diff --git a/docs.it4i/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md b/docs.it4i/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
index e7aedb555028acd76b243a8d1876e0dfd005ada1..0231f61a1e6b2e576b391601f57ba1db7ad1ebeb 100644
--- a/docs.it4i/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
+++ b/docs.it4i/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
@@ -25,27 +25,27 @@ VPN client installation
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.
@@ -56,31 +56,31 @@ You can use graphical user interface or command line interface to run VPN client
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**.
\ No newline at end of file
diff --git a/docs.it4i/anselm-cluster-documentation/compute-nodes.md b/docs.it4i/anselm-cluster-documentation/compute-nodes.md
index 4ab91620251da545090def7ffbf1be0c894e7c4f..f1bcc05718de34cdd9e2a4b4521532e9187aa68f 100644
--- a/docs.it4i/anselm-cluster-documentation/compute-nodes.md
+++ b/docs.it4i/anselm-cluster-documentation/compute-nodes.md
@@ -48,7 +48,7 @@ Anselm is cluster of x86-64 Intel based nodes built on Bull Extreme Computing bu
- bullx R423-E3 servers
- cn[208-209]
-
+
**Figure Anselm bullx B510 servers**
diff --git a/docs.it4i/anselm-cluster-documentation/prace.md b/docs.it4i/anselm-cluster-documentation/prace.md
index f2641aa702dba17d2059bed250a2ae8c98d8456d..6e854b72f2a23996317a265dee52c930c51d0862 100644
--- a/docs.it4i/anselm-cluster-documentation/prace.md
+++ b/docs.it4i/anselm-cluster-documentation/prace.md
@@ -237,7 +237,8 @@ PRACE users should check their project accounting using the [PRACE Accounting To
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".
->The **it4ifree** command is a part of it4i.portal.clients package, located here: <https://pypi.python.org/pypi/it4i.portal.clients>
+!!! Note "Note"
+ The **it4ifree** command is a part of it4i.portal.clients package, located here: <https://pypi.python.org/pypi/it4i.portal.clients>
```bash
$ it4ifree
diff --git a/docs.it4i/anselm-cluster-documentation/remote-visualization.md b/docs.it4i/anselm-cluster-documentation/remote-visualization.md
index b21396878c7f6eecb3c2d6a22399380eeff713c6..bf415fb3623ae7890f460eb11d8fa5ac93ca5828 100644
--- a/docs.it4i/anselm-cluster-documentation/remote-visualization.md
+++ b/docs.it4i/anselm-cluster-documentation/remote-visualization.md
@@ -21,9 +21,9 @@ Currently two compute nodes are dedicated for this service with following config
Schematic overview
------------------
-
+
-
+
How to use the service
----------------------
@@ -130,7 +130,7 @@ $ vncserver -kill :1
Access the visualization node
-----------------------------
-To access the node use a dedicated PBS Professional scheduler queue
+**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 |
@@ -205,18 +205,18 @@ Tips and Tricks
---------------
If you want to increase the responsibility of the visualization, please djust your TurboVNC client settings in this way:
-
+
To have an idea how the settings are affecting the resulting picture uality three levels of "JPEG image quality" are demonstrated:
1. JPEG image quality = 30
-
+
2. JPEG image quality = 15
-
+
3. JPEG image quality = 10
-
\ No newline at end of file
+
\ No newline at end of file
diff --git a/docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md b/docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
index 9e3406cc6535b9209ed2b69e8e82c507a57d77db..b871d1228c7e45259fcd05d888c853775e2ac2af 100644
--- a/docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
+++ b/docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
@@ -28,7 +28,7 @@ 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.
@@ -50,7 +50,7 @@ Eligible time can be seen as eligible_time attribute of job.
Job execution priority (job sort formula) is calculated as:
-
+
### Job backfilling
diff --git a/docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md b/docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
index b286c4e18a709a51a4ea10f1eb4f96741b728c5c..d7f49f6a3724482d4893432c9d5a35ce699158f0 100644
--- a/docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
+++ b/docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
@@ -36,7 +36,7 @@ Anselm users may check current queue configuration at <https://extranet.it4i.cz/
>Check the status of jobs, queues and compute nodes at <https://extranet.it4i.cz/anselm/>
-
+
Display the queue status on Anselm:
diff --git a/docs.it4i/anselm-cluster-documentation/software/ansys/Fluent_Licence_1.jpg b/docs.it4i/anselm-cluster-documentation/software/ansys/Fluent_Licence_1.jpg
deleted file mode 100644
index 786e9ce1f0c190e5ef83bfe691596d298b9efc15..0000000000000000000000000000000000000000
Binary files a/docs.it4i/anselm-cluster-documentation/software/ansys/Fluent_Licence_1.jpg and /dev/null differ
diff --git a/docs.it4i/anselm-cluster-documentation/software/ansys/Fluent_Licence_2.jpg b/docs.it4i/anselm-cluster-documentation/software/ansys/Fluent_Licence_2.jpg
deleted file mode 100644
index 77dc3d7cfeddad08626234586cdf4228fdb69ee9..0000000000000000000000000000000000000000
Binary files a/docs.it4i/anselm-cluster-documentation/software/ansys/Fluent_Licence_2.jpg and /dev/null differ
diff --git a/docs.it4i/anselm-cluster-documentation/software/ansys/Fluent_Licence_3.jpg b/docs.it4i/anselm-cluster-documentation/software/ansys/Fluent_Licence_3.jpg
deleted file mode 100644
index 9a9d57cba8fc61ee756b49ced8888a95da46737b..0000000000000000000000000000000000000000
Binary files a/docs.it4i/anselm-cluster-documentation/software/ansys/Fluent_Licence_3.jpg and /dev/null differ
diff --git a/docs.it4i/anselm-cluster-documentation/software/ansys/Fluent_Licence_4.jpg b/docs.it4i/anselm-cluster-documentation/software/ansys/Fluent_Licence_4.jpg
deleted file mode 100644
index 3027bc33158c70fd3b2844de87dbd3e0649300c2..0000000000000000000000000000000000000000
Binary files a/docs.it4i/anselm-cluster-documentation/software/ansys/Fluent_Licence_4.jpg and /dev/null differ
diff --git a/docs.it4i/anselm-cluster-documentation/software/ansys/ansys-fluent.md b/docs.it4i/anselm-cluster-documentation/software/ansys/ansys-fluent.md
index 09acb0b0945d802369eaa7c37b570191e506a67f..57177b84a70468bf0b23080ff38a20530a650b50 100644
--- a/docs.it4i/anselm-cluster-documentation/software/ansys/ansys-fluent.md
+++ b/docs.it4i/anselm-cluster-documentation/software/ansys/ansys-fluent.md
@@ -153,12 +153,12 @@ Fluent could be run in parallel only under Academic Research license. To do so t
ANSLIC_ADMIN Utility will be run
-
+
-
+
-
+
ANSYS Academic Research license should be moved up to the top of the list.
-
\ No newline at end of file
+
\ No newline at end of file
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-ddt.md b/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
index 0667baee80682d505c13955de13497268464d3bd..efca43d2e5b858615f600f2c8b72741f731e52b3 100644
--- a/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
+++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
@@ -78,7 +78,7 @@ Then launch the debugger with the ddt command followed by the name of the execut
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 " box.
-
+
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".
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/cube.md b/docs.it4i/anselm-cluster-documentation/software/debuggers/cube.md
index ccc237e4411d64c20f95f674314174094fbcb3d8..4bfc6f68360e20b08a2d0ce0f6642bca9fbf9667 100644
--- a/docs.it4i/anselm-cluster-documentation/software/debuggers/cube.md
+++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/cube.md
@@ -11,7 +11,7 @@ CUBE is a graphical performance report explorer for displaying data from Score-P
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.*
@@ -28,7 +28,8 @@ Usage
-----
CUBE is a graphical application. Refer to Graphical User Interface documentation 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.
+!!! Note "Note"
+ 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 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.
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md b/docs.it4i/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
index 7eca1cd6258e932ae6a61f36f02338e52e7184b7..97d46065b217b6bcf0289978e2dc37e2f48cd9d1 100644
--- a/docs.it4i/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
+++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
@@ -95,7 +95,7 @@ Sample output :
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;
+ 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
@@ -265,7 +265,7 @@ Sample output:
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;
+ 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
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md b/docs.it4i/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
index 4876db7c303a2b1b999e9a116b23ed131baf6a3c..c1f2801837c61801fb4a3aec3c797020e5736983 100644
--- a/docs.it4i/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
+++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
@@ -11,7 +11,7 @@ Intel*® *VTune™ Amplifier, part of Intel Parallel studio, is a GUI profilin
bandwidth
- Power usage analysis - frequency and sleep states.
-
+
Usage
-----
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/papi.md b/docs.it4i/anselm-cluster-documentation/software/debuggers/papi.md
index 83149f3b6961a2a2d00f89a370a228884522067c..83d9a00147760dd63468815d63c4fd51f92487a4 100644
--- a/docs.it4i/anselm-cluster-documentation/software/debuggers/papi.md
+++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/papi.md
@@ -66,7 +66,7 @@ Prints which preset events are available on the current CPU. The third column in
Prints which native events are available on the current CPU.
-### class="s1">papi_cost
+### papi_cost
Measures the cost (in cycles) of basic PAPI operations.
@@ -193,7 +193,8 @@ Now the compiler won't remove the multiplication loop. (However it is still not
### 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.
+!!! Note "Note"
+ 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/) native applications, you need to load module with " -mic" suffix, for example " papi/5.3.2-mic" :
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/score-p.md b/docs.it4i/anselm-cluster-documentation/software/debuggers/score-p.md
index bf551f73c0dfbffc78eeabaa085bd3826ad890da..2e401424a3177060649e85d795230b71c7fc3bc9 100644
--- a/docs.it4i/anselm-cluster-documentation/software/debuggers/score-p.md
+++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/score-p.md
@@ -16,7 +16,7 @@ There are currently two versions of Score-P version 1.2.6 [modules](../../enviro
Instrumentation
---------------
-There are three ways to instrument your parallel applications in order to enable performance data collection :
+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
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/total-view.md b/docs.it4i/anselm-cluster-documentation/software/debuggers/total-view.md
index 2cc11cd85b4c8830cff4a8fcd3c0cd62b98982fa..a4f33d610f910d392c077e5da0cf17a888de100e 100644
--- a/docs.it4i/anselm-cluster-documentation/software/debuggers/total-view.md
+++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/total-view.md
@@ -135,11 +135,11 @@ Now you can run the parallel debugger using:
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
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/vampir.md b/docs.it4i/anselm-cluster-documentation/software/debuggers/vampir.md
index 8be78cd36ba4129fb94160622821226fac64b915..780b38f8dcb075cf0c13ea711774505aeb5b17b1 100644
--- a/docs.it4i/anselm-cluster-documentation/software/debuggers/vampir.md
+++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/vampir.md
@@ -3,7 +3,7 @@ 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](../../../salomon/software/debuggers/score-p/)) first to collect the traces.
