formatting style

.gitlab-ci.yml

@@ -9,7 +9,7 @@ docs:
   image: davidhrbac/docker-mdcheck:latest
   allow_failure: true
   script:
-  - mdl -r ~MD013 *.md docs.it4i/
+  - mdl -r ~MD013,~MD033,~MD014 *.md docs.it4i/
 
 two spaces:
   stage: test

docs.it4i/anselm-cluster-documentation/compute-nodes.md

-Compute Nodes
-=============
+# Compute Nodes
+
+## Nodes Configuration
 
-Nodes Configuration
--------------------
 Anselm is cluster of x86-64 Intel based nodes built on Bull Extreme Computing bullx technology. The cluster contains four types of compute nodes.
 
-###Compute Nodes Without Accelerator
-
--    180 nodes
--    2880 cores in total
--    two Intel Sandy Bridge E5-2665, 8-core, 2.4GHz processors per node
--    64 GB of physical memory per node
--    one 500GB SATA 2,5” 7,2 krpm HDD per node
--    bullx B510 blade servers
--    cn[1-180]
-
-###Compute Nodes With GPU Accelerator
-
--    23 nodes
--    368 cores in total
--    two Intel Sandy Bridge E5-2470, 8-core, 2.3GHz processors per node
--    96 GB of physical memory per node
--    one 500GB SATA 2,5” 7,2 krpm HDD per node
--    GPU accelerator 1x NVIDIA Tesla Kepler K20 per node
--    bullx B515 blade servers
--    cn[181-203]
-
-###Compute Nodes With MIC Accelerator
-
--    4 nodes
--    64 cores in total
--    two Intel Sandy Bridge E5-2470, 8-core, 2.3GHz processors per node
--    96 GB of physical memory per node
--    one 500GB SATA 2,5” 7,2 krpm HDD per node
--    MIC accelerator 1x Intel Phi 5110P per node
--    bullx B515 blade servers
--    cn[204-207]
-
-###Fat Compute Nodes
-
--    2 nodes
--    32 cores in total
--    2 Intel Sandy Bridge E5-2665, 8-core, 2.4GHz processors per node
--    512 GB of physical memory per node
--    two 300GB SAS 3,5”15krpm HDD (RAID1) per node
--    two 100GB SLC SSD per node
--    bullx R423-E3 servers
--    cn[208-209]
+### Compute Nodes Without Accelerator
+
+* 180 nodes
+* 2880 cores in total
+* two Intel Sandy Bridge E5-2665, 8-core, 2.4GHz processors per node
+* 64 GB of physical memory per node
+* one 500GB SATA 2,5” 7,2 krpm HDD per node
+* bullx B510 blade servers
+* cn[1-180]
+
+### Compute Nodes With GPU Accelerator
+
+* 23 nodes
+* 368 cores in total
+* two Intel Sandy Bridge E5-2470, 8-core, 2.3GHz processors per node
+* 96 GB of physical memory per node
+* one 500GB SATA 2,5” 7,2 krpm HDD per node
+* GPU accelerator 1x NVIDIA Tesla Kepler K20 per node
+* bullx B515 blade servers
+* cn[181-203]
+
+### Compute Nodes With MIC Accelerator
+
+* 4 nodes
+* 64 cores in total
+* two Intel Sandy Bridge E5-2470, 8-core, 2.3GHz processors per node
+* 96 GB of physical memory per node
+* one 500GB SATA 2,5” 7,2 krpm HDD per node
+* MIC accelerator 1x Intel Phi 5110P per node
+* bullx B515 blade servers
+* cn[204-207]
+
+### Fat Compute Nodes
+
+* 2 nodes
+* 32 cores in total
+* 2 Intel Sandy Bridge E5-2665, 8-core, 2.4GHz processors per node
+* 512 GB of physical memory per node
+* two 300GB SAS 3,5”15krpm HDD (RAID1) per node
+* two 100GB SLC SSD per node
+* bullx R423-E3 servers
+* cn[208-209]
 
 ![](../img/bullxB510.png)
-
 **Figure Anselm bullx B510 servers**
 
 ### Compute Nodes Summary
@@ -61,31 +59,29 @@ Anselm is cluster of x86-64 Intel based nodes built on Bull Extreme Computing bu
   |Nodes with MIC accelerator|4|cn[204-207]|96GB|16 @ 2.3GHz|qmic, qprod|
   |Fat compute nodes|2|cn[208-209]|512GB|16 @ 2.4GHz|qfat, qprod|
 
-Processor Architecture
-----------------------
+## Processor Architecture
+
 Anselm is equipped with Intel Sandy Bridge processors Intel Xeon E5-2665 (nodes without accelerator and fat nodes) and Intel Xeon E5-2470 (nodes with accelerator). Processors support Advanced Vector Extensions (AVX) 256-bit instruction set.
 
 ### Intel Sandy Bridge E5-2665 Processor
 
--   eight-core
--   speed: 2.4 GHz, up to 3.1 GHz using Turbo Boost Technology
--   peak performance:  19.2 GFLOP/s per
-    core
--   caches:
-    -   L2: 256 KB per core
-    -   L3: 20 MB per processor
--   memory bandwidth at the level of the processor: 51.2 GB/s
+* eight-core
+* speed: 2.4 GHz, up to 3.1 GHz using Turbo Boost Technology
+* peak performance:  19.2 GFLOP/s per core
+* caches:
+  * L2: 256 KB per core
+  * L3: 20 MB per processor
+* memory bandwidth at the level of the processor: 51.2 GB/s
 
 ### Intel Sandy Bridge E5-2470 Processor
 
--   eight-core
--   speed: 2.3 GHz, up to 3.1 GHz using Turbo Boost Technology
--   peak performance:  18.4 GFLOP/s per
-    core
--   caches:
-    -   L2: 256 KB per core
-    -   L3: 20 MB per processor
--   memory bandwidth at the level of the processor: 38.4 GB/s
+* eight-core
+* speed: 2.3 GHz, up to 3.1 GHz using Turbo Boost Technology
+* peak performance:  18.4 GFLOP/s per core
+* caches:
+  * L2: 256 KB per core
+  * L3: 20 MB per processor
+* memory bandwidth at the level of the processor: 38.4 GB/s
 
 Nodes equipped with Intel Xeon E5-2665 CPU have set PBS resource attribute cpu_freq = 24, nodes equipped with Intel Xeon E5-2470 CPU have set PBS resource attribute cpu_freq = 23.
 
