file mode 100644
index 1747c4f45a3fc7c229fd4372629ba53e039f4bd0..0000000000000000000000000000000000000000
--- a/whats-new/news-feed.md
+++ /dev/null
@@ -1,2 +0,0 @@
- [Allinea Forge 6.0](news-feed/allinea-forge-6.html){.contenttype-news-item .state-published .url}
-
diff --git a/whats-new/news-feed/issue-with-intel-mpi-4-1-1-on-salomon.md b/whats-new/news-feed/issue-with-intel-mpi-4-1-1-on-salomon.md
deleted file mode 100644
index 53252e5338bd9fe8658d5ec845a20edd692d2bf4..0000000000000000000000000000000000000000
--- a/whats-new/news-feed/issue-with-intel-mpi-4-1-1-on-salomon.md
+++ /dev/null
@@ -1 +0,0 @@
-There is an issue with running MPI programs compiled with Intel MPI
diff --git a/whats-new/news-feed/new-modules-for-parallel-programming-in-modern-fortran-course.md b/whats-new/news-feed/new-modules-for-parallel-programming-in-modern-fortran-course.md
deleted file mode 100644
index e7319263bbd81725a764f3dec7b2a50ce887f07e..0000000000000000000000000000000000000000
--- a/whats-new/news-feed/new-modules-for-parallel-programming-in-modern-fortran-course.md
+++ /dev/null
@@ -1,11 +0,0 @@
-New modules for Parallel programming in modern Fortran course
-=============================================================
-Following the [course by Salvatore
-Filippone](http//prace.it4i.cz/FORT-04-2016), we have prepared the
-following modules for testing new features of Coarray Fortran in
-development version of GCC on Salomon
-- GCC/5.3.1-snapshot-20160419-2.25
-- MPICH/3.2-GCC-5.3.1-snapshot-20160419-2.25
-- OpenCoarrays/1.4.0-GCC-5.3.1-snapshot-20160419-2.25
-The following modules are for PSBLAS and MLD2P4 with GPU support on
-Anselm