-
+
Installed versions
------------------
diff --git a/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-compilers.md b/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-compilers.md
index 23eb1d13cc1cb5c42c2f938ea951d4dd6fe852ac..ab52b214871d56c008f157112e3610a08ef387f3 100644
--- a/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-compilers.md
+++ b/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-compilers.md
@@ -31,7 +31,7 @@ Read more at <http://software.intel.com/sites/products/documentation/doclib/stdx
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:
+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): -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): -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.
\ No newline at end of file
diff --git a/docs.it4i/anselm-cluster-documentation/software/kvirtualization.md b/docs.it4i/anselm-cluster-documentation/software/kvirtualization.md
index 9768507353678dd57368a6a4e2806a3232c597b7..6cacfbf5e6317660657a30c4e34cea53afc94e82 100644
--- a/docs.it4i/anselm-cluster-documentation/software/kvirtualization.md
+++ b/docs.it4i/anselm-cluster-documentation/software/kvirtualization.md
@@ -50,7 +50,7 @@ IT4Innovations does not provide any licenses for operating systems and software
We propose this 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 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](virtualization/#snapshot-mode), image is immutable - image does not change, so one image can be used for many concurrent jobs.
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab 2013-2014.md b/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab 2013-2014.md
index 7f54854eab6f51c4e5c23b6946a676d952bbd15a..f5b62facdb304d30c8cfdeb2b806872f8c4b527c 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab 2013-2014.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab 2013-2014.md
@@ -47,7 +47,7 @@ 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 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.
-
+
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:
diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/diagnostic-component-team.md b/docs.it4i/anselm-cluster-documentation/software/omics-master/diagnostic-component-team.md
index 610e6a072821b8a0ea0ca54681e2d57bf6ec6284..58051b735498cb64c12b0b6409a453ac776e42bd 100644
--- a/docs.it4i/anselm-cluster-documentation/software/omics-master/diagnostic-component-team.md
+++ b/docs.it4i/anselm-cluster-documentation/software/omics-master/diagnostic-component-team.md
@@ -14,6 +14,6 @@ VCF files are scanned by this diagnostic tool for known diagnostic disease-assoc
TEAM (27) 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.
-
+
**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.
\ No newline at end of file
diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md b/docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md
index 26bce4ba613cd4982c6e793f4b978b91213ed7d6..c10bb716f91c891e34a7b041e4e85ffb9adfa384 100644
--- a/docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md
+++ b/docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md
@@ -10,7 +10,7 @@ The scope of this OMICS MASTER solution is restricted to human genomics research
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.
+them, depending of the experimental design carried out.](../../../img/fig1.png)
**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 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.
@@ -43,7 +43,7 @@ Output: **FASTQ file plus an HTML file containing statistics on the data.**
FASTQ format It represents the nucleotide sequence and its corresponding quality scores.
-
+
**Figure 2.**FASTQ file.
#### Mapping
@@ -83,7 +83,7 @@ corresponding information is unavailable.
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.
-
+
**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 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.
@@ -121,7 +121,7 @@ A VCF file consists of a header section and a data section. The header contains
+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.](../../../img/fig4.png)
**Figure 4.** (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.
@@ -341,7 +341,7 @@ The output folder contains all the subfolders with the intermediate data. This f
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), ClinVar (29)^ and COSMIC (23).
-
+
**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. 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 them back (action **H**).*
@@ -353,7 +353,7 @@ For variant discovering/filtering we should upload the VCF file into BierApp by
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 the Genome Maps Tool (30).
-
+
**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 7:132481242 C>T is associated to the phenotype: large intestine tumor.
diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/priorization-component-bierapp.md b/docs.it4i/anselm-cluster-documentation/software/omics-master/priorization-component-bierapp.md
index 5bffe9edab2e21f208707dc01d687e94eb72e5f8..99d907d7f73d0df3565b8bad9c80fda56bbbc94a 100644
--- a/docs.it4i/anselm-cluster-documentation/software/omics-master/priorization-component-bierapp.md
+++ b/docs.it4i/anselm-cluster-documentation/software/omics-master/priorization-component-bierapp.md
@@ -14,7 +14,7 @@ BiERApp is available at the following address:Â <http://omics.it4i.cz/bierapp/>
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 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.
diff --git a/docs.it4i/anselm-cluster-documentation/software/openfoam.md b/docs.it4i/anselm-cluster-documentation/software/openfoam.md
index ed28468da5509550ff24d6ae29b6472bab9cd82f..24019c9ee801811970c989450b2c0c36076f6336 100644
--- a/docs.it4i/anselm-cluster-documentation/software/openfoam.md
+++ b/docs.it4i/anselm-cluster-documentation/software/openfoam.md
@@ -147,7 +147,8 @@ Job submission
This job create simple block mesh and domain decomposition. Check your decomposition, and submit parallel computation:
-> Create a PBS script testParallel.pbs:
+!!! Note "Note"
+ Create a PBS script testParallel.pbs:
```bash
#!/bin/bash
@@ -168,7 +169,7 @@ This job create simple block mesh and domain decomposition. Check your decomposi
mpirun -hostfile ${PBS_NODEFILE} -np $nproc potentialFoam -noFunctionObject-writep -parallel | tee potentialFoam.log
- mpirun -hostfile ${PBS_NODEFILE} -np $nproc simpleFoam -parallel | tee simpleFoam.log
+ mpirun -hostfile ${PBS_NODEFILE} -np $nproc simpleFoam -parallel | tee simpleFoam.log
```
nproc – number of subdomains
diff --git a/docs.it4i/downtimes_history.md b/docs.it4i/downtimes_history.md
new file mode 100644
index 0000000000000000000000000000000000000000..ae419d058b916ca0486ca7f20d7f17abfd193c7f
--- /dev/null
+++ b/docs.it4i/downtimes_history.md
@@ -0,0 +1,52 @@
+History of Downtimes
+====================
+
+Full history of important announcements related to IT4I infrastructure, planned downtimes, outages etc.
+
+ |Date and time |Title and description |
+ | --- | --- |
+ |2016-08-29 00:00:00 |**Salomon Maintenance** The Salomon supercomputer will be down for the updates from 2016-09-19 11:00 CEST to 2016-09-21 11:00 CEST. |
+ |2016-07-29 00:00:00 |**Anselm outage** There was an unplanned outage of Anselm cluster due to network problems. Anselm is now back in production. |
+ |2016-07-27 13:28:51 |**Back in Production** The Salomon and Anselm supercomputers are online! The flooding in the computer room caused by the failed coolant water pipe is now cleared, damage to infrastructure is virtually none.The 8th Open Access Call deadline is extended till Friday 2016-07-29 to compensate the inaccessibility of the extranet.it4i.cz portal. |
+ |2016-07-20 08:45:00 |**Anselm planned downtime** There's a planned maintenance window from 2016-08-16 07:00 till 2016-08-18 16:00 CEST. |
+ |2016-06-29 13:50:00 |**Salomon cluster maintenance outage prolonged** Important! Salomon cluster maintenance outage will be prolonged till 2016-06-29 20:00 CEST. |
+ |2016-06-16 00:00:00 |**Salomon planned downtime** There's a planned maintenance window from 2016-06-28 09:00 till 2016-06-29 20:00 CEST.Thank you for understanding,the IT4Innovations team |
+ |2016-05-26 10:31:44 |**Salomon planned downtime** There's a planned maintenance window from 2016-06-08 09:00 till 2016-06-09 09:00 CEST.Thank you for understanding,the IT4Innovations team |
+ |2016-04-27 15:57:28 |**Salomon cluster maintenance outage prolonged** Important! Salomon cluster maintenance outage will be prolonged till 2016-04-28 14:00 CEST |
+ |2016-03-31 19:03:25 |**Failure on Salomon Cooling System** We have very serious issue with Salomon cooling system since 2016-03-31 10:00. We are working to resolve the issue. |
+ |2016-03-31 18:59:04 |**Salomon Back in Production** As of 2016-03-31 19:30 CET, the Salomon is back in production. The outage was caused by an issue in cooling system. |
+ |2016-03-30 15:57:57 |**PBS malfunction** We've had several issues with PBS scheduler since 2016-03-30 13:00 CEST. We are still working on it. |
+ |2016-03-26 09:52:41 |**Salomon back to production** We have recovered all the issues with the Salomon cluster. |
+ |2016-03-26 09:51:16 |**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 14:57:51 |**Infrastructure Maintenance** The Salomon supercomputer will be down for the maintenance from 2016-03-22 10:00 CEST to 2016-03-22 17:00 CEST. |
+ |2016-02-24 12:30:00 |**Anselm Upgrade** The Anselm supercomputer will be down for the updates from 2016-02-01 to 2016-02-29. |
+ |2016-02-23 08:45:45 |**Anselm Upgrade** The Anselm supercomputer will be down for the updates from 2016-02-01 to 2016-02-29. |
+ |2016-02-14 08:07:46 |**Failure on Salomon Infiniband Network** 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. |
+ |2016-02-04 11:53:30 |**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 11:52:37 |**Salomon Upgrade** The Salomon supercomputer will be down for the updates from 2016-02-16 09:00 CEST to 2016-02-16 13:00 CEST. |
+ |2016-02-04 11:52:25 |**Salomon Upgrade** The Salomon supercomputer will be down for the updates from 2016-02-16 09:00 CEST to 2016-02-16 13:00 CEST. |
+ |2015-11-26 08:11:25 |**/home downtime** Dear HPC usersThere'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 09:10:15 |**The /home filesystem was down** On 23.11.2015, 13:55 - 14:55, the /home filesystem was down due to acute technical problems.>We apologize for inconvenience. |
+ |2015-09-04 16:14:12 |**SCRATCH downtime** Dear IT4I usersSalomon's SCRATCH will *not* be accessible on Thursday (10th September 2015) from 13:00 till 18:00 CEST.Thank you for understanding,the IT4Innovations team |
+ |2015-08-27 00:00:00 |**Today's SCRATCH downtime** Dear IT4I usersWe 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 00:00:00 |**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 00:00:00 |**SCRATCH downtime** Dear IT4I usersSalomon's SCRATCH will not be accessible tomorrow (7th August 2015) from 08:30 till 11:00 CEST.Thank you for understanding,the IT4Innovations team |
+ |2014-11-14 10:27:51 |**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 10:27:50 |**Login1 troubles** Login1 had a short unplanned downtime. Sorry for the troubles. |
+ |2014-10-14 20:30:00 |**Unexpected power failure** Dear Anselm users,>>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. The system was back on-line with all services approximately at 21:00 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, Anselm Administrators |
+ |2014-07-17 13:50:00 |**Login2(!) downtime** Dear Anselm users,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.Thank you for understanding,Anselm Admins |
+ |2014-07-16 13:11:34 |**Login1 downtime** Dear Anselm users,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.Thank you for understanding,Anselm Admins |
+ |2014-06-18 10:51:56 |**Login2 downtime** Dear Anselm users,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.Thank you for understanding,Anselm Admins |
+ |2014-05-22 00:00:00 |**Outage** Dear Anselm users.As of today (20140523 10:45) 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 11:30:00 |**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](https://docs.it4i.cz/heartbleed-bug) Thank you for your understanding.IT4Innovations team |
+ |2014-04-02 13:05:00 |**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 15:50:00 |**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 13:10:00 |**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 22:05:00 |**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 00:00:00 |**Planned Downtime** 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.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 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 00:00:00 |**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 13:30 CEST.Thank you for understanding.Sincerely yours,Anselm admins |
+ |2013-09-17 15:50:00 |**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 15:25:00 |**Infiniband Maintenance Window** Dear Anselm users,We would like to inform you about a planned Infiniband maintenance window, on Wednesday, 28th August from 09:00 till 16:30 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 17:10:00 |**Planned Upgrade / Scheduler Downtime** Dear Anselm users,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.Thank you for understanding,Anselm Admins |
+ |2013-07-16 13:45:00 |**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 07:00 to 20:00 CEST.Sorry for the inconvenience,Anselm admins--Anselm cluster documentation can be found at:[http://support.it4i.cz/docs/anselm-cluster-documentation/"](http://support.it4i.cz/docs/anselm-cluster-documentation/) |
+ |2013-06-27 09:35:00 |**SSH Password Authentication** Dear Anselm users.If you are experiencing some troubles when using SSH PasswordAuthentication on the client side, please switch to PubkeyAuthentication instead.We are trying hard to resolve this issue.Sincerely yours,Anselm admins |
\ No newline at end of file
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md
index 5a2841520fb30afb272c0f3d9c2c0bf426095fd9..ffd66e9747645b8e16897566e4e7204bd7760f65 100644
--- a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md
+++ b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md
@@ -19,9 +19,9 @@ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connect
to
C:*cygwin64binXWin.exe -listen tcp*
-
+
2. Check Putty settings:
Enable X11 forwarding
- 
\ No newline at end of file
+ 
\ No newline at end of file
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md
index 0eb37ff947a8f41b101fa2e576fe1462205251ae..7472bb4a3570023495eeb713a2f39527a372fe93 100644
--- a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md
+++ b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md
@@ -3,14 +3,12 @@ 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**](x-window-system/).