@@ -101,35 +97,34 @@ Intel Turbo Boost Technology is used by default,  you can disable it for all nod
     $ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=16 -l cpu_turbo_boost=0 -I
 ```
 
-Memory Architecture
--------------------
+## Memory Architecture
 
 ### Compute Node Without Accelerator
 
--   2 sockets
--   Memory Controllers are integrated into processors.
-    -   8 DDR3 DIMMs per node
-    -   4 DDR3 DIMMs per CPU
-    -   1 DDR3 DIMMs per channel
-    -   Data rate support: up to 1600MT/s
--   Populated memory: 8 x 8 GB DDR3 DIMM 1600 MHz
+* 2 sockets
+* Memory Controllers are integrated into processors.
+  * 8 DDR3 DIMMs per node
+  * 4 DDR3 DIMMs per CPU
+  * 1 DDR3 DIMMs per channel
+  * Data rate support: up to 1600MT/s
+* Populated memory: 8 x 8 GB DDR3 DIMM 1600 MHz
 
 ### Compute Node With GPU or MIC Accelerator
 
--   2 sockets
--   Memory Controllers are integrated into processors.
-    -   6 DDR3 DIMMs per node
-    -   3 DDR3 DIMMs per CPU
-    -   1 DDR3 DIMMs per channel
-    -   Data rate support: up to 1600MT/s
--   Populated memory: 6 x 16 GB DDR3 DIMM 1600 MHz
+* 2 sockets
+* Memory Controllers are integrated into processors.
+  * 6 DDR3 DIMMs per node
+  * 3 DDR3 DIMMs per CPU
+  * 1 DDR3 DIMMs per channel
+  * Data rate support: up to 1600MT/s
+* Populated memory: 6 x 16 GB DDR3 DIMM 1600 MHz
 
 ### Fat Compute Node
 
--   2 sockets
--   Memory Controllers are integrated into processors.
-    -   16 DDR3 DIMMs per node
-    -   8 DDR3 DIMMs per CPU
-    -   2 DDR3 DIMMs per channel
-    -   Data rate support: up to 1600MT/s
--   Populated memory: 16 x 32 GB DDR3 DIMM 1600 MHz
+* 2 sockets
+* Memory Controllers are integrated into processors.
+  * 16 DDR3 DIMMs per node
+  * 8 DDR3 DIMMs per CPU
+  * 2 DDR3 DIMMs per channel
+  * Data rate support: up to 1600MT/s
+* Populated memory: 16 x 32 GB DDR3 DIMM 1600 MHz

docs.it4i/anselm-cluster-documentation/introduction.md

-Introduction
-============
+# Introduction
 
 Welcome to Anselm supercomputer cluster. The Anselm cluster consists of 209 compute nodes, totaling 3344 compute cores with 15 TB RAM and giving over 94 TFLOP/s theoretical peak performance. Each node is a powerful x86-64 computer, equipped with 16 cores, at least 64 GB RAM, and 500 GB hard disk drive. Nodes are interconnected by fully non-blocking fat-tree InfiniBand network and equipped with Intel Sandy Bridge processors. A few nodes are also equipped with NVIDIA Kepler GPU or Intel Xeon Phi MIC accelerators. Read more in [Hardware Overview](hardware-overview/).
 
-The cluster runs bullx Linux ([bull](http://www.bull.com/bullx-logiciels/systeme-exploitation.html)) [operating system](software/operating-system/), which is compatible with the  RedHat [ Linux family.](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg) We have installed a wide range of software packages targeted at different scientific domains. These packages are accessible via the [modules environment](environment-and-modules/).
+The cluster runs [operating system](software/operating-system/), which is compatible with the  RedHat [Linux family.](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg) We have installed a wide range of software packages targeted at different scientific domains. These packages are accessible via the [modules environment](environment-and-modules/).
 
 User data shared file-system (HOME, 320 TB) and job data shared file-system (SCRATCH, 146 TB) are available to users.
 
 The PBS Professional workload manager provides [computing resources allocations and job execution](resources-allocation-policy/).
 
 Read more on how to [apply for resources](../get-started-with-it4innovations/applying-for-resources/), [obtain login credentials,](../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials/) and [access the cluster](shell-and-data-access/).
-

docs.it4i/anselm-cluster-documentation/job-submission-and-execution.md

-Job submission and execution
-============================
+# Job submission and execution
+
+## Job Submission
 
-Job Submission
---------------
 When allocating computational resources for the job, please specify
 
-1.  suitable queue for your job (default is qprod)
-2.  number of computational nodes required
-3.  number of cores per node required
-4.  maximum wall time allocated to your calculation, note that jobs exceeding maximum wall time will be killed
-5.  Project ID
-6.  Jobscript or interactive switch
+1. suitable queue for your job (default is qprod)
+1. number of computational nodes required
+1. number of cores per node required
+1. maximum wall time allocated to your calculation, note that jobs exceeding maximum wall time will be killed
+1. Project ID
+1. Jobscript or interactive switch
 
 !!! Note "Note"
-	Use the **qsub** command to submit your job to a queue for allocation of the computational resources.
+    Use the **qsub** command to submit your job to a queue for allocation of the computational resources.
 
 Submit the job using the qsub command:
 
@@ -61,8 +60,7 @@ By default, the PBS batch system sends an e-mail only when the job is aborted. D
 $ qsub -m n
 ```
 
-Advanced job placement
-----------------------
+## Advanced job placement
 
 ### Placement by name
 
@@ -103,8 +101,7 @@ We recommend allocating compute nodes of a single switch when best possible comp
 
 In this example, we request all the 18 nodes sharing the isw11 switch for 24 hours. Full chassis will be allocated.
 
