Commit 7d998a7e authored by Lukáš Krupčík's avatar Lukáš Krupčík

change css external links

parent cc100afd
......@@ -73,7 +73,7 @@ To establish local proxy server on your workstation, install and run SOCKS proxy
local $ ssh -D 1080 localhost
```
On Windows, install and run the free, open source [Sock Puppet](http://sockspuppet.com/)![external](../../img/external.png) server.
On Windows, install and run the free, open source [Sock 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](outgoing-connections/#port-forwarding-from-login-nodes).
......@@ -81,4 +81,4 @@ Once the proxy server is running, establish ssh port forwarding from Anselm to t
local $ ssh -R 6000:localhost:1080 anselm.it4i.cz
```
Now, configure the applications proxy settings to **localhost:6000**. Use port forwarding  to access the [proxy server from compute nodes](outgoing-connections/#port-forwarding-from-compute-nodes) as well .
\ No newline at end of file
Now, configure the applications proxy settings to **localhost:6000**. Use port forwarding  to access the [proxy server from compute nodes](outgoing-connections/#port-forwarding-from-compute-nodes) as well .
......@@ -56,7 +56,7 @@ Last login: Tue Jul 9 15:57:38 2013 from your-host.example.com
Data Transfer
-------------
Data in and out of the system may be transferred by the [scp](http://en.wikipedia.org/wiki/Secure_copy)![external](../../img/external.png) and sftp protocols.  (Not available yet.) In case large volumes of data are transferred, use dedicated data mover node dm1.anselm.it4i.cz for increased performance.
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 volumes of data are transferred, use dedicated data mover node dm1.anselm.it4i.cz for increased performance.
|Address|Port|Protocol|
|---|---|
......@@ -109,6 +109,6 @@ $ man scp
$ man sshfs
```
On Windows, use [WinSCP client](http://winscp.net/eng/download.php)![external](../../img/external.png) to transfer the data. The [win-sshfs client](http://code.google.com/p/win-sshfs/)![external](../../img/external.png) provides a way to mount the Anselm filesystems directly as an external disc.
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](../../storage/storage/).
\ No newline at end of file
More information about the shared file systems is available [here](../../storage/storage/).
......@@ -7,7 +7,7 @@ Accessing IT4Innovations internal resources via VPN
!!! Note "Note"
**Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS patch**
Workaround can be found at [vpn-connection-fail-in-win-8.1](../../vpn-connection-fail-in-win-8.1.html)
Workaround can be found at [vpn-connection-fail-in-win-8.1](../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.html)
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:
......@@ -83,4 +83,4 @@ After a successful logon, you can see a green circle with a tick mark on the loc
![](../../img/successfullconnection.jpg)
For disconnecting, right-click on the AnyConnect client icon in the system tray and select **VPN Disconnect**.
\ No newline at end of file
For disconnecting, right-click on the AnyConnect client icon in the system tray and select **VPN Disconnect**.
......@@ -63,7 +63,6 @@ Anselm is cluster of x86-64 Intel based nodes built on Bull Extreme Computing bu
Processor Architecture
----------------------
Anselm is equipped with Intel Sandy Bridge processors Intel Xeon E5-2665 (nodes without accelerator and fat nodes) and Intel Xeon E5-2470 (nodes with accelerator). Processors support Advanced Vector Extensions (AVX) 256-bit instruction set.
### Intel Sandy Bridge E5-2665 Processor
......@@ -133,4 +132,4 @@ Memory Architecture
- 8 DDR3 DIMMS per CPU
- 2 DDR3 DIMMS per channel
- Data rate support: up to 1600MT/s
- Populated memory: 16x 32GB DDR3 DIMM 1600Mhz
\ No newline at end of file
- Populated memory: 16x 32GB DDR3 DIMM 1600Mhz
......@@ -78,10 +78,10 @@ PrgEnv-intel sets up the INTEL development environment in conjunction with the I
### 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")![external](../img/external.png). In case that you want to use some applications that are build by EasyBuild already, you have to modify your MODULEPATH environment variable.
All application modules on Salomon cluster (and further) will be build using tool called [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.