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").
Read more about configuring **[VNC](vnc/)**.
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md
index d7901fecff064e7f18ddf6c70da6a21415ec19e4..9dc8493787654cb7b71c73a8e90fe30e9465e764 100644
--- a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md
+++ b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md
@@ -125,13 +125,13 @@ On the PuTTY Configuration screen go to Connection->SSH->Tunnels to set up
Fill the Source port and Destination fields. **Do not forget to click the Add button**.
-
+
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.
@@ -139,24 +139,24 @@ In this example, we connect to VNC server on port 5961, via the ssh tunnel, usin
Use your VNC password to log using TightVNC Viewer and start a Gnome Session on the login node.
-
+
Gnome session
-------------
You should see after the successful login.
-
+
###Disable your Gnome session screensaver
Open Screensaver preferences dialog:
-
+
Uncheck both options below the slider:
-
+
### Kill screensaver if locked screen
@@ -188,12 +188,11 @@ Or this way:
GUI applications on compute nodes over VNC
------------------------------------------
-
The very same methods as described above, 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.
-
+
Allow incoming X11 graphics from the compute nodes at the login node:
@@ -215,4 +214,4 @@ $ xterm
Example described above:
-
\ No newline at end of file
+
\ No newline at end of file
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/pageant.md b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/pageant.md
index ca2c2b620a95606ff048177681e0ab241b2993c4..e064dad2cb7d8519c5e78e22121df27d71007be9 100644
--- a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/pageant.md
+++ b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/pageant.md
@@ -8,5 +8,5 @@ Pageant holds your private key in memory without needing to retype a passphrase
- Enter your passphrase.
- Now you have your private key in memory without needing to retype a passphrase on every login.
-
+
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md
index 1ddd2d5f39e8b303d657594cde48c9b32662dcde..24416dbb3577c974f95a388d6689a2e8d9454e00 100644
--- a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md
+++ b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md
@@ -31,22 +31,22 @@ PuTTY - how to connect to the IT4Innovations cluster
- Run PuTTY
- Enter Host name and Save session fields with [Login address](../../../salomon/accessing-the-cluster/accessing-the-cluster/) 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 **"salomon.it4i.cz"**.
-
+
- Category -> Connection - > SSH -> Auth:
Select Attempt authentication using Pageant.
Select Allow agent forwarding.
Browse and select your [private key](ssh-keys/) file.
-
+
- Return to Session page and Save selected configuration with *Save* button.
-
+
- Now you can log in using *Open* button.
-
+
- 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/) file if Pageant **SSH authentication agent is not used.**
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md
index c818903d420073690c2f3080e7d7905a37893a48..c5be24d6e86bed0037d6d4b1e17463aee59ff807 100644
--- a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md
+++ b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md
@@ -13,7 +13,7 @@ You can change the password of your SSH key with "PuTTY Key Generator". Make sur
- Confirm key passphrase.
- Save your private key with *Save private key* button.
-
+
### Generate a New Public/Private key
@@ -21,31 +21,31 @@ You can generate an additional public/private key pair and insert public key in
- Start with *Generate* button.
-
+
- Generate some randomness.
-
+
- Wait.
-
+
- Enter a *comment* for your key using format 'username@organization.example.com'.
Enter key passphrase.
Confirm key passphrase.
Save your new private key `in "*.ppk" `format with *Save private key* button.
-
+
- 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.
-
+
- Export private key in OpenSSH format "id_rsa" using Conversion -> Export OpenSSH key
-
+
- 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](../shell-access-and-data-transfer/ssh-keys/).
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
index 7c2ba9fa75188fd6eec6ba49f62bd183e388cd3d..de26dfc187fc4a8791b547b9b85a734472efbba3 100644
--- a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
+++ b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
@@ -18,7 +18,8 @@ After logging in, you can see .ssh/ directory with SSH keys and authorized_keys
-rw-r--r-- 1 username username 392 May 21 2014 id_rsa.pub
```
->Please note that private keys in .ssh directory are without passphrase and allow you to connect within the cluster.
+!!! Note "Note"
+ Please note that private keys in .ssh directory are without passphrase and allow you to connect within the cluster.
### Access privileges on .ssh folder
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md
index 84f67742753b08b04c6f6ff6e68c95902e7f0f08..03e8702677432f344a816a28378c2a9780007ece 100644
--- a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md
+++ b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md
@@ -15,5 +15,5 @@ AnyConnect users on Windows 8.1 will receive a "Failed to initialize connection
- Click 'Test Program'. This will open the program.
- Close
-
+
diff --git a/docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md b/docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
index ed36270e581f42543a96d9359c72a1bafd8a65ee..40c2ad36b45c21d760afbf57d7008f83d07ccf4b 100644
--- a/docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
+++ b/docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
@@ -5,7 +5,7 @@ Obtaining Authorization
-----------------------
The computational resources of IT4I  are allocated by the Allocation Committee to a [Project](/), 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:
-
+
You need to either [become the PI](../applying-for-resources/) or [be named as a collaborator](obtaining-login-credentials/#authorization-of-collaborator-by-pi) by a PI in order to access and use the clusters.