-Advanced job handling
----------------------
+## Advanced job handling
 
 ### Selecting Turbo Boost off
 
@@ -133,10 +130,10 @@ The MPI processes will be distributed differently on the nodes connected to the
 
 Although this example is somewhat artificial, it demonstrates the flexibility of the qsub command options.
 
-Job Management
---------------
+## Job Management
+
 !!! Note "Note"
-	Check status of your jobs using the **qstat** and **check-pbs-jobs** commands
+    Check status of your jobs using the **qstat** and **check-pbs-jobs** commands
 
 ```bash
 $ qstat -a
@@ -217,7 +214,7 @@ Run loop 3
 In this example, we see actual output (some iteration loops) of the job 35141.dm2
 
 !!! Note "Note"
-	Manage your queued or running jobs, using the **qhold**, **qrls**, **qdel**, **qsig** or **qalter** commands
+    Manage your queued or running jobs, using the **qhold**, **qrls**, **qdel**, **qsig** or **qalter** commands
 
 You may release your allocation at any time, using qdel command
 
@@ -237,18 +234,17 @@ Learn more by reading the pbs man page
 $ man pbs_professional
 ```
 
-Job Execution
--------------
+## Job Execution
 
 ### Jobscript
 
 !!! Note "Note"
-	Prepare the jobscript to run batch jobs in the PBS queue system
+    Prepare the jobscript to run batch jobs in the PBS queue system
 
 The Jobscript is a user made script, controlling sequence of commands for executing the calculation. It is often written in bash, other scripts may be used as well. The jobscript is supplied to PBS **qsub** command as an argument and executed by the PBS Professional workload manager.
 