```bash
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.
\ No newline at end of file
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.
......@@ -3,7 +3,7 @@ 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, 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 interlinked by high speed InfiniBand and Ethernet networks. All nodes share 320TB /home disk storage to store the user files. The 146TB shared /scratch storage is available for the scratch data.
The Fat nodes are equipped with large amount (512GB) of memory. 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)![external](../img/external.png) made by a PI.
The Fat nodes are equipped with large amount (512GB) of memory. 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.
Schematic representation of the Anselm cluster. Each box represents a node (computer) or storage capacity:
......@@ -518,4 +518,4 @@ The parameters are summarized in the following tables:
|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/), [Storage](storage/storage/), and [Network](network/).
\ No newline at end of file
For more details please refer to the [Compute nodes](compute-nodes/), [Storage](storage/storage/), and [Network](network/).
......@@ -3,7 +3,7 @@ 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 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/).
The cluster runs bullx Linux ([bull](http://www.bull.com/bullx-logiciels/systeme-exploitation.html)![external](../img/external.png)) [operating system](software/operating-system/), which is compatible with the RedHat [ Linux family.](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)![external](../img/external.png) We have installed a wide range of software packages targeted at different scientific domains. These packages are accessible via the [modules environment](environment-and-modules/).
The cluster runs bullx Linux ([bull](http://www.bull.com/bullx-logiciels/systeme-exploitation.html)) [operating system](software/operating-system/), 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 packages targeted at different scientific domains. These packages are accessible via the [modules environment](environment-and-modules/).
User data shared file-system (HOME, 320TB) and job data shared file-system (SCRATCH, 146TB) are available to users.
......
Network
=======
All compute and login nodes of Anselm are interconnected by [Infiniband](http://en.wikipedia.org/wiki/InfiniBand)![external](../img/external.png) QDR network and by Gigabit [Ethernet](http://en.wikipedia.org/wiki/Ethernet)![external](../img/external.png) network. Both networks may be used to transfer user data.
All compute and login nodes of Anselm are interconnected by [Infiniband](http://en.wikipedia.org/wiki/InfiniBand) QDR network and by Gigabit [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)![external](../img/external.png) QDR network (IB 4x QDR, 40 Gbps). The network topology is a fully non-blocking fat-tree.
All compute and login nodes of Anselm are interconnected by a high-bandwidth, low-latency [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 network interface, in address range 10.2.1.1-209. The MPI may be used to establish native Infiniband connection among the nodes.
......@@ -34,4 +34,4 @@ $ 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.
\ No newline at end of file
In this example, we access the node cn110 by Infiniband network via the ib0 interface, then from cn110 to cn108 by Ethernet network.
......@@ -5,11 +5,11 @@ Intro
-----
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 [Obtaining Login Credentials section](../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/)![external](../img/external.png) should be read before continuing reading the local documentation here.
All general [PRACE User 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/)![external](../img/external.png).
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/).
Information about the local services are provided in the [introduction of general user 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.
......@@ -30,11 +30,11 @@ The user will need a valid certificate and to be present in the PRACE LDAP (plea
Most of the information needed by PRACE users accessing the Anselm TIER-1 system can be found here:
- [General user's FAQ](http://www.prace-ri.eu/Users-General-FAQs)![external](../img/external.png)
- [Certificates FAQ](http://www.prace-ri.eu/Certificates-FAQ)![external](../img/external.png)
- [Interactive access using GSISSH](http://www.prace-ri.eu/Interactive-Access-Using-gsissh)![external](../img/external.png)
- [Data transfer with GridFTP](http://www.prace-ri.eu/Data-Transfer-with-GridFTP-Details)![external](../img/external.png)
- [Data transfer with gtransfer](http://www.prace-ri.eu/Data-Transfer-with-gtransfer)![external](../img/external.png)
- [General user's FAQ](http://www.prace-ri.eu/Users-General-FAQs)
- [Certificates FAQ](http://www.prace-ri.eu/Certificates-FAQ)
- [Interactive access using GSISSH](http://www.prace-ri.eu/Interactive-Access-Using-gsissh)
- [Data transfer with GridFTP](http://www.prace-ri.eu/Data-Transfer-with-GridFTP-Details)
- [Data transfer with gtransfer](http://www.prace-ri.eu/Data-Transfer-with-gtransfer)
Before you start to use any of the services don't forget to create a proxy certificate from your certificate:
......@@ -209,7 +209,7 @@ For production runs always use scratch file systems, either the global shared or
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/).