diff --git a/docs.it4i/salomon/network/7D_Enhanced_hypercube.png b/docs.it4i/img/7D_Enhanced_hypercube.png
similarity index 100%
rename from docs.it4i/salomon/network/7D_Enhanced_hypercube.png
rename to docs.it4i/img/7D_Enhanced_hypercube.png
diff --git a/docs.it4i/salomon/software/ansys/AMsetPar1.png b/docs.it4i/img/AMsetPar1.png
similarity index 100%
rename from docs.it4i/salomon/software/ansys/AMsetPar1.png
rename to docs.it4i/img/AMsetPar1.png
diff --git a/docs.it4i/anselm-cluster-documentation/accessing-the-cluster/Anselmprofile.jpg b/docs.it4i/img/Anselmprofile.jpg
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/accessing-the-cluster/Anselmprofile.jpg
rename to docs.it4i/img/Anselmprofile.jpg
diff --git a/docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/Authorization_chain.png b/docs.it4i/img/Authorization_chain.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/Authorization_chain.png
rename to docs.it4i/img/Authorization_chain.png
diff --git a/docs.it4i/salomon/software/ansys/Fluent_Licence_1.jpg b/docs.it4i/img/Fluent_Licence_1.jpg
similarity index 100%
rename from docs.it4i/salomon/software/ansys/Fluent_Licence_1.jpg
rename to docs.it4i/img/Fluent_Licence_1.jpg
diff --git a/docs.it4i/salomon/software/ansys/Fluent_Licence_2.jpg b/docs.it4i/img/Fluent_Licence_2.jpg
similarity index 100%
rename from docs.it4i/salomon/software/ansys/Fluent_Licence_2.jpg
rename to docs.it4i/img/Fluent_Licence_2.jpg
diff --git a/docs.it4i/salomon/software/ansys/Fluent_Licence_3.jpg b/docs.it4i/img/Fluent_Licence_3.jpg
similarity index 100%
rename from docs.it4i/salomon/software/ansys/Fluent_Licence_3.jpg
rename to docs.it4i/img/Fluent_Licence_3.jpg
diff --git a/docs.it4i/salomon/software/ansys/Fluent_Licence_4.jpg b/docs.it4i/img/Fluent_Licence_4.jpg
similarity index 100%
rename from docs.it4i/salomon/software/ansys/Fluent_Licence_4.jpg
rename to docs.it4i/img/Fluent_Licence_4.jpg
diff --git a/docs.it4i/salomon/network/IBsingleplanetopologyAcceleratednodessmall.png b/docs.it4i/img/IBsingleplanetopologyAcceleratednodessmall.png
similarity index 100%
rename from docs.it4i/salomon/network/IBsingleplanetopologyAcceleratednodessmall.png
rename to docs.it4i/img/IBsingleplanetopologyAcceleratednodessmall.png
diff --git a/docs.it4i/salomon/network/IBsingleplanetopologyICEXMcellsmall.png b/docs.it4i/img/IBsingleplanetopologyICEXMcellsmall.png
similarity index 100%
rename from docs.it4i/salomon/network/IBsingleplanetopologyICEXMcellsmall.png
rename to docs.it4i/img/IBsingleplanetopologyICEXMcellsmall.png
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/Matlab.png b/docs.it4i/img/Matlab.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/software/numerical-languages/Matlab.png
rename to docs.it4i/img/Matlab.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PageantV.png b/docs.it4i/img/PageantV.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PageantV.png
rename to docs.it4i/img/PageantV.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuTTY_host_Salomon.png b/docs.it4i/img/PuTTY_host_Salomon.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuTTY_host_Salomon.png
rename to docs.it4i/img/PuTTY_host_Salomon.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuTTY_keyV.png b/docs.it4i/img/PuTTY_keyV.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuTTY_keyV.png
rename to docs.it4i/img/PuTTY_keyV.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuTTY_open_Salomon.png b/docs.it4i/img/PuTTY_open_Salomon.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuTTY_open_Salomon.png
rename to docs.it4i/img/PuTTY_open_Salomon.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuTTY_save_Salomon.png b/docs.it4i/img/PuTTY_save_Salomon.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuTTY_save_Salomon.png
rename to docs.it4i/img/PuTTY_save_Salomon.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygeneratorV.png b/docs.it4i/img/PuttyKeygeneratorV.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygeneratorV.png
rename to docs.it4i/img/PuttyKeygeneratorV.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_001V.png b/docs.it4i/img/PuttyKeygenerator_001V.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_001V.png
rename to docs.it4i/img/PuttyKeygenerator_001V.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_002V.png b/docs.it4i/img/PuttyKeygenerator_002V.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_002V.png
rename to docs.it4i/img/PuttyKeygenerator_002V.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_003V.png b/docs.it4i/img/PuttyKeygenerator_003V.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_003V.png
rename to docs.it4i/img/PuttyKeygenerator_003V.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_004V.png b/docs.it4i/img/PuttyKeygenerator_004V.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_004V.png
rename to docs.it4i/img/PuttyKeygenerator_004V.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_005V.png b/docs.it4i/img/PuttyKeygenerator_005V.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_005V.png
rename to docs.it4i/img/PuttyKeygenerator_005V.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_006V.png b/docs.it4i/img/PuttyKeygenerator_006V.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_006V.png
rename to docs.it4i/img/PuttyKeygenerator_006V.png
diff --git a/docs.it4i/salomon/network/Salomon_IB_topology.png b/docs.it4i/img/Salomon_IB_topology.png
similarity index 100%
rename from docs.it4i/salomon/network/Salomon_IB_topology.png
rename to docs.it4i/img/Salomon_IB_topology.png
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/Snmekobrazovky20141204v12.56.36.png b/docs.it4i/img/Snmekobrazovky20141204v12.56.36.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/software/debuggers/Snmekobrazovky20141204v12.56.36.png
rename to docs.it4i/img/Snmekobrazovky20141204v12.56.36.png
diff --git a/docs.it4i/salomon/software/intel-suite/Snmekobrazovky20151204v15.35.12.png b/docs.it4i/img/Snmekobrazovky20151204v15.35.12.png
similarity index 100%
rename from docs.it4i/salomon/software/intel-suite/Snmekobrazovky20151204v15.35.12.png
rename to docs.it4i/img/Snmekobrazovky20151204v15.35.12.png
diff --git a/docs.it4i/salomon/software/debuggers/Snmekobrazovky20160211v14.27.45.png b/docs.it4i/img/Snmekobrazovky20160211v14.27.45.png
similarity index 100%
rename from docs.it4i/salomon/software/debuggers/Snmekobrazovky20160211v14.27.45.png
rename to docs.it4i/img/Snmekobrazovky20160211v14.27.45.png
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/Snmekobrazovky20160708v12.33.35.png b/docs.it4i/img/Snmekobrazovky20160708v12.33.35.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/software/debuggers/Snmekobrazovky20160708v12.33.35.png
rename to docs.it4i/img/Snmekobrazovky20160708v12.33.35.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/TightVNC_login.png b/docs.it4i/img/TightVNC_login.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/TightVNC_login.png
rename to docs.it4i/img/TightVNC_login.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/XWinlistentcp.png b/docs.it4i/img/XWinlistentcp.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/XWinlistentcp.png
rename to docs.it4i/img/XWinlistentcp.png
diff --git a/docs.it4i/anselm-cluster-documentation/accessing-the-cluster/anyconnectcontextmenu.jpg b/docs.it4i/img/anyconnectcontextmenu.jpg
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/accessing-the-cluster/anyconnectcontextmenu.jpg
rename to docs.it4i/img/anyconnectcontextmenu.jpg
diff --git a/docs.it4i/anselm-cluster-documentation/accessing-the-cluster/anyconnecticon.jpg b/docs.it4i/img/anyconnecticon.jpg
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/accessing-the-cluster/anyconnecticon.jpg
rename to docs.it4i/img/anyconnecticon.jpg
diff --git a/docs.it4i/img/application.png b/docs.it4i/img/application.png
new file mode 100644
index 0000000000000000000000000000000000000000..006a93a202327e57ca9bb57f0c63f38b43d6411a
Binary files /dev/null and b/docs.it4i/img/application.png differ
diff --git a/docs.it4i/anselm-cluster-documentation/bullxB510.png b/docs.it4i/img/bullxB510.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/bullxB510.png
rename to docs.it4i/img/bullxB510.png
diff --git a/docs.it4i/img/cn_m_cell b/docs.it4i/img/cn_m_cell
new file mode 100644
index 0000000000000000000000000000000000000000..6a882034ba55b29e04eebe4801c727088c677c8d
Binary files /dev/null and b/docs.it4i/img/cn_m_cell differ
diff --git a/docs.it4i/img/cn_mic b/docs.it4i/img/cn_mic
new file mode 100644
index 0000000000000000000000000000000000000000..4e895b76c3c7b94ae1062eb6e06392ba15242338
Binary files /dev/null and b/docs.it4i/img/cn_mic differ
diff --git a/docs.it4i/img/cn_mic-1 b/docs.it4i/img/cn_mic-1
new file mode 100644
index 0000000000000000000000000000000000000000..210eb3d3ba9d9cc4339d0a0b97fb9610aafe9aaa
Binary files /dev/null and b/docs.it4i/img/cn_mic-1 differ
diff --git a/docs.it4i/salomon/accessing-the-cluster/copy_of_vpn_web_install_3.png b/docs.it4i/img/copy_of_vpn_web_install_3.png
similarity index 100%
rename from docs.it4i/salomon/accessing-the-cluster/copy_of_vpn_web_install_3.png
rename to docs.it4i/img/copy_of_vpn_web_install_3.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwinX11forwarding.png b/docs.it4i/img/cygwinX11forwarding.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwinX11forwarding.png
rename to docs.it4i/img/cygwinX11forwarding.png
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/ddt1.png b/docs.it4i/img/ddt1.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/software/debuggers/ddt1.png
rename to docs.it4i/img/ddt1.png
diff --git a/docs.it4i/anselm-cluster-documentation/accessing-the-cluster/downloadfilesuccessfull.jpeg b/docs.it4i/img/downloadfilesuccessfull.jpeg
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/accessing-the-cluster/downloadfilesuccessfull.jpeg
rename to docs.it4i/img/downloadfilesuccessfull.jpeg
diff --git a/docs.it4i/anselm-cluster-documentation/accessing-the-cluster/executionaccess.jpeg b/docs.it4i/img/executionaccess.jpeg
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/accessing-the-cluster/executionaccess.jpeg
rename to docs.it4i/img/executionaccess.jpeg
diff --git a/docs.it4i/anselm-cluster-documentation/accessing-the-cluster/executionaccess2.jpeg b/docs.it4i/img/executionaccess2.jpeg
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/accessing-the-cluster/executionaccess2.jpeg
rename to docs.it4i/img/executionaccess2.jpeg
diff --git a/docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/fairshare_formula.png b/docs.it4i/img/fairshare_formula.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/fairshare_formula.png
rename to docs.it4i/img/fairshare_formula.png
diff --git a/docs.it4i/img/favicon.ico b/docs.it4i/img/favicon.ico
new file mode 100644
index 0000000000000000000000000000000000000000..d51e1c2571169b49424f1ab0f91f59c0b4e63b34
Binary files /dev/null and b/docs.it4i/img/favicon.ico differ
diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/fig1.png b/docs.it4i/img/fig1.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/software/omics-master/fig1.png