 !!! Note "Note"
-	The jobscript or interactive shell is executed on first of the allocated nodes.
+    The jobscript or interactive shell is executed on first of the allocated nodes.
 
 ```bash
 $ qsub -q qexp -l select=4:ncpus=16 -N Name0 ./myjob
@@ -278,7 +274,7 @@ $ pwd
 In this example, 4 nodes were allocated interactively for 1 hour via the qexp queue. The interactive shell is executed in the home directory.
 
 !!! Note "Note"
-	All nodes within the allocation may be accessed via ssh.  Unallocated nodes are not accessible to user.
+    All nodes within the allocation may be accessed via ssh.  Unallocated nodes are not accessible to user.
 
 The allocated nodes are accessible via ssh from login nodes. The nodes may access each other via ssh as well.
 
@@ -310,7 +306,7 @@ In this example, the hostname program is executed via pdsh from the interactive
 ### Example Jobscript for MPI Calculation
 
 !!! Note "Note"
-	Production jobs must use the /scratch directory for I/O
+    Production jobs must use the /scratch directory for I/O
 
 The recommended way to run production jobs is to change to /scratch directory early in the jobscript, copy all inputs to /scratch, execute the calculations and copy outputs to home directory.
 
@@ -342,12 +338,12 @@ exit
 In this example, some directory on the /home holds the input file input and executable mympiprog.x . We create a directory myjob on the /scratch filesystem, copy input and executable files from the /home directory where the qsub was invoked ($PBS_O_WORKDIR) to /scratch, execute the MPI programm mympiprog.x and copy the output file back to the /home directory. The mympiprog.x is executed as one process per node, on all allocated nodes.
 
 !!! Note "Note"
-	Consider preloading inputs and executables onto [shared scratch](storage/) before the calculation starts.
+    Consider preloading inputs and executables onto [shared scratch](storage/) before the calculation starts.
 
 In some cases, it may be impractical to copy the inputs to scratch and outputs to home. This is especially true when very large input and output files are expected, or when the files should be reused by a subsequent calculation. In such a case, it is users responsibility to preload the input files on shared /scratch before the job submission and retrieve the outputs manually, after all calculations are finished.
 
 !!! Note "Note"
-	Store the qsub options within the jobscript. Use **mpiprocs** and **ompthreads** qsub options to control the MPI job execution.
+    Store the qsub options within the jobscript. Use **mpiprocs** and **ompthreads** qsub options to control the MPI job execution.
 
 Example jobscript for an MPI job with preloaded inputs and executables, options for qsub are stored within the script :
 
@@ -380,7 +376,7 @@ sections.
 ### Example Jobscript for Single Node Calculation
 
 !!! Note "Note"
-	Local scratch directory is often useful for single node jobs. Local scratch will be deleted immediately after the job ends.
+    Local scratch directory is often useful for single node jobs. Local scratch will be deleted immediately after the job ends.
 
 Example jobscript for single node calculation, using [local scratch](storage/) on the node:
 

docs.it4i/anselm-cluster-documentation/prace.md

-PRACE User Support
-==================
+# PRACE User Support
+
+## Intro
 
-Intro
------
 PRACE users coming to Anselm as to TIER-1 system offered through the DECI calls are in general treated as standard users and so most of the general documentation applies to them as well. This section shows the main differences for quicker orientation, but often uses references to the original documentation. PRACE users who don't undergo the full procedure (including signing the IT4I AuP on top of the PRACE AuP) will not have a password and thus access to some services intended for regular users. This can lower their comfort, but otherwise they should be able to use the TIER-1 system as intended. Please see the [Obtaining Login Credentials section](../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials/), if the same level of access is required.
 
 All general [PRACE User Documentation](http://www.prace-ri.eu/user-documentation/) should be read before continuing reading the local documentation here.
 
-Help and Support
---------------------
+## 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/).
 
 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.
 
-Obtaining Login Credentials
----------------------------
+## Obtaining Login Credentials
+
 In general PRACE users already have a PRACE account setup through their HOMESITE (institution from their country) as a result of rewarded PRACE project proposal. This includes signed PRACE AuP, generated and registered certificates, etc.
 
 If there's a special need a PRACE user can get a standard (local) account at IT4Innovations. To get an account on the Anselm cluster, the user needs to obtain the login credentials. The procedure is the same as for general users of the cluster, so please see the corresponding section of the general documentation here.
 
-Accessing the cluster
----------------------
+## Accessing the cluster
 
 ### Access with GSI-SSH
 
@@ -30,11 +28,11 @@ The user will need a valid certificate and to be present in the PRACE LDAP (plea
 
 Most of the information needed by PRACE users accessing the Anselm TIER-1 system can be found here:
 
--   [General user's FAQ](http://www.prace-ri.eu/Users-General-FAQs)
--   [Certificates FAQ](http://www.prace-ri.eu/Certificates-FAQ)
--   [Interactive access using GSISSH](http://www.prace-ri.eu/Interactive-Access-Using-gsissh)
--   [Data transfer with GridFTP](http://www.prace-ri.eu/Data-Transfer-with-GridFTP-Details)
--   [Data transfer with gtransfer](http://www.prace-ri.eu/Data-Transfer-with-gtransfer)
+* [General user's FAQ](http://www.prace-ri.eu/Users-General-FAQs)
+* [Certificates FAQ](http://www.prace-ri.eu/Certificates-FAQ)
+* [Interactive access using GSISSH](http://www.prace-ri.eu/Interactive-Access-Using-gsissh)
+* [Data transfer with GridFTP](http://www.prace-ri.eu/Data-Transfer-with-GridFTP-Details)
+* [Data transfer with gtransfer](http://www.prace-ri.eu/Data-Transfer-with-gtransfer)
 
 Before you start to use any of the services don't forget to create a proxy certificate from your certificate:
 
@@ -116,8 +114,8 @@ If the user uses GSI SSH based access, then the procedure is similar to the SSH
 
 After successful obtainment of login credentials for the local IT4Innovations account, the PRACE users can access the cluster as regular users using SSH. For more information please see the section in general documentation.
 
-File transfers
-------------------
+## File transfers
+
 PRACE users can use the same transfer mechanisms as regular users (if they've undergone the full registration procedure). For information about this, please see the section in the general documentation.
 
 Apart from the standard mechanisms, for PRACE users to transfer data to/from Anselm cluster, a GridFTP server running Globus Toolkit GridFTP service is available. The service is available from public Internet as well as from the internal PRACE network (accessible only from other PRACE partners).
@@ -199,9 +197,9 @@ Generally both shared file systems are available through GridFTP:
 
 More information about the shared file systems is available [here](storage/).
 
-Usage of the cluster
---------------------
- There are some limitations for PRACE user when using the cluster. By default PRACE users aren't allowed to access special queues in the PBS Pro to have high priority or exclusive access to some special equipment like accelerated nodes and high memory (fat) nodes. There may be also restrictions obtaining a working license for the commercial software installed on the cluster, mostly because of the license agreement or because of insufficient amount of licenses.
+## Usage of the cluster
+
+There are some limitations for PRACE user when using the cluster. By default PRACE users aren't allowed to access special queues in the PBS Pro to have high priority or exclusive access to some special equipment like accelerated nodes and high memory (fat) nodes. There may be also restrictions obtaining a working license for the commercial software installed on the cluster, mostly because of the license agreement or because of insufficient amount of licenses.
 
 For production runs always use scratch file systems, either the global shared or the local ones. The available file systems are described [here](hardware-overview/).
 
@@ -225,7 +223,7 @@ For PRACE users, the default production run queue is "qprace". PRACE users can a
 |---|---|---|---|---|---|---|
 |**qexp** Express queue|no|none required|2 reserved, 8 total|high|no|1 / 1h|
 |**qprace** Production queue|yes|> 0|178 w/o accelerator|medium|no|24 / 48 h|
-|**qfree** Free resource queue|yes|none required|178 w/o accelerator|very low|no|	12 / 12 h|
+|**qfree** Free resource queue|yes|none required|178 w/o accelerator|very low|no|12 / 12 h|
 
 **qprace**, the PRACE: This queue is intended for normal production runs. It is required that active project with nonzero remaining resources is specified to enter the qprace. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qprace is 12 hours. If the job needs longer time, it must use checkpoint/restart functionality.
 
@@ -238,7 +236,7 @@ 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".
 
 !!! Note "Note"
-	The **it4ifree** command is a part of it4i.portal.clients package, located here: <https://pypi.python.org/pypi/it4i.portal.clients>
+    The **it4ifree** command is a part of it4i.portal.clients package, located here: <https://pypi.python.org/pypi/it4i.portal.clients>
 
 ```bash
     $ it4ifree

docs.it4i/anselm-cluster-documentation/resources-allocation-policy.md

-Resources Allocation Policy
-===========================
+# Resources Allocation Policy
+
+## Introduction
 
-Resources Allocation Policy
----------------------------
 The resources are allocated to the job in a fair-share fashion, subject to constraints set by the queue and resources available to the Project. The Fair-share at Anselm ensures that individual users may consume approximately equal amount of resources per week. Detailed information in the [Job scheduling](job-priority/) section. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following table provides the queue partitioning overview:
 