PRACE users can use the "prace" module to use the [PRACE Common Production Environment](http://www.prace-ri.eu/PRACE-common-production)![external](../img/external.png).
PRACE users can use the "prace" module to use the [PRACE Common Production Environment](http://www.prace-ri.eu/PRACE-common-production).
```bash
$ module load prace
......@@ -231,14 +231,14 @@ qprace**, the PRACE \***: This queue is intended for normal production runs. It
### Accounting & Quota
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 [example in the general documentation](resource-allocation-and-job-execution/resources-allocation-policy/)![external](../img/external.png).
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 [example in the general 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/)![external](../img/external.png).
PRACE users should check their project accounting using the [PRACE Accounting 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 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".
!!! Note "Note"
The **it4ifree** command is a part of it4i.portal.clients package, located here: <https://pypi.python.org/pypi/it4i.portal.clients>![external](../img/external.png)
The **it4ifree** command is a part of it4i.portal.clients package, located here: <https://pypi.python.org/pypi/it4i.portal.clients>
```bash
$ it4ifree
......@@ -256,4 +256,4 @@ By default file system quota is applied. To check the current status of the quot
$ lfs quota -u USER_LOGIN /scratch
```
If the quota is insufficient, please contact the [support](prace/#help-and-support) and request an increase.
\ No newline at end of file
If the quota is insufficient, please contact the [support](prace/#help-and-support) and request an increase.
......@@ -30,7 +30,7 @@ How to use the service
### 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: <http://sourceforge.net/projects/turbovnc/>![external](../img/external.png)
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: <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.
......@@ -219,4 +219,4 @@ To have an idea how the settings are affecting the resulting picture uality thre
3. JPEG image quality = 10
![rem_vis_q1](../img/quality1.png "rem_vis_q1")
\ No newline at end of file
![rem_vis_q1](../img/quality1.png "rem_vis_q1")
......@@ -312,4 +312,4 @@ Unzip the archive in an empty directory on Anselm and follow the instructions in
```bash
$ unzip capacity.zip
$ cat README
```
\ No newline at end of file
```
......@@ -36,4 +36,4 @@ 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/) page.
\ No newline at end of file
Read more on [Capacity computing](capacity-computing/) page.
......@@ -18,7 +18,7 @@ Queue priority is priority of queue where job is queued before execution.
Queue priority has the biggest impact on job execution priority. 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 <https://extranet.it4i.cz/anselm/queues>![external](../../img/external.png)
Queue priorities can be seen at <https://extranet.it4i.cz/anselm/queues>
### Fairshare priority
......@@ -34,7 +34,7 @@ where MAX_FAIRSHARE has value 1E6, usage~Project~ is cumulated usage by all memb
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 <https://extranet.it4i.cz/anselm/projects>.![external](../../img/external.png)
>Calculated usage and fairshare priority can be seen at <https://extranet.it4i.cz/anselm/projects>.
Calculated fairshare priority can be also seen as Resource_List.fairshare attribute of a job.
......@@ -65,4 +65,4 @@ It means, that jobs with lower execution priority can be run before jobs with hi
!!! Note "Note"
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.
\ No newline at end of file
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.
......@@ -408,4 +408,4 @@ In this example, some directory on the home holds the input file input and execu
### Other Jobscript Examples
Further jobscript examples may be found in the software section and the [Capacity computing](capacity-computing/) section.
\ No newline at end of file
Further jobscript examples may be found in the software section and the [Capacity computing](capacity-computing/) section.
......@@ -30,11 +30,11 @@ The job wall clock time defaults to **half the maximum time**, see table above.
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>![external](../../img/external.png).