rename to docs.it4i/img/fig1.png
diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/fig2.png b/docs.it4i/img/fig2.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/software/omics-master/fig2.png
rename to docs.it4i/img/fig2.png
diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/fig3.png b/docs.it4i/img/fig3.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/software/omics-master/fig3.png
rename to docs.it4i/img/fig3.png
diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/fig4.png b/docs.it4i/img/fig4.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/software/omics-master/fig4.png
rename to docs.it4i/img/fig4.png
diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/fig5.png b/docs.it4i/img/fig5.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/software/omics-master/fig5.png
rename to docs.it4i/img/fig5.png
diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/fig6.png b/docs.it4i/img/fig6.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/software/omics-master/fig6.png
rename to docs.it4i/img/fig6.png
diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/fig7.png b/docs.it4i/img/fig7.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/software/omics-master/fig7.png
rename to docs.it4i/img/fig7.png
diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/fig7x.png b/docs.it4i/img/fig7x.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/software/omics-master/fig7x.png
rename to docs.it4i/img/fig7x.png
diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/fig8.png b/docs.it4i/img/fig8.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/software/omics-master/fig8.png
rename to docs.it4i/img/fig8.png
diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/fig9.png b/docs.it4i/img/fig9.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/software/omics-master/fig9.png
rename to docs.it4i/img/fig9.png
diff --git a/docs.it4i/anselm-cluster-documentation/accessing-the-cluster/firstrun.jpg b/docs.it4i/img/firstrun.jpg
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/accessing-the-cluster/firstrun.jpg
rename to docs.it4i/img/firstrun.jpg
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gdmdisablescreensaver.png b/docs.it4i/img/gdmdisablescreensaver.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gdmdisablescreensaver.png
rename to docs.it4i/img/gdmdisablescreensaver.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gdmscreensaver.png b/docs.it4i/img/gdmscreensaver.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gdmscreensaver.png
rename to docs.it4i/img/gdmscreensaver.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gnome-compute-nodes-over-vnc.png b/docs.it4i/img/gnome-compute-nodes-over-vnc.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gnome-compute-nodes-over-vnc.png
rename to docs.it4i/img/gnome-compute-nodes-over-vnc.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gnome-terminal.png b/docs.it4i/img/gnome-terminal.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gnome-terminal.png
rename to docs.it4i/img/gnome-terminal.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gnome_screen.png b/docs.it4i/img/gnome_screen.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gnome_screen.png
rename to docs.it4i/img/gnome_screen.png
diff --git a/docs.it4i/anselm-cluster-documentation/accessing-the-cluster/instalationfile.jpeg b/docs.it4i/img/instalationfile.jpeg
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/accessing-the-cluster/instalationfile.jpeg
rename to docs.it4i/img/instalationfile.jpeg
diff --git a/docs.it4i/anselm-cluster-documentation/accessing-the-cluster/java_detection.jpeg b/docs.it4i/img/java_detection.jpeg
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/accessing-the-cluster/java_detection.jpeg
rename to docs.it4i/img/java_detection.jpeg
diff --git a/docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/job_sort_formula.png b/docs.it4i/img/job_sort_formula.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/job_sort_formula.png
rename to docs.it4i/img/job_sort_formula.png
diff --git a/docs.it4i/anselm-cluster-documentation/legend.png b/docs.it4i/img/legend.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/legend.png
rename to docs.it4i/img/legend.png
diff --git a/docs.it4i/anselm-cluster-documentation/accessing-the-cluster/login.jpeg b/docs.it4i/img/login.jpeg
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/accessing-the-cluster/login.jpeg
rename to docs.it4i/img/login.jpeg
diff --git a/docs.it4i/anselm-cluster-documentation/accessing-the-cluster/logingui.jpg b/docs.it4i/img/logingui.jpg
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/accessing-the-cluster/logingui.jpg
rename to docs.it4i/img/logingui.jpg
diff --git a/docs.it4i/anselm-cluster-documentation/accessing-the-cluster/loginwithprofile.jpeg b/docs.it4i/img/loginwithprofile.jpeg
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/accessing-the-cluster/loginwithprofile.jpeg
rename to docs.it4i/img/loginwithprofile.jpeg
diff --git a/docs.it4i/img/logo.png b/docs.it4i/img/logo.png
new file mode 100644
index 0000000000000000000000000000000000000000..fbb51c7f5ee2e361a0cb3ebb69a46dc23a2818fc
Binary files /dev/null and b/docs.it4i/img/logo.png differ
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/putty-tunnel.png b/docs.it4i/img/putty-tunnel.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/putty-tunnel.png
rename to docs.it4i/img/putty-tunnel.png
diff --git a/docs.it4i/anselm-cluster-documentation/quality1.png b/docs.it4i/img/quality1.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/quality1.png
rename to docs.it4i/img/quality1.png
diff --git a/docs.it4i/anselm-cluster-documentation/quality2.png b/docs.it4i/img/quality2.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/quality2.png
rename to docs.it4i/img/quality2.png
diff --git a/docs.it4i/anselm-cluster-documentation/quality3.png b/docs.it4i/img/quality3.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/quality3.png
rename to docs.it4i/img/quality3.png
diff --git a/docs.it4i/salomon/software/debuggers/report.png b/docs.it4i/img/report.png
similarity index 100%
rename from docs.it4i/salomon/software/debuggers/report.png
rename to docs.it4i/img/report.png
diff --git a/docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/rsweb.png b/docs.it4i/img/rsweb.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution/rsweb.png
rename to docs.it4i/img/rsweb.png
diff --git a/docs.it4i/salomon/resource-allocation-and-job-execution/rswebsalomon.png b/docs.it4i/img/rswebsalomon.png
similarity index 100%
rename from docs.it4i/salomon/resource-allocation-and-job-execution/rswebsalomon.png
rename to docs.it4i/img/rswebsalomon.png
diff --git a/docs.it4i/salomon/salomon b/docs.it4i/img/salomon
similarity index 100%
rename from docs.it4i/salomon/salomon
rename to docs.it4i/img/salomon
diff --git a/docs.it4i/salomon/salomon-1.jpeg b/docs.it4i/img/salomon-1.jpeg
similarity index 100%
rename from docs.it4i/salomon/salomon-1.jpeg
rename to docs.it4i/img/salomon-1.jpeg
diff --git a/docs.it4i/salomon/salomon-2 b/docs.it4i/img/salomon-2
similarity index 100%
rename from docs.it4i/salomon/salomon-2
rename to docs.it4i/img/salomon-2
diff --git a/docs.it4i/salomon/salomon-3.jpeg b/docs.it4i/img/salomon-3.jpeg
similarity index 100%
rename from docs.it4i/salomon/salomon-3.jpeg
rename to docs.it4i/img/salomon-3.jpeg
diff --git a/docs.it4i/salomon/salomon-4.jpeg b/docs.it4i/img/salomon-4.jpeg
similarity index 100%
rename from docs.it4i/salomon/salomon-4.jpeg
rename to docs.it4i/img/salomon-4.jpeg
diff --git a/docs.it4i/anselm-cluster-documentation/scheme.png b/docs.it4i/img/scheme.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/scheme.png
rename to docs.it4i/img/scheme.png
diff --git a/docs.it4i/img/search_icon.png b/docs.it4i/img/search_icon.png
new file mode 100644
index 0000000000000000000000000000000000000000..eb31b322f7eb54819810f5013404c6995312ec0a
Binary files /dev/null and b/docs.it4i/img/search_icon.png differ
diff --git a/docs.it4i/salomon/sgi-c1104-gp1.jpeg b/docs.it4i/img/sgi-c1104-gp1.jpeg
similarity index 100%
rename from docs.it4i/salomon/sgi-c1104-gp1.jpeg
rename to docs.it4i/img/sgi-c1104-gp1.jpeg
diff --git a/docs.it4i/img/sh.png b/docs.it4i/img/sh.png
new file mode 100644
index 0000000000000000000000000000000000000000..f553447d731f19e73e3fb5819a667eda3b1254bd
Binary files /dev/null and b/docs.it4i/img/sh.png differ
diff --git a/docs.it4i/anselm-cluster-documentation/accessing-the-cluster/successfullconnection.jpg b/docs.it4i/img/successfullconnection.jpg
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/accessing-the-cluster/successfullconnection.jpg
rename to docs.it4i/img/successfullconnection.jpg
diff --git a/docs.it4i/anselm-cluster-documentation/accessing-the-cluster/successfullinstalation.jpeg b/docs.it4i/img/successfullinstalation.jpeg
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/accessing-the-cluster/successfullinstalation.jpeg
rename to docs.it4i/img/successfullinstalation.jpeg
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/totalview1.png b/docs.it4i/img/totalview1.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/software/debuggers/totalview1.png
rename to docs.it4i/img/totalview1.png
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/totalview2.png b/docs.it4i/img/totalview2.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/software/debuggers/totalview2.png
rename to docs.it4i/img/totalview2.png
diff --git a/docs.it4i/anselm-cluster-documentation/turbovncclientsetting.png b/docs.it4i/img/turbovncclientsetting.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/turbovncclientsetting.png
rename to docs.it4i/img/turbovncclientsetting.png
diff --git a/docs.it4i/salomon/uv-2000.jpeg b/docs.it4i/img/uv-2000.jpeg
similarity index 100%
rename from docs.it4i/salomon/uv-2000.jpeg
rename to docs.it4i/img/uv-2000.jpeg
diff --git a/docs.it4i/anselm-cluster-documentation/software/virtualization-job-workflow b/docs.it4i/img/virtualization-job-workflow
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/software/virtualization-job-workflow
rename to docs.it4i/img/virtualization-job-workflow
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vncviewer.png b/docs.it4i/img/vncviewer.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vncviewer.png
rename to docs.it4i/img/vncviewer.png
diff --git a/docs.it4i/salomon/accessing-the-cluster/vpn_contacting.png b/docs.it4i/img/vpn_contacting.png
similarity index 100%
rename from docs.it4i/salomon/accessing-the-cluster/vpn_contacting.png
rename to docs.it4i/img/vpn_contacting.png
diff --git a/docs.it4i/salomon/accessing-the-cluster/vpn_contacting_https.png b/docs.it4i/img/vpn_contacting_https.png
similarity index 100%
rename from docs.it4i/salomon/accessing-the-cluster/vpn_contacting_https.png
rename to docs.it4i/img/vpn_contacting_https.png
diff --git a/docs.it4i/salomon/accessing-the-cluster/vpn_contacting_https_cluster.png b/docs.it4i/img/vpn_contacting_https_cluster.png