 !!! Note "Note"
-	Check the queue status at https://extranet.it4i.cz/anselm/
+    Check the queue status at [https://extranet.it4i.cz/anselm/](https://extranet.it4i.cz/anselm/)
 
- |queue |active project |project resources |nodes|min ncpus|priority|authorization|walltime |
- | --- | --- | --- | --- | --- | --- | --- | --- |
- |qexp |no |none required |2 reserved, 31 totalincluding MIC, GPU and FAT nodes |1 |150 |no |1 h |
- |qprod |yes |0 |178 nodes w/o accelerator |16 |0 |no |24/48 h |
- |qlong |yes |0 |60 nodes w/o accelerator |16 |0 |no |72/144 h |
- |qnvidia, qmic, qfat |yes |0 |23 total qnvidia4 total qmic2 total qfat |16 |200 |yes |24/48 h |
- |qfree |yes |none required |178 w/o accelerator |16 |-1024 |no |12 h |
+|queue|active project|project resources|nodes|min ncpus|priority|authorization|walltime|
+|---|---|---|---|---|---|---|---|
+|qexp|no|none required|2 reserved, 31 totalincluding MIC, GPU and FAT nodes|1|150|no|1 h|
+|qprod|yes|0|178 nodes w/o accelerator|16|0|no|24/48 h|
+|qlong|yes|0|60 nodes w/o accelerator|16|0|no|72/144 h|
+|qnvidia, qmic, qfat|yes|0|23 total qnvidia4 total qmic2 total qfat|16|200|yes|24/48 h|
+|qfree|yes|none required|178 w/o accelerator|16|-1024|no|12 h|
 
 !!! Note "Note"
-	**The qfree queue is not free of charge**. [Normal accounting](#resources-accounting-policy) applies. However, it allows for utilization of free resources, once a Project exhausted all its allocated computational resources. This does not apply for Directors Discreation's projects (DD projects) by default. Usage of qfree after exhaustion of DD projects computational resources is allowed after request for this queue.
+ **The qfree queue is not free of charge**. [Normal accounting](#resources-accounting-policy) applies. However, it allows for utilization of free resources, once a Project exhausted all its allocated computational resources. This does not apply for Directors Discreation's projects (DD projects) by default. Usage of qfree after exhaustion of DD projects computational resources is allowed after request for this queue.
 
-    **The qexp queue is equipped with the nodes not having the very same CPU clock speed.** Should you need the very same CPU speed, you have to select the proper nodes during the PSB job submission.
+**The qexp queue is equipped with the nodes not having the very same CPU clock speed.** Should you need the very same CPU speed, you have to select the proper nodes during the PSB job submission.
 
-- **qexp**, the Express queue: This queue is dedicated for testing and running very small jobs. It is not required to specify a project to enter the qexp. There are 2 nodes always reserved for this queue (w/o accelerator), maximum 8 nodes are available via the qexp for a particular user, from a pool of nodes containing Nvidia accelerated nodes (cn181-203), MIC accelerated nodes (cn204-207) and Fat nodes with 512GB RAM (cn208-209). This enables to test and tune also accelerated code or code with higher RAM requirements. The nodes may be allocated on per core basis. No special authorization is required to use it. The maximum runtime in qexp is 1 hour.
-- **qprod**, the Production queue: This queue is intended for normal production runs. It is required that active project with nonzero remaining resources is specified to enter the qprod. All nodes may be accessed via the qprod queue, except the reserved ones. 178 nodes without accelerator are included. Full nodes, 16 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qprod is 48 hours.
-- **qlong**, the Long queue: This queue is intended for long production runs. It is required that active project with nonzero remaining resources is specified to enter the qlong. Only 60 nodes without acceleration may be accessed via the qlong queue. Full nodes, 16 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qlong is 144 hours (three times of the standard qprod time - 3 * 48 h).
-- **qnvidia**, qmic, qfat, the Dedicated queues: The queue qnvidia is dedicated to access the Nvidia accelerated nodes, the qmic to access MIC nodes and qfat the Fat nodes. It is required that active project with nonzero remaining resources is specified to enter these queues. 23 nvidia, 4 mic and 2 fat nodes are included. Full nodes, 16 cores per node are allocated. The queues run with very high priority, the jobs will be scheduled before the jobs coming from the qexp queue. An PI needs explicitly ask [support](https://support.it4i.cz/rt/) for authorization to enter the dedicated queues for all users associated to her/his Project.
-- **qfree**, The Free resource queue: The queue qfree is intended for utilization of free resources, after a Project exhausted all its allocated computational resources (Does not apply to DD projects by default. DD projects have to request for persmission on qfree after exhaustion of computational resources.). It is required that active project is specified to enter the queue, however no remaining resources are required. Consumed resources will be accounted to the Project. Only 178 nodes without accelerator may be accessed from this queue. Full nodes, 16 cores per node are allocated. The queue runs with very low priority and no special authorization is required to use it. The maximum runtime in qfree is 12 hours.
+* **qexp**, the Express queue: This queue is dedicated for testing and running very small jobs. It is not required to specify a project to enter the qexp. There are 2 nodes always reserved for this queue (w/o accelerator), maximum 8 nodes are available via the qexp for a particular user, from a pool of nodes containing Nvidia accelerated nodes (cn181-203), MIC accelerated nodes (cn204-207) and Fat nodes with 512GB RAM (cn208-209). This enables to test and tune also accelerated code or code with higher RAM requirements. The nodes may be allocated on per core basis. No special authorization is required to use it. The maximum runtime in qexp is 1 hour.
+* **qprod**, the Production queue: This queue is intended for normal production runs. It is required that active project with nonzero remaining resources is specified to enter the qprod. All nodes may be accessed via the qprod queue, except the reserved ones. 178 nodes without accelerator are included. Full nodes, 16 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qprod is 48 hours.
+* **qlong**, the Long queue: This queue is intended for long production runs. It is required that active project with nonzero remaining resources is specified to enter the qlong. Only 60 nodes without acceleration may be accessed via the qlong queue. Full nodes, 16 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qlong is 144 hours (three times of the standard qprod time - 3 * 48 h).
+* **qnvidia**, qmic, qfat, the Dedicated queues: The queue qnvidia is dedicated to access the Nvidia accelerated nodes, the qmic to access MIC nodes and qfat the Fat nodes. It is required that active project with nonzero remaining resources is specified to enter these queues. 23 nvidia, 4 mic and 2 fat nodes are included. Full nodes, 16 cores per node are allocated. The queues run with very high priority, the jobs will be scheduled before the jobs coming from the qexp queue. An PI needs explicitly ask [support](https://support.it4i.cz/rt/) for authorization to enter the dedicated queues for all users associated to her/his Project.
+* **qfree**, The Free resource queue: The queue qfree is intended for utilization of free resources, after a Project exhausted all its allocated computational resources (Does not apply to DD projects by default. DD projects have to request for persmission on qfree after exhaustion of computational resources.). It is required that active project is specified to enter the queue, however no remaining resources are required. Consumed resources will be accounted to the Project. Only 178 nodes without accelerator may be accessed from this queue. Full nodes, 16 cores per node are allocated. The queue runs with very low priority and no special authorization is required to use it. The maximum runtime in qfree is 12 hours.
 
 ### Notes
 
@@ -37,7 +36,8 @@ Anselm users may check current queue configuration at <https://extranet.it4i.cz/
 
 ### Queue status
 
->Check the status of jobs, queues and compute nodes at <https://extranet.it4i.cz/anselm/>
+!!! tip
+    Check the status of jobs, queues and compute nodes at <https://extranet.it4i.cz/anselm/>
 
 ![rspbs web interface](../img/rsweb.png)
 
@@ -105,8 +105,7 @@ Options:
   --incl-finished       Include finished jobs
 ```
 
-Resources Accounting Policy
--------------------------------
+## Resources Accounting Policy
 
 ### The Core-Hour
 
@@ -115,7 +114,7 @@ The resources that are currently subject to accounting are the core-hours. The c
 ### Check consumed resources
 
 !!! Note "Note"
-	The **it4ifree** command is a part of it4i.portal.clients package, located here: <https://pypi.python.org/pypi/it4i.portal.clients>
+    The **it4ifree** command is a part of it4i.portal.clients package, located here: <https://pypi.python.org/pypi/it4i.portal.clients>
 
 User may check at any time, how many core-hours have been consumed by himself/herself and his/her projects. The command is available on clusters' login nodes.
 

docs.it4i/anselm-cluster-documentation/shell-and-data-access.md

-Accessing the Cluster
-==============================
+# Accessing the Cluster
+
+## Shell Access
 
-Shell Access
------------------
 The Anselm cluster is accessed by SSH protocol via login nodes login1 and login2 at address anselm.it4i.cz. The login nodes may be addressed specifically, by prepending the login node name to the address.
 
 |Login address|Port|Protocol|Login node|
@@ -13,11 +12,11 @@ The Anselm cluster is accessed by SSH protocol via login nodes login1 and login2
 
 The authentication is by the [private key](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/)
 
-!!! Note "Note"
-	Please verify SSH fingerprints during the first logon. They are identical on all login nodes:
+!!! note
+    Please verify SSH fingerprints during the first logon. They are identical on all login nodes:
 
-	29:b3:f4:64:b0:73:f5:6f:a7:85:0f:e0:0d:be:76:bf (DSA)
-	d4:6f:5c:18:f4:3f:70:ef:bc:fc:cc:2b:fd:13:36:b7 (RSA)
+    29:b3:f4:64:b0:73:f5:6f:a7:85:0f:e0:0d:be:76:bf (DSA)
+    d4:6f:5c:18:f4:3f:70:ef:bc:fc:cc:2b:fd:13:36:b7 (RSA)
 
 Private key authentication:
 
@@ -55,10 +54,10 @@ Last login: Tue Jul  9 15:57:38 2013 from your-host.example.com
 Example to the cluster login:
 
 !!! Note "Note"
-	The environment is **not** shared between login nodes, except for [shared filesystems](storage/#shared-filesystems).
+    The environment is **not** shared between login nodes, except for [shared filesystems](storage/#shared-filesystems).
+
+## Data Transfer
 
-Data Transfer
--------------
 Data in and out of the system may be transferred by the [scp](http://en.wikipedia.org/wiki/Secure_copy) and sftp protocols.  (Not available yet.) In case large volumes of data are transferred, use dedicated data mover node dm1.anselm.it4i.cz for increased performance.
 
 |Address|Port|Protocol|
@@ -71,14 +70,14 @@ Data in and out of the system may be transferred by the [scp](http://en.wikipedi
 The authentication is by the [private key](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/)
 
 !!! Note "Note"
-	Data transfer rates up to **160MB/s** can be achieved with scp or sftp.
+    Data transfer rates up to **160MB/s** can be achieved with scp or sftp.
 
     1TB may be transferred in 1:50h.
 
 To achieve 160MB/s transfer rates, the end user must be connected by 10G line all the way to IT4Innovations and use computer with fast processor for the transfer. Using Gigabit ethernet connection, up to 110MB/s may be expected.  Fast cipher (aes128-ctr) should be used.
 
 !!! Note "Note"
-	If you experience degraded data transfer performance, consult your local network provider.
+    If you experience degraded data transfer performance, consult your local network provider.
 
 On linux or Mac, use scp or sftp client to transfer the data to Anselm:
 
@@ -116,9 +115,8 @@ On Windows, use [WinSCP client](http://winscp.net/eng/download.php) to transfer
 
 More information about the shared file systems is available [here](storage/).
 
+## Connection restrictions
 
-Connection restrictions
------------------------
 Outgoing connections, from Anselm Cluster login nodes to the outside world, are restricted to following ports:
 
 |Port|Protocol|
@@ -129,17 +127,16 @@ Outgoing connections, from Anselm Cluster login nodes to the outside world, are
 |9418|git|
 
 !!! Note "Note"
-	Please use **ssh port forwarding** and proxy servers to connect from Anselm to all other remote ports.
+    Please use **ssh port forwarding** and proxy servers to connect from Anselm to all other remote ports.
 
 Outgoing connections, from Anselm Cluster compute nodes are restricted to the internal network. Direct connections form compute nodes to outside world are cut.
 
-Port forwarding
----------------
+## Port forwarding
 
 ### Port forwarding from login nodes
 
 !!! Note "Note"
-	Port forwarding allows an application running on Anselm to connect to arbitrary remote host and port.
+    Port forwarding allows an application running on Anselm to connect to arbitrary remote host and port.
 
 It works by tunneling the connection from Anselm back to users workstation and forwarding from the workstation to the remote host.
 
@@ -159,7 +156,8 @@ Port forwarding may be established directly to the remote host. However, this re
 $ ssh -L 6000:localhost:1234 remote.host.com
 ```
 
-Note: Port number 6000 is chosen as an example only. Pick any free port.
+!!! note
+    Port number 6000 is chosen as an example only. Pick any free port.
 
 ### Port forwarding from compute nodes
 
@@ -180,7 +178,7 @@ In this example, we assume that port forwarding from login1:6000 to remote.host.
 Port forwarding is static, each single port is mapped to a particular port on remote host. Connection to other remote host, requires new forward.
 
 !!! Note "Note"
-	Applications with inbuilt proxy support, experience unlimited access to remote hosts, via single proxy server.
+    Applications with inbuilt proxy support, experience unlimited access to remote hosts, via single proxy server.
 
 To establish local proxy server on your workstation, install and run SOCKS proxy server software. On Linux, sshd demon provides the functionality. To establish SOCKS proxy server listening on port 1080 run:
 
@@ -198,13 +196,11 @@ local $ ssh -R 6000:localhost:1080 anselm.it4i.cz
 
 Now, configure the applications proxy settings to **localhost:6000**. Use port forwarding  to access the [proxy server from compute nodes](#port-forwarding-from-compute-nodes) as well.
 
-Graphical User Interface
-------------------------
+## Graphical User Interface
 
--   The [X Window system](../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/) is a principal way to get GUI access to the clusters.
--   The [Virtual Network Computing](../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/) is a graphical [desktop sharing](http://en.wikipedia.org/wiki/Desktop_sharing) system that uses the [Remote Frame Buffer protocol](http://en.wikipedia.org/wiki/RFB_protocol) to remotely control another [computer](http://en.wikipedia.org/wiki/Computer).
+* The [X Window system](../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/) is a principal way to get GUI access to the clusters.
+* The [Virtual Network Computing](../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/) is a graphical [desktop sharing](http://en.wikipedia.org/wiki/Desktop_sharing) system that uses the [Remote Frame Buffer protocol](http://en.wikipedia.org/wiki/RFB_protocol) to remotely control another [computer](http://en.wikipedia.org/wiki/Computer).
 
-VPN Access
-----------
+## VPN Access
 
--   Access to IT4Innovations internal resources via [VPN](../get-started-with-it4innovations/accessing-the-clusters/vpn-access/).
+* Access to IT4Innovations internal resources via [VPN](../get-started-with-it4innovations/accessing-the-clusters/vpn-access/).

docs.it4i/anselm-cluster-documentation/software/gpi2.md

-GPI-2
-=====
+# GPI-2
 
-##A library that implements the GASPI specification
+## Introduction
 
-Introduction
-------------
 Programming Next Generation Supercomputers: GPI-2 is an API library for asynchronous interprocess, cross-node communication. It provides a flexible, scalable and fault tolerant interface for parallel applications.
 
 The GPI-2 library ([www.gpi-site.com/gpi2/](http://www.gpi-site.com/gpi2/)) implements the GASPI specification (Global Address Space Programming Interface, [www.gaspi.de](http://www.gaspi.de/en/project.html)). GASPI is a Partitioned Global Address Space (PGAS) API. It aims at scalable, flexible and failure tolerant computing in massively parallel environments.
 
-Modules
--------
+## Modules
+
 The GPI-2, version 1.0.2 is available on Anselm via module gpi2:
 
 ```bash
@@ -19,10 +16,10 @@ The GPI-2, version 1.0.2 is available on Anselm via module gpi2:
 
 The module sets up environment variables, required for linking and running GPI-2 enabled applications. This particular command loads the default module, which is gpi2/1.0.2
 
-Linking
--------
-!!! Note "Note"
-	Link with -lGPI2 -libverbs
+## Linking
+
+!!! note
+    Link with -lGPI2 -libverbs
 
 Load the gpi2 module. Link using **-lGPI2** and **-libverbs** switches to link your code against GPI-2. The GPI-2 requires the OFED infinband communication library ibverbs.
 
@@ -42,11 +39,10 @@ Load the gpi2 module. Link using **-lGPI2** and **-libverbs** switches to link y
     $ gcc myprog.c -o myprog.x -Wl,-rpath=$LIBRARY_PATH -lGPI2 -libverbs
 ```
 
-Running the GPI-2 codes
------------------------
+## Running the GPI-2 codes
 
-!!! Note "Note"
-	gaspi_run starts the GPI-2 application
+!!! note
+    gaspi_run starts the GPI-2 application
 
 The gaspi_run utility is used to start and run GPI-2 applications:
 
@@ -54,7 +50,7 @@ The gaspi_run utility is used to start and run GPI-2 applications:
     $ gaspi_run -m machinefile ./myprog.x
 ```
 
-A machine file (**machinefile**) with the hostnames of nodes where the application will run, must be provided. The machinefile lists all nodes on which to run, one entry per node per process. This file may be hand created or obtained from standard $PBS_NODEFILE:
+A machine file (** machinefile **) with the hostnames of nodes where the application will run, must be provided. The machinefile lists all nodes on which to run, one entry per node per process. This file may be hand created or obtained from standard $PBS_NODEFILE:
 
 ```bash
     $ cut -f1 -d"." $PBS_NODEFILE > machinefile
@@ -80,8 +76,8 @@ machinefle:
 
 This machinefile will run 4 GPI-2 processes, 2 on node cn79 o 2 on node cn80.
 
-!!! Note "Note"
-	Use the **mpiprocs** to control how many GPI-2 processes will run per node
+!!! note
+    Use the **mpiprocs**to control how many GPI-2 processes will run per node
 
 Example:
 
@@ -93,13 +89,12 @@ This example will produce $PBS_NODEFILE with 16 entries per node.
 
 ### gaspi_logger
 
-!!! Note "Note"
-	gaspi_logger views the output form GPI-2 application ranks
+!!! note
+    gaspi_logger views the output form GPI-2 application ranks
 
 The gaspi_logger utility is used to view the output from all nodes except the master node (rank 0). The gaspi_logger is started, on another session, on the master node - the node where the gaspi_run is executed. The output of the application, when called with gaspi_printf(), will be redirected to the gaspi_logger. Other I/O routines (e.g. printf) will not.
 
-Example
--------
+## Example
 
 Following is an example GPI-2 enabled code:
 
@@ -169,4 +164,4 @@ At the same time, in another session, you may start the gaspi logger:
     [cn80:0] Hello from rank 1 of 2
 ```
 
-In this example, we compile the helloworld_gpi.c code using the **gnu compiler** (gcc) and link it to the GPI-2 and ibverbs library. The library search path is compiled in. For execution, we use the qexp queue, 2 nodes 1 core each. The GPI module must be loaded on the master compute node (in this example the cn79), gaspi_logger is used from different session to view the output of the second process.
+In this example, we compile the helloworld_gpi.c code using the **gnu compiler**(gcc) and link it to the GPI-2 and ibverbs library. The library search path is compiled in. For execution, we use the qexp queue, 2 nodes 1 core each. The GPI module must be loaded on the master compute node (in this example the cn79), gaspi_logger is used from different session to view the output of the second process.

docs.it4i/anselm-cluster-documentation/software/omics-master/diagnostic-component-team.md

-Diagnostic component (TEAM)
-===========================
+# Diagnostic component (TEAM)
 
-### Access
+## Access
 
 TEAM is available at the [following address](http://omics.it4i.cz/team/)
 
-!!! Note "Note"
-	The address is accessible only via VPN.
+!!! note
+    The address is accessible only via VPN.
 
-### Diagnostic component (TEAM)
+## Diagnostic component
 
 VCF files are scanned by this diagnostic tool for known diagnostic disease-associated variants. When no diagnostic mutation is found, the file can be sent to the disease-causing gene discovery tool to see whether new disease associated variants can be found.
 
@@ -16,4 +15,4 @@ TEAM (27) is an intuitive and easy-to-use web tool that fills the gap between th
 
 ![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.](../../../img/fig5.png)
 
-**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.
+** 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.

docs.it4i/anselm-cluster-documentation/software/omics-master/priorization-component-bierapp.md

-Prioritization component (BiERapp)
-================================
+# Prioritization component (BiERapp)
 
-### Access
+## Access
 
 BiERapp is available at the [following address](http://omics.it4i.cz/bierapp/)
 
-!!! Note "Note"
-	The address is accessible onlyvia VPN.
+!!! note
+    The address is accessible only via VPN.
 
-###BiERapp
+## BiERapp
 
-**This tool is aimed to discover new disease genes or variants by studying affected families or cases and controls. It carries out a filtering process to sequentially remove: (i) variants which are not no compatible with the disease because are not expected to have impact on the protein function; (ii) variants that exist at frequencies incompatible with the disease; (iii) variants that do not segregate with the disease. The result is a reduced set of disease gene candidates that should be further validated experimentally.**
+** This tool is aimed to discover new disease genes or variants by studying affected families or cases and controls. It carries out a filtering process to sequentially remove: (i) variants which are not no compatible with the disease because are not expected to have impact on the protein function; (ii) variants that exist at frequencies incompatible with the disease; (iii) variants that do not segregate with the disease. The result is a reduced set of disease gene candidates that should be further validated experimentally. **
 
 BiERapp (28) efficiently helps in the identification of causative variants in family and sporadic genetic diseases. The program reads lists of predicted variants (nucleotide substitutions and indels) in affected individuals or tumor samples and controls. In family studies, different modes of inheritance can easily be defined to filter out variants that do not segregate with the disease along the family. Moreover, BiERapp integrates additional information such as allelic frequencies in the general population and the most popular damaging scores to further narrow down the number of putative variants in successive filtering steps. BiERapp provides an interactive and user-friendly interface that implements the filtering strategy used in the context of a large-scale genomic project carried out by the Spanish Network for Research, in Rare Diseases (CIBERER) and the Medical Genome Project. in which more than 800 exomes have been analyzed.
 
 ![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.](../../../img/fig6.png)
 
-**Figure 6**. Web interface to the prioritization tool. This figure shows the interface of the web tool for candidate gene
+** 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.