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 <https://extranet.it4i.cz/anselm/>![external](../../img/external.png)
>Check the status of jobs, queues and compute nodes at <https://extranet.it4i.cz/anselm/>
![rspbs web interface](../../img/rsweb.png)
......@@ -112,7 +112,7 @@ The resources that are currently subject to accounting are the core-hours. The c
### Check consumed resources
!!! Note "Note"
The **it4ifree** command is a part of it4i.portal.clients package, located here: <https://pypi.python.org/pypi/it4i.portal.clients>![external](../../img/external.png)
The **it4ifree** command is a part of it4i.portal.clients package, 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.
......@@ -123,4 +123,4 @@ Password:
   -------- ------- ------ -------- -------
   OPEN-0-0 1500000 400644   225265 1099356
   DD-13-1    10000 2606 2606 7394
```
\ No newline at end of file
```
ANSYS CFX
=========
[ANSYS CFX](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+CFX)![external](../../../img/external.png)
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.
[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.
......@@ -54,4 +53,4 @@ Header of the pbs file (above) is common and description can be find on [this s
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** should be selected by parameter -P (Big letter **P**). Licensed products are the following: aa_r (ANSYS **Academic** Research), ane3fl (ANSYS Multiphysics)-**Commercial**.
[More about licensing here](licensing/)
\ No newline at end of file
[More about licensing here](licensing/)
ANSYS Fluent
============
[ANSYS Fluent](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent)![external](../../../img/external.png)
[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.
```bash
......@@ -161,4 +161,4 @@ ANSLIC_ADMIN Utility will be run
ANSYS Academic Research license should be moved up to the top of the list.
![](../../../img/Fluent_Licence_4.jpg)
\ No newline at end of file
![](../../../img/Fluent_Licence_4.jpg)
ANSYS LS-DYNA
=============
**[ANSYSLS-DYNA](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/Explicit+Dynamics/ANSYS+LS-DYNA)![external](../../../img/external.png)** 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.
**[ANSYSLS-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.
......@@ -51,6 +51,6 @@ 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/). [SVS FEM](http://www.svsfem.cz)![external](../../../img/external.png) 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.
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/). [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=
\ No newline at end of file
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=
ANSYS MAPDL
===========
**[ANSYS Multiphysics](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics)![external](../../../img/external.png)**
**[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.
......@@ -50,9 +50,9 @@ echo Machines: $hl
/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.md). [SVS FEM](http://www.svsfem.cz)![external](../../../img/external.png) 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.
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.md). [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/)
\ No newline at end of file
[More about licensing here](licensing/)
Overview of ANSYS Products
==========================
**[SVS FEM](http://www.svsfem.cz/)![external](../../../img/external.png)** as **[ANSYS Channel partner](http://www.ansys.com/)** 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)
**[SVS FEM](http://www.svsfem.cz/)** as **[ANSYS Channel partner](http://www.ansys.com/)** 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)
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). [ More about licensing here](ansys/licensing/)
......
LS-DYNA
=======
[LS-DYNA](http://www.lstc.com/)![external](../../../img/external.png) 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.
[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.
......@@ -31,6 +31,6 @@ 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)![external](../../../img/external.png) 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.
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=
\ No newline at end of file
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=
......@@ -5,13 +5,13 @@ Molpro is a complete system of ab initio programs for molecular electronic struc
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/)![external](../../../img/external.png).
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)![external](../../../img/external.png).
To run Molpro, you need to have a valid license token present in " $HOME/.molpro/token". You can download the token from [Molpro website](https://www.molpro.net/licensee/?portal=licensee).
Installed version
-----------------
......@@ -31,7 +31,7 @@ Compilation parameters are default:
Running
------
Molpro is compiled for parallel execution using MPI and OpenMP. By default, Molpro reads the number of allocated nodes from PBS and launches a data server on one node. On the remaining allocated nodes, compute processes are launched, one process per node, each with 16 threads. You can modify this behavior by using -n, -t and helper-server options. Please refer to the [Molpro documentation](http://www.molpro.net/info/2010.1/doc/manual/node9.html)![external](../../../img/external.png) for more details.
Molpro is compiled for parallel execution using MPI and OpenMP. By default, Molpro reads the number of allocated nodes from PBS and launches a data server on one node. On the remaining allocated nodes, compute processes are launched, one process per node, each with 16 threads. You can modify this behavior by using -n, -t and helper-server options. Please refer to the [Molpro documentation](http://www.molpro.net/info/2010.1/doc/manual/node9.html) for more details.
!!! Note "Note"
The OpenMP parallelization in Molpro is limited and has been observed to produce limited scaling. We therefore recommend to use MPI parallelization only. This can be achieved by passing option mpiprocs=16:ompthreads=1 to PBS.
......@@ -61,4 +61,4 @@ You are advised to use the -d option to point to a directory in [SCRATCH filesys
# delete scratch directory
rm -rf /scratch/$USER/$PBS_JOBID
```
\ No newline at end of file
```
......@@ -7,11 +7,10 @@ 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)![external](../../../img/external.png)
[Homepage](http://www.nwchem-sw.org/index.php/Main_Page)
Installed versions
------------------
The following versions are currently installed:
- 6.1.1, not recommended, problems have been observed with this version
......@@ -40,7 +39,7 @@ NWChem is compiled for parallel MPI execution. Normal procedure for MPI jobs app
Options
--------------------
Please refer to [the documentation](http://www.nwchem-sw.org/index.php/Release62:Top-level)![external](../../../img/external.png) and in the input file set the following directives :
Please refer to [the documentation](http://www.nwchem-sw.org/index.php/Release62:Top-level) 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/storage/#scratch) (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"
\ No newline at end of file
- SCRATCH_DIR : set this to a directory in [SCRATCH filesystem](../../storage/storage/#scratch) (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"
......@@ -3,15 +3,15 @@ COMSOL Multiphysics®
Introduction
-------------------------
[COMSOL](http://www.comsol.com)![external](../../img/external.png) 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
[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)![external](../../img/external.png),
- [Heat Transfer Module](http://www.comsol.com/heat-transfer-module)![external](../../img/external.png),
- [CFD Module](http://www.comsol.com/cfd-module)![external](../../img/external.png),
- [Acoustics Module](http://www.comsol.com/acoustics-module)![external](../../img/external.png),
- and [many others](http://www.comsol.com/products)![external](../../img/external.png)
- [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.
......@@ -118,4 +118,4 @@ 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.
\ No newline at end of file
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.
......@@ -94,4 +94,4 @@ Users can find original User Guide after loading the DDT module:
$DDTPATH/doc/userguide.pdf
```
[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)![external](../../../img/external.png)
\ No newline at end of file
[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)
......@@ -59,4 +59,4 @@ Now lets profile the code:
$ perf-report mpirun ./mympiprog.x
```
Performance report files [mympiprog_32p*.txt](mympiprog_32p_2014-10-15_16-56.txt)![external](../../../img/external.png) and [mympiprog_32p*.html](mympiprog_32p_2014-10-15_16-56.html)![external](../../../img/external.png) were created. We can see that the code is very efficient on MPI and is CPU bounded.
\ No newline at end of file
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.
......@@ -19,7 +19,7 @@ Each node in the tree is colored by severity (the color scheme is displayed at t
Installed versions
------------------
Currently, there are two versions of CUBE 4.2.3 available as [modules](../../environment-and-modules/) :
Currently, there are two versions of CUBE 4.2.3 available as [modules](../../environment-and-modules/):
- cube/4.2.3-gcc, compiled with GCC
- cube/4.2.3-icc, compiled with Intel compiler
......@@ -34,5 +34,5 @@ CUBE is a graphical application. Refer to Graphical User Interface documentation
After loading the apropriate module, simply launch 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.
References
1. <http://www.scalasca.org/software/cube-4.x/download.html>![external](../../../img/external.png)
1. <http://www.scalasca.org/software/cube-4.x/download.html>
......@@ -58,4 +58,4 @@ Vampir is a GUI trace analyzer for traces in OTF format.
$ vampir
```
Read more at the [Vampir](../../salomon/software/debuggers/vampir/) page.
\ No newline at end of file
Read more at the [Vampir](../../salomon/software/debuggers/vampir/) page.
......@@ -191,7 +191,7 @@ Can be used as a sensor for ksysguard GUI, which is currently not installed on A
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)![external](../../../img/external.png) for details of the 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.
!!! Note "Note"
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)
......@@ -277,6 +277,6 @@ Sample output:
References
----------
1. <https://software.intel.com/en-us/articles/intel-performance-counter-monitor-a-better-way-to-measure-cpu-utilization>![external](../../../img/external.png)
2. <https://software.intel.com/sites/default/files/m/3/2/2/xeon-e5-2600-uncore-guide.pdf>![external](../../../img/external.png) Intel® Xeon® Processor E5-2600 Product Family Uncore Performance Monitoring Guide.
3. <http://intel-pcm-api-documentation.github.io/classPCM.html>![external](../../../img/external.png) API Documentation
\ No newline at end of file
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> API Documentation
......@@ -71,4 +71,4 @@ You may also use remote analysis to collect data from the MIC and then analyze i
References
----------
1. <https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf>![external](../../../img/external.png) Performance Tuning for Intel® Xeon Phi™ Coprocessors
\ No newline at end of file
1. <https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf> Performance Tuning for Intel® Xeon Phi™ Coprocessors
......@@ -3,7 +3,6 @@ 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.
......@@ -92,19 +91,19 @@ The include path is automatically added by papi module to $INCLUDE.
### High level API
Please refer to <http://icl.cs.utk.edu/projects/papi/wiki/PAPIC:High_Level>![external](../../../img/external.png) for a description of the 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>![external](../../../img/external.png) for a description of the 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>![external](../../../img/external.png)
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>![external](../../../img/external.png)
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
-------
......@@ -235,6 +234,6 @@ To use PAPI in offload mode, you need to provide both host and MIC versions of P
References
----------
1. <http://icl.cs.utk.edu/papi/>![external](../../../img/external.png) Main project page
2. <http://icl.cs.utk.edu/projects/papi/wiki/Main_Page>![external](../../../img/external.png) Wiki
3. <http://icl.cs.utk.edu/papi/docs/>![external](../../../img/external.png) API Documentation
\ No newline at end of file
1. <http://icl.cs.utk.edu/papi/> Main project page
2. <http://icl.cs.utk.edu/projects/papi/wiki/Main_Page> Wiki
3. <http://icl.cs.utk.edu/papi/docs/> API Documentation
......@@ -3,7 +3,7 @@ Scalasca
Introduction
-------------------------
[Scalasca](http://www.scalasca.org/)![external](../../../img/external.png) 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](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.
......@@ -68,4 +68,4 @@ Refer to [CUBE documentation](cube/) on usage of the GUI viewer.
References
----------
1. <http://www.scalasca.org/>![external](../../../img/external.png)
\ No newline at end of file
1. <http://www.scalasca.org/>
......@@ -3,7 +3,7 @@ Score-P
Introduction
------------
The [Score-P measurement infrastructure](http://www.vi-hps.org/projects/score-p/)![external](../../../img/external.png) is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications.
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.
Score-P can be used as an instrumentation tool for [Scalasca](scalasca/).
......@@ -75,7 +75,7 @@ An example in C/C++ :
end subroutine foo
```
Please refer to the [documentation for description of the API](https://silc.zih.tu-dresden.de/scorep-current/pdf/scorep.pdf)![external](../../../img/external.png).
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
......@@ -115,4 +115,4 @@ and in Fortran :
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)![external](../../../img/external.png) for a more elaborate description.
\ No newline at end of file
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.
......@@ -159,4 +159,4 @@ More information regarding the command line parameters of the TotalView can be f
Documentation
-------------
[1] The [TotalView documentation](http://www.roguewave.com/support/product-documentation/totalview-family.aspx#totalview)![external](../../../img/external.png) web page is a good resource for learning more about some of the advanced TotalView features.
\ No newline at end of file
[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.
......@@ -5,10 +5,9 @@ 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)![external](../../../img/external.png). 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.
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 :