similarity index 100%
rename from docs.it4i/salomon/accessing-the-cluster/vpn_contacting_https_cluster.png
rename to docs.it4i/img/vpn_contacting_https_cluster.png
diff --git a/docs.it4i/salomon/accessing-the-cluster/vpn_login.png b/docs.it4i/img/vpn_login.png
similarity index 100%
rename from docs.it4i/salomon/accessing-the-cluster/vpn_login.png
rename to docs.it4i/img/vpn_login.png
diff --git a/docs.it4i/salomon/accessing-the-cluster/vpn_successfull_connection.png b/docs.it4i/img/vpn_successfull_connection.png
similarity index 100%
rename from docs.it4i/salomon/accessing-the-cluster/vpn_successfull_connection.png
rename to docs.it4i/img/vpn_successfull_connection.png
diff --git a/docs.it4i/salomon/accessing-the-cluster/vpn_web_download.png b/docs.it4i/img/vpn_web_download.png
similarity index 100%
rename from docs.it4i/salomon/accessing-the-cluster/vpn_web_download.png
rename to docs.it4i/img/vpn_web_download.png
diff --git a/docs.it4i/salomon/accessing-the-cluster/vpn_web_download_2.png b/docs.it4i/img/vpn_web_download_2.png
similarity index 100%
rename from docs.it4i/salomon/accessing-the-cluster/vpn_web_download_2.png
rename to docs.it4i/img/vpn_web_download_2.png
diff --git a/docs.it4i/salomon/accessing-the-cluster/vpn_web_install_2.png b/docs.it4i/img/vpn_web_install_2.png
similarity index 100%
rename from docs.it4i/salomon/accessing-the-cluster/vpn_web_install_2.png
rename to docs.it4i/img/vpn_web_install_2.png
diff --git a/docs.it4i/salomon/accessing-the-cluster/vpn_web_install_4.png b/docs.it4i/img/vpn_web_install_4.png
similarity index 100%
rename from docs.it4i/salomon/accessing-the-cluster/vpn_web_install_4.png
rename to docs.it4i/img/vpn_web_install_4.png
diff --git a/docs.it4i/salomon/accessing-the-cluster/vpn_web_login.png b/docs.it4i/img/vpn_web_login.png
similarity index 100%
rename from docs.it4i/salomon/accessing-the-cluster/vpn_web_login.png
rename to docs.it4i/img/vpn_web_login.png
diff --git a/docs.it4i/salomon/accessing-the-cluster/vpn_web_login_2.png b/docs.it4i/img/vpn_web_login_2.png
similarity index 100%
rename from docs.it4i/salomon/accessing-the-cluster/vpn_web_login_2.png
rename to docs.it4i/img/vpn_web_login_2.png
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpnuiV.png b/docs.it4i/img/vpnuiV.png
similarity index 100%
rename from docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpnuiV.png
rename to docs.it4i/img/vpnuiV.png
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/vtune-amplifier.png b/docs.it4i/img/vtune-amplifier.png
similarity index 100%
rename from docs.it4i/anselm-cluster-documentation/software/debuggers/vtune-amplifier.png
rename to docs.it4i/img/vtune-amplifier.png
diff --git a/docs.it4i/new.md b/docs.it4i/new.md
new file mode 100644
index 0000000000000000000000000000000000000000..0307689c63e7be3940fd0f7858b98e48e481496c
--- /dev/null
+++ b/docs.it4i/new.md
@@ -0,0 +1,24 @@
+|Datum účinnosti|Nadpis|
+|---|---|
+|Středa 13.07.2016 15:40|[MATLAB 2015b](https://docs.it4i.cz/whats-new/news-feed/matlab-2015b "MATLAB 2015b")|
+|Pátek 08.07.2016 00:00|[Vampir installed](https://docs.it4i.cz/whats-new/news-feed/vampir-installed "Vampir installed")|
+|ÄŚtvrtek 30.06.2016 00:00|[Allinea Tools updated to 6.0.6](https://docs.it4i.cz/whats-new/news-feed/allinea-tools-updated-to-6-0.6 "Allinea Tools updated to 6.0.6")|
+|ÄŚtvrtek 30.06.2016 00:00|[Intel VTune Amplifier support for Xeon Phi on Salomon](https://docs.it4i.cz/whats-new/news-feed/intel-vtune-amplifier-support-for-xeon-phi-on-salomon "Intel VTune Amplifier support for Xeon Phi on Salomon")|
+|ÄŚtvrtek 23.06.2016 00:00|[New method to execute parallel MATLAB jobs](https://docs.it4i.cz/whats-new/news-feed/new-method-to-execute-parallel-matlab-jobs "New method to execute parallel MATLAB jobs")|
+|Středa 08.06.2016 00:00|[New versions of Allinea Forge and Performance Reports](https://docs.it4i.cz/whats-new/news-feed/new-versions-of-allinea-forge-and-performance-version "New versions of Allinea Forge and Performance Reports")|
+|Pondělà 06.06.2016 00:00|[Intel VTune is working](https://docs.it4i.cz/whats-new/news-feed/intel-vtune-is-working "Intel VTune is working")|
+|ĂšterĂ˝ 31.05.2016 14:00|[Intel Parallel Studio 2016 update 3](https://docs.it4i.cz/whats-new/news-feed/intel-parallel-studio-2016-update-3 "Intel Parallel Studio 2016 update 3")|
+|ÄŚtvrtek 05.05.2016 15:58|[ANSYS 17.0 Installed](https://docs.it4i.cz/whats-new/news-feed/ansys-17-0-installed "ANSYS 17.0 Installed")|
+|Pátek 29.04.2016 14:25|[Allinea Forge 6.0](https://docs.it4i.cz/whats-new/news-feed/allinea-forge-6.0 "Allinea Forge 6.0")|
+|Pátek 29.04.2016 14:23|[Issue with Intel MPI 4.1.1 on Salomon](https://docs.it4i.cz/whats-new/news-feed/issue-with-intel-mpi-4-1-1-on-salomon "Issue with Intel MPI 4.1.1 on Salomon")|
+|Pátek 22.04.2016 14:35|[New modules for Parallel programming in modern Fortran course](https://docs.it4i.cz/whats-new/news-feed/new-modules-for-parallel-programming-in-modern-fortran-course "New modules for Parallel programming in modern Fortran course")|
+|Středa 13.04.2016 14:20|[Octave updated to 4.0.1 on Anselm](https://docs.it4i.cz/whats-new/news-feed/octave-updated-to-4-0-1-on-anselm "Octave updated to 4.0.1 on Anselm")|
+|Pátek 01.04.2016 00:00|[Allinea Forge 5.1 installed on Anselm](https://docs.it4i.cz/whats-new/news-feed/allinea-forge-5-1-installed-on-anselm "Allinea Forge 5.1 installed on Anselm")|
+|Pondělà 07.03.2016 00:00|[Cuda 7.5 is now installed on Anselm](https://docs.it4i.cz/whats-new/news-feed/cuda-7-5-is-now-installed-on-anselm "Cuda 7.5 is now installed on Anselm")|
+|Středa 24.02.2016 00:00|[Added basic documentation for Intel Advisor and Intel Inspector](https://docs.it4i.cz/whats-new/news-feed/added-basic-documentation-for-intel-advisor-and-intel-inspector "Added basic documentation for Intel Advisor and Intel Inspector")|
+|Středa 24.02.2016 00:00|[Anselm downtime has been extended to Feb 26th.](https://docs.it4i.cz/whats-new/news-feed/anselm-downtime-has-been-extended-to-feb-26th "Anselm downtime has been extended to Feb 26th.")|
+|ÄŚtvrtek 11.02.2016 00:00|[Allinea Forge documentation updated](https://docs.it4i.cz/whats-new/news-feed/allinea-forge-documentation-updated "Allinea Forge documentation updated")|
+|ĂšterĂ˝ 09.02.2016 00:00|[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](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 "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")
+|ĂšterĂ˝ 26.01.2016 00:00|[Salomon PBS changes](https://docs.it4i.cz/whats-new/news-feed/salomon-pbs-changes "Salomon PBS changes")|
+|Pátek 15.01.2016 00:00|[Capacity computing updated for Salomon](https://docs.it4i.cz/whats-new/news-feed/capacity-computing-updated-for-salomon "Capacity computing updated for Salomon")|
+|Středa 13.01.2016 00:00|[Mono 4.2.2 and MPI.NET 1.2 on Salomon](https://docs.it4i.cz/whats-new/news-feed/mono-4-2-2-and-mpi-net-1-2-on-salomon "Mono 4.2.2 and MPI.NET 1.2 on Salomon")|
\ No newline at end of file
diff --git a/docs.it4i/salomon/accessing-the-cluster/accessing-the-cluster.md b/docs.it4i/salomon/accessing-the-cluster/accessing-the-cluster.md
index 2637565a859c3cf6d3bbd90259e1f5024c77fe55..af5e36a46bea39e96385164221342d4ea5afba60 100644
--- a/docs.it4i/salomon/accessing-the-cluster/accessing-the-cluster.md
+++ b/docs.it4i/salomon/accessing-the-cluster/accessing-the-cluster.md
@@ -18,9 +18,11 @@ The Salomon cluster is accessed by SSH protocol via login nodes login1, login2,
The authentication is by the [private key](../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:
-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)
+!!! Note "Note"
+ Please verify SSH fingerprints during the first logon. They are identical on all login nodes:
+
+ 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)
Private key authentication:
diff --git a/docs.it4i/salomon/accessing-the-cluster/anyconnectcontextmenu.jpg b/docs.it4i/salomon/accessing-the-cluster/anyconnectcontextmenu.jpg
deleted file mode 100644
index 26122f2f5965ce71489267d359eff21c39ed7960..0000000000000000000000000000000000000000
Binary files a/docs.it4i/salomon/accessing-the-cluster/anyconnectcontextmenu.jpg and /dev/null differ
diff --git a/docs.it4i/salomon/accessing-the-cluster/anyconnecticon.jpg b/docs.it4i/salomon/accessing-the-cluster/anyconnecticon.jpg
deleted file mode 100644
index d7397f5c43f659d71a6fe8413ad89dca8157bb48..0000000000000000000000000000000000000000
Binary files a/docs.it4i/salomon/accessing-the-cluster/anyconnecticon.jpg and /dev/null differ
diff --git a/docs.it4i/salomon/accessing-the-cluster/vpn-access.md b/docs.it4i/salomon/accessing-the-cluster/vpn-access.md
index 4b7c86509d2a7540a5ed19595482639521c99ae7..4b45bc5b236e52fd67f3c39d580071ceb5c34e0a 100644
--- a/docs.it4i/salomon/accessing-the-cluster/vpn-access.md
+++ b/docs.it4i/salomon/accessing-the-cluster/vpn-access.md
@@ -18,25 +18,25 @@ VPN client installation
------------------------------------
You can install VPN client from web interface after successful login with LDAP credentials on address <https://vpn.it4i.cz/user>
-
+
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.
@@ -47,30 +47,30 @@ You can use graphical user interface or command line interface to run VPN client
Before the first login to VPN, you have to fill URLÂ **[https://vpn.it4i.cz/user](https://vpn.it4i.cz/user)** 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 "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.
-
+
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**.
\ No newline at end of file
diff --git a/docs.it4i/salomon/compute-nodes.md b/docs.it4i/salomon/compute-nodes.md
new file mode 100644
index 0000000000000000000000000000000000000000..b8845ff256642ee1d005a979aebaffc6061a5da7
--- /dev/null
+++ b/docs.it4i/salomon/compute-nodes.md
@@ -0,0 +1,110 @@
+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](network-1/ib-single-plane-topology/).
+
+###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
+
+
+
+###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
+
+
+
+
+
+
+
+### 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<p>32GB\ |<p>24 @ 2.5Ghz<p>61 @ 1.238GHz\ |
+ |UV2000 SMP node |1 |3328GB\ |<p>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 to 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: 68 GB/s
+
+### MIC Accelerator Intel Xeon Phi 7120PÂ Processor
+
+- 61-core
+- speed:Â 1.238
+ GHz, up to 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: 352 GB/s
+
+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
\ No newline at end of file
diff --git a/docs.it4i/salomon/hardware-overview.md b/docs.it4i/salomon/hardware-overview.md
index 0fffddcc3fd6599716e6c85ed637984fa30df5c9..088117ac899b950a91cfe53c9962d3695e6bd4e0 100644
--- a/docs.it4i/salomon/hardware-overview.md
+++ b/docs.it4i/salomon/hardware-overview.md
@@ -7,7 +7,7 @@ The Salomon cluster consists of 1008 computational nodes of which 576 are regula
[More about schematic representation of the Salomon cluster compute nodes IB topology](../network/ib-single-plane-topology/).
-
+
The parameters are summarized in the following tables:
@@ -57,4 +57,4 @@ For large memory computations a special SMP/NUMA SGI UV 2000 server is available
| --- | --- |
|UV2000 |1 |14x Intel Xeon E5-4627v2, 3.3GHz, 8cores |112 |3328GB DDR3@1866MHz |2x 400GB local SSD1x NVIDIA GM200(GeForce GTX TITAN X),12GB RAM\ |
-
\ No newline at end of file
+
\ No newline at end of file
diff --git a/docs.it4i/salomon/introduction.md b/docs.it4i/salomon/introduction.md
index c18d771b2603ba5dc21dd61abe7e9e128cc2c884..5a698254fa2ede99f0e444543b40b3ebf191a7c9 100644
--- a/docs.it4i/salomon/introduction.md
+++ b/docs.it4i/salomon/introduction.md
@@ -7,12 +7,12 @@ The cluster runs [CentOS Linux](http://www.bull.com/bullx-logiciels/systeme-expl
**Water-cooled Compute Nodes With MIC Accelerator**
-
+
-
+
**Tape Library T950B**
-
+
-
\ No newline at end of file
+
\ No newline at end of file
diff --git a/docs.it4i/salomon/network/7d-enhanced-hypercube.md b/docs.it4i/salomon/network/7d-enhanced-hypercube.md
index a8b8060d402091d6d70edd6c16a8bcb77956140a..ab096378c2cff98abee5e1e8cd9e15545f161c07 100644
--- a/docs.it4i/salomon/network/7d-enhanced-hypercube.md
+++ b/docs.it4i/salomon/network/7d-enhanced-hypercube.md
@@ -19,7 +19,7 @@ Nodes may be selected via the PBS resource attribute ehc_[1-7]d .
### 7D Enhanced Hypercube {#d-enhanced-hypercube}
-
+
|Node type|Count|Short name|Long name|Rack|
|---|---|
@@ -28,5 +28,5 @@ Nodes may be selected via the PBS resource attribute ehc_[1-7]d .
### Â IB Topology
-
+
diff --git a/docs.it4i/salomon/network/ib-single-plane-topology.md b/docs.it4i/salomon/network/ib-single-plane-topology.md
index 5a0ded2af2ec72396bc208ff309cb568e5d606a6..2ee89058e1750e6972e69e096f18f821f8b244c1 100644
--- a/docs.it4i/salomon/network/ib-single-plane-topology.md
+++ b/docs.it4i/salomon/network/ib-single-plane-topology.md
@@ -13,16 +13,16 @@ The SGI ICE X IB Premium Blade provides the first level of interconnection via d
Each colour in each physical IRU represents one dual-switch ASIC switch.
-
+
### 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/).
-As shown in a diagram 
+As shown in a diagram 
- 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.
-
\ No newline at end of file
+
\ No newline at end of file
diff --git a/docs.it4i/salomon/prace.md b/docs.it4i/salomon/prace.md
index eb5872a3d971d0d9de4481e206e2609994dcabb6..1025fb3ddbb0d75ddead8d44bb31bdd9129599cc 100644
--- a/docs.it4i/salomon/prace.md
+++ b/docs.it4i/salomon/prace.md
@@ -9,8 +9,7 @@ All general [PRACE User Documentation](http://www.prace-ri.eu/user-documentation
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/).
+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.
diff --git a/docs.it4i/salomon/resource-allocation-and-job-execution/fairshare_formula.png b/docs.it4i/salomon/resource-allocation-and-job-execution/fairshare_formula.png
deleted file mode 100644
index 6a5a1443fa08cd9d3c62bea52bbb48136b2501dc..0000000000000000000000000000000000000000
Binary files a/docs.it4i/salomon/resource-allocation-and-job-execution/fairshare_formula.png and /dev/null differ
diff --git a/docs.it4i/salomon/resource-allocation-and-job-execution/job-priority.md b/docs.it4i/salomon/resource-allocation-and-job-execution/job-priority.md
index e03bcc7f63cff859b689751aba597a4f57c94cba..c6ba19b458bcfe1bd6c2b7f97e54c814a336693d 100644
--- a/docs.it4i/salomon/resource-allocation-and-job-execution/job-priority.md
+++ b/docs.it4i/salomon/resource-allocation-and-job-execution/job-priority.md
@@ -27,7 +27,7 @@ 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.
@@ -50,7 +50,7 @@ Eligible time can be seen as eligible_time attribute of job.
Job execution priority (job sort formula) is calculated as:
-
+
### Job backfilling
diff --git a/docs.it4i/salomon/resource-allocation-and-job-execution/job_sort_formula.png b/docs.it4i/salomon/resource-allocation-and-job-execution/job_sort_formula.png
deleted file mode 100644
index 6078911559aa56effb4b342fa4ffd074cfaed46f..0000000000000000000000000000000000000000
Binary files a/docs.it4i/salomon/resource-allocation-and-job-execution/job_sort_formula.png and /dev/null differ
diff --git a/docs.it4i/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md b/docs.it4i/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
index 24ab7b583953c53ed969ebad8c9c709c7061f9ec..366dad1cf21742bb8320aef06ec23fbc92a62bdb 100644
--- a/docs.it4i/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
+++ b/docs.it4i/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
@@ -42,7 +42,7 @@ Salomon users may check current queue configuration at <https://extranet.it4i.cz
!!! Note "Note"
Check the status of jobs, queues and compute nodes at [https://extranet.it4i.cz/rsweb/salomon/](https://extranet.it4i.cz/rsweb/salomon)
-
+
Display the queue status on Salomon:
diff --git a/docs.it4i/salomon/software/ansys/ansys-fluent.md b/docs.it4i/salomon/software/ansys/ansys-fluent.md
index e81ededc9e2c930ec870cd8befbc4270b6b45eb5..aa43f6a9b8ad1229ee37fabb6bcf41366d9f4c36 100644
--- a/docs.it4i/salomon/software/ansys/ansys-fluent.md
+++ b/docs.it4i/salomon/software/ansys/ansys-fluent.md
@@ -153,12 +153,12 @@ Fluent could be run in parallel only under Academic Research license. To do so t
ANSLIC_ADMIN Utility will be run
-
+
-
+
-
+
ANSYS Academic Research license should be moved up to the top of the list.
-
\ No newline at end of file
+
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md b/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md
index 78da5be845044685ae194580cc439934940fc049..9bb3cdb458d5f14fd0fd13f237cf8edec20d0394 100644
--- a/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md
+++ b/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md
@@ -54,5 +54,4 @@ Header of the pbs file (above) is common and description can be find on [this si
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
+**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
diff --git a/docs.it4i/salomon/software/ansys/setting-license-preferences.md b/docs.it4i/salomon/software/ansys/setting-license-preferences.md
index 2132ca04c32e13253dc55cbc0e1bbd1e30bfd78c..3b673a6af32ba0cb442298fa32e553923f1f8b3a 100644
--- a/docs.it4i/salomon/software/ansys/setting-license-preferences.md
+++ b/docs.it4i/salomon/software/ansys/setting-license-preferences.md
@@ -13,12 +13,12 @@ Launch the ANSLIC_ADMIN utility in a graphical environment:
ANSLIC_ADMIN Utility will be run
-
+
-
+
-
+
ANSYS Academic Research license should be moved up to the top or down to the bottom of the list.
-
\ No newline at end of file
+
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/ansys/workbench.md b/docs.it4i/salomon/software/ansys/workbench.md
index 4877593a2b7bbcee39e0056847b145452bf274c3..929019f1459affda975c4c9f6e93660defd0cf45 100644
--- a/docs.it4i/salomon/software/ansys/workbench.md
+++ b/docs.it4i/salomon/software/ansys/workbench.md
@@ -5,7 +5,7 @@ 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 ...
-
+
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:
diff --git a/docs.it4i/salomon/software/compilers.md b/docs.it4i/salomon/software/compilers.md
index d1030b0e3208efd3c460679d027ce03aa6d7fabf..03b33da7e84fbb8cb30d35cf0ab259a4fb06d6ce 100644
--- a/docs.it4i/salomon/software/compilers.md
+++ b/docs.it4i/salomon/software/compilers.md
@@ -53,7 +53,7 @@ PGDBG OpenMP/MPI debugger and PGPROF OpenMP/MPI profiler are available
$ pgprof &
```
-For more information, see the [PGI page](http://www.pgroup.com/products/pgicdk.htm).
+For more information, see the [PGI page](http://www.pgroup.com/products/pgicdk.htm).
GNU
---
@@ -184,11 +184,10 @@ To run the example on two compute nodes using all 48 cores, with 48 threads, iss
For more informations see the man pages.
-Java
-----
+##Java
For information how to use Java (runtime and/or compiler), please read the [Java page](java/).
-nVidia CUDA
+##nVidia CUDA
For information how to work with nVidia CUDA, please read the [nVidia CUDA page](../../anselm-cluster-documentation/software/nvidia-cuda/).
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png b/docs.it4i/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png
deleted file mode 100644
index d8ea15508f0714eeacfadff6d85fe8cafe5c406b..0000000000000000000000000000000000000000
Binary files a/docs.it4i/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png and /dev/null differ
diff --git a/docs.it4i/salomon/software/debuggers/TightVNC_login.png b/docs.it4i/salomon/software/debuggers/TightVNC_login.png
deleted file mode 100644
index 078dfc73a90b2b3ffc1648fa82ba4b0a109fbc29..0000000000000000000000000000000000000000
Binary files a/docs.it4i/salomon/software/debuggers/TightVNC_login.png and /dev/null differ
diff --git a/docs.it4i/salomon/software/debuggers/aislinn.md b/docs.it4i/salomon/software/debuggers/aislinn.md
index 3e77a68122a629f6136fb2d23c5eeade84812205..59dfd3bd84138b17cfaee8dbd36e1e54375ff23d 100644
--- a/docs.it4i/salomon/software/debuggers/aislinn.md
+++ b/docs.it4i/salomon/software/debuggers/aislinn.md
@@ -80,7 +80,7 @@ Aislinn found an error and produced HTML report. To view it, we can use any brow
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:
- Error occurs in process 0 in test.cpp on line 16.
diff --git a/docs.it4i/salomon/software/debuggers/allinea-ddt.md b/docs.it4i/salomon/software/debuggers/allinea-ddt.md
index 240a92c15a6a015b90f3259178e1d9da9bedf024..f09f506293fb3d7e157128b45de7730a43a40891 100644
--- a/docs.it4i/salomon/software/debuggers/allinea-ddt.md
+++ b/docs.it4i/salomon/software/debuggers/allinea-ddt.md
@@ -78,7 +78,7 @@ Then launch the debugger with the ddt command followed by the name of the execut
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 " box.
-
+
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".
diff --git a/docs.it4i/salomon/software/debuggers/ddt1.png b/docs.it4i/salomon/software/debuggers/ddt1.png
deleted file mode 100644
index 57a18f48908f0b8a4857bc14a820b450fcdd9652..0000000000000000000000000000000000000000
Binary files a/docs.it4i/salomon/software/debuggers/ddt1.png and /dev/null differ
diff --git a/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md b/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md
index b146345508acdd7f269eb304ddbdd09c97c8f762..b4c1a4ad9a962fa12475df6afcd361a300a40c35 100644
--- a/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md
+++ b/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md
@@ -10,7 +10,7 @@ Intel*® *VTune™ Amplifier, part of Intel Parallel studio, is a GUI profilin
- Low level specific counters, such as branch analysis and memory bandwidth
- Power usage analysis - frequency and sleep states.
-
+
Usage
-----
diff --git a/docs.it4i/salomon/software/debuggers/total-view.md b/docs.it4i/salomon/software/debuggers/total-view.md
index ddfb173e9dba005aec5711c46aac4d83324c5f17..ea7df97257837a03dbd7215a06fb17f4cb04e063 100644
--- a/docs.it4i/salomon/software/debuggers/total-view.md
+++ b/docs.it4i/salomon/software/debuggers/total-view.md
@@ -126,11 +126,11 @@ Now you can run the parallel debugger using:
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
diff --git a/docs.it4i/salomon/software/debuggers/totalview1.png b/docs.it4i/salomon/software/debuggers/totalview1.png
deleted file mode 100644
index 09678f174b4f5d05ccda08cc11de059ee53e7e09..0000000000000000000000000000000000000000
Binary files a/docs.it4i/salomon/software/debuggers/totalview1.png and /dev/null differ
diff --git a/docs.it4i/salomon/software/debuggers/totalview2.png b/docs.it4i/salomon/software/debuggers/totalview2.png
deleted file mode 100644
index 9d26ffd97db190a6b8161dd6358fc759ad2cb2ca..0000000000000000000000000000000000000000
Binary files a/docs.it4i/salomon/software/debuggers/totalview2.png and /dev/null differ
diff --git a/docs.it4i/salomon/software/debuggers/vampir.md b/docs.it4i/salomon/software/debuggers/vampir.md
index 1ca43b4b5df6f16ae06fc6e4c90d541dd1b02ce6..60d9c4e12c1c66341cc7a8747782d1dc7527d610 100644
--- a/docs.it4i/salomon/software/debuggers/vampir.md
+++ b/docs.it4i/salomon/software/debuggers/vampir.md
@@ -3,7 +3,7 @@ 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](score-p/)) first to collect the traces.
-
+
Installed versions
------------------
diff --git a/docs.it4i/salomon/software/debuggers/vtune-amplifier.png b/docs.it4i/salomon/software/debuggers/vtune-amplifier.png
deleted file mode 100644
index 75ee99d84b87649151f22edad65de021ec348f1c..0000000000000000000000000000000000000000
Binary files a/docs.it4i/salomon/software/debuggers/vtune-amplifier.png and /dev/null differ
diff --git a/docs.it4i/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md b/docs.it4i/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
index c8ae0919a6440ce106fa25edb97ba3c9a10f2ee9..f90d945e291cedf2fcc42db4c68fdf2f0c0695b6 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
@@ -31,7 +31,7 @@ To view and analyze the trace, open ITAC GUI in a [graphical environment](../../
The GUI will launch and you can open the produced *.stf file.
-
+
Please refer to Intel documenation about usage of the GUI tool.
diff --git a/docs.it4i/salomon/software/intel-xeon-phi.md b/docs.it4i/salomon/software/intel-xeon-phi.md
index b9cc6d1c734a943b542550e5bc80ea5406bbf8a2..eba38dca8a6600f0ad8f06e2d29bf01e33b9718d 100644
--- a/docs.it4i/salomon/software/intel-xeon-phi.md
+++ b/docs.it4i/salomon/software/intel-xeon-phi.md
@@ -417,13 +417,14 @@ If the code is parallelized using OpenMP a set of additional libraries is requir
For your information the list of libraries and their location required for execution of an OpenMP parallel code on Intel Xeon Phi is:
->/apps/intel/composer_xe_2013.5.192/compiler/lib/mic
+!!! Note "Note"
+ /apps/intel/composer_xe_2013.5.192/compiler/lib/mic
->libiomp5.so
-libimf.so
-libsvml.so
-libirng.so
-libintlc.so.5
+ - libiomp5.so
+ - libimf.so
+ - libsvml.so
+ - libirng.so
+ - libintlc.so.5
Finally, to run the compiled code use:
diff --git a/docs.it4i/salomon/storage/cesnet-data-storage.md b/docs.it4i/salomon/storage/cesnet-data-storage.md
index e7e2c02930982e719cc701d4858e2b88c62518c3..ff73c3b0ee01746f00b818ee1329e90631d439c1 100644
--- a/docs.it4i/salomon/storage/cesnet-data-storage.md
+++ b/docs.it4i/salomon/storage/cesnet-data-storage.md
@@ -5,7 +5,8 @@ Introduction
------------
Do not use shared filesystems at IT4Innovations as a backup for large 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/).
+!!! Note "Note"
+../../img/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/).
The CESNET Storage service can be used for research purposes, mainly by academic staff and students of research institutions in the Czech Republic.
@@ -24,13 +25,15 @@ CESNET storage access
### Understanding Cesnet storage
->It is very important to understand the Cesnet storage before uploading data. Please read <https://du.cesnet.cz/en/navody/home-migrace-plzen/start> first.
+!!! Note "Note"
+ It is very important to understand the Cesnet storage before uploading data. Please read <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 number of ways. We recommend the SSHFS and RSYNC methods.
### SSHFS Access
->SSHFS: The storage will be mounted like a local hard drive
+!!! Note "Note"
+ SSHFS: The 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 than copied in and out in a usual fashion.
@@ -74,7 +77,8 @@ Once done, please remember to unmount the storage
### Rsync access
->Rsync provides delta transfer for best performance, can resume interrupted transfers
+!!! Note "Note"
+ Rsync provides delta transfer for best performance, can resume interrupted transfers
Rsync is a fast and extraordinarily versatile file copying tool. It is famous for its delta-transfer algorithm, which reduces the amount of 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.
diff --git a/docs.it4i/salomon/storage/storage.md b/docs.it4i/salomon/storage/storage.md
index 2e352602e64843963a2dcda7c0cbfc19820f7bc8..3f96799587aca0fa93babce92da5f8df55bb8c41 100644
--- a/docs.it4i/salomon/storage/storage.md
+++ b/docs.it4i/salomon/storage/storage.md
@@ -3,17 +3,18 @@ Storage
Introduction
------------
-There are two main shared file systems on Salomon cluster, the [HOME](storage/#home)and [SCRATCH](storage/#shared-filesystems).
+There are two main shared file systems on Salomon cluster, the [HOME](storage/storage/#home)and [SCRATCH](storage/#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.
Policy (in a nutshell)
----------------------
->Use [ for your most valuable data and programs.
-Use [WORK](storage/#work) for your large project files.
-Use [TEMP](storage/#temp) for large scratch data.
+!!! Note "Note"
+ Use [ for your most valuable data and programs.
+ Use [WORK](storage/#work) for your large project files.
+ Use [TEMP](storage/#temp) for large scratch data.
->Do not use for [archiving](storage/#archiving)!
+ Do not use for [archiving](storage/#archiving)!
Archiving
-------------
@@ -59,7 +60,8 @@ There is default stripe configuration for Salomon Lustre filesystems. However, u
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 OST where the first stripe is to be placed; default is -1 which results in random selection; using a non-default value is NOT recommended.
->Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.
+!!! Note "Note"
+ 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.
@@ -92,13 +94,15 @@ $ man lfs
### Hints on Lustre Stripping
->Increase the stripe_count for parallel I/O to the same file.
+!!! Note "Note"
+ 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
+!!! Note "Note"
+ 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.
@@ -216,7 +220,8 @@ Shared Workspaces
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), the quota may be lifted upon request.
->The HOME filesystem is intended for preparation, evaluation, processing and storage of data generated by active Projects.
+!!! Note "Note"
+ 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.
@@ -236,13 +241,15 @@ The workspace is backed up, such that it can be restored in case of catasthropi
The WORK workspace resides on SCRATCH filesystem. Users may create 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.
->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.
+!!! Note "Note"
+ 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.
+ 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 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 54 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.
+!!! Note "Note"
+ Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.
|WORK workspace||
|---|---|
@@ -259,15 +266,17 @@ The WORK workspace is hosted on SCRATCH filesystem. The SCRATCH is realized as L
The TEMP workspace resides on SCRATCH filesystem. The TEMP workspace accesspoint is /scratch/temp. Users may freely create subdirectories 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 insufficient for particular user, please contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
->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.
+!!! Note "Note"
+ 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.
+ 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**.
+ 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 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 54 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.
+!!! Note "Note"
+ Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.
|TEMP workspace||
|---|---|
@@ -284,13 +293,15 @@ 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.
+!!! Note "Note"
+ 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.
+!!! Note "Note"
+ 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||
|---|---|
diff --git a/mkdocs.yml b/mkdocs.yml
index 24849b44b07e19d192f910ddd2940334ea773985..f0faac923f8eb947698acb12cbec6b9815cad762 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -5,6 +5,8 @@ copyright: "Build at "
pages:
- Home: index.md
+ - News: new.md
+ - History of Downtimes: downtimes_history.md
- Get Started with IT4Innovations:
- Applying for Resources: get-started-with-it4innovations/applying-for-resources.md
- Get Started with IT4Innovations-Obtaining Login Credentials:
@@ -114,6 +116,11 @@ pages:
- PRACE User Support: salomon/prace.md
- Environment and Modules: salomon/environment-and-modules.md
- Hardware Overview: salomon/hardware-overview.md
+ - Compute Nodes: salomon/compute-nodes.md
+ - Salomon Cluster Documentation-Accessing the Cluster:
+ - Outgoing connections: salomon/accessing-the-cluster/outgoing-connections.md
+ - VPN Access: salomon/accessing-the-cluster/vpn-access.md
+ - Accessing the Cluster: salomon/accessing-the-cluster/accessing-the-cluster.md
- Salomon Cluster Documentation-Network:
- Introduction: salomon/network/network.md
- IB single-plane topology: salomon/network/ib-single-plane-topology.md
@@ -127,10 +134,6 @@ pages:
- Salomon Cluster Documentation-Storage:
- CESNET Data Storage: salomon/storage/cesnet-data-storage.md
- Storage: salomon/storage/storage.md
- - Salomon Cluster Documentation-Accessing the Cluster:
- - Outgoing connections: salomon/accessing-the-cluster/outgoing-connections.md
- - VPN Access: salomon/accessing-the-cluster/vpn-access.md
- - Accessing the Cluster: salomon/accessing-the-cluster/accessing-the-cluster.md
- Salomon Cluster Documentation-Software:
- Compilers: salomon/software/compilers.md
- Intel Xeon Phi: salomon/software/intel-xeon-phi.md
@@ -184,5 +187,5 @@ pages:
markdown_extensions:
- toc:
- permalink: ď
+ permalink: yes
- admonition: