diff --git a/docs.it4i/anselm-cluster-documentation/capacity-computing.md b/docs.it4i/anselm-cluster-documentation/capacity-computing.md
index e916a14128f321a024e092e7c1e0a94e2c58fbd1..a1372efcb635bb757c6c828805d8c216a165ce23 100644
--- a/docs.it4i/anselm-cluster-documentation/capacity-computing.md
+++ b/docs.it4i/anselm-cluster-documentation/capacity-computing.md
@@ -1,8 +1,7 @@
-Capacity computing
-==================
+# Capacity computing
+
+## Introduction
-Introduction
-------------
In many cases, it is useful to submit huge (>100+) number of computational jobs into the PBS queue system. Huge number of (small) jobs is one of the most effective ways to execute embarrassingly parallel calculations, achieving best runtime, throughput and computer utilization.
However, executing huge number of jobs via the PBS queue may strain the system. This strain may result in slow response to commands, inefficient scheduling and overall degradation of performance and user experience, for all users. For this reason, the number of jobs is **limited to 100 per user, 1000 per job array**
@@ -14,14 +13,12 @@ However, executing huge number of jobs via the PBS queue may strain the system.
- Use [GNU parallel](capacity-computing/#gnu-parallel) when running single core jobs
- Combine [GNU parallel with Job arrays](capacity-computing/#job-arrays-and-gnu-parallel) when running huge number of single core jobs
-Policy
-------
+## Policy
1. A user is allowed to submit at most 100 jobs. Each job may be [a job array](capacity-computing/#job-arrays).
2. The array size is at most 1000 subjobs.
-Job arrays
---------------
+## Job arrays
!!! Note "Note"
Huge number of jobs may be easily submitted and managed as a job array.
@@ -73,7 +70,7 @@ cp $PBS_O_WORKDIR/$TASK input ; cp $PBS_O_WORKDIR/myprog.x .
cp output $PBS_O_WORKDIR/$TASK.out
```
-In this example, the submit directory holds the 900 input files, executable myprog.x and the jobscript file. As input for each run, we take the filename of input file from created tasklist file. We copy the input file to local scratch /lscratch/$PBS_JOBID, execute the myprog.x and copy the output file back to >the submit directory, under the $TASK.out name. The myprog.x runs on one node only and must use threads to run in parallel. Be aware, that if the myprog.x **is not multithreaded**, then all the **jobs are run as single thread programs in sequential** manner. Due to allocation of the whole node, the accounted time is equal to the usage of whole node**, while using only 1/16 of the node!
+In this example, the submit directory holds the 900 input files, executable myprog.x and the jobscript file. As input for each run, we take the filename of input file from created tasklist file. We copy the input file to local scratch /lscratch/$PBS_JOBID, execute the myprog.x and copy the output file back to >the submit directory, under the $TASK.out name. The myprog.x runs on one node only and must use threads to run in parallel. Be aware, that if the myprog.x **is not multithreaded**, then all the **jobs are run as single thread programs in sequential** manner. Due to allocation of the whole node, the accounted time is equal to the usage of whole node\*\*, while using only 1/16 of the node!
If huge number of parallel multicore (in means of multinode multithread, e. g. MPI enabled) jobs is needed to run, then a job array approach should also be used. The main difference compared to previous example using one node is that the local scratch should not be used (as it's not shared between nodes) and MPI or other technique for parallel multinode run has to be used properly.
@@ -150,8 +147,7 @@ $ qstat -u $USER -tJ
Read more on job arrays in the [PBSPro Users guide](../../pbspro-documentation/).
-GNU parallel
-----------------
+## GNU parallel
!!! Note "Note"
Use GNU parallel to run many single core tasks on one node.
@@ -222,8 +218,7 @@ In this example, we submit a job of 101 tasks. 16 input files will be processed
Please note the #PBS directives in the beginning of the jobscript file, dont' forget to set your valid PROJECT_ID and desired queue.
-Job arrays and GNU parallel
----------------------------
+## Job arrays and GNU parallel
!!! Note "Note"
Combine the Job arrays and GNU parallel for best throughput of single core jobs
@@ -290,7 +285,7 @@ In this example, the jobscript executes in multiple instances in parallel, on al
When deciding this values, think about following guiding rules:
-1. Let n=N/16. Inequality (n+1) * T < W should hold. The N is number of tasks per subjob, T is expected single task walltime and W is subjob walltime. Short subjob walltime improves scheduling and job throughput.
+1. Let n=N/16. Inequality (n+1) \* T < W should hold. The N is number of tasks per subjob, T is expected single task walltime and W is subjob walltime. Short subjob walltime improves scheduling and job throughput.
2. Number of tasks should be modulo 16.
3. These rules are valid only when all tasks have similar task walltimes T.
@@ -307,8 +302,7 @@ In this example, we submit a job array of 31 subjobs. Note the -J 1-992:**32**,
Please note the #PBS directives in the beginning of the jobscript file, dont' forget to set your valid PROJECT_ID and desired queue.
-Examples
---------
+## Examples
Download the examples in [capacity.zip](capacity.zip), illustrating the above listed ways to run huge number of jobs. We recommend to try out the examples, before using this for running production jobs.
diff --git a/docs.it4i/anselm-cluster-documentation/compute-nodes.md b/docs.it4i/anselm-cluster-documentation/compute-nodes.md
index f7b65a0f137a065f3a39e12670497ca11ecc5592..6cd3c18f75ce9886bf315073d0ec6adeba51768c 100644
--- a/docs.it4i/anselm-cluster-documentation/compute-nodes.md
+++ b/docs.it4i/anselm-cluster-documentation/compute-nodes.md
@@ -6,58 +6,58 @@ Anselm is cluster of x86-64 Intel based nodes built on Bull Extreme Computing bu
### 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]
+- 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]
+- 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]
+- 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]
+- 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]
**Figure Anselm bullx B510 servers**
### Compute Nodes Summary
- |Node type|Count|Range|Memory|Cores|[Access](resources-allocation-policy/)|
- |---|---|---|---|---|---|
- |Nodes without accelerator|180|cn[1-180]|64GB|16 @ 2.4Ghz|qexp, qprod, qlong, qfree|
- |Nodes with GPU accelerator|23|cn[181-203]|96GB|16 @ 2.3Ghz|qgpu, qprod|
- |Nodes with MIC accelerator|4|cn[204-207]|96GB|16 @ 2.3GHz|qmic, qprod|
- |Fat compute nodes|2|cn[208-209]|512GB|16 @ 2.4GHz|qfat, qprod|
+| Node type | Count | Range | Memory | Cores | [Access](resources-allocation-policy/) |
+| -------------------------- | ----- | ----------- | ------ | ----------- | -------------------------------------- |
+| Nodes without accelerator | 180 | cn[1-180] | 64GB | 16 @ 2.4Ghz | qexp, qprod, qlong, qfree |
+| Nodes with GPU accelerator | 23 | cn[181-203] | 96GB | 16 @ 2.3Ghz | qgpu, qprod |
+| Nodes with MIC accelerator | 4 | cn[204-207] | 96GB | 16 @ 2.3GHz | qmic, qprod |
+| Fat compute nodes | 2 | cn[208-209] | 512GB | 16 @ 2.4GHz | qfat, qprod |
## Processor Architecture
@@ -65,23 +65,23 @@ Anselm is equipped with Intel Sandy Bridge processors Intel Xeon E5-2665 (nodes
### 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.
@@ -101,30 +101,30 @@ Intel Turbo Boost Technology is used by default, you can disable it for all nod
### 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
diff --git a/docs.it4i/anselm-cluster-documentation/environment-and-modules.md b/docs.it4i/anselm-cluster-documentation/environment-and-modules.md
index 45b23263a0a2f5b0f49c8c41279b716ee043621b..ae50c883237578e18cc94c4141890b78c394c741 100644
--- a/docs.it4i/anselm-cluster-documentation/environment-and-modules.md
+++ b/docs.it4i/anselm-cluster-documentation/environment-and-modules.md
@@ -1,5 +1,4 @@
-Environment and Modules
-=======================
+# Environment and Modules
### Environment Customization
@@ -77,7 +76,7 @@ PrgEnv-gnu sets up the GNU development environment in conjunction with the bullx
PrgEnv-intel sets up the INTEL development environment in conjunction with the Intel MPI library
How to using modules in examples:
-<tty-player controls src=/src/anselm/modules_anselm.ttyrec></tty-player>
+<tty-player controls src=/src/anselm/modules_anselm.ttyrec></tty-player>
### Application Modules Path Expansion
diff --git a/docs.it4i/anselm-cluster-documentation/hardware-overview.md b/docs.it4i/anselm-cluster-documentation/hardware-overview.md
index a13b08f2d82759b5385515ef1ae053590876f96c..84e05272bd3765b79b12fb66abf793992b148819 100644
--- a/docs.it4i/anselm-cluster-documentation/hardware-overview.md
+++ b/docs.it4i/anselm-cluster-documentation/hardware-overview.md
@@ -1,5 +1,4 @@
-Hardware Overview
-=================
+# Hardware Overview
The Anselm cluster consists of 209 computational nodes named cn[1-209] of which 180 are regular compute nodes, 23 GPU Kepler K20 accelerated nodes, 4 MIC Xeon Phi 5110P accelerated nodes and 2 fat nodes. Each node is a powerful x86-64 computer, equipped with 16 cores (two eight-core Intel Sandy Bridge processors), at least 64 GB RAM, and local hard drive. The user access to the Anselm cluster is provided by two login nodes login[1,2]. The nodes are interlinked by high speed InfiniBand and Ethernet networks. All nodes share 320 TB /home disk storage to store the user files. The 146 TB shared /scratch storage is available for the scratch data.
@@ -31,31 +30,31 @@ The user access to the Anselm cluster is provided by two login nodes login1, log
The parameters are summarized in the following tables:
-|**In general**||
-|---|---|
-|Primary purpose|High Performance Computing|
-|Architecture of compute nodes|x86-64|
-|Operating system|Linux|
-|[**Compute nodes**](compute-nodes/)||
-|Totally|209|
-|Processor cores|16 (2 x 8 cores)|
-|RAM|min. 64 GB, min. 4 GB per core|
-|Local disk drive|yes - usually 500 GB|
-|Compute network|InfiniBand QDR, fully non-blocking, fat-tree|
-|w/o accelerator|180, cn[1-180]|
-|GPU accelerated|23, cn[181-203]|
-|MIC accelerated|4, cn[204-207]|
-|Fat compute nodes|2, cn[208-209]|
-|**In total**||
-|Total theoretical peak performance (Rpeak)|94 TFLOP/s|
-|Total max. LINPACK performance (Rmax)|73 TFLOP/s|
-|Total amount of RAM|15.136 TB|
-
- |Node|Processor|Memory|Accelerator|
- |---|---|---|---|
- |w/o accelerator|2 x Intel Sandy Bridge E5-2665, 2.4 GHz|64 GB|-|
- |GPU accelerated|2 x Intel Sandy Bridge E5-2470, 2.3 GHz|96 GB|NVIDIA Kepler K20|
- |MIC accelerated|2 x Intel Sandy Bridge E5-2470, 2.3 GHz|96 GB|Intel Xeon Phi 5110P|
- |Fat compute node|2 x Intel Sandy Bridge E5-2665, 2.4 GHz|512 GB|-|
+| **In general** | |
+| ------------------------------------------- | -------------------------------------------- |
+| Primary purpose | High Performance Computing |
+| Architecture of compute nodes | x86-64 |
+| Operating system | Linux |
+| [**Compute nodes**](compute-nodes/) | |
+| Totally | 209 |
+| Processor cores | 16 (2 x 8 cores) |
+| RAM | min. 64 GB, min. 4 GB per core |
+| Local disk drive | yes - usually 500 GB |
+| Compute network | InfiniBand QDR, fully non-blocking, fat-tree |
+| w/o accelerator | 180, cn[1-180] |
+| GPU accelerated | 23, cn[181-203] |
+| MIC accelerated | 4, cn[204-207] |
+| Fat compute nodes | 2, cn[208-209] |
+| **In total** | |
+| Total theoretical peak performance (Rpeak) | 94 TFLOP/s |
+| Total max. LINPACK performance (Rmax) | 73 TFLOP/s |
+| Total amount of RAM | 15.136 TB |
+
+| Node | Processor | Memory | Accelerator |
+| ---------------- | --------------------------------------- | ------ | -------------------- |
+| w/o accelerator | 2 x Intel Sandy Bridge E5-2665, 2.4 GHz | 64 GB | - |
+| GPU accelerated | 2 x Intel Sandy Bridge E5-2470, 2.3 GHz | 96 GB | NVIDIA Kepler K20 |
+| MIC accelerated | 2 x Intel Sandy Bridge E5-2470, 2.3 GHz | 96 GB | Intel Xeon Phi 5110P |
+| Fat compute node | 2 x Intel Sandy Bridge E5-2665, 2.4 GHz | 512 GB | - |
For more details please refer to the [Compute nodes](compute-nodes/), [Storage](storage/), and [Network](network/).
diff --git a/docs.it4i/anselm-cluster-documentation/job-priority.md b/docs.it4i/anselm-cluster-documentation/job-priority.md
index 454bbf200ae2a540f473765501cb768224ea1793..b0724da7cb04fbdf8f17fc2f3d7c08499f2a3e96 100644
--- a/docs.it4i/anselm-cluster-documentation/job-priority.md
+++ b/docs.it4i/anselm-cluster-documentation/job-priority.md
@@ -1,8 +1,6 @@
-Job scheduling
-==============
+# Job scheduling
-Job execution priority
-----------------------
+## Job execution priority
Scheduler gives each job an execution priority and then uses this job execution priority to select which job(s) to run.
@@ -31,8 +29,8 @@ Fair-share priority is calculated as
where MAX_FAIRSHARE has value 1E6,
-usage*Project* is cumulated usage by all members of selected project,
-usage*Total* is total usage by all users, by all projects.
+usage_Project_ is cumulated usage by all members of selected project,
+usage_Total_ is total usage by all users, by all projects.
Usage counts allocated core-hours (`ncpus x walltime`). Usage is decayed, or cut in half periodically, at the interval 168 hours (one week).
Jobs queued in queue qexp are not calculated to project's usage.
@@ -42,7 +40,7 @@ Jobs queued in queue qexp are not calculated to project's usage.
Calculated fair-share priority can be also seen as Resource_List.fairshare attribute of a job.
-###Eligible time
+\###Eligible time
Eligible time is amount (in seconds) of eligible time job accrued while waiting to run. Jobs with higher eligible time gains higher priority.
diff --git a/docs.it4i/anselm-cluster-documentation/job-submission-and-execution.md b/docs.it4i/anselm-cluster-documentation/job-submission-and-execution.md
index a7dd204066f718ced9ca569f865c8cc5c9e4b9ff..c63517b096542386b83f2cfe52973e5038f13930 100644
--- a/docs.it4i/anselm-cluster-documentation/job-submission-and-execution.md
+++ b/docs.it4i/anselm-cluster-documentation/job-submission-and-execution.md
@@ -4,12 +4,12 @@
When allocating computational resources for the job, please specify
-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
+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
!!! Note "Note"
Use the **qsub** command to submit your job to a queue for allocation of the computational resources.
@@ -76,10 +76,10 @@ In this example, we allocate nodes cn171 and cn172, all 16 cores per node, for 2
Nodes equipped with Intel Xeon E5-2665 CPU have base clock frequency 2.4GHz, nodes equipped with Intel Xeon E5-2470 CPU have base frequency 2.3 GHz (see section Compute Nodes for details). Nodes may be selected via the PBS resource attribute cpu_freq .
-|CPU Type|base freq.|Nodes|cpu_freq attribute|
-|---|---|---|---|
-|Intel Xeon E5-2665|2.4GHz|cn[1-180], cn[208-209]|24|
-|Intel Xeon E5-2470|2.3GHz|cn[181-207]|23|
+| CPU Type | base freq. | Nodes | cpu_freq attribute |
+| ------------------ | ---------- | ---------------------- | ------------------ |
+| Intel Xeon E5-2665 | 2.4GHz | cn[1-180], cn[208-209] | 24 |
+| Intel Xeon E5-2470 | 2.3GHz | cn[181-207] | 23 |
```bash
$ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=16:cpu_freq=24 -I
@@ -156,7 +156,7 @@ Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
16547.srv11 user2 qprod job3x 13516 2 32 -- 48:00 R 00:58
```
-In this example user1 and user2 are running jobs named job1, job2 and job3x. The jobs job1 and job2 are using 4 nodes, 16 cores per node each. The job1 already runs for 38 hours and 25 minutes, job2 for 17 hours 44 minutes. The job1 already consumed 64*38.41 = 2458.6 core hours. The job3x already consumed 0.96*32 = 30.93 core hours. These consumed core hours will be accounted on the respective project accounts, regardless of whether the allocated cores were actually used for computations.
+In this example user1 and user2 are running jobs named job1, job2 and job3x. The jobs job1 and job2 are using 4 nodes, 16 cores per node each. The job1 already runs for 38 hours and 25 minutes, job2 for 17 hours 44 minutes. The job1 already consumed 64_38.41 = 2458.6 core hours. The job3x already consumed 0.96_32 = 30.93 core hours. These consumed core hours will be accounted on the respective project accounts, regardless of whether the allocated cores were actually used for computations.
Check status of your jobs using check-pbs-jobs command. Check presence of user's PBS jobs' processes on execution hosts. Display load, processes. Display job standard and error output. Continuously display (tail -f) job standard or error output.
diff --git a/docs.it4i/anselm-cluster-documentation/network.md b/docs.it4i/anselm-cluster-documentation/network.md
index 24fe0881bab6b1629a3096493d409f5c5b0702b9..307931a5d350f697be4679358a7e1c74e57a7cb5 100644
--- a/docs.it4i/anselm-cluster-documentation/network.md
+++ b/docs.it4i/anselm-cluster-documentation/network.md
@@ -1,10 +1,9 @@
-Network
-=======
+# Network
All compute and login nodes of Anselm are interconnected by [InfiniBand](http://en.wikipedia.org/wiki/InfiniBand) QDR network and by Gigabit [Ethernet](http://en.wikipedia.org/wiki/Ethernet) network. Both networks may be used to transfer user data.
-InfiniBand Network
-------------------
+## InfiniBand Network
+
All compute and login nodes of Anselm are interconnected by a high-bandwidth, low-latency [InfiniBand](http://en.wikipedia.org/wiki/InfiniBand) QDR network (IB 4 x QDR, 40 Gbps). The network topology is a fully non-blocking fat-tree.
The compute nodes may be accessed via the InfiniBand network using ib0 network interface, in address range 10.2.1.1-209. The MPI may be used to establish native InfiniBand connection among the nodes.
@@ -14,12 +13,11 @@ The compute nodes may be accessed via the InfiniBand network using ib0 network i
The Fat tree topology ensures that peak transfer rates are achieved between any two nodes, independent of network traffic exchanged among other nodes concurrently.
-Ethernet Network
-----------------
+## Ethernet Network
+
The compute nodes may be accessed via the regular Gigabit Ethernet network interface eth0, in address range 10.1.1.1-209, or by using aliases cn1-cn209. The network provides **114 MB/s** transfer rates via the TCP connection.
-Example
--------
+## Example
```bash
$ qsub -q qexp -l select=4:ncpus=16 -N Name0 ./myjob
diff --git a/docs.it4i/anselm-cluster-documentation/prace.md b/docs.it4i/anselm-cluster-documentation/prace.md
index 0b12438381379f4ce57dbeb46fc18720f745c74a..9cbbb19a14b369f6872092b7c5bc0b20f8ee413d 100644
--- a/docs.it4i/anselm-cluster-documentation/prace.md
+++ b/docs.it4i/anselm-cluster-documentation/prace.md
@@ -28,11 +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:
@@ -52,11 +52,11 @@ To access Anselm cluster, two login nodes running GSI SSH service are available.
It is recommended to use the single DNS name anselm-prace.it4i.cz which is distributed between the two login nodes. If needed, user can login directly to one of the login nodes. The addresses are:
-|Login address|Port|Protocol|Login node|
-|---|---|---|---|
-|anselm-prace.it4i.cz|2222|gsissh|login1 or login2|
-|login1-prace.anselm.it4i.cz|2222|gsissh|login1|
-|login2-prace.anselm.it4i.cz|2222|gsissh|login2|
+| Login address | Port | Protocol | Login node |
+| --------------------------- | ---- | -------- | ---------------- |
+| anselm-prace.it4i.cz | 2222 | gsissh | login1 or login2 |
+| login1-prace.anselm.it4i.cz | 2222 | gsissh | login1 |
+| login2-prace.anselm.it4i.cz | 2222 | gsissh | login2 |
```bash
$ gsissh -p 2222 anselm-prace.it4i.cz
@@ -72,11 +72,11 @@ When logging from other PRACE system, the prace_service script can be used:
It is recommended to use the single DNS name anselm.it4i.cz which is distributed between the two login nodes. If needed, user can login directly to one of the login nodes. The addresses are:
-|Login address|Port|Protocol|Login node|
-|---|---|---|---|
-|anselm.it4i.cz|2222|gsissh|login1 or login2|
-|login1.anselm.it4i.cz|2222|gsissh|login1|
-|login2.anselm.it4i.cz|2222|gsissh|login2|
+| Login address | Port | Protocol | Login node |
+| --------------------- | ---- | -------- | ---------------- |
+| anselm.it4i.cz | 2222 | gsissh | login1 or login2 |
+| login1.anselm.it4i.cz | 2222 | gsissh | login1 |
+| login2.anselm.it4i.cz | 2222 | gsissh | login2 |
```bash
$ gsissh -p 2222 anselm.it4i.cz
@@ -124,12 +124,12 @@ There's one control server and three backend servers for striping and/or backup
**Access from PRACE network:**
-|Login address|Port|Node role|
-|---|---|---|
-|gridftp-prace.anselm.it4i.cz|2812|Front end /control server|
-|login1-prace.anselm.it4i.cz|2813|Backend / data mover server|
-|login2-prace.anselm.it4i.cz|2813|Backend / data mover server|
-|dm1-prace.anselm.it4i.cz|2813|Backend / data mover server|
+| Login address | Port | Node role |
+| ---------------------------- | ---- | --------------------------- |
+| gridftp-prace.anselm.it4i.cz | 2812 | Front end /control server |
+| login1-prace.anselm.it4i.cz | 2813 | Backend / data mover server |
+| login2-prace.anselm.it4i.cz | 2813 | Backend / data mover server |
+| dm1-prace.anselm.it4i.cz | 2813 | Backend / data mover server |
Copy files **to** Anselm by running the following commands on your local machine:
@@ -157,12 +157,12 @@ Or by using prace_service script:
**Access from public Internet:**
-|Login address|Port|Node role|
-|---|---|---|
-|gridftp.anselm.it4i.cz|2812|Front end /control server|
-|login1.anselm.it4i.cz|2813|Backend / data mover server|
-|login2.anselm.it4i.cz|2813|Backend / data mover server|
-|dm1.anselm.it4i.cz|2813|Backend / data mover server|
+| Login address | Port | Node role |
+| ---------------------- | ---- | --------------------------- |
+| gridftp.anselm.it4i.cz | 2812 | Front end /control server |
+| login1.anselm.it4i.cz | 2813 | Backend / data mover server |
+| login2.anselm.it4i.cz | 2813 | Backend / data mover server |
+| dm1.anselm.it4i.cz | 2813 | Backend / data mover server |
Copy files **to** Anselm by running the following commands on your local machine:
@@ -190,10 +190,10 @@ Or by using prace_service script:
Generally both shared file systems are available through GridFTP:
-|File system mount point|Filesystem|Comment|
-|---|---|---|
-|/home|Lustre|Default HOME directories of users in format /home/prace/login/|
-|/scratch|Lustre|Shared SCRATCH mounted on the whole cluster|
+| File system mount point | Filesystem | Comment |
+| ----------------------- | ---------- | -------------------------------------------------------------- |
+| /home | Lustre | Default HOME directories of users in format /home/prace/login/ |
+| /scratch | Lustre | Shared SCRATCH mounted on the whole cluster |
More information about the shared file systems is available [here](storage/).
@@ -219,11 +219,11 @@ General information about the resource allocation, job queuing and job execution
For PRACE users, the default production run queue is "qprace". PRACE users can also use two other queues "qexp" and "qfree".
-|queue|Active project|Project resources|Nodes|priority|authorization|walltime|
-|---|---|---|---|---|---|---|
-|**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|
+| queue | Active project | Project resources | Nodes | priority | authorization | walltime |
+| ----------------------------- | -------------- | ----------------- | ------------------- | -------- | ------------- | --------- |
+| **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 |
**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.
diff --git a/docs.it4i/anselm-cluster-documentation/remote-visualization.md b/docs.it4i/anselm-cluster-documentation/remote-visualization.md
index af1ef71fb5b044a1c227be8f3f3567491e7ce852..7e2ed7bacd27fef656a19351f77e78802e95c931 100644
--- a/docs.it4i/anselm-cluster-documentation/remote-visualization.md
+++ b/docs.it4i/anselm-cluster-documentation/remote-visualization.md
@@ -8,14 +8,14 @@ The service is based on integration of open source tools VirtualGL and TurboVNC
Currently two compute nodes are dedicated for this service with following configuration for each node:
-|[**Visualization node configuration**](compute-nodes/)||
-|---|---|
-|CPU|2 x Intel Sandy Bridge E5-2670, 2.6 GHz|
-|Processor cores|16 (2 x 8 cores)|
-|RAM|64 GB, min. 4 GB per core|
-|GPU|NVIDIA Quadro 4000, 2 GB RAM|
-|Local disk drive|yes - 500 GB|
-|Compute network|InfiniBand QDR|
+| [**Visualization node configuration**](compute-nodes/) | |
+| ------------------------------------------------------ | --------------------------------------- |
+| CPU | 2 x Intel Sandy Bridge E5-2670, 2.6 GHz |
+| Processor cores | 16 (2 x 8 cores) |
+| RAM | 64 GB, min. 4 GB per core |
+| GPU | NVIDIA Quadro 4000, 2 GB RAM |
+| Local disk drive | yes - 500 GB |
+| Compute network | InfiniBand QDR |
## Schematic overview
@@ -41,7 +41,7 @@ Please [follow the documentation](shell-and-data-access/).
To have the OpenGL acceleration, **24 bit color depth must be used**. Otherwise only the geometry (desktop size) definition is needed.
-*At first VNC server run you need to define a password.*
+_At first VNC server run you need to define a password._
This example defines desktop with dimensions 1200x700 pixels and 24 bit color depth.
@@ -97,7 +97,7 @@ $ ssh login2.anselm.it4i.cz -L 5901:localhost:5901
```
x-window-system/
-*If you use Windows and Putty, please refer to port forwarding setup in the documentation:*
+_If you use Windows and Putty, please refer to port forwarding setup in the documentation:_
[x-window-and-vnc#section-12](../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/)
#### 7. If you don't have Turbo VNC installed on your workstation
@@ -112,15 +112,15 @@ Mind that you should connect through the SSH tunneled port. In this example it i
$ vncviewer localhost:5901
```
-*If you use Windows version of TurboVNC Viewer, just run the Viewer and use address **localhost:5901**.*
+_If you use Windows version of TurboVNC Viewer, just run the Viewer and use address **localhost:5901**._
#### 9. Proceed to the chapter "Access the visualization node"
-*Now you should have working TurboVNC session connected to your workstation.*
+_Now you should have working TurboVNC session connected to your workstation._
#### 10. After you end your visualization session
-*Don't forget to correctly shutdown your own VNC server on the login node!*
+_Don't forget to correctly shutdown your own VNC server on the login node!_
```bash
$ vncserver -kill :1
@@ -131,17 +131,17 @@ $ vncserver -kill :1
**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 |
- | --- | --- | --- | --- | --- | --- | --- | --- |
- |**qviz** Visualization queue |yes |none required |2 |4 |150 |no |1 hour / 8 hours |
+| queue | active project | project resources | nodes | min ncpus | priority | authorization | walltime |
+| ---------------------------- | -------------- | ----------------- | ----- | --------- | -------- | ------------- | ---------------- |
+| **qviz** Visualization queue | yes | none required | 2 | 4 | 150 | no | 1 hour / 8 hours |
-Currently when accessing the node, each user gets 4 cores of a CPU allocated, thus approximately 16 GB of RAM and 1/4 of the GPU capacity. *If more GPU power or RAM is required, it is recommended to allocate one whole node per user, so that all 16 cores, whole RAM and whole GPU is exclusive. This is currently also the maximum allowed allocation per one user. One hour of work is allocated by default, the user may ask for 2 hours maximum.*
+Currently when accessing the node, each user gets 4 cores of a CPU allocated, thus approximately 16 GB of RAM and 1/4 of the GPU capacity. _If more GPU power or RAM is required, it is recommended to allocate one whole node per user, so that all 16 cores, whole RAM and whole GPU is exclusive. This is currently also the maximum allowed allocation per one user. One hour of work is allocated by default, the user may ask for 2 hours maximum._
To access the visualization node, follow these steps:
#### 1. In your VNC session, open a terminal and allocate a node using PBSPro qsub command
-*This step is necessary to allow you to proceed with next steps.*
+_This step is necessary to allow you to proceed with next steps._
```bash
$ qsub -I -q qviz -A PROJECT_ID
@@ -153,7 +153,7 @@ In this example the default values for CPU cores and usage time are used.
$ qsub -I -q qviz -A PROJECT_ID -l select=1:ncpus=16 -l walltime=02:00:00
```
-*Substitute **PROJECT_ID** with the assigned project identification string.*
+_Substitute **PROJECT_ID** with the assigned project identification string._
In this example a whole node for 2 hours is requested.
diff --git a/docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution.md b/docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution.md
index 4d4d9f50da7853e981136cec182a274bdcae6f9e..7eecefdca112cf3c111a18847b381de96c61027b 100644
--- a/docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution.md
+++ b/docs.it4i/anselm-cluster-documentation/resource-allocation-and-job-execution.md
@@ -1,25 +1,24 @@
-Resource Allocation and Job Execution
-=====================================
+# Resource Allocation and Job Execution
To run a [job](../introduction/), [computational resources](../introduction/) for this particular job must be allocated. This is done via the PBS Pro job workload manager software, which efficiently distributes workloads across the supercomputer. Extensive information about PBS Pro can be found in the [official documentation here](../pbspro-documentation/pbspro/), especially in the PBS Pro User's Guide.
-Resources Allocation Policy
----------------------------
+## 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](job-priority/) at Anselm ensures that individual users may consume approximately equal amount of resources per week. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following queues are available to Anselm users:
-- **qexp**, the Express queue
-- **qprod**, the Production queue
-- **qlong**, the Long queue, regula
-- **qnvidia**, **qmic**, **qfat**, the Dedicated queues
-- **qfree**, the Free resource utilization queue
+- **qexp**, the Express queue
+- **qprod**, the Production queue
+- **qlong**, the Long queue, regula
+- **qnvidia**, **qmic**, **qfat**, the Dedicated queues
+- **qfree**, the Free resource utilization queue
!!! Note "Note"
Check the queue status at <https://extranet.it4i.cz/anselm/>
Read more on the [Resource AllocationPolicy](resources-allocation-policy/) page.
-Job submission and execution
-----------------------------
+## Job submission and execution
+
!!! Note "Note"
Use the **qsub** command to submit your jobs.
@@ -27,8 +26,8 @@ The qsub submits the job into the queue. The qsub command creates a request to t
Read more on the [Job submission and execution](job-submission-and-execution/) page.
-Capacity computing
-------------------
+## Capacity computing
+
!!! Note "Note"
Use Job arrays when running huge number of jobs.
diff --git a/docs.it4i/anselm-cluster-documentation/resources-allocation-policy.md b/docs.it4i/anselm-cluster-documentation/resources-allocation-policy.md
index 92d338d84563e33b39153afcf687f5e76fe9ba6d..16a090cd40ba27f92d1ac2b54994be3d170b82ab 100644
--- a/docs.it4i/anselm-cluster-documentation/resources-allocation-policy.md
+++ b/docs.it4i/anselm-cluster-documentation/resources-allocation-policy.md
@@ -5,26 +5,26 @@
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/](https://extranet.it4i.cz/anselm/)
+ Check the queue status at <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 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
diff --git a/docs.it4i/anselm-cluster-documentation/shell-and-data-access.md b/docs.it4i/anselm-cluster-documentation/shell-and-data-access.md
index 1b318ba453cc225458d8f52150ff04b7697cd2cf..08978df2cbfe81e7a4d6d9f3a1ebd4313654e065 100644
--- a/docs.it4i/anselm-cluster-documentation/shell-and-data-access.md
+++ b/docs.it4i/anselm-cluster-documentation/shell-and-data-access.md
@@ -4,11 +4,11 @@
The Anselm cluster is accessed by SSH protocol via login nodes login1 and login2 at address anselm.it4i.cz. The login nodes may be addressed specifically, by prepending the login node name to the address.
-|Login address|Port|Protocol|Login node|
-|---|---|---|---|
-|anselm.it4i.cz|22|ssh|round-robin DNS record for login1 and login2|
-|login1.anselm.it4i.cz|22|ssh|login1|
-|login2.anselm.it4i.cz|22|ssh|login2|
+| Login address | Port | Protocol | Login node |
+| --------------------- | ---- | -------- | -------------------------------------------- |
+| anselm.it4i.cz | 22 | ssh | round-robin DNS record for login1 and login2 |
+| login1.anselm.it4i.cz | 22 | ssh | login1 |
+| login2.anselm.it4i.cz | 22 | ssh | login2 |
The authentication is by the [private key](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/)
@@ -60,12 +60,12 @@ Example to the cluster login:
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|
-|---|---|---|
-|anselm.it4i.cz|22|scp, sftp|
-|login1.anselm.it4i.cz|22|scp, sftp|
-|login2.anselm.it4i.cz|22|scp, sftp|
-|dm1.anselm.it4i.cz|22|scp, sftp|
+| Address | Port | Protocol |
+| --------------------- | ---- | --------- |
+| anselm.it4i.cz | 22 | scp, sftp |
+| login1.anselm.it4i.cz | 22 | scp, sftp |
+| login2.anselm.it4i.cz | 22 | scp, sftp |
+| dm1.anselm.it4i.cz | 22 | scp, sftp |
The authentication is by the [private key](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/)
@@ -119,12 +119,12 @@ More information about the shared file systems is available [here](storage/).
Outgoing connections, from Anselm Cluster login nodes to the outside world, are restricted to following ports:
-|Port|Protocol|
-|---|---|
-|22|ssh|
-|80|http|
-|443|https|
-|9418|git|
+| Port | Protocol |
+| ---- | -------- |
+| 22 | ssh |
+| 80 | http |
+| 443 | https |
+| 9418 | git |
!!! Note "Note"
Please use **ssh port forwarding** and proxy servers to connect from Anselm to all other remote ports.
@@ -148,7 +148,7 @@ local $ ssh -R 6000:remote.host.com:1234 anselm.it4i.cz
In this example, we establish port forwarding between port 6000 on Anselm and port 1234 on the remote.host.com. By accessing localhost:6000 on Anselm, an application will see response of remote.host.com:1234. The traffic will run via users local workstation.
-Port forwarding may be done **using PuTTY** as well. On the PuTTY Configuration screen, load your Anselm configuration first. Then go to Connection->SSH->Tunnels to set up the port forwarding. Click Remote radio button. Insert 6000 to Source port textbox. Insert remote.host.com:1234. Click Add button, then Open.
+Port forwarding may be done **using PuTTY** as well. On the PuTTY Configuration screen, load your Anselm configuration first. Then go to Connection->SSH->Tunnels to set up the port forwarding. Click Remote radio button. Insert 6000 to Source port textbox. Insert remote.host.com:1234. Click Add button, then Open.
Port forwarding may be established directly to the remote host. However, this requires that user has ssh access to remote.host.com
@@ -198,9 +198,9 @@ Now, configure the applications proxy settings to **localhost:6000**. Use port f
## 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
-* 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/).
diff --git a/docs.it4i/anselm-cluster-documentation/software/ansys/ansys-cfx.md b/docs.it4i/anselm-cluster-documentation/software/ansys/ansys-cfx.md
index 03edb80891c5f9c1fe08a5888eb93b96fa5b1a68..34069a554e8108df81a8af468f360d42f7b1c6a5 100644
--- a/docs.it4i/anselm-cluster-documentation/software/ansys/ansys-cfx.md
+++ b/docs.it4i/anselm-cluster-documentation/software/ansys/ansys-cfx.md
@@ -1,5 +1,4 @@
-ANSYS CFX
-=========
+# ANSYS CFX
[ANSYS CFX](http://www.ansys.com/products/fluids/ansys-cfx) software is a high-performance, general purpose fluid dynamics program that has been applied to solve wide-ranging fluid flow problems for over 20 years. At the heart of ANSYS CFX is its advanced solver technology, the key to achieving reliable and accurate solutions quickly and robustly. The modern, highly parallelized solver is the foundation for an abundant choice of physical models to capture virtually any type of phenomena related to fluid flow. The solver and its many physical models are wrapped in a modern, intuitive, and flexible GUI and user environment, with extensive capabilities for customization and automation using session files, scripting and a powerful expression language.
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 04dd0b56251aef1f17bbb52b94d0730111fe42de..8e6d19481644c2c46c633bda8bfac20d5c5acb28 100644
--- a/docs.it4i/anselm-cluster-documentation/software/ansys/ansys-fluent.md
+++ b/docs.it4i/anselm-cluster-documentation/software/ansys/ansys-fluent.md
@@ -1,11 +1,12 @@
-ANSYS Fluent
-============
+# ANSYS Fluent
[ANSYS Fluent](http://www.ansys.com/products/fluids/ansys-fluent)
software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants. Special models that give the software the ability to model in-cylinder combustion, aeroacoustics, turbomachinery, and multiphase systems have served to broaden its reach.
-1. Common way to run Fluent over PBS file
------------------------------------------
+1. Common way to run Fluent over PBS file
+
+* * *
+
To run ANSYS Fluent in batch mode you can utilize/modify the default fluent.pbs script and execute it via the qsub command.
```bash
@@ -57,17 +58,20 @@ Journal file with definition of the input geometry and boundary conditions and d
The appropriate dimension of the problem has to be set by parameter (2d/3d).
-2. Fast way to run Fluent from command line
---------------------------------------------------------
+2. Fast way to run Fluent from command line
+
+* * *
```bash
fluent solver_version [FLUENT_options] -i journal_file -pbs
```
-This syntax will start the ANSYS FLUENT job under PBS Professional using the qsub command in a batch manner. When resources are available, PBS Professional will start the job and return a job ID, usually in the form of *job_ID.hostname*. This job ID can then be used to query, control, or stop the job using standard PBS Professional commands, such as qstat or qdel. The job will be run out of the current working directory, and all output will be written to the file fluent.o *job_ID*.
+This syntax will start the ANSYS FLUENT job under PBS Professional using the qsub command in a batch manner. When resources are available, PBS Professional will start the job and return a job ID, usually in the form of _job_ID.hostname_. This job ID can then be used to query, control, or stop the job using standard PBS Professional commands, such as qstat or qdel. The job will be run out of the current working directory, and all output will be written to the file fluent.o _job_ID_.
+
+3. Running Fluent via user's config file
+
+* * *
-3. Running Fluent via user's config file
-----------------------------------------
The sample script uses a configuration file called pbs_fluent.conf if no command line arguments are present. This configuration file should be present in the directory from which the jobs are submitted (which is also the directory in which the jobs are executed). The following is an example of what the content of pbs_fluent.conf can be:
```bash
@@ -143,8 +147,10 @@ To run ANSYS Fluent in batch mode with user's config file you can utilize/modify
It runs the jobs out of the directory from which they are submitted (PBS_O_WORKDIR).
-4. Running Fluent in parralel
------------------------------
+4. Running Fluent in parralel
+
+* * *
+
Fluent could be run in parallel only under Academic Research license. To do so this ANSYS Academic Research license must be placed before ANSYS CFD license in user preferences. To make this change anslic_admin utility should be run
```bash
diff --git a/docs.it4i/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md b/docs.it4i/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
index 269e44a7cb7b55b2181f6e752ccb6cc56c94c575..e033709fd65858003bbfcb8bd931b74e455ee499 100644
--- a/docs.it4i/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
+++ b/docs.it4i/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
@@ -1,5 +1,4 @@
-ANSYS LS-DYNA
-=============
+# ANSYS LS-DYNA
**[ANSYSLS-DYNA](http://www.ansys.com/products/structures/ansys-ls-dyna)** software provides convenient and easy-to-use access to the technology-rich, time-tested explicit solver without the need to contend with the complex input requirements of this sophisticated program. Introduced in 1996, ANSYS LS-DYNA capabilities have helped customers in numerous industries to resolve highly intricate design issues. ANSYS Mechanical users have been able take advantage of complex explicit solutions for a long time utilizing the traditional ANSYS Parametric Design Language (APDL) environment. These explicit capabilities are available to ANSYS Workbench users as well. The Workbench platform is a powerful, comprehensive, easy-to-use environment for engineering simulation. CAD import from all sources, geometry cleanup, automatic meshing, solution, parametric optimization, result visualization and comprehensive report generation are all available within a single fully interactive modern graphical user environment.
diff --git a/docs.it4i/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md b/docs.it4i/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
index 1168d089cfbecfaf9187324ffbf144f097ae9266..d99fe416ada838585b509d0de20998286fa2bb32 100644
--- a/docs.it4i/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
+++ b/docs.it4i/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
@@ -1,5 +1,4 @@
-ANSYS MAPDL
-===========
+# ANSYS MAPDL
**[ANSYS Multiphysics](http://www.ansys.com/products/multiphysics)**
software offers a comprehensive product solution for both multiphysics and single-physics analysis. The product includes structural, thermal, fluid and both high- and low-frequency electromagnetic analysis. The product also contains solutions for both direct and sequentially coupled physics problems including direct coupled-field elements and the ANSYS multi-field solver.
diff --git a/docs.it4i/anselm-cluster-documentation/software/ansys/ansys.md b/docs.it4i/anselm-cluster-documentation/software/ansys/ansys.md
index 8d0a501e6f6ccc91ad6e32cbb1e69b19416540c1..1ab4477c2f3c477695b072bfec6340c371d37f12 100644
--- a/docs.it4i/anselm-cluster-documentation/software/ansys/ansys.md
+++ b/docs.it4i/anselm-cluster-documentation/software/ansys/ansys.md
@@ -1,9 +1,8 @@
-Overview of ANSYS Products
-==========================
+# Overview of ANSYS Products
**[SVS FEM](http://www.svsfem.cz/)** as **[ANSYS Channel partner](http://www.ansys.com/)** for Czech Republic provided all ANSYS licenses for ANSELM cluster and supports of all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent, Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging to problem of ANSYS functionality contact please [hotline@svsfem.cz](mailto:hotline@svsfem.cz?subject=Ostrava%20-%20ANSELM)
-Anselm provides commercial as well as academic variants. Academic variants are distinguished by "**Academic...**" word in the name of license or by two letter preposition "**aa_**" in the license feature name. Change of license is realized on command line respectively directly in user's PBS file (see individual products). [ More about licensing here](ansys/licensing/)
+Anselm provides commercial as well as academic variants. Academic variants are distinguished by "**Academic...**" word in the name of license or by two letter preposition "**aa\_**" in the license feature name. Change of license is realized on command line respectively directly in user's PBS file (see individual products). [ More about licensing here](ansys/licensing/)
To load the latest version of any ANSYS product (Mechanical, Fluent, CFX, MAPDL,...) load the module:
@@ -14,4 +13,3 @@ To load the latest version of any ANSYS product (Mechanical, Fluent, CFX, MAPDL,
ANSYS supports interactive regime, but due to assumed solution of extremely difficult tasks it is not recommended.
If user needs to work in interactive regime we recommend to configure the RSM service on the client machine which allows to forward the solution to the Anselm directly from the client's Workbench project (see ANSYS RSM service).
-
diff --git a/docs.it4i/anselm-cluster-documentation/software/ansys/ls-dyna.md b/docs.it4i/anselm-cluster-documentation/software/ansys/ls-dyna.md
index dc9ca58c1dd83e44411ec3af34d63dc5cfb06636..dd5682a25ba7846e49f179f3bf72666316f97aaf 100644
--- a/docs.it4i/anselm-cluster-documentation/software/ansys/ls-dyna.md
+++ b/docs.it4i/anselm-cluster-documentation/software/ansys/ls-dyna.md
@@ -1,5 +1,4 @@
-LS-DYNA
-=======
+# LS-DYNA
[LS-DYNA](http://www.lstc.com/) is a multi-purpose, explicit and implicit finite element program used to analyze the nonlinear dynamic response of structures. Its fully automated contact analysis capability, a wide range of constitutive models to simulate a whole range of engineering materials (steels, composites, foams, concrete, etc.), error-checking features and the high scalability have enabled users worldwide to solve successfully many complex problems. Additionally LS-DYNA is extensively used to simulate impacts on structures from drop tests, underwater shock, explosions or high-velocity impacts. Explosive forming, process engineering, accident reconstruction, vehicle dynamics, thermal brake disc analysis or nuclear safety are further areas in the broad range of possible applications. In leading-edge research LS-DYNA is used to investigate the behavior of materials like composites, ceramics, concrete, or wood. Moreover, it is used in biomechanics, human modeling, molecular structures, casting, forging, or virtual testing.
diff --git a/docs.it4i/anselm-cluster-documentation/software/chemistry/molpro.md b/docs.it4i/anselm-cluster-documentation/software/chemistry/molpro.md
index f345e50536c19178295df237e80f0b035a09a524..af3115a8a03fb7434b1bba2b198c1133c88fe500 100644
--- a/docs.it4i/anselm-cluster-documentation/software/chemistry/molpro.md
+++ b/docs.it4i/anselm-cluster-documentation/software/chemistry/molpro.md
@@ -1,36 +1,35 @@
-Molpro
-======
+# Molpro
Molpro is a complete system of ab initio programs for molecular electronic structure calculations.
-About Molpro
-------------
+## About Molpro
+
Molpro is a software package used for accurate ab-initio quantum chemistry calculations. More information can be found at the [official webpage](http://www.molpro.net/).
-License
--------
+## License
+
Molpro software package is available only to users that have a valid license. Please contact support to enable access to Molpro if you have a valid license appropriate for running on our cluster (eg. academic research group licence, parallel execution).
To run Molpro, you need to have a valid license token present in " $HOME/.molpro/token". You can download the token from [Molpro website](https://www.molpro.net/licensee/?portal=licensee).
-Installed version
------------------
+## Installed version
+
Currently on Anselm is installed version 2010.1, patch level 45, parallel version compiled with Intel compilers and Intel MPI.
Compilation parameters are default:
-|Parameter|Value|
-|---|---|
-|max number of atoms|200|
-|max number of valence orbitals|300|
-|max number of basis functions|4095|
-|max number of states per symmmetry|20|
-|max number of state symmetries|16|
-|max number of records|200|
-|max number of primitives|maxbfn x [2]|
-
-Running
-------
+| Parameter | Value |
+| ---------------------------------- | ------------ |
+| max number of atoms | 200 |
+| max number of valence orbitals | 300 |
+| max number of basis functions | 4095 |
+| max number of states per symmmetry | 20 |
+| max number of state symmetries | 16 |
+| max number of records | 200 |
+| max number of primitives | maxbfn x [2] |
+
+## Running
+
Molpro is compiled for parallel execution using MPI and OpenMP. By default, Molpro reads the number of allocated nodes from PBS and launches a data server on one node. On the remaining allocated nodes, compute processes are launched, one process per node, each with 16 threads. You can modify this behavior by using -n, -t and helper-server options. Please refer to the [Molpro documentation](http://www.molpro.net/info/2010.1/doc/manual/node9.html) for more details.
!!! Note "Note"
diff --git a/docs.it4i/anselm-cluster-documentation/software/chemistry/nwchem.md b/docs.it4i/anselm-cluster-documentation/software/chemistry/nwchem.md
index 0318c4a119730a4cabb6163287bb3dc5d2ef236d..a578fb9d8e0c7ec115bbbeab83ed7d9845b9b2ab 100644
--- a/docs.it4i/anselm-cluster-documentation/software/chemistry/nwchem.md
+++ b/docs.it4i/anselm-cluster-documentation/software/chemistry/nwchem.md
@@ -1,16 +1,15 @@
-NWChem
-======
+# NWChem
**High-Performance Computational Chemistry**
-Introduction
--------------------------
+## Introduction
+
NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.
[Homepage](http://www.nwchem-sw.org/index.php/Main_Page)
-Installed versions
-------------------
+## Installed versions
+
The following versions are currently installed:
- 6.1.1, not recommended, problems have been observed with this version
@@ -24,8 +23,8 @@ For a current list of installed versions, execute:
module avail nwchem
```
-Running
--------
+## Running
+
NWChem is compiled for parallel MPI execution. Normal procedure for MPI jobs applies. Sample jobscript:
```bash
@@ -37,8 +36,8 @@ NWChem is compiled for parallel MPI execution. Normal procedure for MPI jobs app
mpirun -np 16 nwchem h2o.nw
```
-Options
---------------------
+## Options
+
Please refer to [the documentation](http://www.nwchem-sw.org/index.php/Release62:Top-level) and in the input file set the following directives :
- MEMORY : controls the amount of memory NWChem will use
diff --git a/docs.it4i/anselm-cluster-documentation/software/compilers.md b/docs.it4i/anselm-cluster-documentation/software/compilers.md
index 8d5cabd42ea244a6ef2eea78251d0d50bb905e64..919c95a107201787b7afe8a13ba4f100a12b1c87 100644
--- a/docs.it4i/anselm-cluster-documentation/software/compilers.md
+++ b/docs.it4i/anselm-cluster-documentation/software/compilers.md
@@ -1,7 +1,6 @@
-Compilers
-=========
+# Compilers
-##Available compilers, including GNU, INTEL and UPC compilers
+\##Available compilers, including GNU, INTEL and UPC compilers
Currently there are several compilers for different programming languages available on the Anselm cluster:
@@ -13,12 +12,12 @@ Currently there are several compilers for different programming languages availa
The C/C++ and Fortran compilers are divided into two main groups GNU and Intel.
-Intel Compilers
----------------
+## Intel Compilers
+
For information about the usage of Intel Compilers and other Intel products, please read the [Intel Parallel studio](intel-suite/) page.
-GNU C/C++ and Fortran Compilers
--------------------------------
+## GNU C/C++ and Fortran Compilers
+
For compatibility reasons there are still available the original (old 4.4.6-4) versions of GNU compilers as part of the OS. These are accessible in the search path by default.
It is strongly recommended to use the up to date version (4.8.1) which comes with the module gcc:
@@ -42,8 +41,8 @@ With the module loaded two environment variables are predefined. One for maximum
For more information about the possibilities of the compilers, please see the man pages.
-Unified Parallel C
-------------------
+## Unified Parallel C
+
UPC is supported by two compiler/runtime implementations:
- GNU - SMP/multi-threading support only
@@ -146,10 +145,10 @@ To run the example on two compute nodes using all 32 cores, with 32 threads, iss
For more information 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 on how to work with NVIDIA CUDA, please read the [NVIDIA CUDA page](nvidia-cuda/).
diff --git a/docs.it4i/anselm-cluster-documentation/software/comsol-multiphysics.md b/docs.it4i/anselm-cluster-documentation/software/comsol-multiphysics.md
index ee61c219bafd9c04cad860204863c68a1cb34c54..d19b6766b865722e2d65bb79dddadc11da84985b 100644
--- a/docs.it4i/anselm-cluster-documentation/software/comsol-multiphysics.md
+++ b/docs.it4i/anselm-cluster-documentation/software/comsol-multiphysics.md
@@ -1,8 +1,7 @@
-COMSOL Multiphysics®
-====================
+# COMSOL Multiphysics®
+
+## Introduction
-Introduction
--------------------------
[COMSOL](http://www.comsol.com) is a powerful environment for modelling and solving various engineering and scientific problems based on partial differential equations. COMSOL is designed to solve coupled or multiphysics phenomena. For many
standard engineering problems COMSOL provides add-on products such as electrical, mechanical, fluid flow, and chemical
applications.
@@ -15,8 +14,8 @@ applications.
COMSOL also allows an interface support for equation-based modelling of partial differential equations.
-Execution
-----------------------
+## Execution
+
On the Anselm cluster COMSOL is available in the latest stable version. There are two variants of the release:
- **Non commercial** or so called **EDU variant**, which can be used for research and educational purposes.
@@ -72,8 +71,8 @@ comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tm
Working directory has to be created before sending the (comsol.pbs) job script into the queue. Input file (name_input_f.mph) has to be in working directory or full path to input file has to be specified. The appropriate path to the temp directory of the job has to be set by command option (-tmpdir).
-LiveLink™* *for MATLAB®^
--------------------------
+## LiveLink™\* \*for MATLAB®^
+
COMSOL is the software package for the numerical solution of the partial differential equations. LiveLink for MATLAB allows connection to the COMSOL**®** API (Application Programming Interface) with the benefits of the programming language and computing environment of the MATLAB.
LiveLink for MATLAB is available in both **EDU** and **COM** **variant** of the COMSOL release. On Anselm 1 commercial (**COM**) license and the 5 educational (**EDU**) licenses of LiveLink for MATLAB (please see the [ISV Licenses](../isv_licenses/)) are available.
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 4daa5a06639b74d38891844805ef87f93fe1aa4c..576d46674ebe89458dbba7c39680ff25477a1be5 100644
--- a/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
+++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
@@ -1,5 +1,4 @@
-Allinea Forge (DDT,MAP)
-=======================
+# Allinea Forge (DDT,MAP)
Allinea Forge consist of two tools - debugger DDT and profiler MAP.
@@ -7,8 +6,8 @@ Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or Op
Allinea MAP is a profiler for C/C++/Fortran HPC codes. It is designed for profiling parallel code, which uses pthreads, OpenMP or MPI.
-License and Limitations for Anselm Users
-----------------------------------------
+## License and Limitations for Anselm Users
+
On Anselm users can debug OpenMP or MPI code that runs up to 64 parallel processes. In case of debugging GPU or Xeon Phi accelerated codes the limit is 8 accelerators. These limitation means that:
- 1 user can debug up 64 processes, or
@@ -19,8 +18,7 @@ In case of debugging on accelerators:
- 1 user can debug on up to 8 accelerators, or
- 8 users can debug on single accelerator.
-Compiling Code to run with DDT
-------------------------------
+## Compiling Code to run with DDT
### Modules
@@ -50,12 +48,12 @@ $ mpif90 -g -O0 -o test_debug test.f
Before debugging, you need to compile your code with theses flags:
!!! Note "Note"
- - **g** : Generates extra debugging information usable by GDB. -g3 includes even more debugging information. This option is available for GNU and INTEL C/C++ and Fortran compilers.
+ \- **g** : Generates extra debugging information usable by GDB. -g3 includes even more debugging information. This option is available for GNU and INTEL C/C++ and Fortran compilers.
+
+ - **O0** : Suppress all optimizations.
- - **O0** : Suppress all optimizations.
+## Starting a Job with DDT
-Starting a Job with DDT
------------------------
Be sure to log in with an X window forwarding enabled. This could mean using the -X in the ssh:
```bash
@@ -86,8 +84,8 @@ To start the debugging directly without the submission window, user can specify
ddt -start -np 4 ./hello_debug_impi
```
-Documentation
--------------
+## Documentation
+
Users can find original User Guide after loading the DDT module:
```bash
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md b/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
index a563ec561798a03620183c58d3b647527a1316ab..6cbed37781d67e3fe6dbd1cdfc2aef91f8fa1af3 100644
--- a/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
+++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
@@ -1,18 +1,17 @@
-Allinea Performance Reports
-===========================
+# Allinea Performance Reports
-##quick application profiling
+\##quick application profiling
+
+## Introduction
-Introduction
-------------
Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs.
The Allinea Performance Reports is most useful in profiling MPI programs.
Our license is limited to 64 MPI processes.
-Modules
--------
+## Modules
+
Allinea Performance Reports version 6.0 is available
```bash
@@ -21,8 +20,8 @@ Allinea Performance Reports version 6.0 is available
The module sets up environment variables, required for using the Allinea Performance Reports. This particular command loads the default module, which is performance reports version 4.2.
-Usage
------
+## Usage
+
!!! Note "Note"
Use the the perf-report wrapper on your (MPI) program.
@@ -32,10 +31,10 @@ Instead of [running your MPI program the usual way](../mpi/), use the the perf r
$ perf-report mpirun ./mympiprog.x
```
-The mpi program will run as usual. The perf-report creates two additional files, in *.txt and *.html format, containing the performance report. Note that [demanding MPI codes should be run within the queue system](../../resource-allocation-and-job-execution/job-submission-and-execution/).
+The mpi program will run as usual. The perf-report creates two additional files, in _.txt and _.html format, containing the performance report. Note that [demanding MPI codes should be run within the queue system](../../resource-allocation-and-job-execution/job-submission-and-execution/).
+
+## Example
-Example
--------
In this example, we will be profiling the mympiprog.x MPI program, using Allinea performance reports. Assume that the code is compiled with Intel compilers and linked against Intel MPI library:
First, we allocate some nodes via the express queue:
@@ -59,4 +58,4 @@ Now lets profile the code:
$ perf-report mpirun ./mympiprog.x
```
-Performance report files [mympiprog_32p*.txt](mympiprog_32p_2014-10-15_16-56.txt) and [mympiprog_32p*.html](mympiprog_32p_2014-10-15_16-56.html) were created. We can see that the code is very efficient on MPI and is CPU bounded.
+Performance report files [mympiprog_32p\*.txt](mympiprog_32p_2014-10-15_16-56.txt) and [mympiprog_32p\*.html](mympiprog_32p_2014-10-15_16-56.html) were created. We can see that the code is very efficient on MPI and is CPU bounded.
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/cube.md b/docs.it4i/anselm-cluster-documentation/software/debuggers/cube.md
index a416deab5cd4873a6e9a19877d6b0545c7ea5dfc..2a11e646f6b76fc5c8365fd6fe8fd30fd05f60c3 100644
--- a/docs.it4i/anselm-cluster-documentation/software/debuggers/cube.md
+++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/cube.md
@@ -1,8 +1,7 @@
-CUBE
-====
+# CUBE
+
+## Introduction
-Introduction
-------------
CUBE is a graphical performance report explorer for displaying data from Score-P and Scalasca (and other compatible tools). The name comes from the fact that it displays performance data in a three-dimensions :
- **performance metric**, where a number of metrics are available, such as communication time or cache misses,
@@ -13,19 +12,19 @@ Each dimension is organized in a tree, for example the time performance metric i
-*Figure 1. Screenshot of CUBE displaying data from Scalasca.*
+_Figure 1. Screenshot of CUBE displaying data from Scalasca._
Each node in the tree is colored by severity (the color scheme is displayed at the bottom of the window, ranging from the least severe blue to the most severe being red). For example in Figure 1, we can see that most of the point-to-point MPI communication happens in routine exch_qbc, colored red.
-Installed versions
-------------------
+## Installed versions
+
Currently, there are two versions of CUBE 4.2.3 available as [modules](../../environment-and-modules/):
-- cube/4.2.3-gcc, compiled with GCC
-- cube/4.2.3-icc, compiled with Intel compiler
+- cube/4.2.3-gcc, compiled with GCC
+- cube/4.2.3-icc, compiled with Intel compiler
+
+## Usage
-Usage
------
CUBE is a graphical application. Refer to Graphical User Interface documentation for a list of methods to launch graphical applications on Anselm.
!!! Note "Note"
@@ -34,5 +33,4 @@ CUBE is a graphical application. Refer to Graphical User Interface documentation
After loading the appropriate module, simply launch cube command, or alternatively you can use scalasca -examine command to launch the GUI. Note that for Scalasca datasets, if you do not analyze the data with scalasca -examine before to opening them with CUBE, not all performance data will be available.
References
-1. <http://www.scalasca.org/software/cube-4.x/download.html>
-
+1\. <http://www.scalasca.org/software/cube-4.x/download.html>
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/debuggers.md b/docs.it4i/anselm-cluster-documentation/software/debuggers/debuggers.md
index b36213ce422ff4e93328be866b62cd86c0ef74bc..11335363e21cc51a9e693ad9e342fec5acac40e4 100644
--- a/docs.it4i/anselm-cluster-documentation/software/debuggers/debuggers.md
+++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/debuggers.md
@@ -1,12 +1,11 @@
-Debuggers and profilers summary
-===============================
+# Debuggers and profilers summary
+
+## Introduction
-Introduction
-------------
We provide state of the art programms and tools to develop, profile and debug HPC codes at IT4Innovations. On these pages, we provide an overview of the profiling and debugging tools available on Anslem at IT4I.
-Intel debugger
---------------
+## Intel debugger
+
The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use X display for running the GUI.
```bash
@@ -16,8 +15,8 @@ The intel debugger version 13.0 is available, via module intel. The debugger wor
Read more at the [Intel Debugger](intel-suite/intel-debugger/) page.
-Allinea Forge (DDT/MAP)
------------------------
+## Allinea Forge (DDT/MAP)
+
Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel Xeon Phi accelerators. DDT provides all the standard debugging features (stack trace, breakpoints, watches, view variables, threads etc.) for every thread running as part of your program, or for every process even if these processes are distributed across a cluster using an MPI implementation.
```bash
@@ -27,8 +26,8 @@ Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or Op
Read more at the [Allinea DDT](debuggers/allinea-ddt/) page.
-Allinea Performance Reports
----------------------------
+## Allinea Performance Reports
+
Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs. Our license is limited to 64 MPI processes.
```bash
@@ -38,8 +37,8 @@ Allinea Performance Reports characterize the performance of HPC application runs
Read more at the [Allinea Performance Reports](debuggers/allinea-performance-reports/) page.
-RougeWave Totalview
--------------------
+## RougeWave Totalview
+
TotalView is a source- and machine-level debugger for multi-process, multi-threaded programs. Its wide range of tools provides ways to analyze, organize, and test programs, making it easy to isolate and identify problems in individual threads and processes in programs of great complexity.
```bash
@@ -49,8 +48,8 @@ TotalView is a source- and machine-level debugger for multi-process, multi-threa
Read more at the [Totalview](debuggers/total-view/) page.
-Vampir trace analyzer
----------------------
+## Vampir trace analyzer
+
Vampir is a GUI trace analyzer for traces in OTF format.
```bash
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 5ff0b98220f8253d40e360c981943793f9d742e7..be48242e4d3aa5a8dc0300f11c3d62c57277b3c4 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
@@ -1,20 +1,19 @@
-Intel Performance Counter Monitor
-=================================
+# Intel Performance Counter Monitor
+
+## Introduction
-Introduction
-------------
Intel PCM (Performance Counter Monitor) is a tool to monitor performance hardware counters on Intel>® processors, similar to [PAPI](papi/). The difference between PCM and PAPI is that PCM supports only Intel hardware, but PCM can monitor also uncore metrics, like memory controllers and >QuickPath Interconnect links.
-Installed version
-------------------------------
+## Installed version
+
Currently installed version 2.6. To load the [module](../../environment-and-modules/), issue:
```bash
$ module load intelpcm
```
-Command line tools
-------------------
+## Command line tools
+
PCM provides a set of tools to monitor system/or application.
### pcm-memory
@@ -66,15 +65,15 @@ NUMA monitoring utility does not work on Anselm.
### pcm-pcie
-Can be used to monitor PCI Express bandwith. Usage: pcm-pcie.x <delay>
+Can be used to monitor PCI Express bandwith. Usage: pcm-pcie.x <delay>
### pcm-power
-Displays energy usage and thermal headroom for CPU and DRAM sockets. Usage: pcm-power.x <delay> | <external program>
+Displays energy usage and thermal headroom for CPU and DRAM sockets. Usage: pcm-power.x <delay> \| <external program>
### pcm
-This command provides an overview of performance counters and memory usage. Usage: pcm.x <delay> | <external program>
+This command provides an overview of performance counters and memory usage. Usage: pcm.x <delay> \| <external program>
Sample output :
@@ -189,8 +188,8 @@ Sample output :
Can be used as a sensor for ksysguard GUI, which is currently not installed on Anselm.
-API
----
+## API
+
In a similar fashion to PAPI, PCM provides a C++ API to access the performance counter from within your application. Refer to the [Doxygen documentation](http://intel-pcm-api-documentation.github.io/classPCM.html) for details of the API.
!!! Note "Note"
@@ -275,8 +274,8 @@ Sample output:
Bytes read:12513408
```
-References
-----------
+## References
+
1. <https://software.intel.com/en-us/articles/intel-performance-counter-monitor-a-better-way-to-measure-cpu-utilization>
2. <https://software.intel.com/sites/default/files/m/3/2/2/xeon-e5-2600-uncore-guide.pdf> Intel® Xeon® Processor E5-2600 Product Family Uncore Performance Monitoring Guide.
3. <http://intel-pcm-api-documentation.github.io/classPCM.html> API Documentation
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 fac34c5e8fa3b822b27ac40f5a70a15b839198e0..278c69ba3f1cb550815195d98b527974fa02247a 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
@@ -1,9 +1,8 @@
-Intel VTune Amplifier
-=====================
+# Intel VTune Amplifier
-Introduction
-------------
-Intel*® *VTune™ Amplifier, part of Intel Parallel studio, is a GUI profiling tool designed for Intel processors. It offers a graphical performance analysis of single core and multithreaded applications. A highlight of the features:
+## Introduction
+
+Intel_® _VTune™ Amplifier, part of Intel Parallel studio, is a GUI profiling tool designed for Intel processors. It offers a graphical performance analysis of single core and multithreaded applications. A highlight of the features:
- Hotspot analysis
- Locks and waits analysis
@@ -13,8 +12,8 @@ Intel*® *VTune™ Amplifier, part of Intel Parallel studio, is a GUI profiling
-Usage
------
+## Usage
+
To launch the GUI, first load the module:
```bash
@@ -30,13 +29,13 @@ and launch the GUI :
!!! Note "Note"
To profile an application with VTune Amplifier, special kernel modules need to be loaded. The modules are not loaded on Anselm login nodes, thus direct profiling on login nodes is not possible. Use VTune on compute nodes and refer to the documentation on using GUI applications.
-The GUI will open in new window. Click on "*New Project...*" to create a new project. After clicking *OK*, a new window with project properties will appear. At "*Application:*", select the bath to your binary you want to profile (the binary should be compiled with -g flag). Some additional options such as command line arguments can be selected. At "*Managed code profiling mode:*" select "*Native*" (unless you want to profile managed mode .NET/Mono applications). After clicking *OK*, your project is created.
+The GUI will open in new window. Click on "_New Project..._" to create a new project. After clicking _OK_, a new window with project properties will appear. At "_Application:_", select the bath to your binary you want to profile (the binary should be compiled with -g flag). Some additional options such as command line arguments can be selected. At "_Managed code profiling mode:_" select "_Native_" (unless you want to profile managed mode .NET/Mono applications). After clicking _OK_, your project is created.
+
+To run a new analysis, click "_New analysis..._". You will see a list of possible analysis. Some of them will not be possible on the current CPU (e.g. Intel Atom analysis is not possible on Sandy Bridge CPU), the GUI will show an error box if you select the wrong analysis. For example, select "_Advanced Hotspots_". Clicking on _Start _will start profiling of the application.
-To run a new analysis, click "*New analysis...*". You will see a list of possible analysis. Some of them will not be possible on the current CPU (e.g. Intel Atom analysis is not possible on Sandy Bridge CPU), the GUI will show an error box if you select the wrong analysis. For example, select "*Advanced Hotspots*". Clicking on *Start *will start profiling of the application.
+## Remote Analysis
-Remote Analysis
----------------
-VTune Amplifier also allows a form of remote analysis. In this mode, data for analysis is collected from the command line without GUI, and the results are then loaded to GUI on another machine. This allows profiling without interactive graphical jobs. To perform a remote analysis, launch a GUI somewhere, open the new analysis window and then click the button "*Command line*" in bottom right corner. It will show the command line needed to perform the selected analysis.
+VTune Amplifier also allows a form of remote analysis. In this mode, data for analysis is collected from the command line without GUI, and the results are then loaded to GUI on another machine. This allows profiling without interactive graphical jobs. To perform a remote analysis, launch a GUI somewhere, open the new analysis window and then click the button "_Command line_" in bottom right corner. It will show the command line needed to perform the selected analysis.
The command line will look like this:
@@ -44,10 +43,10 @@ The command line will look like this:
/apps/all/VTune/2016_update1/vtune_amplifier_xe_2016.1.1.434111/bin64/amplxe-cl -collect advanced-hotspots -knob collection-detail=stack-and-callcount -mrte-mode=native -target-duration-type=veryshort -app-working-dir /home/sta545/test -- /home/sta545/test_pgsesv
```
-Copy the line to clipboard and then you can paste it in your jobscript or in command line. After the collection is run, open the GUI once again, click the menu button in the upper right corner, and select "*Open > Result...*". The GUI will load the results from the run.
+Copy the line to clipboard and then you can paste it in your jobscript or in command line. After the collection is run, open the GUI once again, click the menu button in the upper right corner, and select "_Open > Result..._". The GUI will load the results from the run.
+
+## Xeon Phi
-Xeon Phi
---------
!!! Note "Note"
This section is outdated. It will be updated with new information soon.
@@ -69,6 +68,6 @@ You may also use remote analysis to collect data from the MIC and then analyze i
"export LD_LIBRARY_PATH=/apps/intel/composer_xe_2015.2.164/compiler/lib/mic/:/apps/intel/composer_xe_2015.2.164/mkl/lib/mic/; export KMP_AFFINITY=compact; /tmp/app.mic"
```
-References
-----------
+## References
+
1. <https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf> Performance Tuning for Intel® Xeon Phi™ Coprocessors
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/papi.md b/docs.it4i/anselm-cluster-documentation/software/debuggers/papi.md
index 3bc686243940268ae0f58a52ea06ac6904a156f4..f449dcc88209910298a450bfd93fc68ba86f410e 100644
--- a/docs.it4i/anselm-cluster-documentation/software/debuggers/papi.md
+++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/papi.md
@@ -1,16 +1,15 @@
-PAPI
-====
+# PAPI
+
+## Introduction
-Introduction
-------------
Performance Application Programming Interface (PAPI) is a portable interface to access hardware performance counters (such as instruction counts and cache misses) found in most modern architectures. With the new component framework, PAPI is not limited only to CPU counters, but offers also components for CUDA, network, Infiniband etc.
PAPI provides two levels of interface - a simpler, high level interface and more detailed low level interface.
PAPI can be used with parallel as well as serial programs.
-Usage
------
+## Usage
+
To use PAPI, load [module](../../environment-and-modules/) papi:
```bash
@@ -19,8 +18,8 @@ To use PAPI, load [module](../../environment-and-modules/) papi:
This will load the default version. Execute module avail papi for a list of installed versions.
-Utilities
---------
+## Utilities
+
The bin directory of PAPI (which is automatically added to $PATH upon loading the module) contains various utilites.
### papi_avail
@@ -65,16 +64,16 @@ Prints which preset events are available on the current CPU. The third column in
Prints which native events are available on the current CPU.
-### papi_cost
+### papi_cost
Measures the cost (in cycles) of basic PAPI operations.
-###papi_mem_info
+\###papi_mem_info
Prints information about the memory architecture of the current CPU.
-PAPI API
---------
+## PAPI API
+
PAPI provides two kinds of events:
- **Preset events** is a set of predefined common CPU events, standardized across platforms.
@@ -82,10 +81,10 @@ PAPI provides two kinds of events:
To use PAPI in your application, you need to link the appropriate include file.
-- papi.h for C
-- f77papi.h for Fortran 77
-- f90papi.h for Fortran 90
-- fpapi.h for Fortran with preprocessor
+- papi.h for C
+- f77papi.h for Fortran 77
+- f90papi.h for Fortran 90
+- fpapi.h for Fortran with preprocessor
The include path is automatically added by papi module to $INCLUDE.
@@ -105,8 +104,7 @@ PAPI provides the most accurate timers the platform can support. See <http://icl
PAPI can be used to query some system infromation, such as CPU name and MHz. See <http://icl.cs.utk.edu/projects/papi/wiki/PAPIC:System_Information>
-Example
--------
+## Example
The following example prints MFLOPS rate of a naive matrix-matrix multiplication:
@@ -232,8 +230,8 @@ To use PAPI in offload mode, you need to provide both host and MIC versions of P
$ icc matrix-offload.c -o matrix-offload -offload-option,mic,compiler,"-L$PAPI_HOME-mic/lib -lpapi" -lpapi
```
-References
-----------
+## References
+
1. <http://icl.cs.utk.edu/papi/> Main project page
2. <http://icl.cs.utk.edu/projects/papi/wiki/Main_Page> Wiki
3. <http://icl.cs.utk.edu/papi/docs/> API Documentation
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/scalasca.md b/docs.it4i/anselm-cluster-documentation/software/debuggers/scalasca.md
index 76e227f196f4e834457f4becc4648b917e6cf2a8..56032e03a42a50c0c229f2c29d1e5e54ff4e6285 100644
--- a/docs.it4i/anselm-cluster-documentation/software/debuggers/scalasca.md
+++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/scalasca.md
@@ -1,21 +1,20 @@
-Scalasca
-========
+# Scalasca
+
+## Introduction
-Introduction
--------------------------
[Scalasca](http://www.scalasca.org/) is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks – in particular those concerning communication and synchronization – and offers guidance in exploring their causes.
Scalasca supports profiling of MPI, OpenMP and hybrid MPI+OpenMP applications.
-Installed versions
-------------------
+## Installed versions
+
There are currently two versions of Scalasca 2.0 [modules](../../environment-and-modules/) installed on Anselm:
- scalasca2/2.0-gcc-openmpi, for usage with [GNU Compiler](../compilers/) and [OpenMPI](../mpi/Running_OpenMPI/),
- scalasca2/2.0-icc-impi, for usage with [Intel Compiler](../compilers.html) and [Intel MPI](../mpi/running-mpich2/).
-Usage
------
+## Usage
+
Profiling a parallel application with Scalasca consists of three steps:
1. Instrumentation, compiling the application such way, that the profiling data can be generated.
@@ -30,7 +29,7 @@ Instrumentation via " scalasca -instrument" is discouraged. Use [Score-P instrum
After the application is instrumented, runtime measurement can be performed with the " scalasca -analyze" command. The syntax is:
-scalasca -analyze [scalasca options] [launcher] [launcher options] [program] [program options]
+scalasca -analyze [scalasca options][launcher] [launcher options][program] [program options]
An example :
@@ -41,7 +40,7 @@ An example :
Some notable Scalasca options are:
**-t Enable trace data collection. By default, only summary data are collected.**
-**-e <directory> Specify a directory to save the collected data to. By default, Scalasca saves the data to a directory with prefix scorep_, followed by name of the executable and launch configuration.**
+**-e <directory> Specify a directory to save the collected data to. By default, Scalasca saves the data to a directory with prefix scorep\_, followed by name of the executable and launch configuration.**
!!! Note "Note"
Scalasca can generate a huge amount of data, especially if tracing is enabled. Please consider saving the data to a [scratch directory](../../storage/storage/).
@@ -66,6 +65,6 @@ Alternatively you can open CUBE and load the data directly from here. Keep in mi
Refer to [CUBE documentation](cube/) on usage of the GUI viewer.
-References
-----------
+## References
+
1. <http://www.scalasca.org/>
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 c51794fb87d2943cdd7dffb06d23aa154d7c0f6a..fb909a7734b1f972b3d3d405356dcdf49c2fb263 100644
--- a/docs.it4i/anselm-cluster-documentation/software/debuggers/score-p.md
+++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/score-p.md
@@ -1,21 +1,20 @@
-Score-P
-=======
+# Score-P
+
+## Introduction
-Introduction
-------------
The [Score-P measurement infrastructure](http://www.vi-hps.org/projects/score-p/) is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications.
Score-P can be used as an instrumentation tool for [Scalasca](scalasca/).
-Installed versions
-------------------
+## Installed versions
+
There are currently two versions of Score-P version 1.2.6 [modules](../../environment-and-modules/) installed on Anselm :
- scorep/1.2.3-gcc-openmpi, for usage with [GNU Compiler](../compilers/) and [OpenMPI](../mpi/Running_OpenMPI/)
- scorep/1.2.3-icc-impi, for usage with [Intel Compiler](../compilers.html)> and [Intel MPI](../mpi/running-mpich2/)>.
-Instrumentation
----------------
+## Instrumentation
+
There are three ways to instrument your parallel applications in order to enable performance data collection:
1. Automated instrumentation using compiler
@@ -44,7 +43,7 @@ Usually your program is compiled using a Makefile or similar script, so it advis
It is important that scorep is prepended also to the linking command, in order to link with Score-P instrumentation libraries.
-###Manual instrumentation using API calls
+\###Manual instrumentation using API calls
To use this kind of instrumentation, use scorep with switch --user. You will then mark regions to be instrumented by inserting API calls.
@@ -77,7 +76,7 @@ An example in C/C++ :
Please refer to the [documentation for description of the API](https://silc.zih.tu-dresden.de/scorep-current/pdf/scorep.pdf).
-###Manual instrumentation using directives
+\###Manual instrumentation using directives
This method uses POMP2 directives to mark regions to be instrumented. To use this method, use command scorep --pomp.
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 6df6ba9b95bfe15c151de6700b17a7e0e8d5f4c6..b48b9527ee7bc8c608259f85a7df49e40ed005d0 100644
--- a/docs.it4i/anselm-cluster-documentation/software/debuggers/total-view.md
+++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/total-view.md
@@ -1,10 +1,9 @@
-Total View
-==========
+# Total View
-##TotalView is a GUI-based source code multi-process, multi-thread debugger.
+\##TotalView is a GUI-based source code multi-process, multi-thread debugger.
+
+## License and Limitations for Anselm Users
-License and Limitations for Anselm Users
-----------------------------------------
On Anselm users can debug OpenMP or MPI code that runs up to 64 parallel processes. These limitation means that:
```bash
@@ -28,8 +27,8 @@ You can check the status of the licenses here:
CUDA 64 0 64
```
-Compiling Code to run with TotalView
-------------------------------------
+## Compiling Code to run with TotalView
+
### Modules
Load all necessary modules to compile the code. For example:
@@ -61,10 +60,10 @@ Before debugging, you need to compile your code with theses flags:
!!! Note "Note"
**-g** : Generates extra debugging information usable by GDB. **-g3** includes even more debugging information. This option is available for GNU and INTEL C/C++ and Fortran compilers.
- **-O0** : Suppress all optimizations.
+ **-O0** : Suppress all optimizations.
+
+## Starting a Job with TotalView
-Starting a Job with TotalView
------------------------------
Be sure to log in with an X window forwarding enabled. This could mean using the -X in the ssh:
```bash
@@ -115,6 +114,7 @@ To debug a parallel code compiled with **OpenMPI** you need to setup your TotalV
dlappend TV::image_load_callbacks mpi_auto_run_starter
```
+
The source code of this function can be also found in
```bash
@@ -157,6 +157,6 @@ After running previous command you will see the same window as shown in the scre
More information regarding the command line parameters of the TotalView can be found TotalView Reference Guide, Chapter 7: TotalView Command Syntax.
-Documentation
--------------
+## Documentation
+
[1] The [TotalView documentation](http://www.roguewave.com/support/product-documentation/totalview-family.aspx#totalview) web page is a good resource for learning more about some of the advanced TotalView features.
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/valgrind.md b/docs.it4i/anselm-cluster-documentation/software/debuggers/valgrind.md
index 1b0919431ac1fcb01425837d0087374d6ac6685e..dec4485389dd4a2e57bdd4cef466a80600e73f06 100644
--- a/docs.it4i/anselm-cluster-documentation/software/debuggers/valgrind.md
+++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/valgrind.md
@@ -1,10 +1,9 @@
-Valgrind
-========
+# Valgrind
Valgrind is a tool for memory debugging and profiling.
-About Valgrind
---------------
+## About Valgrind
+
Valgrind is an open-source tool, used mainly for debuggig memory-related problems, such as memory leaks, use of uninitalized memory etc. in C/C++ applications. The toolchain was however extended over time with more functionality, such as debugging of threaded applications, cache profiling, not limited only to C/C++.
Valgind is an extremely useful tool for debugging memory errors such as [off-by-one](http://en.wikipedia.org/wiki/Off-by-one_error). Valgrind uses a virtual machine and dynamic recompilation of binary code, because of that, you can expect that programs being debugged by Valgrind run 5-100 times slower.
@@ -18,15 +17,15 @@ The main tools available in Valgrind are :
- **Callgrind**, a callgraph analyzer.
- For a full list and detailed documentation, please refer to the [official Valgrind documentation](http://valgrind.org/docs/).
-Installed versions
-------------------
+## Installed versions
+
There are two versions of Valgrind available on Anselm.
- Version 3.6.0, installed by operating system vendor in /usr/bin/valgrind. This version is available by default, without the need to load any module. This version however does not provide additional MPI support.
- Version 3.9.0 with support for Intel MPI, available in [module](../../environment-and-modules/) valgrind/3.9.0-impi. After loading the module, this version replaces the default valgrind.
-Usage
------
+## Usage
+
Compile the application which you want to debug as usual. It is advisable to add compilation flags -g (to add debugging information to the binary so that you will see original source code lines in the output) and -O0 (to disable compiler optimizations).
For example, lets look at this C code, which has two problems :
@@ -56,7 +55,7 @@ Now, compile it with Intel compiler :
Now, lets run it with Valgrind. The syntax is :
- *valgrind [valgrind options] <your program binary> [your program options]*
+ _valgrind [valgrind options] <your program binary> [your program options]_
If no Valgrind options are specified, Valgrind defaults to running Memcheck tool. Please refer to the Valgrind documentation for a full description of command line options.
@@ -132,8 +131,8 @@ In the output we can see that Valgrind has detected both errors - the off-by-one
Now we can see that the memory leak is due to the malloc() at line 6.
-Usage with MPI
----------------------------
+## Usage with MPI
+
Although Valgrind is not primarily a parallel debugger, it can be used to debug parallel applications as well. When launching your parallel applications, prepend the valgrind command. For example :
```bash
diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/vampir.md b/docs.it4i/anselm-cluster-documentation/software/debuggers/vampir.md
index 129eb41ddbf9443e606f8254bb654846fe570877..15509457b9735703e8ad8d6139c6813cdb03cdd8 100644
--- a/docs.it4i/anselm-cluster-documentation/software/debuggers/vampir.md
+++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/vampir.md
@@ -1,12 +1,11 @@
-hVampir
-======
+# hVampir
Vampir is a commercial trace analysis and visualization 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
-------------------
+## Installed versions
+
Version 8.5.0 is currently installed as module Vampir/8.5.0 :
```bash
@@ -14,10 +13,10 @@ Version 8.5.0 is currently installed as module Vampir/8.5.0 :
$ vampir &
```
-User manual
------------
+## User manual
+
You can find the detailed user manual in PDF format in $EBROOTVAMPIR/doc/vampir-manual.pdf
-References
-----------
+## References
+
[1]. <https://www.vampir.eu>
diff --git a/docs.it4i/anselm-cluster-documentation/software/index.md b/docs.it4i/anselm-cluster-documentation/software/index.md
index 2cbcedb9cf9af259990f7eb19b93a97858793ed4..760656e5b60f6d3036e5b5dfd122f0b39717ba7c 100644
--- a/docs.it4i/anselm-cluster-documentation/software/index.md
+++ b/docs.it4i/anselm-cluster-documentation/software/index.md
@@ -1,86 +1,86 @@
-Anselm Cluster Software
-===
+# Anselm Cluster Software
## [Modules](../../modules-anselm)
-* List of available modules
-## [COMSOL](comsol-multiphysics)
-* A finite element analysis, solver and Simulation software
-## [ParaView](paraview)
-* An open-source, multi-platform data analysis and visualization application
-## [Compilers](compilers)
-* Available compilers, including GNU, INTEL and UPC compilers
-## [NVIDIA CUDA](nvidia-cuda)
-* A guide to NVIDIA CUDA programming and GPU usage
-## [GPI-2](gpi2)
-* A library that implements the GASPI specification
-## [OpenFOAM](openfoam)
-* A free, open source CFD software package
-## [ISV Licenses](isv_licenses)
-* A guide to managing Independent Software Vendor licenses
-## [Intel Xeon Phi](intel-xeon-phi)
-* A guide to Intel Xeon Phi usage
-## [Virtualization](kvirtualization)
-## [Java](java)
-* Java on ANSELM
-## [Operating System](operating-system)
-* The operating system, deployed on ANSELM
-## Intel Suite
-* The Intel Parallel Studio XE
-### [Introduction](intel-suite/introduction)
-### [Intel MKL](intel-suite/intel-mkl)
-### [Intel Compilers](intel-suite/intel-compilers)
-### [Intel IPP](intel-suite/intel-integrated-performance-primitives)
-### [Intel TBB](intel-suite/intel-tbb)
-### [Intel Debugger](intel-suite/intel-debugger)
-## MPI
-* Message Passing Interface libraries
-### [Introduction](mpi/mpi)
-### [MPI4Py (MPI for Python)](mpi/mpi4py-mpi-for-python)
-### [Running OpenMPI](mpi/Running_OpenMPI)
-### [Running MPICH2](mpi/running-mpich2)
-## Numerical Libraries
-* Libraries for numerical computations
-### [Intel numerical libraries](numerical-libraries/intel-numerical-libraries)
-### [PETSc](numerical-libraries/petsc)
-### [Trilinos](numerical-libraries/trilinos)
-### [FFTW](numerical-libraries/fftw)
-### [GSL](numerical-libraries/gsl)
-### [MAGMA for Intel Xeon Phi](numerical-libraries/magma-for-intel-xeon-phi)
-### [HDF5](numerical-libraries/hdf5)
-## Omics Master
-### [Diagnostic component (TEAM)](omics-master/diagnostic-component-team)
-### [Prioritization component (BiERapp)](omics-master/priorization-component-bierapp)
-### [Overview](omics-master/overview)
-## Debuggers
-* A collection of development tools
-### [Valgrind](debuggers/valgrind)
-### [PAPI](debuggers/papi)
-### [Allinea Forge (DDT,MAP)](debuggers/allinea-ddt)
-### [Total View](debuggers/total-view)
-### [CUBE](debuggers/cube)
-### [Intel VTune Amplifier](debuggers/intel-vtune-amplifier)
-### [VNC](debuggers/debuggers)
-### [Scalasca](debuggers/scalasca)
-### [Score-P](debuggers/score-p)
-### [Intel Performance Counter Monitor](debuggers/intel-performance-counter-monitor)
-### [Allinea Performance Reports](debuggers/allinea-performance-reports)
-### [Vampir](debuggers/vampir)
-## Numerical Languages
-* Interpreted languages for numerical computations
-### [Introduction](numerical-languages/introduction)
-### [R](numerical-languages/r)
-### [MATLAB 2013-2014](numerical-languages/matlab_1314)
-### [MATLAB](numerical-languages/matlab)
-### [Octave](numerical-languages/octave)
-## Chemistry
-* Tools for computational chemistry
-### [Molpro](chemistry/molpro)
-### [NWChem](chemistry/nwchem)
-## ANSYS
-* An engineering simulation software
-### [Introduction](ansys/ansys)
-### [ANSYS CFX](ansys/ansys-cfx)
-### [ANSYS LS-DYNA](ansys/ansys-ls-dyna)
-### [ANSYS MAPDL](ansys/ansys-mechanical-apdl)
-### [LS-DYNA](ansys/ls-dyna)
-### [ANSYS Fluent](ansys/ansys-fluent)
+
+- List of available modules
+ ## [COMSOL](comsol-multiphysics)
+- A finite element analysis, solver and Simulation software
+ ## [ParaView](paraview)
+- An open-source, multi-platform data analysis and visualization application
+ ## [Compilers](compilers)
+- Available compilers, including GNU, INTEL and UPC compilers
+ ## [NVIDIA CUDA](nvidia-cuda)
+- A guide to NVIDIA CUDA programming and GPU usage
+ ## [GPI-2](gpi2)
+- A library that implements the GASPI specification
+ ## [OpenFOAM](openfoam)
+- A free, open source CFD software package
+ ## [ISV Licenses](isv_licenses)
+- A guide to managing Independent Software Vendor licenses
+ ## [Intel Xeon Phi](intel-xeon-phi)
+- A guide to Intel Xeon Phi usage
+ ## [Virtualization](kvirtualization)
+ ## [Java](java)
+- Java on ANSELM
+ ## [Operating System](operating-system)
+- The operating system, deployed on ANSELM
+ ## Intel Suite
+- The Intel Parallel Studio XE
+ ### [Introduction](intel-suite/introduction)
+ ### [Intel MKL](intel-suite/intel-mkl)
+ ### [Intel Compilers](intel-suite/intel-compilers)
+ ### [Intel IPP](intel-suite/intel-integrated-performance-primitives)
+ ### [Intel TBB](intel-suite/intel-tbb)
+ ### [Intel Debugger](intel-suite/intel-debugger)
+ ## MPI
+- Message Passing Interface libraries
+ ### [Introduction](mpi/mpi)
+ ### [MPI4Py (MPI for Python)](mpi/mpi4py-mpi-for-python)
+ ### [Running OpenMPI](mpi/Running_OpenMPI)
+ ### [Running MPICH2](mpi/running-mpich2)
+ ## Numerical Libraries
+- Libraries for numerical computations
+ ### [Intel numerical libraries](numerical-libraries/intel-numerical-libraries)
+ ### [PETSc](numerical-libraries/petsc)
+ ### [Trilinos](numerical-libraries/trilinos)
+ ### [FFTW](numerical-libraries/fftw)
+ ### [GSL](numerical-libraries/gsl)
+ ### [MAGMA for Intel Xeon Phi](numerical-libraries/magma-for-intel-xeon-phi)
+ ### [HDF5](numerical-libraries/hdf5)
+ ## Omics Master
+ ### [Diagnostic component (TEAM)](omics-master/diagnostic-component-team)
+ ### [Prioritization component (BiERapp)](omics-master/priorization-component-bierapp)
+ ### [Overview](omics-master/overview)
+ ## Debuggers
+- A collection of development tools
+ ### [Valgrind](debuggers/valgrind)
+ ### [PAPI](debuggers/papi)
+ ### [Allinea Forge (DDT,MAP)](debuggers/allinea-ddt)
+ ### [Total View](debuggers/total-view)
+ ### [CUBE](debuggers/cube)
+ ### [Intel VTune Amplifier](debuggers/intel-vtune-amplifier)
+ ### [VNC](debuggers/debuggers)
+ ### [Scalasca](debuggers/scalasca)
+ ### [Score-P](debuggers/score-p)
+ ### [Intel Performance Counter Monitor](debuggers/intel-performance-counter-monitor)
+ ### [Allinea Performance Reports](debuggers/allinea-performance-reports)
+ ### [Vampir](debuggers/vampir)
+ ## Numerical Languages
+- Interpreted languages for numerical computations
+ ### [Introduction](numerical-languages/introduction)
+ ### [R](numerical-languages/r)
+ ### [MATLAB 2013-2014](numerical-languages/matlab_1314)
+ ### [MATLAB](numerical-languages/matlab)
+ ### [Octave](numerical-languages/octave)
+ ## Chemistry
+- Tools for computational chemistry
+ ### [Molpro](chemistry/molpro)
+ ### [NWChem](chemistry/nwchem)
+ ## ANSYS
+- An engineering simulation software
+ ### [Introduction](ansys/ansys)
+ ### [ANSYS CFX](ansys/ansys-cfx)
+ ### [ANSYS LS-DYNA](ansys/ansys-ls-dyna)
+ ### [ANSYS MAPDL](ansys/ansys-mechanical-apdl)
+ ### [LS-DYNA](ansys/ls-dyna)
+ ### [ANSYS Fluent](ansys/ansys-fluent)
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 75ea441489d47ed7d5ea7f4e575e54ccffeba6c6..e78535a1d4491e8adf0ab1eecd2d8f0ea7a4b775 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
@@ -1,5 +1,4 @@
-Intel Compilers
-===============
+# Intel Compilers
The Intel compilers version 13.1.1 are available, via module intel. The compilers include the icc C and C++ compiler and the ifort fortran 77/90/95 compiler.
@@ -29,8 +28,8 @@ The compiler recognizes the omp, simd, vector and ivdep pragmas for OpenMP paral
Read more at <http://software.intel.com/sites/products/documentation/doclib/stdxe/2013/composerxe/compiler/cpp-lin/index.htm>
-Sandy Bridge/Haswell binary compatibility
------------------------------------------
+## Sandy Bridge/Haswell binary compatibility
+
Anselm nodes are currently equipped with Sandy Bridge CPUs, while Salomon will use Haswell architecture. >The new processors are backward compatible with the Sandy Bridge nodes, so all programs that ran on the Sandy Bridge processors, should also run on the new Haswell nodes. >To get optimal performance out of the Haswell processors a program should make use of the special AVX2 instructions for this processor. One can do this by recompiling codes with the compiler flags >designated to invoke these instructions. For the Intel compiler suite, there are two ways of doing this:
- Using compiler flag (both for Fortran and C): -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.
diff --git a/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-debugger.md b/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-debugger.md
index 92e19f9c03e985fc8660d19a4a5df5a09942f4be..f63f338b9241f5427c32b8b5230083b750feb5cd 100644
--- a/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-debugger.md
+++ b/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-debugger.md
@@ -1,8 +1,7 @@
-Intel Debugger
-==============
+# Intel Debugger
+
+## Debugging serial applications
-Debugging serial applications
------------------------------
The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use X display for running the GUI.
```bash
@@ -33,8 +32,8 @@ Example:
In this example, we allocate 1 full compute node, compile program myprog.c with debugging options -O0 -g and run the idb debugger interactively on the myprog.x executable. The GUI access is via X11 port forwarding provided by the PBS workload manager.
-Debugging parallel applications
--------------------------------
+## Debugging parallel applications
+
Intel debugger is capable of debugging multithreaded and MPI parallel programs as well.
### Small number of MPI ranks
@@ -69,7 +68,6 @@ Run the idb debugger from within the MPI debug option. This will cause the debug
Run the idb debugger in GUI mode. The menu Parallel contains number of tools for debugging multiple threads. One of the most useful tools is the **Serialize Execution** tool, which serializes execution of concurrent threads for easy orientation and identification of concurrency related bugs.
-Further information
--------------------
-Exhaustive manual on idb features and usage is published at [Intel website](http://software.intel.com/sites/products/documentation/doclib/stdxe/2013/composerxe/debugger/user_guide/index.htm)
+## Further information
+Exhaustive manual on idb features and usage is published at [Intel website](http://software.intel.com/sites/products/documentation/doclib/stdxe/2013/composerxe/debugger/user_guide/index.htm)
diff --git a/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md b/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
index 08067b718f70cd6ad18bd7d62ceb3997c5799223..fc9ad019cd10b5c83df92d2abe2b0cecd031d444 100644
--- a/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
+++ b/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
@@ -1,8 +1,7 @@
-Intel IPP
-=========
+# Intel IPP
+
+## Intel Integrated Performance Primitives
-Intel Integrated Performance Primitives
----------------------------------------
Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX vector instructions is available, via module ipp. The IPP is a very rich library of highly optimized algorithmic building blocks for media and data applications. This includes signal, image and frame processing algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax, as well as cryptographic functions, linear algebra functions and many more.
!!! Note "Note"
@@ -14,8 +13,7 @@ Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX vector
The module sets up environment variables, required for linking and running ipp enabled applications.
-IPP example
------------
+## IPP example
```cpp
#include "ipp.h"
@@ -76,8 +74,8 @@ You will need the ipp module loaded to run the ipp enabled executable. This may
$ icc testipp.c -o testipp.x -Wl,-rpath=$LIBRARY_PATH -lippi -lipps -lippcore
```
-Code samples and documentation
-------------------------------
+## Code samples and documentation
+
Intel provides number of [Code Samples for IPP](https://software.intel.com/en-us/articles/code-samples-for-intel-integrated-performance-primitives-library), illustrating use of IPP.
Read full documentation on IPP [on Intel website,](http://software.intel.com/sites/products/search/search.php?q=&x=15&y=6&product=ipp&version=7.1&docos=lin) in particular the [IPP Reference manual.](http://software.intel.com/sites/products/documentation/doclib/ipp_sa/71/ipp_manual/index.htm)
diff --git a/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-mkl.md b/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-mkl.md
index 62bb0fae83c406ddec06615a41e91a071806962d..f06365e8fa6c86614a4da6f3c2e533041caaccac 100644
--- a/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-mkl.md
+++ b/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-mkl.md
@@ -1,17 +1,16 @@
-Intel MKL
-=========
+# Intel MKL
+
+## Intel Math Kernel Library
-Intel Math Kernel Library
--------------------------
Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, extensively threaded and optimized for maximum performance. Intel MKL provides these basic math kernels:
-- BLAS (level 1, 2, and 3) and LAPACK linear algebra routines, offering vector, vector-matrix, and matrix-matrix operations.
-- The PARDISO direct sparse solver, an iterative sparse solver, and supporting sparse BLAS (level 1, 2, and 3) routines for solving sparse systems of equations.
-- ScaLAPACK distributed processing linear algebra routines for Linux* and Windows* operating systems, as well as the Basic Linear Algebra Communications Subprograms (BLACS) and the Parallel Basic Linear Algebra Subprograms (PBLAS).
-- Fast Fourier transform (FFT) functions in one, two, or three dimensions with support for mixed radices (not limited to sizes that are powers of 2), as well as distributed versions of these functions.
-- Vector Math Library (VML) routines for optimized mathematical operations on vectors.
-- Vector Statistical Library (VSL) routines, which offer high-performance vectorized random number generators (RNG) for several probability distributions, convolution and correlation routines, and summary statistics functions.
-- Data Fitting Library, which provides capabilities for spline-based approximation of functions, derivatives and integrals of functions, and search.
+- BLAS (level 1, 2, and 3) and LAPACK linear algebra routines, offering vector, vector-matrix, and matrix-matrix operations.
+- The PARDISO direct sparse solver, an iterative sparse solver, and supporting sparse BLAS (level 1, 2, and 3) routines for solving sparse systems of equations.
+- ScaLAPACK distributed processing linear algebra routines for Linux_ and Windows_ operating systems, as well as the Basic Linear Algebra Communications Subprograms (BLACS) and the Parallel Basic Linear Algebra Subprograms (PBLAS).
+- Fast Fourier transform (FFT) functions in one, two, or three dimensions with support for mixed radices (not limited to sizes that are powers of 2), as well as distributed versions of these functions.
+- Vector Math Library (VML) routines for optimized mathematical operations on vectors.
+- Vector Statistical Library (VSL) routines, which offer high-performance vectorized random number generators (RNG) for several probability distributions, convolution and correlation routines, and summary statistics functions.
+- Data Fitting Library, which provides capabilities for spline-based approximation of functions, derivatives and integrals of functions, and search.
- Extended Eigensolver, a shared memory version of an eigensolver based on the Feast Eigenvalue Solver.
For details see the [Intel MKL Reference Manual](http://software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mklman/index.htm).
@@ -31,10 +30,10 @@ The module sets up environment variables, required for linking and running mkl e
The MKL library provides number of interfaces. The fundamental once are the LP64 and ILP64. The Intel MKL ILP64 libraries use the 64-bit integer type (necessary for indexing large arrays, with more than 231^-1 elements), whereas the LP64 libraries index arrays with the 32-bit integer type.
-|Interface|Integer type|
-|---|---|
-|LP64|32-bit, int, integer(kind=4), MPI_INT|
-|ILP64|64-bit, long int, integer(kind=8), MPI_INT64|
+| Interface | Integer type |
+| --------- | -------------------------------------------- |
+| LP64 | 32-bit, int, integer(kind=4), MPI_INT |
+| ILP64 | 64-bit, long int, integer(kind=8), MPI_INT64 |
### Linking
@@ -60,8 +59,8 @@ For this to work, the application must link the threaded MKL library (default).
The application will run with 16 threads with affinity optimized for fine grain parallelization.
-Examples
-------------
+## Examples
+
Number of examples, demonstrating use of the MKL library and its linking is available on Anselm, in the $MKL_EXAMPLES directory. In the examples below, we demonstrate linking MKL to Intel and GNU compiled program for multi-threaded matrix multiplication.
### Working with examples
@@ -114,10 +113,10 @@ In this example, we compile and link the cblas_dgemm example, using LP64 interf
In this example, we compile, link and run the cblas_dgemm example, using LP64 interface to threaded MKL and gnu OMP threads implementation.
-MKL and MIC accelerators
-------------------------
+## MKL and MIC accelerators
+
The MKL is capable to automatically offload the computations o the MIC accelerator. See section [Intel XeonPhi](../intel-xeon-phi/) for details.
-Further reading
----------------
+## Further reading
+
Read more on [Intel website](http://software.intel.com/en-us/intel-mkl), in particular the [MKL users guide](https://software.intel.com/en-us/intel-mkl/documentation/linux).
diff --git a/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-tbb.md b/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-tbb.md
index ccf79fef061da0c6078779f0d29f417a266216e6..681f16d3c8f4e1be93099848e6bf569090ba8704 100644
--- a/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-tbb.md
+++ b/docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-tbb.md
@@ -1,8 +1,7 @@
-Intel TBB
-=========
+# Intel TBB
+
+## Intel Threading Building Blocks
-Intel Threading Building Blocks
--------------------------------
Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner. The tasks are executed by a runtime scheduler and may
be offloaded to [MIC accelerator](../intel-xeon-phi/).
@@ -17,8 +16,8 @@ The module sets up environment variables, required for linking and running tbb e
!!! Note "Note"
Link the tbb library, using -ltbb
-Examples
---------
+## Examples
+
Number of examples, demonstrating use of TBB and its built-in scheduler is available on Anselm, in the $TBB_EXAMPLES directory.
```bash
@@ -38,7 +37,6 @@ You will need the tbb module loaded to run the tbb enabled executable. This may
$ icc -O2 -o primes.x main.cpp primes.cpp -Wl,-rpath=$LIBRARY_PATH -ltbb
```
-Further reading
----------------
-Read more on Intel website, <http://software.intel.com/sites/products/documentation/doclib/tbb_sa/help/index.htm>
+## Further reading
+Read more on Intel website, <http://software.intel.com/sites/products/documentation/doclib/tbb_sa/help/index.htm>
diff --git a/docs.it4i/anselm-cluster-documentation/software/intel-suite/introduction.md b/docs.it4i/anselm-cluster-documentation/software/intel-suite/introduction.md
index 206c70444ca5dcb00613409a3ef27a17f9730ceb..fda98aa7c9a03a57e483bb446c1fcb42ba8224d3 100644
--- a/docs.it4i/anselm-cluster-documentation/software/intel-suite/introduction.md
+++ b/docs.it4i/anselm-cluster-documentation/software/intel-suite/introduction.md
@@ -1,18 +1,17 @@
-Intel Parallel Studio
-=====================
+# Intel Parallel Studio
The Anselm cluster provides following elements of the Intel Parallel Studio XE
|Intel Parallel Studio XE|
-|-------------------------------------------------|
+\|-------------------------------------------------\|
|Intel Compilers|
|Intel Debugger|
|Intel MKL Library|
|Intel Integrated Performance Primitives Library|
|Intel Threading Building Blocks Library|
-Intel compilers
----------------
+## Intel compilers
+
The Intel compilers version 13.1.3 are available, via module intel. The compilers include the icc C and C++ compiler and the ifort fortran 77/90/95 compiler.
```bash
@@ -23,8 +22,8 @@ The Intel compilers version 13.1.3 are available, via module intel. The compiler
Read more at the [Intel Compilers](intel-compilers/) page.
-Intel debugger
---------------
+## Intel debugger
+
The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use X display for running the GUI.
```bash
@@ -34,8 +33,8 @@ The intel debugger version 13.0 is available, via module intel. The debugger wor
Read more at the [Intel Debugger](intel-debugger/) page.
-Intel Math Kernel Library
--------------------------
+## Intel Math Kernel Library
+
Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, extensively threaded and optimized for maximum performance. Intel MKL unites and provides these basic components: BLAS, LAPACK, ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and many more.
```bash
@@ -44,8 +43,8 @@ Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, e
Read more at the [Intel MKL](intel-mkl/) page.
-Intel Integrated Performance Primitives
----------------------------------------
+## Intel Integrated Performance Primitives
+
Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is available, via module ipp. The IPP is a library of highly optimized algorithmic building blocks for media and data applications. This includes signal, image and frame processing algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many more.
```bash
@@ -54,8 +53,8 @@ Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is avai
Read more at the [Intel IPP](intel-integrated-performance-primitives/) page.
-Intel Threading Building Blocks
--------------------------------
+## Intel Threading Building Blocks
+
Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. It is designed to promote scalable data parallel programming. Additionally, it fully supports nested parallelism, so you can build larger parallel components from smaller parallel components. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner.
```bash
diff --git a/docs.it4i/anselm-cluster-documentation/software/intel-xeon-phi.md b/docs.it4i/anselm-cluster-documentation/software/intel-xeon-phi.md
index 80e76efecfacbe0a7158a13c0ca4658a695053ff..c9f5c39c01dd2fdb91eebcadaf7dc5e357462843 100644
--- a/docs.it4i/anselm-cluster-documentation/software/intel-xeon-phi.md
+++ b/docs.it4i/anselm-cluster-documentation/software/intel-xeon-phi.md
@@ -1,12 +1,11 @@
-Intel Xeon Phi
-==============
+# Intel Xeon Phi
-##A guide to Intel Xeon Phi usage
+\##A guide to Intel Xeon Phi usage
Intel Xeon Phi can be programmed in several modes. The default mode on Anselm is offload mode, but all modes described in this document are supported.
-Intel Utilities for Xeon Phi
-----------------------------
+## Intel Utilities for Xeon Phi
+
To get access to a compute node with Intel Xeon Phi accelerator, use the PBS interactive session
```bash
@@ -89,8 +88,8 @@ The output of the "micinfo" utility executed on one of the Anselm node is as fol
GDDR Voltage : 1501000 uV
```
-Offload Mode
-------------
+## Offload Mode
+
To compile a code for Intel Xeon Phi a MPSS stack has to be installed on the machine where compilation is executed. Currently the MPSS stack is only installed on compute nodes equipped with accelerators.
```bash
@@ -237,10 +236,10 @@ Some interesting compiler flags useful not only for code debugging are:
vec-report[0|1|2] - controls the OpenMP parallelizer diagnostic level
Performance ooptimization
- xhost - FOR HOST ONLY - to generate AVX (Advanced Vector Extensions) instructions.
+ xhost - FOR HOST ONLY - to generate AVX (Advanced Vector Extensions) instructions.
+
+## Automatic Offload using Intel MKL Library
-Automatic Offload using Intel MKL Library
------------------------------------------
Intel MKL includes an Automatic Offload (AO) feature that enables computationally intensive MKL functions called in user code to benefit from attached Intel Xeon Phi coprocessors automatically and transparently.
Behavioral of automatic offload mode is controlled by functions called within the program or by environmental variables. Complete list of controls is listed [ here](http://software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mkl_userguide_lnx/GUID-3DC4FC7D-A1E4-423D-9C0C-06AB265FFA86.htm).
@@ -358,8 +357,8 @@ The output of a code should look similar to following listing, where lines start
Done
```
-Native Mode
------------
+## Native Mode
+
In the native mode a program is executed directly on Intel Xeon Phi without involvement of the host machine. Similarly to offload mode, the code is compiled on the host computer with Intel compilers.
To compile a code user has to be connected to a compute with MIC and load Intel compilers module. To get an interactive session on a compute node with an Intel Xeon Phi and load the module use following commands:
@@ -423,10 +422,9 @@ For your information the list of libraries and their location required for execu
- libiomp5.so
- libimf.so
- - libsvml.so
- - libirng.so
- - libintlc.so.5
-
+ - libsvml.so
+ - libirng.so
+ - libintlc.so.5
Finally, to run the compiled code use:
@@ -434,8 +432,8 @@ Finally, to run the compiled code use:
$ ~/path_to_binary/vect-add-mic
```
-OpenCL
--------------------
+## OpenCL
+
OpenCL (Open Computing Language) is an open standard for general-purpose parallel programming for diverse mix of multi-core CPUs, GPU coprocessors, and other parallel processors. OpenCL provides a flexible execution model and uniform programming environment for software developers to write portable code for systems running on both the CPU and graphics processors or accelerators like the Intel® Xeon Phi.
On Anselm OpenCL is installed only on compute nodes with MIC accelerator, therefore OpenCL code can be compiled only on these nodes.
@@ -543,8 +541,7 @@ To see the performance of Intel Xeon Phi performing the DGEMM run the example as
!!! Note "Note"
Please note: GNU compiler is used to compile the OpenCL codes for Intel MIC. You do not need to load Intel compiler module.
-MPI
------------------
+## MPI
### Environment setup and compilation
@@ -562,15 +559,15 @@ The only supported implementation of MPI standard for Intel Xeon Phi is Intel MP
To compile an MPI code for host use:
-```bash
- $ mpiicc -xhost -o mpi-test mpi-test.c
-```bash
+````bash
+ $ mpiicc -xhost -o mpi-test mpi-test.c
+ ```bash
-To compile the same code for Intel Xeon Phi architecture use:
+ To compile the same code for Intel Xeon Phi architecture use:
-```bash
- $ mpiicc -mmic -o mpi-test-mic mpi-test.c
-```
+ ```bash
+ $ mpiicc -mmic -o mpi-test-mic mpi-test.c
+````
An example of basic MPI version of "hello-world" example in C language, that can be executed on both host and Xeon Phi is (can be directly copy and pasted to a .c file)
@@ -606,11 +603,11 @@ Intel MPI for the Xeon Phi coprocessors offers different MPI programming models:
!!! Note "Note"
**Host-only model** - all MPI ranks reside on the host. The coprocessors can be used by using offload pragmas. (Using MPI calls inside offloaded code is not supported.)
- **Coprocessor-only model** - all MPI ranks reside only on the coprocessors.
+ **Coprocessor-only model** - all MPI ranks reside only on the coprocessors.
- **Symmetric model** - the MPI ranks reside on both the host and the coprocessor. Most general MPI case.
+ **Symmetric model** - the MPI ranks reside on both the host and the coprocessor. Most general MPI case.
-###Host-only model
+\###Host-only model
In this case all environment variables are set by modules, so to execute the compiled MPI program on a single node, use:
@@ -652,8 +649,8 @@ Similarly to execution of OpenMP programs in native mode, since the environmenta
!!! Note "Note"
Please note:
- - this file sets up both environmental variable for both MPI and OpenMP libraries.
- - this file sets up the paths to a particular version of Intel MPI library and particular version of an Intel compiler. These versions have to match with loaded modules.
+ \- this file sets up both environmental variable for both MPI and OpenMP libraries.
+ \- this file sets up the paths to a particular version of Intel MPI library and particular version of an Intel compiler. These versions have to match with loaded modules.
To access a MIC accelerator located on a node that user is currently connected to, use:
@@ -706,8 +703,8 @@ or using mpirun
!!! Note "Note"
Please note:
- - the full path to the binary has to specified (here: "**>~/mpi-test-mic**")
- - the LD_LIBRARY_PATH has to match with Intel MPI module used to compile the MPI code
+ \- the full path to the binary has to specified (here: "**>~/mpi-test-mic**")
+ \- the LD_LIBRARY_PATH has to match with Intel MPI module used to compile the MPI code
The output should be again similar to:
@@ -754,9 +751,9 @@ This output means that the PBS allocated nodes cn204 and cn205, which means that
!!! Note "Note"
Please note: At this point user can connect to any of the allocated nodes or any of the allocated MIC accelerators using ssh:
- - to connect to the second node : ** $ ssh cn205**
- - to connect to the accelerator on the first node from the first node: **$ ssh cn204-mic0** or **$ ssh mic0**
- - to connect to the accelerator on the second node from the first node: **$ ssh cn205-mic0**
+ - to connect to the second node : ** $ ssh cn205**
+ - to connect to the accelerator on the first node from the first node: **$ ssh cn204-mic0** or **$ ssh mic0**
+ - to connect to the accelerator on the second node from the first node: **$ ssh cn205-mic0**
At this point we expect that correct modules are loaded and binary is compiled. For parallel execution the mpiexec.hydra is used. Again the first step is to tell mpiexec that the MPI can be executed on MIC accelerators by setting up the environmental variable "I_MPI_MIC"
@@ -774,6 +771,7 @@ The launch the MPI program use:
-host cn204-mic0 -n 4 ~/mpi-test-mic
: -host cn205-mic0 -n 6 ~/mpi-test-mic
```
+
or using mpirun:
```bash
@@ -811,7 +809,7 @@ The same way MPI program can be executed on multiple hosts:
: -host cn205 -n 6 ~/mpi-test
```
-###Symmetric model
+\###Symmetric model
In a symmetric mode MPI programs are executed on both host computer(s) and MIC accelerator(s). Since MIC has a different
architecture and requires different binary file produced by the Intel compiler two different files has to be compiled before MPI program is executed.
@@ -899,6 +897,6 @@ PBS also generates a set of node-files that can be used instead of manually crea
Please note each host or accelerator is listed only per files. User has to specify how many jobs should be executed per node using "-n" parameter of the mpirun command.
-Optimization
-------------
-For more details about optimization techniques please read Intel document [Optimization and Performance Tuning for Intel® Xeon Phi™ Coprocessors](http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization "http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization")
+## Optimization
+
+For more details about optimization techniques please read Intel document [Optimization and Performance Tuning for Intel® Xeon Phi™ Coprocessors](http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization "http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization")
diff --git a/docs.it4i/anselm-cluster-documentation/software/isv_licenses.md b/docs.it4i/anselm-cluster-documentation/software/isv_licenses.md
index 2303a969bfbf19d0ae5c1ca4b05ef955a3bd86b2..61d77e17a7610a6ecfc03aa6f1ed97d36831b204 100644
--- a/docs.it4i/anselm-cluster-documentation/software/isv_licenses.md
+++ b/docs.it4i/anselm-cluster-documentation/software/isv_licenses.md
@@ -1,7 +1,6 @@
-ISV Licenses
-============
+# ISV Licenses
-##A guide to managing Independent Software Vendor licenses
+\##A guide to managing Independent Software Vendor licenses
On Anselm cluster there are also installed commercial software applications, also known as ISV (Independent Software Vendor), which are subjects to licensing. The licenses are limited and their usage may be restricted only to some users or user groups.
@@ -9,8 +8,8 @@ Currently Flex License Manager based licensing is supported on the cluster for p
If an ISV application was purchased for educational (research) purposes and also for commercial purposes, then there are always two separate versions maintained and suffix "edu" is used in the name of the non-commercial version.
-Overview of the licenses usage
-------------------------------
+## Overview of the licenses usage
+
!!! Note "Note"
The overview is generated every minute and is accessible from web or command line interface.
@@ -23,13 +22,13 @@ For each license there is a table, which provides the information about the name
For each license there is a unique text file, which provides the information about the name, number of available (purchased/licensed), number of used and number of free license features. The text files are accessible from the Anselm command prompt.
-|Product|File with license state|Note|
-|---|---|
-|ansys|/apps/user/licenses/ansys_features_state.txt|Commercial|
-|comsol|/apps/user/licenses/comsol_features_state.txt|Commercial|
-|comsol-edu|/apps/user/licenses/comsol-edu_features_state.txt|Non-commercial only|
-|matlab|/apps/user/licenses/matlab_features_state.txt|Commercial|
-|matlab-edu|/apps/user/licenses/matlab-edu_features_state.txt|Non-commercial only|
+| Product | File with license state | Note |
+| ---------- | ------------------------------------------------- | ------------------- |
+| ansys | /apps/user/licenses/ansys_features_state.txt | Commercial |
+| comsol | /apps/user/licenses/comsol_features_state.txt | Commercial |
+| comsol-edu | /apps/user/licenses/comsol-edu_features_state.txt | Non-commercial only |
+| matlab | /apps/user/licenses/matlab_features_state.txt | Commercial |
+| matlab-edu | /apps/user/licenses/matlab-edu_features_state.txt | Non-commercial only |
The file has a header which serves as a legend. All the info in the legend starts with a hash (#) so it can be easily filtered when parsing the file via a script.
@@ -54,13 +53,13 @@ Example of the Commercial Matlab license state:
Statistics_Toolbox 1 0 1
```
-License tracking in PBS Pro scheduler and users usage
------------------------------------------------------
+## License tracking in PBS Pro scheduler and users usage
+
Each feature of each license is accounted and checked by the scheduler of PBS Pro. If you ask for certain licenses, the scheduler won't start the job until the asked licenses are free (available). This prevents to crash batch jobs, just because of unavailability of the needed licenses.
The general format of the name is:
-**feature__APP__FEATURE**
+**feature**APP**FEATURE**
Names of applications (APP):
@@ -73,26 +72,27 @@ Names of applications (APP):
To get the FEATUREs of a license take a look into the corresponding state file ([see above](isv_licenses/#Licence)), or use:
**Application and List of provided features**
-- **ansys** $ grep -v "#" /apps/user/licenses/ansys_features_state.txt | cut -f1 -d' '
-- **comsol** $ grep -v "#" /apps/user/licenses/comsol_features_state.txt | cut -f1 -d' '
-- **comsol-ed** $ grep -v "#" /apps/user/licenses/comsol-edu_features_state.txt | cut -f1 -d' '
-- **matlab** $ grep -v "#" /apps/user/licenses/matlab_features_state.txt | cut -f1 -d' '
-- **matlab-edu** $ grep -v "#" /apps/user/licenses/matlab-edu_features_state.txt | cut -f1 -d' '
+
+- **ansys** $ grep -v "#" /apps/user/licenses/ansys_features_state.txt | cut -f1 -d' '
+- **comsol** $ grep -v "#" /apps/user/licenses/comsol_features_state.txt | cut -f1 -d' '
+- **comsol-ed** $ grep -v "#" /apps/user/licenses/comsol-edu_features_state.txt | cut -f1 -d' '
+- **matlab** $ grep -v "#" /apps/user/licenses/matlab_features_state.txt | cut -f1 -d' '
+- **matlab-edu** $ grep -v "#" /apps/user/licenses/matlab-edu_features_state.txt | cut -f1 -d' '
Example of PBS Pro resource name, based on APP and FEATURE name:
- |Application |Feature |PBS Pro resource name |
- | --- | --- |
- |ansys |acfd |feature_ansys_acfd |
- |ansys |aa_r |feature_ansys_aa_r |
- |comsol |COMSOL |feature_comsol_COMSOL |
- |comsol |HEATTRANSFER |feature_comsol_HEATTRANSFER |
- |comsol-edu |COMSOLBATCH |feature_comsol-edu_COMSOLBATCH |
- |comsol-edu |STRUCTURALMECHANICS |feature_comsol-edu_STRUCTURALMECHANICS |
- |matlab |MATLAB |feature_matlab_MATLAB |
- |matlab |Image_Toolbox |feature_matlab_Image_Toolbox |
- |matlab-edu |MATLAB_Distrib_Comp_Engine |feature_matlab-edu_MATLAB_Distrib_Comp_Engine |
- |matlab-edu |Image_Acquisition_Toolbox |feature_matlab-edu_Image_Acquisition_Toolbox\ |
+| Application | Feature | PBS Pro resource name |
+| ----------- | -------------------------- | ----------------------------------------------- |
+| ansys | acfd | feature_ansys_acfd |
+| ansys | aa_r | feature_ansys_aa_r |
+| comsol | COMSOL | feature_comsol_COMSOL |
+| comsol | HEATTRANSFER | feature_comsol_HEATTRANSFER |
+| comsol-edu | COMSOLBATCH | feature_comsol-edu_COMSOLBATCH |
+| comsol-edu | STRUCTURALMECHANICS | feature_comsol-edu_STRUCTURALMECHANICS |
+| matlab | MATLAB | feature_matlab_MATLAB |
+| matlab | Image_Toolbox | feature_matlab_Image_Toolbox |
+| matlab-edu | MATLAB_Distrib_Comp_Engine | feature_matlab-edu_MATLAB_Distrib_Comp_Engine |
+| matlab-edu | Image_Acquisition_Toolbox | feature_matlab-edu_Image_Acquisition_Toolbox\\ |
**Be aware, that the resource names in PBS Pro are CASE SENSITIVE!**
diff --git a/docs.it4i/anselm-cluster-documentation/software/java.md b/docs.it4i/anselm-cluster-documentation/software/java.md
index 7159f790b9f39ed904caeeae78893bba3ebf05b5..a9aa360e91b97b7dbbdc441d225b4b14b40f2f00 100644
--- a/docs.it4i/anselm-cluster-documentation/software/java.md
+++ b/docs.it4i/anselm-cluster-documentation/software/java.md
@@ -1,7 +1,6 @@
-Java
-====
+# Java
-##Java on ANSELM
+\##Java on ANSELM
Java is available on Anselm cluster. Activate java by loading the java module
@@ -26,4 +25,3 @@ With the module loaded, not only the runtime environment (JRE), but also the dev
```
Java applications may use MPI for inter-process communication, in conjunction with OpenMPI. Read more on <http://www.open-mpi.org/faq/?category=java>. This functionality is currently not supported on Anselm cluster. In case you require the java interface to MPI, please contact [Anselm support](https://support.it4i.cz/rt/).
-
diff --git a/docs.it4i/anselm-cluster-documentation/software/kvirtualization.md b/docs.it4i/anselm-cluster-documentation/software/kvirtualization.md
index 508fe8bf91326cf468ce398d2e2ae275a02c8ff4..3c37ed9b153a8f206d89352e454561befd6691c3 100644
--- a/docs.it4i/anselm-cluster-documentation/software/kvirtualization.md
+++ b/docs.it4i/anselm-cluster-documentation/software/kvirtualization.md
@@ -1,10 +1,9 @@
-Virtualization
-==============
+# Virtualization
-##Running virtual machines on compute nodes
+\##Running virtual machines on compute nodes
+
+## Introduction
-Introduction
-------------
There are situations when Anselm's environment is not suitable for user needs.
- Application requires different operating system (e.g Windows), application is not available for Linux
@@ -17,8 +16,7 @@ We offer solution for these cases - **virtualization**. Anselm's environment giv
Solution is based on QEMU-KVM software stack and provides hardware-assisted x86 virtualization.
-Limitations
------------
+## Limitations
Anselm's infrastructure was not designed for virtualization. Anselm's environment is not intended primary for virtualization, compute nodes, storages and all infrastructure of Anselm is intended and optimized for running HPC jobs, this implies suboptimal configuration of virtualization and limitations.
@@ -31,20 +29,18 @@ Solution described in chapter [HOWTO](virtualization/#howto) is suitable for si
!!! Note "Note"
Please consider virtualization as last resort solution for your needs.
- Please consult use of virtualization with IT4Innovation's support.
+ Please consult use of virtualization with IT4Innovation's support.
- For running Windows application (when source code and Linux native application are not available) consider use of Wine, Windows compatibility layer. Many Windows applications can be run using Wine with less effort and better performance than when using virtualization.
+ For running Windows application (when source code and Linux native application are not available) consider use of Wine, Windows compatibility layer. Many Windows applications can be run using Wine with less effort and better performance than when using virtualization.
-Licensing
----------
+## Licensing
IT4Innovations does not provide any licenses for operating systems and software of virtual machines. Users are ( in accordance with [Acceptable use policy document](http://www.it4i.cz/acceptable-use-policy.pdf)) fully responsible for licensing all software running in virtual machines on Anselm. Be aware of complex conditions of licensing software in virtual environments.
!!! Note "Note"
Users are responsible for licensing OS e.g. MS Windows and all software running in their virtual machines.
- HOWTO
-----------
+## HOWTO
### Virtual Machine Job Workflow
@@ -100,10 +96,10 @@ Your image should run some kind of operating system startup script. Startup scri
We recommend, that startup script
-- maps Job Directory from host (from compute node)
-- runs script (we call it "run script") from Job Directory and waits for application's exit
- - for management purposes if run script does not exist wait for some time period (few minutes)
-- shutdowns/quits OS
+- maps Job Directory from host (from compute node)
+- runs script (we call it "run script") from Job Directory and waits for application's exit
+ - for management purposes if run script does not exist wait for some time period (few minutes)
+- shutdowns/quits OS
For Windows operating systems we suggest using Local Group Policy Startup script, for Linux operating systems rc.local, runlevel init script or similar service.
@@ -222,6 +218,7 @@ Get help
```bash
$ man qemu
```
+
Run virtual machine (simple)
```bash
@@ -340,9 +337,9 @@ Interface tap0 has IP address 192.168.1.1 and network mask 255.255.255.0 (/24).
Redirected ports:
-- DNS udp/53->udp/3053, tcp/53->tcp3053
-- DHCP udp/67->udp3067
-- SMB tcp/139->tcp3139, tcp/445->tcp3445).
+- DNS udp/53->udp/3053, tcp/53->tcp3053
+- DHCP udp/67->udp3067
+- SMB tcp/139->tcp3139, tcp/445->tcp3445).
You can configure IP address of virtual machine statically or dynamically. For dynamic addressing provide your DHCP server on port 3067 of tap0 interface, you can also provide your DNS server on port 3053 of tap0 interface for example:
diff --git a/docs.it4i/anselm-cluster-documentation/software/mpi/Running_OpenMPI.md b/docs.it4i/anselm-cluster-documentation/software/mpi/Running_OpenMPI.md
index 4f0168872215e74c6114899674bd1b15bec2c730..e2376523a96ba461422fe63335aa3bf913679bd4 100644
--- a/docs.it4i/anselm-cluster-documentation/software/mpi/Running_OpenMPI.md
+++ b/docs.it4i/anselm-cluster-documentation/software/mpi/Running_OpenMPI.md
@@ -1,8 +1,7 @@
-Running OpenMPI
-==============
+# Running OpenMPI
+
+## OpenMPI program execution
-OpenMPI program execution
--------------------------
The OpenMPI programs may be executed only via the PBS Workload manager, by entering an appropriate queue. On Anselm, the **bullxmpi-1.2.4.1** and **OpenMPI 1.6.5** are OpenMPI based MPI implementations.
### Basic usage
@@ -109,19 +108,19 @@ In the previous two examples with one or two MPI processes per node, the operati
or this one for Intel OpenMP:
-```bash
- $ export KMP_AFFINITY=granularity=fine,compact,1,0
-``
+````bash
+ $ export KMP_AFFINITY=granularity=fine,compact,1,0
+ ``
-As of OpenMP 4.0 (supported by GCC 4.9 and later and Intel 14.0 and later) the following variables may be used for Intel or GCC:
+ As of OpenMP 4.0 (supported by GCC 4.9 and later and Intel 14.0 and later) the following variables may be used for Intel or GCC:
-```bash
- $ export OMP_PROC_BIND=true
- $ export OMP_PLACES=cores
-```
+ ```bash
+ $ export OMP_PROC_BIND=true
+ $ export OMP_PLACES=cores
+````
+
+## OpenMPI Process Mapping and Binding
-OpenMPI Process Mapping and Binding
-------------------------------------------------
The mpiexec allows for precise selection of how the MPI processes will be mapped to the computational nodes and how these processes will bind to particular processor sockets and cores.
MPI process mapping may be specified by a hostfile or rankfile input to the mpiexec program. Altough all implementations of MPI provide means for process mapping and binding, following examples are valid for the openmpi only.
@@ -203,15 +202,15 @@ In all cases, binding and threading may be verified by executing for example:
$ mpiexec -bysocket -bind-to-socket echo $OMP_NUM_THREADS
```
-Changes in OpenMPI 1.8
-----------------------
+## Changes in OpenMPI 1.8
+
Some options have changed in OpenMPI version 1.8.
- |version 1.6.5 |version 1.8.1 |
- | --- | --- |
- |--bind-to-none |--bind-to none |
- |--bind-to-core |--bind-to core |
- |--bind-to-socket |--bind-to socket |
- |-bysocket |--map-by socket |
- |-bycore |--map-by core |
- |-pernode |--map-by ppr:1:node |
+| version 1.6.5 | version 1.8.1 |
+| ---------------- | ------------------- |
+| --bind-to-none | --bind-to none |
+| --bind-to-core | --bind-to core |
+| --bind-to-socket | --bind-to socket |
+| -bysocket | --map-by socket |
+| -bycore | --map-by core |
+| -pernode | --map-by ppr:1:node |
diff --git a/docs.it4i/anselm-cluster-documentation/software/mpi/mpi.md b/docs.it4i/anselm-cluster-documentation/software/mpi/mpi.md
index 5f81e8ee4eb3855c549bf3f558431afd3073e3f7..ade0bc2e6284c37f40acc73be8a5934e982de580 100644
--- a/docs.it4i/anselm-cluster-documentation/software/mpi/mpi.md
+++ b/docs.it4i/anselm-cluster-documentation/software/mpi/mpi.md
@@ -1,17 +1,16 @@
-MPI
-===
+# MPI
+
+## Setting up MPI Environment
-Setting up MPI Environment
---------------------------
The Anselm cluster provides several implementations of the MPI library:
- |MPI Library |Thread support |
- | --- | --- |
- |The highly optimized and stable **bullxmpi 1.2.4.1** |Partial thread support up to MPI_THREAD_SERIALIZED |
- |The **Intel MPI 4.1** |Full thread support up to MPI_THREAD_MULTIPLE |
- |The [OpenMPI 1.6.5](href="http://www.open-mpi.org)| Full thread support up to MPI_THREAD_MULTIPLE, BLCR c/r support |
- |The OpenMPI 1.8.1 |Full thread support up to MPI_THREAD_MULTIPLE, MPI-3.0 support |
- |The **mpich2 1.9** |Full thread support up to MPI_THREAD_MULTIPLE, BLCR c/r support |
+| MPI Library | Thread support |
+| ---------------------------------------------------- | --------------------------------------------------------------- |
+| The highly optimized and stable **bullxmpi 1.2.4.1** | Partial thread support up to MPI_THREAD_SERIALIZED |
+| The **Intel MPI 4.1** | Full thread support up to MPI_THREAD_MULTIPLE |
+| The [OpenMPI 1.6.5](href="http://www.open-mpi.org) | Full thread support up to MPI_THREAD_MULTIPLE, BLCR c/r support |
+| The OpenMPI 1.8.1 | Full thread support up to MPI_THREAD_MULTIPLE, MPI-3.0 support |
+| The **mpich2 1.9** | Full thread support up to MPI_THREAD_MULTIPLE, BLCR c/r support |
MPI libraries are activated via the environment modules.
@@ -32,15 +31,15 @@ Look up section modulefiles/mpi in module avail
There are default compilers associated with any particular MPI implementation. The defaults may be changed, the MPI libraries may be used in conjunction with any compiler. The defaults are selected via the modules in following way
-|Module|MPI|Compiler suite|
-|-------- |---|---|
-|PrgEnv-gnu|bullxmpi-1.2.4.1|bullx GNU 4.4.6|
-|PrgEnv-intel|Intel MPI 4.1.1|Intel 13.1.1|
-|bullxmpi|bullxmpi-1.2.4.1|none, select via module|
-|impi|Intel MPI 4.1.1|none, select via module|
-|openmpi|OpenMPI 1.6.5|GNU compilers 4.8.1, GNU compilers 4.4.6, Intel Compilers|
-|openmpi|OpenMPI 1.8.1|GNU compilers 4.8.1, GNU compilers 4.4.6, GNU compilers 4.9.0, Intel Compilers|
-|mvapich2|MPICH2 1.9|GNU compilers 4.8.1, GNU compilers 4.4.6, Intel Compilers|
+| Module | MPI | Compiler suite |
+| ------------ | ---------------- | ------------------------------------------------------------------------------ |
+| PrgEnv-gnu | bullxmpi-1.2.4.1 | bullx GNU 4.4.6 |
+| PrgEnv-intel | Intel MPI 4.1.1 | Intel 13.1.1 |
+| bullxmpi | bullxmpi-1.2.4.1 | none, select via module |
+| impi | Intel MPI 4.1.1 | none, select via module |
+| openmpi | OpenMPI 1.6.5 | GNU compilers 4.8.1, GNU compilers 4.4.6, Intel Compilers |
+| openmpi | OpenMPI 1.8.1 | GNU compilers 4.8.1, GNU compilers 4.4.6, GNU compilers 4.9.0, Intel Compilers |
+| mvapich2 | MPICH2 1.9 | GNU compilers 4.8.1, GNU compilers 4.4.6, Intel Compilers |
Examples:
@@ -59,8 +58,8 @@ To use openmpi with the intel compiler suite, use
In this example, the openmpi 1.6.5 using intel compilers is activated
-Compiling MPI Programs
-----------------------
+## Compiling MPI Programs
+
!!! Note "Note"
After setting up your MPI environment, compile your program using one of the mpi wrappers
@@ -106,8 +105,8 @@ Compile the above example with
$ mpicc helloworld_mpi.c -o helloworld_mpi.x
```
-Running MPI Programs
---------------------
+## Running MPI Programs
+
!!! Note "Note"
The MPI program executable must be compatible with the loaded MPI module.
Always compile and execute using the very same MPI module.
@@ -123,9 +122,9 @@ Optimal way to run an MPI program depends on its memory requirements, memory acc
!!! Note "Note"
Consider these ways to run an MPI program:
- 1. One MPI process per node, 16 threads per process
- 2. Two MPI processes per node, 8 threads per process
- 3. 16 MPI processes per node, 1 thread per process.
+ 1. One MPI process per node, 16 threads per process
+ 2. Two MPI processes per node, 8 threads per process
+ 3. 16 MPI processes per node, 1 thread per process.
**One MPI** process per node, using 16 threads, is most useful for memory demanding applications, that make good use of processor cache memory and are not memory bound. This is also a preferred way for communication intensive applications as one process per node enjoys full bandwidth access to the network interface.
diff --git a/docs.it4i/anselm-cluster-documentation/software/mpi/mpi4py-mpi-for-python.md b/docs.it4i/anselm-cluster-documentation/software/mpi/mpi4py-mpi-for-python.md
index df186ef653458832d130aadfcdb6e9c2a684eef3..3738f2ec2d02bb0afd9e221be02c91fdbf24ac5b 100644
--- a/docs.it4i/anselm-cluster-documentation/software/mpi/mpi4py-mpi-for-python.md
+++ b/docs.it4i/anselm-cluster-documentation/software/mpi/mpi4py-mpi-for-python.md
@@ -1,16 +1,15 @@
-MPI4Py (MPI for Python)
-=======================
+# MPI4Py (MPI for Python)
+
+## Introduction
-Introduction
-------------
MPI for Python provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.
This package is constructed on top of the MPI-1/2 specifications and provides an object oriented interface which closely follows MPI-2 C++ bindings. It supports point-to-point (sends, receives) and collective (broadcasts, scatters, gathers) communications of any picklable Python object, as well as optimized communications of Python object exposing the single-segment buffer interface (NumPy arrays, builtin bytes/string/array objects).
On Anselm MPI4Py is available in standard Python modules.
-Modules
--------
+## Modules
+
MPI4Py is build for OpenMPI. Before you start with MPI4Py you need to load Python and OpenMPI modules.
```bash
@@ -18,8 +17,8 @@ MPI4Py is build for OpenMPI. Before you start with MPI4Py you need to load Pytho
$ module load openmpi
```
-Execution
----------
+## Execution
+
You need to import MPI to your python program. Include the following line to the python script:
```cpp
@@ -38,8 +37,7 @@ For example
$ mpiexec python hello_world.py
```
-Examples
---------
+## Examples
### Hello world!
@@ -53,7 +51,7 @@ Examples
comm.Barrier() # wait for everybody to synchronize
```
-###Collective Communication with NumPy arrays
+\###Collective Communication with NumPy arrays
```cpp
from mpi4py import MPI
diff --git a/docs.it4i/anselm-cluster-documentation/software/mpi/running-mpich2.md b/docs.it4i/anselm-cluster-documentation/software/mpi/running-mpich2.md
index d5cf06387e7958d8eb8a8fb8244488d8baffe363..74c882c3bde7a5aff01e4bb205b2c14c59efa45b 100644
--- a/docs.it4i/anselm-cluster-documentation/software/mpi/running-mpich2.md
+++ b/docs.it4i/anselm-cluster-documentation/software/mpi/running-mpich2.md
@@ -1,8 +1,7 @@
-Running MPICH2
-==============
+# Running MPICH2
+
+## MPICH2 program execution
-MPICH2 program execution
-------------------------
The MPICH2 programs use mpd daemon or ssh connection to spawn processes, no PBS support is needed. However the PBS allocation is required to access compute nodes. On Anselm, the **Intel MPI** and **mpich2 1.9** are MPICH2 based MPI implementations.
### Basic usage
@@ -115,8 +114,8 @@ As of OpenMP 4.0 (supported by GCC 4.9 and later and Intel 14.0 and later) the f
$ export OMP_PLACES=cores
```
-MPICH2 Process Mapping and Binding
-----------------------------------
+## MPICH2 Process Mapping and Binding
+
The mpirun allows for precise selection of how the MPI processes will be mapped to the computational nodes and how these processes will bind to particular processor sockets and cores.
### Machinefile
@@ -159,7 +158,6 @@ In all cases, binding and threading may be verified by executing
$ mpirun -bindto numa echo $OMP_NUM_THREADS
```
-Intel MPI on Xeon Phi
----------------------
+## Intel MPI on Xeon Phi
The[MPI section of Intel Xeon Phi chapter](../intel-xeon-phi/) provides details on how to run Intel MPI code on Xeon Phi architecture.
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/introduction.md b/docs.it4i/anselm-cluster-documentation/software/numerical-languages/introduction.md
index 9d54dceac9b0d77e4a4a9ca4313ff2cf0cb3b875..67493f1f7d099c0c9a8986b2118bff77aa4dd38b 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/introduction.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-languages/introduction.md
@@ -1,14 +1,13 @@
-Numerical languages
-===================
+# Numerical languages
Interpreted languages for numerical computations and analysis
-Introduction
-------------
+## Introduction
+
This section contains a collection of high-level interpreted languages, primarily intended for numerical computations.
-Matlab
-------
+## Matlab
+
MATLAB® is a high-level language and interactive environment for numerical computation, visualization, and programming.
```bash
@@ -18,8 +17,8 @@ MATLAB® is a high-level language and interactive environment for numerical comp
Read more at the [Matlab page](matlab/).
-Octave
-------
+## Octave
+
GNU Octave is a high-level interpreted language, primarily intended for numerical computations. The Octave language is quite similar to Matlab so that most programs are easily portable.
```bash
@@ -29,8 +28,7 @@ GNU Octave is a high-level interpreted language, primarily intended for numerica
Read more at the [Octave page](octave/).
-R
----
+## R
The R is an interpreted language and environment for statistical computing and graphics.
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab.md b/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab.md
index 27dd6bb6e7def484ba4847d8ce7c67fb99a06b25..8f09761721deced6e7bd0555a88c4e101b5744c9 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab.md
@@ -1,8 +1,7 @@
-Matlab
-======
+# Matlab
+
+## Introduction
-Introduction
-------------
Matlab is available in versions R2015a and R2015b. There are always two variants of the release:
- Non commercial or so called EDU variant, which can be used for common research and educational purposes.
@@ -40,8 +39,8 @@ To run Matlab in text mode, without the Matlab Desktop GUI environment, use
plots, images, etc... will be still available.
-Running parallel Matlab using Distributed Computing Toolbox / Engine
-------------------------------------------------------------------------
+## Running parallel Matlab using Distributed Computing Toolbox / Engine
+
!!! Note "Note"
Distributed toolbox is available only for the EDU variant
@@ -59,7 +58,7 @@ To use Distributed Computing, you first need to setup a parallel profile. We hav
SalomonPBSPro
```
-Or in the GUI, go to tab HOME -> Parallel -> Manage Cluster Profiles..., click Import and navigate to:
+Or in the GUI, go to tab HOME -> Parallel -> Manage Cluster Profiles..., click Import and navigate to:
/apps/all/MATLAB/2015a-EDU/SalomonPBSPro.settings
@@ -148,6 +147,7 @@ The last step is to start matlabpool with "cluster" object and correct number of
parpool close
```
+
The complete example showing how to use Distributed Computing Toolbox in local mode is shown here.
```bash
@@ -250,7 +250,7 @@ This is an example of m-script using direct mode:
### Non-interactive Session and Licenses
-If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l _feature_matlab_MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please [look here](../isv_licenses/).
+If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l \_feature_matlab_MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please [look here](../isv_licenses/).
In case of non-interactive session please read the [following information](../isv_licenses/) on how to modify the qsub command to test for available licenses prior getting the resource allocation.
@@ -258,15 +258,15 @@ In case of non-interactive session please read the [following information](../is
Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:
- |compute nodes|number of workers|start-up time[s]|
- |---|---|---|
- |16|384|831|
- |8|192|807|
- |4|96|483|
- |2|48|16|
+| compute nodes | number of workers | start-up time[s] |
+| ------------- | ----------------- | ---------------- |
+| 16 | 384 | 831 |
+| 8 | 192 | 807 |
+| 4 | 96 | 483 |
+| 2 | 48 | 16 |
+
+## MATLAB on UV2000
-MATLAB on UV2000
------------------
UV2000 machine available in queue "qfat" can be used for MATLAB computations. This is a SMP NUMA machine with large amount of RAM, which can be beneficial for certain types of MATLAB jobs. CPU cores are allocated in chunks of 8 for this machine.
You can use MATLAB on UV2000 in two parallel modes:
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab_1314.md b/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab_1314.md
index d28bb29cb4d9bbb2bec23336b4dc61a7b7710d81..9ca3aca6ae23e907518d7192529b5923a43dcb25 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab_1314.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab_1314.md
@@ -1,8 +1,7 @@
-Matlab 2013-2014
-================
+# Matlab 2013-2014
+
+## Introduction
-Introduction
-------------
!!! Note "Note"
This document relates to the old versions R2013 and R2014. For MATLAB 2015, please use [this documentation instead](matlab/).
@@ -37,36 +36,34 @@ To run Matlab with GUI, use
To run Matlab in text mode, without the Matlab Desktop GUI environment, use
-```bash```bash
+`bash`bash
$ matlab -nodesktop -nosplash
-```
-plots, images, etc... will be still available.
+ plots, images, etc... will be still available.
-Running parallel Matlab using Distributed Computing Toolbox / Engine
---------------------------------------------------------------------
-Recommended parallel mode for running parallel Matlab on Anselm is MPIEXEC mode. In this mode user allocates resources through PBS prior to starting Matlab. Once resources are granted the main Matlab instance is 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.
+ 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:
+ 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:
-```bash
- $ vim ~/matlab/mpiLibConf.m
+ ```bash
+ $ vim ~/matlab/mpiLibConf.m
- function [lib, extras] = mpiLibConf
- %MATLAB MPI Library overloading for Infiniband Networks
+ function [lib, extras] = mpiLibConf
+ %MATLAB MPI Library overloading for Infiniband Networks
- mpich = '/opt/intel/impi/4.1.1.036/lib64/';
+ mpich = '/opt/intel/impi/4.1.1.036/lib64/';
- disp('Using Intel MPI 4.1.1.036 over Infiniband')
+ disp('Using Intel MPI 4.1.1.036 over Infiniband')
- lib = strcat(mpich, 'libmpich.so');
- mpl = strcat(mpich, 'libmpl.so');
- opa = strcat(mpich, 'libopa.so');
+ lib = strcat(mpich, 'libmpich.so');
+ mpl = strcat(mpich, 'libmpl.so');
+ opa = strcat(mpich, 'libopa.so');
- extras = {};
-```
+ extras = {};
System MPI library allows Matlab to communicate through 40 Gbit/s InfiniBand QDR interconnect instead of slower 1 Gbit Ethernet network.
@@ -192,7 +189,7 @@ You can copy and paste the example in a .m file and execute. Note that the matla
### Non-interactive Session and Licenses
-If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l _feature_matlab_MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please [look here](../isv_licenses/).
+If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l \_feature_matlab_MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please [look here](../isv_licenses/).
In case of non-interactive session please read the [following information](../isv_licenses/) on how to modify the qsub command to test for available licenses prior getting the resource allocation.
@@ -200,9 +197,9 @@ In case of non-interactive session please read the [following information](../is
Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:
- |compute nodes|number of workers|start-up time[s]|
- |---|---|---|
- |16|256|1008|
- |8|128|534|
- |4|64|333|
- |2|32|210|
+| compute nodes | number of workers | start-up time[s] |
+| ------------- | ----------------- | ---------------- |
+| 16 | 256 | 1008 |
+| 8 | 128 | 534 |
+| 4 | 64 | 333 |
+| 2 | 32 | 210 |
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/octave.md b/docs.it4i/anselm-cluster-documentation/software/numerical-languages/octave.md
index db07503afb05f69b39495cc2322fe2465e96f7e8..992bfe1626e7df2f6a806b0713f43b126c26dfb1 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/octave.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-languages/octave.md
@@ -1,20 +1,18 @@
-Octave
-======
+# Octave
+
+## Introduction
-Introduction
-------------
GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to Matlab so that most programs are easily portable. Read more on <http://www.gnu.org/software/octave/>
Two versions of octave are available on Anselm, via module
-|Version|module|
-|---|---|
-|Octave 3.8.2, compiled with GCC and Multithreaded MKL|Octave/3.8.2-gimkl-2.11.5|
-|Octave 4.0.1, compiled with GCC and Multithreaded MKL|Octave/4.0.1-gimkl-2.11.5|
-|Octave 4.0.0, compiled with >GCC and OpenBLAS|Octave/4.0.0-foss-2015g|
+| Version | module |
+| ----------------------------------------------------- | ------------------------- |
+| Octave 3.8.2, compiled with GCC and Multithreaded MKL | Octave/3.8.2-gimkl-2.11.5 |
+| Octave 4.0.1, compiled with GCC and Multithreaded MKL | Octave/4.0.1-gimkl-2.11.5 |
+| Octave 4.0.0, compiled with >GCC and OpenBLAS | Octave/4.0.0-foss-2015g |
- Modules and execution
-----------------------
+## Modules and execution
$ module load Octave
@@ -60,8 +58,8 @@ The octave c compiler mkoctfile calls the GNU gcc 4.8.1 for compiling native c c
Octave may use MPI for interprocess communication This functionality is currently not supported on Anselm cluster. In case you require the octave interface to MPI, please contact [Anselm support](https://support.it4i.cz/rt/).
-Xeon Phi Support
-----------------
+## Xeon Phi Support
+
Octave may take advantage of the Xeon Phi accelerators. This will only work on the [Intel Xeon Phi](../intel-xeon-phi/) [accelerated nodes](../../compute-nodes/).
### Automatic offload support
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/r.md b/docs.it4i/anselm-cluster-documentation/software/numerical-languages/r.md
index 238e7106b70a2da05422d2fa4d089c372eef21bb..e9ffdfe2b6d3d37f46ffb6b77830d2cc7bdcae31 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/r.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-languages/r.md
@@ -1,8 +1,7 @@
-R
-===
+# R
+
+## Introduction
-Introduction
-------------
The R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible.
One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control.
@@ -13,21 +12,21 @@ Extensive support for parallel computing is available within R.
Read more on <http://www.r-project.org/>, <http://cran.r-project.org/doc/manuals/r-release/R-lang.html>
-Modules
--------
+## Modules
+
The R version 3.0.1 is available on Anselm, along with GUI interface Rstudio
-|Application|Version|module|
-|---|---|
-| **R**|R 3.0.1|R|
-|**Rstudio**|Rstudio 0.97|Rstudio|
+| Application | Version | module |
+| ----------- | ------------ | ------- |
+| **R** | R 3.0.1 | R |
+| **Rstudio** | Rstudio 0.97 | Rstudio |
```bash
$ module load R
```
-Execution
----------
+## Execution
+
The R on Anselm is linked to highly optimized MKL mathematical library. This provides threaded parallelization to many R kernels, notably the linear algebra subroutines. The R runs these heavy calculation kernels without any penalty. By default, the R would parallelize to 16 threads. You may control the threads by setting the OMP_NUM_THREADS environment variable.
### Interactive execution
@@ -69,12 +68,12 @@ Example jobscript:
This script may be submitted directly to the PBS workload manager via the qsub command. The inputs are in rscript.R file, outputs in routput.out file. See the single node jobscript example in the [Job execution section](../../resource-allocation-and-job-execution/job-submission-and-execution/).
-Parallel R
-----------
+## Parallel R
+
Parallel execution of R may be achieved in many ways. One approach is the implied parallelization due to linked libraries or specially enabled functions, as [described above](r/#interactive-execution). In the following sections, we focus on explicit parallelization, where parallel constructs are directly stated within the R script.
-Package parallel
---------------------
+## Package parallel
+
The package parallel provides support for parallel computation, including by forking (taken from package multicore), by sockets (taken from package snow) and random-number generation.
The package is activated this way:
@@ -99,9 +98,9 @@ The forking is the most simple to use. Forking family of functions provide paral
!!! Note "Note"
Forking via package parallel provides functionality similar to OpenMP construct
- omp parallel for
+ omp parallel for
- Only cores of single node can be utilized this way!
+ Only cores of single node can be utilized this way!
Forking example:
@@ -145,8 +144,8 @@ The above example is the classic parallel example for calculating the number π.
Every evaluation of the integrad function runs in parallel on different process.
-Package Rmpi
-------------
+## Package Rmpi
+
!!! Note "Note"
package Rmpi provides an interface (wrapper) to MPI APIs.
@@ -160,6 +159,7 @@ When using package Rmpi, both openmpi and R modules must be loaded
$ module load openmpi
$ module load R
```
+
Rmpi may be used in three basic ways. The static approach is identical to executing any other MPI programm. In addition, there is Rslaves dynamic MPI approach and the mpi.apply approach. In the following section, we will use the number π integration example, to illustrate all these concepts.
### static Rmpi
@@ -359,13 +359,11 @@ Execute the example as:
$ R --slave --no-save --no-restore -f pi3parSapply.R
```
-Combining parallel and Rmpi
----------------------------
+## Combining parallel and Rmpi
Currently, the two packages can not be combined for hybrid calculations.
-Parallel execution
-------------------
+## Parallel execution
The R parallel jobs are executed via the PBS queue system exactly as any other parallel jobs. User must create an appropriate jobscript and submit via the **qsub**
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/fftw.md b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/fftw.md
index 8920a402fdc3f1d614a71cebc15bbda6313f115e..67c3fdf090a195dc3cd88d66dd920e0cd6163648 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/fftw.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/fftw.md
@@ -1,5 +1,4 @@
-FFTW
-====
+# FFTW
The discrete Fourier transform in one or more dimensions, MPI parallel
@@ -7,16 +6,16 @@ FFTW is a C subroutine library for computing the discrete Fourier transform in
Two versions, **3.3.3** and **2.1.5** of FFTW are available on Anselm, each compiled for **Intel MPI** and **OpenMPI** using **intel** and **gnu** compilers. These are available via modules:
- |Version |Parallelization |module |linker options |
- | --- | --- |
- |FFTW3 gcc3.3.3 |pthread, OpenMP |fftw3/3.3.3-gcc |-lfftw3, -lfftw3_threads-lfftw3_omp |
- |FFTW3 icc3.3.3 |pthread, OpenMP |fftw3 |-lfftw3, -lfftw3_threads-lfftw3_omp |
- |FFTW2 gcc2.1.5 |pthread |fftw2/2.1.5-gcc |-lfftw, -lfftw_threads |
- |FFTW2 icc2.1.5 |pthread |fftw2 |-lfftw, -lfftw_threads |
- |FFTW3 gcc3.3.3 |OpenMPI |fftw-mpi3/3.3.3-gcc |-lfftw3_mpi |
- |FFTW3 icc3.3.3 |Intel MPI |fftw3-mpi |-lfftw3_mpi |
- |FFTW2 gcc2.1.5 |OpenMPI |fftw2-mpi/2.1.5-gcc |-lfftw_mpi |
- |FFTW2 gcc2.1.5 |IntelMPI |fftw2-mpi/2.1.5-gcc |-lfftw_mpi |
+| Version | Parallelization | module | linker options |
+| -------------- | --------------- | ------------------- | ----------------------------------- |
+| FFTW3 gcc3.3.3 | pthread, OpenMP | fftw3/3.3.3-gcc | -lfftw3, -lfftw3_threads-lfftw3_omp |
+| FFTW3 icc3.3.3 | pthread, OpenMP | fftw3 | -lfftw3, -lfftw3_threads-lfftw3_omp |
+| FFTW2 gcc2.1.5 | pthread | fftw2/2.1.5-gcc | -lfftw, -lfftw_threads |
+| FFTW2 icc2.1.5 | pthread | fftw2 | -lfftw, -lfftw_threads |
+| FFTW3 gcc3.3.3 | OpenMPI | fftw-mpi3/3.3.3-gcc | -lfftw3_mpi |
+| FFTW3 icc3.3.3 | Intel MPI | fftw3-mpi | -lfftw3_mpi |
+| FFTW2 gcc2.1.5 | OpenMPI | fftw2-mpi/2.1.5-gcc | -lfftw_mpi |
+| FFTW2 gcc2.1.5 | IntelMPI | fftw2-mpi/2.1.5-gcc | -lfftw_mpi |
```bash
$ module load fftw3
@@ -24,8 +23,7 @@ Two versions, **3.3.3** and **2.1.5** of FFTW are available on Anselm, each comp
The module sets up environment variables, required for linking and running FFTW enabled applications. Make sure that the choice of FFTW module is consistent with your choice of MPI library. Mixing MPI of different implementations may have unpredictable results.
-Example
--------
+## Example
```cpp
#include <fftw3-mpi.h>
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/gsl.md b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/gsl.md
index ab2efcd3674a0bf83e62f42f5b34fe65b99c3e63..4295fc5d72115f880d1803c325556685b31c419c 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/gsl.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/gsl.md
@@ -1,15 +1,13 @@
-GSL
-===
+# GSL
The GNU Scientific Library. Provides a wide range of mathematical routines.
-Introduction
-------------
+## Introduction
+
The GNU Scientific Library (GSL) provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total. The routines have been written from scratch in C, and present a modern Applications Programming Interface (API) for C programmers, allowing wrappers to be written for very high level languages.
The library covers a wide range of topics in numerical computing. Routines are available for the following areas:
-
Complex Numbers Roots of Polynomials
Special Functions Vectors and Matrices
@@ -44,15 +42,14 @@ The library covers a wide range of topics in numerical computing. Routines are a
Basis Splines Wavelets
-Modules
--------
+## Modules
The GSL 1.16 is available on Anselm, compiled for GNU and Intel compiler. These variants are available via modules:
-|Module|Compiler|
-|---|---|
-| gsl/1.16-gcc|gcc 4.8.6|
-|gsl/1.16-icc(default)|icc|
+| Module | Compiler |
+| --------------------- | --------- |
+| gsl/1.16-gcc | gcc 4.8.6 |
+| gsl/1.16-icc(default) | icc |
```bash
$ module load gsl
@@ -60,8 +57,8 @@ The GSL 1.16 is available on Anselm, compiled for GNU and Intel compiler. These
The module sets up environment variables, required for linking and running GSL enabled applications. This particular command loads the default module, which is gsl/1.16-icc
-Linking
--------
+## Linking
+
Load an appropriate gsl module. Link using **-lgsl** switch to link your code against GSL. The GSL depends on cblas API to BLAS library, which must be supplied for linking. The BLAS may be provided, for example from the MKL library, as well as from the BLAS GSL library (-lgslcblas). Using the MKL is recommended.
### Compiling and linking with Intel compilers
@@ -81,8 +78,8 @@ Load an appropriate gsl module. Link using **-lgsl** switch to link your code ag
$ gcc myprog.c -o myprog.x -Wl,-rpath=$LIBRARY_PATH -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lgsl
```
-Example
--------
+## Example
+
Following is an example of discrete wavelet transform implemented by GSL:
```cpp
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/hdf5.md b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
index ae758f5e09d24495f2e64d340230d59448eb4b37..238d1cb9ad29a458d846ba0922b2f243ca711386 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
@@ -1,5 +1,4 @@
-HDF5
-====
+# HDF5
Hierarchical Data Format library. Serial and MPI parallel version.
@@ -7,15 +6,15 @@ Hierarchical Data Format library. Serial and MPI parallel version.
Versions **1.8.11** and **1.8.13** of HDF5 library are available on Anselm, compiled for **Intel MPI** and **OpenMPI** using **intel** and **gnu** compilers. These are available via modules:
- |Version |Parallelization |module |C linker options|C++ linker options|Fortran linker options |
- | --- | --- |
- |HDF5 icc serial |pthread |hdf5/1.8.11 |$HDF5_INC $HDF5_SHLIB |$HDF5_INC $HDF5_CPP_LIB |$HDF5_INC $HDF5_F90_LIB |
- |HDF5 icc parallel MPI |pthread, IntelMPI |hdf5-parallel/1.8.11 |$HDF5_INC $HDF5_SHLIB |Not supported |$HDF5_INC $HDF5_F90_LIB |
- |HDF5 icc serial |pthread |hdf5/1.8.13 |$HDF5_INC $HDF5_SHLIB |$HDF5_INC $HDF5_CPP_LIB |$HDF5_INC $HDF5_F90_LIB |
- |HDF5 icc parallel MPI |pthread, IntelMPI |hdf5-parallel/1.8.13 |$HDF5_INC $HDF5_SHLIB |Not supported |$HDF5_INC $HDF5_F90_LIB |
- |HDF5 gcc parallel MPI |pthread, OpenMPI 1.6.5, gcc 4.8.1 |hdf5-parallel/1.8.11-gcc |$HDF5_INC $HDF5_SHLIB |Not supported |$HDF5_INC $HDF5_F90_LIB |
- |HDF5 gcc parallel MPI|pthread, OpenMPI 1.6.5, gcc 4.8.1 |hdf5-parallel/1.8.13-gcc |$HDF5_INC $HDF5_SHLIB |Not supported |$HDF5_INC $HDF5_F90_LIB |
- |HDF5 gcc parallel MPI |pthread, OpenMPI 1.8.1, gcc 4.9.0 |hdf5-parallel/1.8.13-gcc49 |$HDF5_INC $HDF5_SHLIB |Not supported |$HDF5_INC $HDF5_F90_LIB |
+| Version | Parallelization | module | C linker options | C++ linker options | Fortran linker options |
+| --------------------- | --------------------------------- | -------------------------- | --------------------- | ----------------------- | ----------------------- |
+| HDF5 icc serial | pthread | hdf5/1.8.11 | $HDF5_INC $HDF5_SHLIB | $HDF5_INC $HDF5_CPP_LIB | $HDF5_INC $HDF5_F90_LIB |
+| HDF5 icc parallel MPI | pthread, IntelMPI | hdf5-parallel/1.8.11 | $HDF5_INC $HDF5_SHLIB | Not supported | $HDF5_INC $HDF5_F90_LIB |
+| HDF5 icc serial | pthread | hdf5/1.8.13 | $HDF5_INC $HDF5_SHLIB | $HDF5_INC $HDF5_CPP_LIB | $HDF5_INC $HDF5_F90_LIB |
+| HDF5 icc parallel MPI | pthread, IntelMPI | hdf5-parallel/1.8.13 | $HDF5_INC $HDF5_SHLIB | Not supported | $HDF5_INC $HDF5_F90_LIB |
+| HDF5 gcc parallel MPI | pthread, OpenMPI 1.6.5, gcc 4.8.1 | hdf5-parallel/1.8.11-gcc | $HDF5_INC $HDF5_SHLIB | Not supported | $HDF5_INC $HDF5_F90_LIB |
+| HDF5 gcc parallel MPI | pthread, OpenMPI 1.6.5, gcc 4.8.1 | hdf5-parallel/1.8.13-gcc | $HDF5_INC $HDF5_SHLIB | Not supported | $HDF5_INC $HDF5_F90_LIB |
+| HDF5 gcc parallel MPI | pthread, OpenMPI 1.8.1, gcc 4.9.0 | hdf5-parallel/1.8.13-gcc49 | $HDF5_INC $HDF5_SHLIB | Not supported | $HDF5_INC $HDF5_F90_LIB |
```bash
$ module load hdf5-parallel
@@ -26,10 +25,9 @@ The module sets up environment variables, required for linking and running HDF5
!!! Note "Note"
Be aware, that GCC version of **HDF5 1.8.11** has serious performance issues, since it's compiled with -O0 optimization flag. This version is provided only for testing of code compiled only by GCC and IS NOT recommended for production computations. For more information, please see: <http://www.hdfgroup.org/ftp/HDF5/prev-releases/ReleaseFiles/release5-1811>
- All GCC versions of **HDF5 1.8.13** are not affected by the bug, are compiled with -O3 optimizations and are recommended for production computations.
+ All GCC versions of **HDF5 1.8.13** are not affected by the bug, are compiled with -O3 optimizations and are recommended for production computations.
-Example
--------
+## Example
```cpp
#include "hdf5.h"
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
index 0683f6bd1a65e784f3277bf980be437ecf07a21d..8a79b9961d7f158bb369dc65f6ea6e21896b09ac 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
@@ -1,10 +1,9 @@
-Intel numerical libraries
-=========================
+# Intel numerical libraries
Intel libraries for high performance in numerical computing
-Intel Math Kernel Library
--------------------------
+## Intel Math Kernel Library
+
Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, extensively threaded and optimized for maximum performance. Intel MKL unites and provides these basic components: BLAS, LAPACK, ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and many more.
```bash
@@ -13,8 +12,8 @@ Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, e
Read more at the [Intel MKL](../intel-suite/intel-mkl/) page.
-Intel Integrated Performance Primitives
----------------------------------------
+## Intel Integrated Performance Primitives
+
Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is available, via module ipp. The IPP is a library of highly optimized algorithmic building blocks for media and data applications. This includes signal, image and frame processing algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many more.
```bash
@@ -23,8 +22,8 @@ Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is avai
Read more at the [Intel IPP](../intel-suite/intel-integrated-performance-primitives/) page.
-Intel Threading Building Blocks
--------------------------------
+## Intel Threading Building Blocks
+
Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. It is designed to promote scalable data parallel programming. Additionally, it fully supports nested parallelism, so you can build larger parallel components from smaller parallel components. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner.
```bash
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
index e8c956b5decbcbc5d757dcb287f7504a735b0784..5c0c9f27f0ec508f3e90d871508c215bab580eef 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
@@ -1,5 +1,4 @@
-MAGMA for Intel Xeon Phi
-========================
+# MAGMA for Intel Xeon Phi
Next generation dense algebra library for heterogeneous systems with accelerators
@@ -75,9 +74,8 @@ To test if the MAGMA server runs properly we can run one of examples that are pa
MAGMA relies on the performance of all CPU cores as well as on the performance of the accelerator. Therefore on Anselm number of CPU OpenMP threads has to be set to 16:
**export OMP_NUM_THREADS=16**
-
See more details at [MAGMA home page](http://icl.cs.utk.edu/magma/).
-References
-----------
-[1] MAGMA MIC: Linear Algebra Library for Intel Xeon Phi Coprocessors, Jack Dongarra et. al, [http://icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf](http://icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf)
+## References
+
+[1] MAGMA MIC: Linear Algebra Library for Intel Xeon Phi Coprocessors, Jack Dongarra et. al, <http://icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf>
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.md b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.md
index 3be05fe85a496fb88fa8cabf153b8b715a481100..cfdffd82dd0338bb5f6544c239378e0308f8e2c5 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.md
@@ -1,22 +1,20 @@
-PETSc
-=====
+# PETSc
PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modeled by partial differential equations. It supports MPI, shared memory, and GPU through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism.
-Introduction
-------------
+## Introduction
+
PETSc (Portable, Extensible Toolkit for Scientific Computation) is a suite of building blocks (data structures and routines) for the scalable solution of scientific and engineering applications modelled by partial differential equations. It allows thinking in terms of high-level objects (matrices) instead of low-level objects (raw arrays). Written in C language but can also be called from FORTRAN, C++, Python and Java codes. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism.
-Resources
----------
+## Resources
+
- [project webpage](http://www.mcs.anl.gov/petsc/)
- [documentation](http://www.mcs.anl.gov/petsc/documentation/)
- [PETSc Users Manual (PDF)](http://www.mcs.anl.gov/petsc/petsc-current/docs/manual.pdf)
- [index of all manual pages](http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/singleindex.html)
- PRACE Video Tutorial [part1](http://www.youtube.com/watch?v=asVaFg1NDqY), [part2](http://www.youtube.com/watch?v=ubp_cSibb9I), [part3](http://www.youtube.com/watch?v=vJAAAQv-aaw), [part4](http://www.youtube.com/watch?v=BKVlqWNh8jY), [part5](http://www.youtube.com/watch?v=iXkbLEBFjlM)
-Modules
--------
+## Modules
You can start using PETSc on Anselm by loading the PETSc module. Module names obey this pattern:
@@ -27,8 +25,8 @@ You can start using PETSc on Anselm by loading the PETSc module. Module names ob
where `variant` is replaced by one of `{dbg, opt, threads-dbg, threads-opt}`. The `opt` variant is compiled without debugging information (no `-g` option) and with aggressive compiler optimizations (`-O3 -xAVX`). This variant is suitable for performance measurements and production runs. In all other cases use the debug (`dbg`) variant, because it contains debugging information, performs validations and self-checks, and provides a clear stack trace and message in case of an error. The other two variants `threads-dbg` and `threads-opt` are `dbg` and `opt`, respectively, built with [OpenMP and pthreads threading support](https://www.mcs.anl.gov/petsc/miscellaneous/petscthreads.html).
-External libraries
-------------------
+## External libraries
+
PETSc needs at least MPI, BLAS and LAPACK. These dependencies are currently satisfied with Intel MPI and Intel MKL in Anselm `petsc` modules.
PETSc can be linked with a plethora of [external numerical libraries](http://www.mcs.anl.gov/petsc/miscellaneous/external.html), extending PETSc functionality, e.g. direct linear system solvers, preconditioners or partitioners. See below a list of libraries currently included in Anselm `petsc` modules.
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/trilinos.md b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
index e4ca472867371b26240e5d5ade9f0c9f441d265e..761a42ca80af58e474eff4e2d9b8480d4943f791 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
@@ -1,5 +1,4 @@
-Trilinos
-========
+# Trilinos
Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization.
diff --git a/docs.it4i/anselm-cluster-documentation/software/nvidia-cuda.md b/docs.it4i/anselm-cluster-documentation/software/nvidia-cuda.md
index 2161674281cbc34891aa015bbdd1a22ba4d55f24..89b88d808b6d0e18ca119d46e0ac45c9a7a5f104 100644
--- a/docs.it4i/anselm-cluster-documentation/software/nvidia-cuda.md
+++ b/docs.it4i/anselm-cluster-documentation/software/nvidia-cuda.md
@@ -1,10 +1,9 @@
-NVIDIA CUDA
-===========
+# NVIDIA CUDA
-##A guide to NVIDIA CUDA programming and GPU usage
+\##A guide to NVIDIA CUDA programming and GPU usage
+
+## CUDA Programming on Anselm
-CUDA Programming on Anselm
---------------------------
The default programming model for GPU accelerators on Anselm is Nvidia CUDA. To set up the environment for CUDA use
```bash
@@ -193,8 +192,7 @@ To run the code use interactive PBS session to get access to one of the GPU acce
$ ./test.cuda
```
-CUDA Libraries
---------------
+## CUDA Libraries
### cuBLAS
@@ -285,8 +283,8 @@ SAXPY function multiplies the vector x by the scalar alpha and adds it to the ve
!!! Note "Note"
Please note: cuBLAS has its own function for data transfers between CPU and GPU memory:
- - [cublasSetVector](http://docs.nvidia.com/cuda/cublas/index.html#cublassetvector) - transfers data from CPU to GPU memory
- - [cublasGetVector](http://docs.nvidia.com/cuda/cublas/index.html#cublasgetvector) - transfers data from GPU to CPU memory
+ - [cublasSetVector](http://docs.nvidia.com/cuda/cublas/index.html#cublassetvector) - transfers data from CPU to GPU memory
+ - [cublasGetVector](http://docs.nvidia.com/cuda/cublas/index.html#cublasgetvector) - transfers data from GPU to CPU memory
To compile the code using NVCC compiler a "-lcublas" compiler flag has to be specified:
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 a02517c34f360d9197d5ab25ff09c9ad3d61a23c..80ae515bd495524c9bdf7806f82a741afdcf38a7 100644
--- a/docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md
+++ b/docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md
@@ -60,22 +60,22 @@ It is a human readable tab-delimited format in which each read and its alignment
The SAM format (1) consists of one header section and one alignment section. The lines in the header section start with character â€@’, and lines in the alignment section do not. All lines are TAB delimited.
-In SAM, each alignment line has 11 mandatory fields and a variable number of optional fields. The mandatory fields are briefly described in Table 1. They must be present but their value can be a â€*’ or a zero (depending on the field) if the
+In SAM, each alignment line has 11 mandatory fields and a variable number of optional fields. The mandatory fields are briefly described in Table 1. They must be present but their value can be a â€\*’ or a zero (depending on the field) if the
corresponding information is unavailable.
- |** No. **|** Name **|** Description **|
- |--|--|--|
- |1|QNAME|Query NAME of the read or the read pai|
- |2|FLAG|Bitwise FLAG (pairing,strand,mate strand,etc.)|
- |3|RNAME|<p>Reference sequence NAME|
- |4|POS|<p>1-Based leftmost POSition of clipped alignment|
- |5|MAPQ|<p>MAPping Quality (Phred-scaled)|
- |6|CIGAR|<p>Extended CIGAR string (operations:MIDNSHP)|
- |7|MRNM|<p>Mate REference NaMe ('=' if same RNAME)|
- |8|MPOS|<p>1-Based leftmost Mate POSition|
- |9|ISIZE|<p>Inferred Insert SIZE|
- |10|SEQ|<p>Query SEQuence on the same strand as the reference|
- |11|QUAL|<p>Query QUALity (ASCII-33=Phred base quality)|
+| ** No. ** | ** Name ** | ** Description ** |
+| --------- | ---------- | ----------------------------------------------------- |
+| 1 | QNAME | Query NAME of the read or the read pai |
+| 2 | FLAG | Bitwise FLAG (pairing,strand,mate strand,etc.) |
+| 3 | RNAME | <p>Reference sequence NAME |
+| 4 | POS | <p>1-Based leftmost POSition of clipped alignment |
+| 5 | MAPQ | <p>MAPping Quality (Phred-scaled) |
+| 6 | CIGAR | <p>Extended CIGAR string (operations:MIDNSHP) |
+| 7 | MRNM | <p>Mate REference NaMe ('=' if same RNAME) |
+| 8 | MPOS | <p>1-Based leftmost Mate POSition |
+| 9 | ISIZE | <p>Inferred Insert SIZE |
+| 10 | SEQ | <p>Query SEQuence on the same strand as the reference |
+| 11 | QUAL | <p>Query QUALity (ASCII-33=Phred base quality) |
** Table 1 **. Mandatory fields in the SAM format.
@@ -95,13 +95,13 @@ BAM is the binary representation of SAM and keeps exactly the same information a
Some features
-* Quality control
- * reads with N errors
- * reads with multiple mappings
- * strand bias
- * paired-end insert
-* Filtering: by number of errors, number of hits
- * Comparator: stats, intersection, ...
+- Quality control
+ - reads with N errors
+ - reads with multiple mappings
+ - strand bias
+ - paired-end insert
+- Filtering: by number of errors, number of hits
+ - Comparator: stats, intersection, ...
** Input: ** BAM file.
@@ -207,7 +207,6 @@ If we launch ngsPipeline with â€-h’, we will get the usage help:
Initial stage
-e END, --end END Final stage
--log Log to file
-
```
Let us see a brief description of the arguments:
@@ -291,55 +290,55 @@ If we want to re-launch the pipeline from stage 4 until stage 20 we should use t
The pipeline calls the following tools
-* [fastqc](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), quality control tool for high throughput sequence data.
-* [gatk](https://www.broadinstitute.org/gatk/), The Genome Analysis Toolkit or GATK is a software package developed at
- the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
-* [hpg-aligner](https://github.com/opencb-hpg/hpg-aligner), HPG Aligner has been designed to align short and long reads with high sensitivity, therefore any number of mismatches or indels are allowed. HPG Aligner implements and combines two well known algorithms: *Burrows-Wheeler Transform* (BWT) to speed-up mapping high-quality reads, and *Smith-Waterman*> (SW) to increase sensitivity when reads cannot be mapped using BWT.
-* [hpg-fastq](http://docs.bioinfo.cipf.es/projects/fastqhpc/wiki), a quality control tool for high throughput sequence data.
-* [hpg-variant](http://docs.bioinfo.cipf.es/projects/hpg-variant/wiki), The HPG Variant suite is an ambitious project aimed to provide a complete suite of tools to work with genomic variation data, from VCF tools to variant profiling or genomic statistics. It is being implemented using High Performance Computing technologies to provide the best performance possible.
-* [picard](http://picard.sourceforge.net/), Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (HTSJDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.
-* [samtools](http://samtools.sourceforge.net/samtools-c.shtml), SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
-* [snpEff](http://snpeff.sourceforge.net/), Genetic variant annotation and effect prediction toolbox.
+- [fastqc](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), quality control tool for high throughput sequence data.
+- [gatk](https://www.broadinstitute.org/gatk/), The Genome Analysis Toolkit or GATK is a software package developed at
+ the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
+- [hpg-aligner](https://github.com/opencb-hpg/hpg-aligner), HPG Aligner has been designed to align short and long reads with high sensitivity, therefore any number of mismatches or indels are allowed. HPG Aligner implements and combines two well known algorithms: _Burrows-Wheeler Transform_ (BWT) to speed-up mapping high-quality reads, and _Smith-Waterman_> (SW) to increase sensitivity when reads cannot be mapped using BWT.
+- [hpg-fastq](http://docs.bioinfo.cipf.es/projects/fastqhpc/wiki), a quality control tool for high throughput sequence data.
+- [hpg-variant](http://docs.bioinfo.cipf.es/projects/hpg-variant/wiki), The HPG Variant suite is an ambitious project aimed to provide a complete suite of tools to work with genomic variation data, from VCF tools to variant profiling or genomic statistics. It is being implemented using High Performance Computing technologies to provide the best performance possible.
+- [picard](http://picard.sourceforge.net/), Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (HTSJDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.
+- [samtools](http://samtools.sourceforge.net/samtools-c.shtml), SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
+- [snpEff](http://snpeff.sourceforge.net/), Genetic variant annotation and effect prediction toolbox.
This listing show which tools are used in each step of the pipeline
-* stage-00: fastqc
-* stage-01: hpg_fastq
-* stage-02: fastqc
-* stage-03: hpg_aligner and samtools
-* stage-04: samtools
-* stage-05: samtools
-* stage-06: fastqc
-* stage-07: picard
-* stage-08: fastqc
-* stage-09: picard
-* stage-10: gatk
-* stage-11: gatk
-* stage-12: gatk
-* stage-13: gatk
-* stage-14: gatk
-* stage-15: gatk
-* stage-16: samtools
-* stage-17: samtools
-* stage-18: fastqc
-* stage-19: gatk
-* stage-20: gatk
-* stage-21: gatk
-* stage-22: gatk
-* stage-23: gatk
-* stage-24: hpg-variant
-* stage-25: hpg-variant
-* stage-26: snpEff
-* stage-27: snpEff
-* stage-28: hpg-variant
+- stage-00: fastqc
+- stage-01: hpg_fastq
+- stage-02: fastqc
+- stage-03: hpg_aligner and samtools
+- stage-04: samtools
+- stage-05: samtools
+- stage-06: fastqc
+- stage-07: picard
+- stage-08: fastqc
+- stage-09: picard
+- stage-10: gatk
+- stage-11: gatk
+- stage-12: gatk
+- stage-13: gatk
+- stage-14: gatk
+- stage-15: gatk
+- stage-16: samtools
+- stage-17: samtools
+- stage-18: fastqc
+- stage-19: gatk
+- stage-20: gatk
+- stage-21: gatk
+- stage-22: gatk
+- stage-23: gatk
+- stage-24: hpg-variant
+- stage-25: hpg-variant
+- stage-26: snpEff
+- stage-27: snpEff
+- stage-28: hpg-variant
## Interpretation
The output folder contains all the subfolders with the intermediate data. This folder contains the final VCF with all the variants. This file can be uploaded into [TEAM](diagnostic-component-team.html) by using the VCF file button. It is important to note here that the entire management of the VCF file is local: no patient’s sequence data is sent over the Internet thus avoiding any problem of data privacy or confidentiality.
-
+![TEAM upload panel. Once the file has been uploaded, a panel must be chosen from the Panel list. Then, pressing the Run button the diagnostic process starts.]\((../../../img/fig7.png)
-** Figure 7. ** *TEAM upload panel.* *Once the file has been uploaded, a panel must be chosen from the Panel* list. Then, pressing the Run button the diagnostic process starts.
+** Figure 7. ** _TEAM upload panel._ _Once the file has been uploaded, a panel must be chosen from the Panel_ list. Then, pressing the Run button the diagnostic process starts.
Once the file has been uploaded, a panel must be chosen from the Panel list. Then, pressing the Run button the diagnostic process starts. TEAM searches first for known diagnostic mutation(s) taken from four databases: HGMD-public (20), [HUMSAVAR](http://www.uniprot.org/docs/humsavar), ClinVar (29) and COSMIC (23).
@@ -349,9 +348,9 @@ Once the file has been uploaded, a panel must be chosen from the Panel list. The
For variant discovering/filtering we should upload the VCF file into BierApp by using the following form:
-**
+__
-** Figure 8 **. *BierApp VCF upload panel. It is recommended to choose a name for the job as well as a description **.
+** Figure 8 **. \*BierApp VCF upload panel. It is recommended to choose a name for the job as well as a description \*\*.
Each prioritization (â€job’) has three associated screens that facilitate 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).
@@ -361,32 +360,32 @@ Each prioritization (â€job’) has three associated screens that facilitate the
## References
-1. Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth5, Goncalo Abecasis6, Richard Durbin and 1000 Genome Project Data Processing Subgroup: The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25: 2078-2079.
-1. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. *Genome Res* >2010, 20:1297-1303.
-1. Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert E. Handsaker, Gerton Lunter, Gabor T. Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin, and 1000 Genomes Project Analysis Group. The variant call format and VCFtools. Bioinformatics 2011, 27: 2156-2158.
-1. Medina I, De Maria A, Bleda M, Salavert F, Alonso R, Gonzalez CY, Dopazo J: VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing. Nucleic Acids Res 2012, 40:W54-58.
-1. Bleda M, Tarraga J, de Maria A, Salavert F, Garcia-Alonso L, Celma M, Martin A, Dopazo J, Medina I: CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. Nucleic Acids Res 2012, 40:W609-614.
-1. Flicek,P., Amode,M.R., Barrell,D., Beal,K., Brent,S., Carvalho-Silva,D., Clapham,P., Coates,G., Fairley,S., Fitzgerald,S. et al. (2012) Ensembl 2012. Nucleic Acids Res., 40, D84–D90.
-1. UniProt Consortium. (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res., 40, D71–D75.
-1. Kozomara,A. and Griffiths-Jones,S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 39, D152–D157.
-1. Xiao,F., Zuo,Z., Cai,G., Kang,S., Gao,X. and Li,T. (2009) miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res., 37, D105–D110.
-1. Hsu,S.D., Lin,F.M., Wu,W.Y., Liang,C., Huang,W.C., Chan,W.L., Tsai,W.T., Chen,G.Z., Lee,C.J., Chiu,C.M. et al. (2011) miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res., 39, D163–D169.
-1. Friedman,R.C., Farh,K.K., Burge,C.B. and Bartel,D.P. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 19, 92–105. 12. Betel,D., Wilson,M., Gabow,A., Marks,D.S. and Sander,C. (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res., 36, D149–D153.
-1. Dreszer,T.R., Karolchik,D., Zweig,A.S., Hinrichs,A.S., Raney,B.J., Kuhn,R.M., Meyer,L.R., Wong,M., Sloan,C.A., Rosenbloom,K.R. et al. (2012) The UCSC genome browser database: extensions and updates 2011. Nucleic Acids Res.,40, D918–D923.
-1. Smith,B., Ashburner,M., Rosse,C., Bard,J., Bug,W., Ceusters,W., Goldberg,L.J., Eilbeck,K., Ireland,A., Mungall,C.J. et al. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol., 25, 1251–1255.
-1. Hunter,S., Jones,P., Mitchell,A., Apweiler,R., Attwood,T.K.,Bateman,A., Bernard,T., Binns,D., Bork,P., Burge,S. et al. (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res.,40, D306–D312.
-1. Sherry,S.T., Ward,M.H., Kholodov,M., Baker,J., Phan,L., Smigielski,E.M. and Sirotkin,K. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res., 29, 308–311.
-1. Altshuler,D.M., Gibbs,R.A., Peltonen,L., Dermitzakis,E., Schaffner,S.F., Yu,F., Bonnen,P.E., de Bakker,P.I., Deloukas,P., Gabriel,S.B. et al. (2010) Integrating common and rare genetic variation in diverse human populations. Nature, 467, 52–58.
-1. 1000 Genomes Project Consortium. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061–1073.
-1. Hindorff,L.A., Sethupathy,P., Junkins,H.A., Ramos,E.M., Mehta,J.P., Collins,F.S. and Manolio,T.A. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA, 106, 9362–9367.
-1. Stenson,P.D., Ball,E.V., Mort,M., Phillips,A.D., Shiel,J.A., Thomas,N.S., Abeysinghe,S., Krawczak,M. and Cooper,D.N. (2003) Human gene mutation database (HGMD): 2003 update. Hum. Mutat., 21, 577–581.
-1. Johnson,A.D. and O’Donnell,C.J. (2009) An open access database of genome-wide association results. BMC Med. Genet, 10, 6.
-1. McKusick,V. (1998) A Catalog of Human Genes and Genetic Disorders, 12th edn. John Hopkins University Press,Baltimore, MD.
-1. Forbes,S.A., Bindal,N., Bamford,S., Cole,C., Kok,C.Y., Beare,D., Jia,M., Shepherd,R., Leung,K., Menzies,A. et al. (2011) COSMIC: mining complete cancer genomes in the catalogue of somatic mutations in cancer. Nucleic Acids Res., 39, D945–D950.
-1. Kerrien,S., Aranda,B., Breuza,L., Bridge,A., Broackes-Carter,F., Chen,C., Duesbury,M., Dumousseau,M., Feuermann,M., Hinz,U. et al. (2012) The Intact molecular interaction database in 2012. Nucleic Acids Res., 40, D841–D846.
-1. Croft,D., O’Kelly,G., Wu,G., Haw,R., Gillespie,M., Matthews,L., Caudy,M., Garapati,P., Gopinath,G., Jassal,B. et al. (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res., 39, D691–D697.
-1. Demir,E., Cary,M.P., Paley,S., Fukuda,K., Lemer,C., Vastrik,I.,Wu,G., D’Eustachio,P., Schaefer,C., Luciano,J. et al. (2010) The BioPAX community standard for pathway data sharing. Nature Biotechnol., 28, 935–942.
-1. Alemán Z, GarcĂa-GarcĂa F, Medina I, Dopazo J (2014): A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications. Nucleic Acids Res 42: W83-7.
-1. [Alemán A](http://www.ncbi.nlm.nih.gov/pubmed?term=Alem%C3%A1n%20A%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Garcia-Garcia F](http://www.ncbi.nlm.nih.gov/pubmed?term=Garcia-Garcia%20F%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Salavert F](http://www.ncbi.nlm.nih.gov/pubmed?term=Salavert%20F%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Medina I](http://www.ncbi.nlm.nih.gov/pubmed?term=Medina%20I%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Dopazo J](http://www.ncbi.nlm.nih.gov/pubmed?term=Dopazo%20J%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)> (2014). A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. [Nucleic Acids Res.](http://www.ncbi.nlm.nih.gov/pubmed/?term=BiERapp "Nucleic acids research.")>42 :W88-93.
-1. Landrum,M.J., Lee,J.M., Riley,G.R., Jang,W., Rubinstein,W.S., Church,D.M. and Maglott,D.R. (2014) ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res., 42, D980–D985.
-1. Medina I, Salavert F, Sanchez R, de Maria A, Alonso R, Escobar P, Bleda M, Dopazo J: Genome Maps, a new generation genome browser. Nucleic Acids Res 2013, 41:W41-46.
+1. Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth5, Goncalo Abecasis6, Richard Durbin and 1000 Genome Project Data Processing Subgroup: The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25: 2078-2079.
+2. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. _Genome Res_ >2010, 20:1297-1303.
+3. Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert E. Handsaker, Gerton Lunter, Gabor T. Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin, and 1000 Genomes Project Analysis Group. The variant call format and VCFtools. Bioinformatics 2011, 27: 2156-2158.
+4. Medina I, De Maria A, Bleda M, Salavert F, Alonso R, Gonzalez CY, Dopazo J: VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing. Nucleic Acids Res 2012, 40:W54-58.
+5. Bleda M, Tarraga J, de Maria A, Salavert F, Garcia-Alonso L, Celma M, Martin A, Dopazo J, Medina I: CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. Nucleic Acids Res 2012, 40:W609-614.
+6. Flicek,P., Amode,M.R., Barrell,D., Beal,K., Brent,S., Carvalho-Silva,D., Clapham,P., Coates,G., Fairley,S., Fitzgerald,S. et al. (2012) Ensembl 2012. Nucleic Acids Res., 40, D84–D90.
+7. UniProt Consortium. (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res., 40, D71–D75.
+8. Kozomara,A. and Griffiths-Jones,S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 39, D152–D157.
+9. Xiao,F., Zuo,Z., Cai,G., Kang,S., Gao,X. and Li,T. (2009) miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res., 37, D105–D110.
+10. Hsu,S.D., Lin,F.M., Wu,W.Y., Liang,C., Huang,W.C., Chan,W.L., Tsai,W.T., Chen,G.Z., Lee,C.J., Chiu,C.M. et al. (2011) miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res., 39, D163–D169.
+11. Friedman,R.C., Farh,K.K., Burge,C.B. and Bartel,D.P. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 19, 92–105. 12. Betel,D., Wilson,M., Gabow,A., Marks,D.S. and Sander,C. (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res., 36, D149–D153.
+12. Dreszer,T.R., Karolchik,D., Zweig,A.S., Hinrichs,A.S., Raney,B.J., Kuhn,R.M., Meyer,L.R., Wong,M., Sloan,C.A., Rosenbloom,K.R. et al. (2012) The UCSC genome browser database: extensions and updates 2011. Nucleic Acids Res.,40, D918–D923.
+13. Smith,B., Ashburner,M., Rosse,C., Bard,J., Bug,W., Ceusters,W., Goldberg,L.J., Eilbeck,K., Ireland,A., Mungall,C.J. et al. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol., 25, 1251–1255.
+14. Hunter,S., Jones,P., Mitchell,A., Apweiler,R., Attwood,T.K.,Bateman,A., Bernard,T., Binns,D., Bork,P., Burge,S. et al. (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res.,40, D306–D312.
+15. Sherry,S.T., Ward,M.H., Kholodov,M., Baker,J., Phan,L., Smigielski,E.M. and Sirotkin,K. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res., 29, 308–311.
+16. Altshuler,D.M., Gibbs,R.A., Peltonen,L., Dermitzakis,E., Schaffner,S.F., Yu,F., Bonnen,P.E., de Bakker,P.I., Deloukas,P., Gabriel,S.B. et al. (2010) Integrating common and rare genetic variation in diverse human populations. Nature, 467, 52–58.
+17. 1000 Genomes Project Consortium. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061–1073.
+18. Hindorff,L.A., Sethupathy,P., Junkins,H.A., Ramos,E.M., Mehta,J.P., Collins,F.S. and Manolio,T.A. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA, 106, 9362–9367.
+19. Stenson,P.D., Ball,E.V., Mort,M., Phillips,A.D., Shiel,J.A., Thomas,N.S., Abeysinghe,S., Krawczak,M. and Cooper,D.N. (2003) Human gene mutation database (HGMD): 2003 update. Hum. Mutat., 21, 577–581.
+20. Johnson,A.D. and O’Donnell,C.J. (2009) An open access database of genome-wide association results. BMC Med. Genet, 10, 6.
+21. McKusick,V. (1998) A Catalog of Human Genes and Genetic Disorders, 12th edn. John Hopkins University Press,Baltimore, MD.
+22. Forbes,S.A., Bindal,N., Bamford,S., Cole,C., Kok,C.Y., Beare,D., Jia,M., Shepherd,R., Leung,K., Menzies,A. et al. (2011) COSMIC: mining complete cancer genomes in the catalogue of somatic mutations in cancer. Nucleic Acids Res., 39, D945–D950.
+23. Kerrien,S., Aranda,B., Breuza,L., Bridge,A., Broackes-Carter,F., Chen,C., Duesbury,M., Dumousseau,M., Feuermann,M., Hinz,U. et al. (2012) The Intact molecular interaction database in 2012. Nucleic Acids Res., 40, D841–D846.
+24. Croft,D., O’Kelly,G., Wu,G., Haw,R., Gillespie,M., Matthews,L., Caudy,M., Garapati,P., Gopinath,G., Jassal,B. et al. (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res., 39, D691–D697.
+25. Demir,E., Cary,M.P., Paley,S., Fukuda,K., Lemer,C., Vastrik,I.,Wu,G., D’Eustachio,P., Schaefer,C., Luciano,J. et al. (2010) The BioPAX community standard for pathway data sharing. Nature Biotechnol., 28, 935–942.
+26. Alemán Z, GarcĂa-GarcĂa F, Medina I, Dopazo J (2014): A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications. Nucleic Acids Res 42: W83-7.
+27. [Alemán A](http://www.ncbi.nlm.nih.gov/pubmed?term=Alem%C3%A1n%20A%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Garcia-Garcia F](http://www.ncbi.nlm.nih.gov/pubmed?term=Garcia-Garcia%20F%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Salavert F](http://www.ncbi.nlm.nih.gov/pubmed?term=Salavert%20F%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Medina I](http://www.ncbi.nlm.nih.gov/pubmed?term=Medina%20I%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Dopazo J](http://www.ncbi.nlm.nih.gov/pubmed?term=Dopazo%20J%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)> (2014). A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. [Nucleic Acids Res.](http://www.ncbi.nlm.nih.gov/pubmed/?term=BiERapp "Nucleic acids research.")>42 :W88-93.
+28. Landrum,M.J., Lee,J.M., Riley,G.R., Jang,W., Rubinstein,W.S., Church,D.M. and Maglott,D.R. (2014) ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res., 42, D980–D985.
+29. Medina I, Salavert F, Sanchez R, de Maria A, Alonso R, Escobar P, Bleda M, Dopazo J: Genome Maps, a new generation genome browser. Nucleic Acids Res 2013, 41:W41-46.
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 53f94e0125e713fa5f902f09047f295cb9fd9ff6..6f88fecc7b92de4bd29a6e022902cb06dbbf1300 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
@@ -17,4 +17,3 @@ BiERapp (28) efficiently helps in the identification of causative variants in fa
** 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 56f9d6985d02b42c09a68cefd8b3a39523955a61..5fefbfdd71c1e673abe4b8528d033852a308b288 100644
--- a/docs.it4i/anselm-cluster-documentation/software/openfoam.md
+++ b/docs.it4i/anselm-cluster-documentation/software/openfoam.md
@@ -1,34 +1,33 @@
-OpenFOAM
-========
+# OpenFOAM
-##A free, open source CFD software package
+\##A free, open source CFD software package
+
+## Introduction
-Introduction
-----------------
OpenFOAM is a free, open source CFD software package developed by [**OpenCFD Ltd**](http://www.openfoam.com/about) at [**ESI Group**](http://www.esi-group.com/) and distributed by the [**OpenFOAM Foundation **](http://www.openfoam.org/). It has a large user base across most areas of engineering and science, from both commercial and academic organisations.
Homepage: <http://www.openfoam.com/>
-###Installed version
+\###Installed version
Currently, several version compiled by GCC/ICC compilers in single/double precision with several version of openmpi are available on Anselm.
For example syntax of available OpenFOAM module is:
-< openfoam/2.2.1-icc-openmpi1.6.5-DP >
+< openfoam/2.2.1-icc-openmpi1.6.5-DP >
this means openfoam version 2.2.1 compiled by ICC compiler with openmpi1.6.5 in double precision.
Naming convection of the installed versions is following:
-openfoam/<>VERSION>>-<>COMPILER<span>>-<</span><span>openmpiVERSION</span><span>>-<</span><span>PRECISION</span><span>></span>
+openfoam/<>VERSION>>-<>COMPILER<span>>-<</span><span>openmpiVERSION</span><span>>-<</span><span>PRECISION</span><span>></span>
-- <VERSION>> - version of openfoam
-- <COMPILER> - version of used compiler
-- <openmpiVERSION> - version of used openmpi/impi
-- <PRECISION> - DP/SP – double/single precision
+- <VERSION>> - version of openfoam
+- <COMPILER> - version of used compiler
+- <openmpiVERSION> - version of used openmpi/impi
+- <PRECISION> - DP/SP – double/single precision
-###Available OpenFOAM modules
+\###Available OpenFOAM modules
To check available modules use
@@ -48,8 +47,7 @@ In /opt/modules/modulefiles/engineering you can see installed engineering softwa
For information how to use modules please [look here](../environment-and-modules/ "Environment and Modules ").
-Getting Started
--------------------
+## Getting Started
To create OpenFOAM environment on ANSELM give the commands:
@@ -62,7 +60,7 @@ To create OpenFOAM environment on ANSELM give the commands:
!!! Note "Note"
Please load correct module with your requirements “compiler - GCC/ICC, precision - DP/SP”.
-Create a project directory within the $HOME/OpenFOAM directory named ><USER>-<OFversion> and create a directory named run within it, e.g. by typing:
+Create a project directory within the $HOME/OpenFOAM directory named ><USER>-<OFversion> and create a directory named run within it, e.g. by typing:
```bash
$ mkdir -p $FOAM_RUN
@@ -74,7 +72,7 @@ Project directory is now available by typing:
$ cd /home/<USER>/OpenFOAM/<USER>-<OFversion>/run
```
-<OFversion> - for example <2.2.1>
+<OFversion> - for example <2.2.1>
or
@@ -90,8 +88,7 @@ Copy the tutorial examples directory in the OpenFOAM distribution to the run dir
Now you can run the first case for example incompressible laminar flow in a cavity.
-Running Serial Applications
--------------------------------
+## Running Serial Applications
Create a Bash script >test.sh
@@ -114,10 +111,11 @@ Job submission
```bash
$ qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=16,walltime=03:00:00 test.sh
```
+
For information about job submission please [look here](../resource-allocation-and-job-execution/job-submission-and-execution/ "Job submission").
-Running applications in parallel
--------------------------------------------------
+## Running applications in parallel
+
Run the second case for example external incompressible turbulent flow - case - motorBike.
First we must run serial application bockMesh and decomposePar for preparation of parallel computation.
@@ -179,8 +177,8 @@ Job submission
```bash
$ qsub testParallel.pbs
```
-Compile your own solver
-----------------------------------------
+
+## Compile your own solver
Initialize OpenFOAM environment before compiling your solver
@@ -210,7 +208,7 @@ Rename icoFoam.C to My_icoFOAM.C
$ mv icoFoam.C My_icoFoam.C
```
-Edit >*files* file in *Make* directory:
+Edit >_files_ file in _Make_ directory:
```bash
icoFoam.C
@@ -230,5 +228,6 @@ In directory My_icoFoam give the compilation command:
$ wmake
```
-------------------------------------------------------------------------
+* * *
+
**Have a fun with OpenFOAM :)**
diff --git a/docs.it4i/anselm-cluster-documentation/software/operating-system.md b/docs.it4i/anselm-cluster-documentation/software/operating-system.md
index 03a9cf45b0da087a378c1555974b53c81e41a09b..6ecbcdabd665b51018b453e7fd043c161dfef3fe 100644
--- a/docs.it4i/anselm-cluster-documentation/software/operating-system.md
+++ b/docs.it4i/anselm-cluster-documentation/software/operating-system.md
@@ -1,7 +1,5 @@
-Operating System
-===============
+# Operating System
The operating system on Anselm is Linux - **bullx Linux Server release 6.x**
bullx Linux is based on Red Hat Enterprise Linux. bullx Linux is a Linux distribution provided by Bull and dedicated to HPC applications.
-
diff --git a/docs.it4i/anselm-cluster-documentation/software/paraview.md b/docs.it4i/anselm-cluster-documentation/software/paraview.md
index b9deba00e7e363e2089427f58dac808daba62585..57802d1c34e32acbf3a551e209f4db07a6a274d4 100644
--- a/docs.it4i/anselm-cluster-documentation/software/paraview.md
+++ b/docs.it4i/anselm-cluster-documentation/software/paraview.md
@@ -1,10 +1,8 @@
-ParaView
-========
+# ParaView
-##An open-source, multi-platform data analysis and visualization application
+\##An open-source, multi-platform data analysis and visualization application
-Introduction
-------------
+## Introduction
**ParaView** is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities.
@@ -12,12 +10,12 @@ ParaView was developed to analyze extremely large datasets using distributed mem
Homepage : <http://www.paraview.org/>
-Installed version
------------------
+## Installed version
+
Currently, version 4.0.1 compiled with GCC 4.8.1 against Bull MPI library and OSMesa 10.0 is installed on Anselm.
-Usage
------
+## Usage
+
On Anselm, ParaView is to be used in client-server mode. A parallel ParaView server is launched on compute nodes by the user, and client is launched on your desktop PC to control and view the visualization. Download ParaView client application for your OS here: <http://paraview.org/paraview/resources/software.php>. Important : **your version must match the version number installed on Anselm** ! (currently v4.0.1)
### Launching server
@@ -55,9 +53,9 @@ Because a direct connection is not allowed to compute nodes on Anselm, you must
ssh -TN -L 12345:cn77:11111 username@anselm.it4i.cz
```
-replace username with your login and cn77 with the name of compute node your ParaView server is running on (see previous step). If you use PuTTY on Windows, load Anselm connection configuration, t>hen go to Connection-> SSH>->Tunnels to set up the port forwarding. Click Remote radio button. Insert 12345 to Source port textbox. Insert cn77:11111. Click Add button, then Open.
+replace username with your login and cn77 with the name of compute node your ParaView server is running on (see previous step). If you use PuTTY on Windows, load Anselm connection configuration, t>hen go to Connection-> SSH>->Tunnels to set up the port forwarding. Click Remote radio button. Insert 12345 to Source port textbox. Insert cn77:11111. Click Add button, then Open.
-Now launch ParaView client installed on your desktop PC. Select File->Connect..., click Add Server. Fill in the following :
+Now launch ParaView client installed on your desktop PC. Select File->Connect..., click Add Server. Fill in the following :
Name : Anselm tunnel
Server Type : Client/Server
@@ -76,6 +74,6 @@ You can now use Parallel ParaView.
Remember to close the interactive session after you finish working with ParaView server, as it will remain launched even after your client is disconnected and will continue to consume resources.
-GPU support
------------
+## GPU support
+
Currently, GPU acceleration is not supported in the server and ParaView will not take advantage of accelerated nodes on Anselm. Support for GPU acceleration might be added in the future.
diff --git a/docs.it4i/anselm-cluster-documentation/storage.md b/docs.it4i/anselm-cluster-documentation/storage.md
index 3cbb15a1de47b6369872c91a8948666fb77e12f3..5f83eabeabb716873a117654d94e4f0c69541c6a 100644
--- a/docs.it4i/anselm-cluster-documentation/storage.md
+++ b/docs.it4i/anselm-cluster-documentation/storage.md
@@ -1,15 +1,12 @@
-Storage
-=======
+# Storage
There are two main shared file systems on Anselm cluster, the [HOME](#home) and [SCRATCH](#scratch). All login and compute nodes may access same data on shared file systems. Compute nodes are also equipped with local (non-shared) scratch, ramdisk and tmp file systems.
-Archiving
----------
+## Archiving
Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use [CESNET storage service](#cesnet-data-storage), which is available via SSHFS.
-Shared Filesystems
-------------------
+## Shared Filesystems
Anselm computer provides two main shared filesystems, the [HOME filesystem](#home) and the [SCRATCH filesystem](#scratch). Both HOME and SCRATCH filesystems are realized as a parallel Lustre filesystem. Both shared file systems are accessible via the Infiniband network. Extended ACLs are provided on both Lustre filesystems for the purpose of sharing data with other users using fine-grained control.
@@ -25,9 +22,9 @@ If multiple clients try to read and write the same part of a file at the same ti
There is default stripe configuration for Anselm Lustre filesystems. However, users can set the following stripe parameters for their own directories or files to get optimum I/O performance:
-1. stripe_size: the size of the chunk in bytes; specify with k, m, or g to use units of KB, MB, or GB, respectively; the size must be an even multiple of 65,536 bytes; default is 1MB for all Anselm Lustre filesystems
-2. stripe_count the number of OSTs to stripe across; default is 1 for Anselm Lustre filesystems one can specify -1 to use all OSTs in the filesystem.
-3. stripe_offset The index of the 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.
+1. stripe_size: the size of the chunk in bytes; specify with k, m, or g to use units of KB, MB, or GB, respectively; the size must be an even multiple of 65,536 bytes; default is 1MB for all Anselm Lustre filesystems
+2. stripe_count the number of OSTs to stripe across; default is 1 for Anselm Lustre filesystems one can specify -1 to use all OSTs in the filesystem.
+3. stripe_offset The index of the 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.
!!! Note "Note"
Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.
@@ -83,25 +80,25 @@ The architecture of Lustre on Anselm is composed of two metadata servers (MDS)
Configuration of the storages
-- HOME Lustre object storage
+- HOME Lustre object storage
- One disk array NetApp E5400
- 22 OSTs
- 227 2TB NL-SAS 7.2krpm disks
- 22 groups of 10 disks in RAID6 (8+2)
- 7 hot-spare disks
-- SCRATCH Lustre object storage
+- SCRATCH Lustre object storage
- Two disk arrays NetApp E5400
- 10 OSTs
- 106 2TB NL-SAS 7.2krpm disks
- 10 groups of 10 disks in RAID6 (8+2)
- 6 hot-spare disks
-- Lustre metadata storage
+- Lustre metadata storage
- One disk array NetApp E2600
- 12 300GB SAS 15krpm disks
- 2 groups of 5 disks in RAID5
- 2 hot-spare disks
-###HOME
+\###HOME
The HOME filesystem is mounted in directory /home. Users home directories /home/username reside on this filesystem. Accessible capacity is 320TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 250GB per user. If 250GB should prove as insufficient for particular user, please contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
@@ -120,17 +117,17 @@ Default stripe size is 1MB, stripe count is 1. There are 22 OSTs dedicated for t
!!! Note "Note"
Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.
-|HOME filesystem||
-|---|---|
-|Mountpoint|/home|
-|Capacity|320 TB|
-|Throughput|2 GB/s|
-|User quota|250 GB|
-|Default stripe size|1 MB|
-|Default stripe count|1|
-|Number of OSTs|22|
+| HOME filesystem | |
+| -------------------- | ------ |
+| Mountpoint | /home |
+| Capacity | 320 TB |
+| Throughput | 2 GB/s |
+| User quota | 250 GB |
+| Default stripe size | 1 MB |
+| Default stripe count | 1 |
+| Number of OSTs | 22 |
-###SCRATCH
+\###SCRATCH
The SCRATCH filesystem is mounted in directory /scratch. Users may freely create subdirectories and files on the filesystem. Accessible capacity is 146TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 100TB per user. The purpose of this quota is to prevent runaway programs from filling the entire filesystem and deny service to other users. If 100TB should prove as insufficient for particular user, please contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
@@ -139,22 +136,22 @@ The SCRATCH filesystem is mounted in directory /scratch. Users may freely create
>Users are advised to save the necessary data from the SCRATCH filesystem to HOME filesystem after the calculations and clean up the scratch files.
- Files on the SCRATCH filesystem that are **not accessed for more than 90 days** will be automatically **deleted**.
+ Files on the SCRATCH filesystem that are **not accessed for more than 90 days** will be automatically **deleted**.
The SCRATCH filesystem is realized as Lustre parallel filesystem and is available from all login and computational nodes. Default stripe size is 1MB, stripe count is 1. There are 10 OSTs dedicated for the SCRATCH filesystem.
!!! Note "Note"
Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.
-|SCRATCH filesystem||
-|---|---|
-|Mountpoint|/scratch|
-|Capacity|146TB|
-|Throughput|6GB/s|
-|User quota|100TB|
-|Default stripe size|1MB|
-|Default stripe count|1|
-|Number of OSTs|10|
+| SCRATCH filesystem | |
+| -------------------- | -------- |
+| Mountpoint | /scratch |
+| Capacity | 146TB |
+| Throughput | 6GB/s |
+| User quota | 100TB |
+| Default stripe size | 1MB |
+| Default stripe count | 1 |
+| Number of OSTs | 10 |
### Disk usage and quota commands
@@ -259,8 +256,7 @@ Default ACL mechanism can be used to replace setuid/setgid permissions on direct
[http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html ](http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html)
-Local Filesystems
------------------
+## Local Filesystems
### Local Scratch
@@ -276,13 +272,13 @@ The local scratch filesystem is intended for temporary scratch data generated d
!!! Note "Note"
The local scratch directory /lscratch/$PBS_JOBID will be deleted immediately after the calculation end. Users should take care to save the output data from within the jobscript.
-|local SCRATCH filesystem||
-|---|---|
-|Mountpoint|/lscratch|
-|Accesspoint|/lscratch/$PBS_JOBID|
-|Capacity|330GB|
-|Throughput|100MB/s|
-|User quota|none|
+| local SCRATCH filesystem | |
+| ------------------------ | -------------------- |
+| Mountpoint | /lscratch |
+| Accesspoint | /lscratch/$PBS_JOBID |
+| Capacity | 330GB |
+| Throughput | 100MB/s |
+| User quota | none |
### RAM disk
@@ -298,31 +294,30 @@ The local RAM disk filesystem is intended for temporary scratch data generated d
!!! Note "Note"
The local RAM disk directory /ramdisk/$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||
-|---|---|
-|Mountpoint| /ramdisk|
-|Accesspoint| /ramdisk/$PBS_JOBID|
-|Capacity|60GB at compute nodes without accelerator, 90GB at compute nodes with accelerator, 500GB at fat nodes|
-|Throughput|over 1.5 GB/s write, over 5 GB/s read, single thread, over 10 GB/s write, over 50 GB/s read, 16 threads|
-|User quota|none|
+| RAM disk | |
+| ----------- | ------------------------------------------------------------------------------------------------------- |
+| Mountpoint | /ramdisk |
+| Accesspoint | /ramdisk/$PBS_JOBID |
+| Capacity | 60GB at compute nodes without accelerator, 90GB at compute nodes with accelerator, 500GB at fat nodes |
+| Throughput | over 1.5 GB/s write, over 5 GB/s read, single thread, over 10 GB/s write, over 50 GB/s read, 16 threads |
+| User quota | none |
### tmp
Each node is equipped with local /tmp directory of few GB capacity. The /tmp directory should be used to work with small temporary files. Old files in /tmp directory are automatically purged.
-Summary
-----------
+## Summary
-|Mountpoint|Usage|Protocol|Net Capacity|Throughput|Limitations|Access|Services|
-|---|---|---|---|---|---|---|---|
-|/home|home directory|Lustre|320 TiB|2 GB/s|Quota 250GB|Compute and login nodes|backed up|
-|/scratch|cluster shared jobs' data|Lustre|146 TiB|6 GB/s|Quota 100TB|Compute and login nodes|files older 90 days removed|
-|/lscratch|node local jobs' data|local|330 GB|100 MB/s|none|Compute nodes|purged after job ends|
-|/ramdisk|node local jobs' data|local|60, 90, 500 GB|5-50 GB/s|none|Compute nodes|purged after job ends|
-|/tmp|local temporary files|local|9.5 GB|100 MB/s|none|Compute and login nodes|auto| purged
+| Mountpoint | Usage | Protocol | Net Capacity | Throughput | Limitations | Access | Services | |
+| ---------- | ------------------------- | -------- | -------------- | ---------- | ----------- | ----------------------- | --------------------------- | ------ |
+| /home | home directory | Lustre | 320 TiB | 2 GB/s | Quota 250GB | Compute and login nodes | backed up | |
+| /scratch | cluster shared jobs' data | Lustre | 146 TiB | 6 GB/s | Quota 100TB | Compute and login nodes | files older 90 days removed | |
+| /lscratch | node local jobs' data | local | 330 GB | 100 MB/s | none | Compute nodes | purged after job ends | |
+| /ramdisk | node local jobs' data | local | 60, 90, 500 GB | 5-50 GB/s | none | Compute nodes | purged after job ends | |
+| /tmp | local temporary files | local | 9.5 GB | 100 MB/s | none | Compute and login nodes | auto | purged |
+
+## CESNET Data Storage
-CESNET Data Storage
-------------
Do not use shared filesystems at IT4Innovations as a backup for large amount of data or long-term archiving purposes.
!!! Note "Note"
@@ -340,8 +335,8 @@ The procedure to obtain the CESNET access is quick and trouble-free.
(source [https://du.cesnet.cz/](https://du.cesnet.cz/wiki/doku.php/en/start "CESNET Data Storage"))
-CESNET storage access
-------------
+## CESNET storage access
+
### Understanding CESNET storage
!!! Note "Note"
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 d392471ef04667686c5226f7dbc6e9055c193b98..f1c3573a84bd0e13a403e0b4b0566120585c1d22 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
@@ -1,17 +1,13 @@
-Graphical User Interface
-========================
+# Graphical User Interface
-X Window System
----------------
+## 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
----
+## 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 eea8cf0cb08c61f102304419fa5223098bd0e612..0e566755baed0ecd16d3e70574034a93eb5ff93f 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
@@ -120,7 +120,7 @@ Search for the localhost and port number (in this case 127.0.0.1:5961).
tcp 0 0 127.0.0.1:5961 0.0.0.0:* LISTEN 24031/Xvnc
```
-On the PuTTY Configuration screen go to Connection->SSH->Tunnels to set up the tunnel.
+On the PuTTY Configuration screen go to Connection->SSH->Tunnels to set up the tunnel.
Fill the Source port and Destination fields. **Do not forget to click the Add button**.
@@ -188,7 +188,7 @@ Or this way:
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.
+Open a Terminal (Applications -> System Tools -> Terminal). Run all the next commands in the terminal.
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
index b275082163a3ed4a30785b5824ab0520c8819def..6e9b37130b299b1ae85f3c7f322681fb87972c80 100644
--- a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
+++ b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
@@ -44,9 +44,9 @@ Mac OS users need to install [XQuartz server](https://www.xquartz.org).
There are variety of X servers available for Windows environment. The commercial Xwin32 is very stable and rich featured. The Cygwin environment provides fully featured open-source XWin X server. For simplicity, we recommend open-source X server by the [Xming project](http://sourceforge.net/projects/xming/). For stability and full features we recommend the
[XWin](http://x.cygwin.com/) X server by Cygwin
- |How to use Xwin |How to use Xming |
- | --- | --- |
- |[Install Cygwin](http://x.cygwin.com/) Find and execute XWin.exeto start the X server on Windows desktop computer.[If no able to forward X11 using PuTTY to CygwinX](#if-no-able-to-forward-x11-using-putty-to-cygwinx) |<p>Use Xlaunch to configure the Xming.<p>Run Xmingto start the X server on Windows desktop computer.|
+| How to use Xwin | How to use Xming |
+| ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------- |
+| [Install Cygwin](http://x.cygwin.com/) Find and execute XWin.exeto start the X server on Windows desktop computer.[If no able to forward X11 using PuTTY to CygwinX](#if-no-able-to-forward-x11-using-putty-to-cygwinx) | <p>Use Xlaunch to configure the Xming.<p>Run Xmingto start the X server on Windows desktop computer. |
Read more on [http://www.math.umn.edu/systems_guide/putty_xwin32.html](http://www.math.umn.edu/systems_guide/putty_xwin32.shtml)
@@ -141,16 +141,16 @@ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connect
(gnome-session:23691): WARNING **: Cannot open display:**
```
-1. Locate and modify Cygwin shortcut that uses [startxwin](http://x.cygwin.com/docs/man1/startxwin.1.html)
+1. Locate and modify Cygwin shortcut that uses [startxwin](http://x.cygwin.com/docs/man1/startxwin.1.html)
locate
C:cygwin64binXWin.exe
change it
to
- C:*cygwin64binXWin.exe -listen tcp*
+ C:_cygwin64binXWin.exe -listen tcp_
-1. Check Putty settings:
+1. Check Putty settings:
Enable X11 forwarding
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 8957f3b1f9304d36db2363165cb748fac540f7ca..9672a2d38d6c89c1022c0f33fcd7a4b593de5d39 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
@@ -15,43 +15,43 @@ We recommned you to download "**A Windows installer for everything except PuTTYt
## PuTTY - how to connect to the IT4Innovations cluster
-* Run PuTTY
-* Enter Host name and Save session fields with [Login address](../../../salomon/shell-and-data-access.md) 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"**.
+- Run PuTTY
+- Enter Host name and Save session fields with [Login address](../../../salomon/shell-and-data-access.md) 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.
+- 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.
+- Return to Session page and Save selected configuration with _Save_ button.
-* Now you can log in using *Open* 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.**
+- 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.**
## Another PuTTY Settings
-* Category - Windows - Translation - Remote character set and select **UTF-8**.
-* Category - Terminal - Features and select **Disable application keypad mode** (enable numpad)
-* Save your configuration on Session page in to Default Settings with *Save* button.
+- Category - Windows - Translation - Remote character set and select **UTF-8**.
+- Category - Terminal - Features and select **Disable application keypad mode** (enable numpad)
+- Save your configuration on Session page in to Default Settings with _Save_ button.
## Pageant SSH agent
Pageant holds your private key in memory without needing to retype a passphrase on every login.
-* Run Pageant.
-* On Pageant Key List press *Add key* and select your private key (id_rsa.ppk).
-* Enter your passphrase.
-* Now you have your private key in memory without needing to retype a passphrase on every login.
+- Run Pageant.
+- On Pageant Key List press _Add key_ and select your private key (id_rsa.ppk).
+- Enter your passphrase.
+- Now you have your private key in memory without needing to retype a passphrase on every login.
@@ -63,11 +63,11 @@ PuTTYgen is the PuTTY key generator. You can load in an existing private key and
You can change the password of your SSH key with "PuTTY Key Generator". Make sure to backup the key.
-* Load your [private key](../shell-access-and-data-transfer/ssh-keys/) file with *Load* button.
-* Enter your current passphrase.
-* Change key passphrase.
-* Confirm key passphrase.
-* Save your private key with *Save private key* button.
+- Load your [private key](../shell-access-and-data-transfer/ssh-keys/) file with _Load_ button.
+- Enter your current passphrase.
+- Change key passphrase.
+- Confirm key passphrase.
+- Save your private key with _Save private key_ button.
@@ -75,33 +75,33 @@ You can change the password of your SSH key with "PuTTY Key Generator". Make sur
You can generate an additional public/private key pair and insert public key into authorized_keys file for authentication with your own private key.
-* Start with *Generate* button.
+- Start with _Generate_ button.
-* Generate some randomness.
+- Generate some randomness.
-* Wait.
+- 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.
+- 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.
+- 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
+- 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/).
+- 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 85fcd1da797fddb65f3258611f7a9de221f2817f..95c3027d2c3f06d7824ce18eb3620dc87e8f2438 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
@@ -21,9 +21,9 @@ After logging in, you can see .ssh/ directory with SSH keys and authorized_keys
## Access privileges on .ssh folder
-* .ssh directory: 700 (drwx------)
-* Authorized_keys, known_hosts and public key (.pub file): 644 (-rw-r--r--)
-* Private key (id_rsa/id_rsa.ppk): 600 (-rw-------)
+- .ssh directory: 700 (drwx------)
+- Authorized_keys, known_hosts and public key (.pub file): 644 (-rw-r--r--)
+- Private key (id_rsa/id_rsa.ppk): 600 (-rw-------)
```bash
cd /home/username/
@@ -76,7 +76,7 @@ An example of private key format:
## Public key
-Public key file in "*.pub" format is used to verify a digital signature. Public key is present on the remote side and allows access to the owner of the matching private key.
+Public key file in "\*.pub" format is used to verify a digital signature. Public key is present on the remote side and allows access to the owner of the matching private key.
An example of public key format:
@@ -107,4 +107,4 @@ In this example, we add an additional public key, stored in file additional_key.
## How to remove your own key
-Removing your key from authorized_keys can be done simply by deleting the corresponding public key which can be identified by a comment at the end of line (eg. *username@organization.example.com*).
+Removing your key from authorized_keys can be done simply by deleting the corresponding public key which can be identified by a comment at the end of line (eg. _username@organization.example.com_).
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 b70bfd7f9d3b1fb97fe2ac41599ecf8816db2e44..decb2210fd03dbe8901262a43318a818671aca01 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
@@ -6,12 +6,12 @@ AnyConnect users on Windows 8.1 will receive a "Failed to initialize connection
## Workaround
-* Close the Cisco AnyConnect Window and the taskbar mini-icon
-* Right click vpnui.exe in the 'Cisco AnyConnect Secure Mobility Client' folder. (C:Program Files (x86)CiscoCisco AnyConnect Secure Mobility Client)
-* Click on the 'Run compatibility troubleshooter' button
-* Choose 'Try recommended settings'
-* The wizard suggests Windows 8 compatibility.
-* Click 'Test Program'. This will open the program.
-* Close
+- Close the Cisco AnyConnect Window and the taskbar mini-icon
+- Right click vpnui.exe in the 'Cisco AnyConnect Secure Mobility Client' folder. (C:Program Files (x86)CiscoCisco AnyConnect Secure Mobility Client)
+- Click on the 'Run compatibility troubleshooter' button
+- Choose 'Try recommended settings'
+- The wizard suggests Windows 8 compatibility.
+- Click 'Test Program'. This will open the program.
+- Close
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/vpn-access.md b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/vpn-access.md
index 40960cee821bb85c826db8dd9f8a92828878c285..2e6348e5d827f8b549aca6de6497e7defa72f7cc 100644
--- a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/vpn-access.md
+++ b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/vpn-access.md
@@ -4,12 +4,12 @@
For using resources and licenses which are located at IT4Innovations local network, it is necessary to VPN connect to this network. We use Cisco AnyConnect Secure Mobility Client, which is supported on the following operating systems:
-* Windows XP
-* Windows Vista
-* Windows 7
-* Windows 8
-* Linux
-* MacOS
+- Windows XP
+- Windows Vista
+- Windows 7
+- Windows 8
+- Linux
+- MacOS
It is impossible to connect to VPN from other operating systems.
@@ -43,7 +43,7 @@ After successful download of installation file, you have to execute this tool wi
You can use graphical user interface or command line interface to run VPN client on all supported operating systems. We suggest using GUI.
-Before the first login to VPN, you have to fill URL **[https://vpn.it4i.cz/user](https://vpn.it4i.cz/user)** into the text field.
+Before the first login to VPN, you have to fill URL **<https://vpn.it4i.cz/user>** into the text field.
diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/vpn1-access.md b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/vpn1-access.md
index d49ab6b1d69dd6004886803dadb9862c25cc84e2..040ffe8144c60fd82c641b3e3c3f3a7fb3b4de2d 100644
--- a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/vpn1-access.md
+++ b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/vpn1-access.md
@@ -9,12 +9,12 @@ Workaround can be found at [vpn-connection-fail-in-win-8.1](../../get-started-wi
For using resources and licenses which are located at IT4Innovations local network, it is necessary to VPN connect to this network. We use Cisco AnyConnect Secure Mobility Client, which is supported on the following operating systems:
-* Windows XP
-* Windows Vista
-* Windows 7
-* Windows 8
-* Linux
-* MacOS
+- Windows XP
+- Windows Vista
+- Windows 7
+- Windows 8
+- Linux
+- MacOS
It is impossible to connect to VPN from other operating systems.
diff --git a/docs.it4i/get-started-with-it4innovations/applying-for-resources.md b/docs.it4i/get-started-with-it4innovations/applying-for-resources.md
index 0467551d3541af5e1c97ac4106ea8eae92c45714..8875ec91b415637f2b90fb7218c980849e1f48f0 100644
--- a/docs.it4i/get-started-with-it4innovations/applying-for-resources.md
+++ b/docs.it4i/get-started-with-it4innovations/applying-for-resources.md
@@ -1,5 +1,4 @@
-Applying for Resources
-======================
+# Applying for Resources
Computational resources may be allocated by any of the following [Computing resources allocation](http://www.it4i.cz/computing-resources-allocation/?lang=en) mechanisms.
diff --git a/docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md b/docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
index 2ab422dece0646d6565df0d38939305787615501..5de00c5ed5270d7e75de4d3b8b8a66d45ae4480a 100644
--- a/docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
+++ b/docs.it4i/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
@@ -8,10 +8,10 @@ IT4Innovations employs X.509 certificates for secure communication (e. g. creden
There are different kinds of certificates, each with a different scope of use. We mention here:
-* User (Private) certificates
-* Certificate Authority (CA) certificates
-* Host certificates
-* Service certificates
+- User (Private) certificates
+- Certificate Authority (CA) certificates
+- Host certificates
+- Service certificates
However, users need only manage User and CA certificates. Note that your user certificate is protected by an associated private key, and this **private key must never be disclosed**.
@@ -41,7 +41,7 @@ The PKCS12 (often abbreviated to ’p12’) format stores your user certificate,
The PEM format (`*`.pem) stores your user certificate and your associated private key in two separate files. This form of your certificate can be used by PRACE’s gsissh-term and with the grid related services like Globus toolkit (GSI-SSH, GridFTP and GRAM5).
-To convert your Certificate from PEM to p12 formats, and *vice versa*, IT4Innovations recommends using the openssl tool (see separate FAQ entry).
+To convert your Certificate from PEM to p12 formats, and _vice versa_, IT4Innovations recommends using the openssl tool (see separate FAQ entry).
JKS is the Java KeyStore and may contain both your personal certificate with your private key and a list of your trusted CA certificates. This form of your certificate can be used by grid services like DART and UNICORE6.
@@ -82,7 +82,7 @@ To convert from PEM to p12, enter the following command:
username.p12
```
-To convert from p12 to PEM, type the following *four* commands:
+To convert from p12 to PEM, type the following _four_ commands:
```bash
openssl pkcs12 -in username.p12 -out usercert.pem -clcerts -nokeys
@@ -148,7 +148,7 @@ If you are an Internet Explorer user, click StartSettingsControl Panel and then
## Q: What is a proxy certificate?
-A proxy certificate is a short-lived certificate which may be employed by UNICORE and the Globus services. The proxy certificate consists of a new user certificate and a newly generated proxy private key. This proxy typically has a rather short lifetime (normally 12 hours) and often only allows a limited delegation of rights. Its default location, for Unix/Linux, is /tmp/x509_u*uid* but can be set via the $X509_USER_PROXY environment variable.
+A proxy certificate is a short-lived certificate which may be employed by UNICORE and the Globus services. The proxy certificate consists of a new user certificate and a newly generated proxy private key. This proxy typically has a rather short lifetime (normally 12 hours) and often only allows a limited delegation of rights. Its default location, for Unix/Linux, is /tmp/x509_u_uid_ but can be set via the $X509_USER_PROXY environment variable.
## Q: What is the MyProxy service?
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 8be289456e028d8602e67c8a0b119512a78672dc..d252c6766a0730f3a68d00c1aeb40e7297ac50bf 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
@@ -24,16 +24,16 @@ This is a preferred way of granting access to project resources. Please, use thi
Log in to the [IT4I Extranet portal](https://extranet.it4i.cz) using IT4I credentials and go to the **Projects** section.
-* **Users:** Please, submit your requests for becoming a project member.
-* **Primary Investigators:** Please, approve or deny users' requests in the same section.
+- **Users:** Please, submit your requests for becoming a project member.
+- **Primary Investigators:** Please, approve or deny users' requests in the same section.
## Authorization by e-mail (an alternative approach)
-In order to authorize a Collaborator to utilize the allocated resources, the PI should contact the [IT4I support](https://support.it4i.cz/rt/) (E-mail: [support[at]it4i.cz](mailto:support@it4i.cz)) and provide following information:
+In order to authorize a Collaborator to utilize the allocated resources, the PI should contact the [IT4I support](https://support.it4i.cz/rt/) (E-mail: [support\[at\]it4i.cz](mailto:support@it4i.cz)) and provide following information:
-1. Identify your project by project ID
-1. Provide list of people, including himself, who are authorized to use the resources allocated to the project. The list must include full name, e-mail and affiliation. Provide usernames as well, if collaborator login access already exists on the IT4I systems.
-1. Include "Authorization to IT4Innovations" into the subject line.
+1. Identify your project by project ID
+2. Provide list of people, including himself, who are authorized to use the resources allocated to the project. The list must include full name, e-mail and affiliation. Provide usernames as well, if collaborator login access already exists on the IT4I systems.
+3. Include "Authorization to IT4Innovations" into the subject line.
Example (except the subject line which must be in English, you may use Czech or Slovak language for communication with us):
@@ -57,14 +57,14 @@ Should the above information be provided by e-mail, the e-mail **must be** digit
## The Login Credentials
-Once authorized by PI, every person (PI or Collaborator) wishing to access the clusters, should contact the [IT4I support](https://support.it4i.cz/rt/) (E-mail: [support[at]it4i.cz](mailto:support@it4i.cz)) providing following information:
+Once authorized by PI, every person (PI or Collaborator) wishing to access the clusters, should contact the [IT4I support](https://support.it4i.cz/rt/) (E-mail: [support\[at\]it4i.cz](mailto:support@it4i.cz)) providing following information:
-1. Project ID
-1. Full name and affiliation
-1. Statement that you have read and accepted the [Acceptable use policy document](http://www.it4i.cz/acceptable-use-policy.pdf) (AUP).
-1. Attach the AUP file.
-1. Your preferred username, max 8 characters long. The preferred username must associate your surname and name or be otherwise derived from it. Only alphanumeric sequences, dash and underscore signs are allowed.
-1. In case you choose [Alternative way to personal certificate](obtaining-login-credentials/#alternative-way-of-getting-personal-certificate), a **scan of photo ID** (personal ID or passport or driver license) is required
+1. Project ID
+2. Full name and affiliation
+3. Statement that you have read and accepted the [Acceptable use policy document](http://www.it4i.cz/acceptable-use-policy.pdf) (AUP).
+4. Attach the AUP file.
+5. Your preferred username, max 8 characters long. The preferred username must associate your surname and name or be otherwise derived from it. Only alphanumeric sequences, dash and underscore signs are allowed.
+6. In case you choose [Alternative way to personal certificate](obtaining-login-credentials/#alternative-way-of-getting-personal-certificate), a **scan of photo ID** (personal ID or passport or driver license) is required
Example (except the subject line which must be in English, you may use Czech or Slovak language for communication with us):
@@ -94,9 +94,9 @@ For various reasons we do not accept PGP keys.** Please, use only X.509 PKI cert
You will receive your personal login credentials by protected e-mail. The login credentials include:
-1. username
-1. ssh private key and private key passphrase
-1. system password
+1. username
+2. ssh private key and private key passphrase
+3. system password
The clusters are accessed by the [private key](../accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/) and username. Username and password is used for login to the [information systems](http://support.it4i.cz/).
@@ -116,11 +116,11 @@ Change password in [your user profile](https://extranet.it4i.cz/user/).
## The Certificates for Digital Signatures
-We accept personal certificates issued by any widely respected certification authority (CA). This includes certificates by CAs organized in [International Grid Trust Federation](http://www.igtf.net/), its European branch [EUGridPMA](https://www.eugridpma.org/) and its member organizations, e.g. the [CESNET certification authority](https://tcs.cesnet.cz). The Czech *"Qualified certificate" (Kvalifikovaný certifikát)* provided by [PostSignum](http://www.postsignum.cz/) or [I.CA](http://www.ica.cz/Kvalifikovany-certifikat.aspx), that is used in electronic contact with Czech authorities is accepted as well.
+We accept personal certificates issued by any widely respected certification authority (CA). This includes certificates by CAs organized in [International Grid Trust Federation](http://www.igtf.net/), its European branch [EUGridPMA](https://www.eugridpma.org/) and its member organizations, e.g. the [CESNET certification authority](https://tcs.cesnet.cz). The Czech _"Qualified certificate" (Kvalifikovaný certifikát)_ provided by [PostSignum](http://www.postsignum.cz/) or [I.CA](http://www.ica.cz/Kvalifikovany-certifikat.aspx), that is used in electronic contact with Czech authorities is accepted as well.
Certificate generation process is well-described here:
-* [How to generate a personal TCS certificate in Mozilla Firefox web browser (in Czech)](http://idoc.vsb.cz/xwiki/wiki/infra/view/uzivatel/moz-cert-gen)
+- [How to generate a personal TCS certificate in Mozilla Firefox web browser (in Czech)](http://idoc.vsb.cz/xwiki/wiki/infra/view/uzivatel/moz-cert-gen)
A FAQ about certificates can be found here: [Certificates FAQ](certificates-faq/).
@@ -128,19 +128,19 @@ A FAQ about certificates can be found here: [Certificates FAQ](certificates-faq/
Follow these steps **only** if you can not obtain your certificate in a standard way. In case you choose this procedure, please attach a **scan of photo ID** (personal ID or passport or drivers license) when applying for [login credentials](obtaining-login-credentials/#the-login-credentials).
-* Go to [CAcert](www.cacert.org).
- * If there's a security warning, just acknowledge it.
-* Click *Join*.
-* Fill in the form and submit it by the *Next* button.
- * Type in the e-mail address which you use for communication with us.
- * Don't forget your chosen *Pass Phrase*.
-* You will receive an e-mail verification link. Follow it.
-* After verifying, go to the CAcert's homepage and login using *Password Login*.
-* Go to *Client Certificates* *New*.
-* Tick *Add* for your e-mail address and click the *Next* button.
-* Click the *Create Certificate Request* button.
-* You'll be redirected to a page from where you can download/install your certificate.
- * Simultaneously you'll get an e-mail with a link to the certificate.
+- Go to [CAcert](www.cacert.org).
+ - If there's a security warning, just acknowledge it.
+- Click _Join_.
+- Fill in the form and submit it by the _Next_ button.
+ - Type in the e-mail address which you use for communication with us.
+ - Don't forget your chosen _Pass Phrase_.
+- You will receive an e-mail verification link. Follow it.
+- After verifying, go to the CAcert's homepage and login using _Password Login_.
+- Go to _Client Certificates_ _New_.
+- Tick _Add_ for your e-mail address and click the _Next_ button.
+- Click the _Create Certificate Request_ button.
+- You'll be redirected to a page from where you can download/install your certificate.
+ - Simultaneously you'll get an e-mail with a link to the certificate.
## Installation of the Certificate Into Your Mail Client
@@ -148,13 +148,13 @@ The procedure is similar to the following guides:
MS Outlook 2010
-* [How to Remove, Import, and Export Digital certificates](http://support.microsoft.com/kb/179380)
-* [Importing a PKCS #12 certificate (in Czech)](http://idoc.vsb.cz/xwiki/wiki/infra/view/uzivatel/outl-cert-imp)
+- [How to Remove, Import, and Export Digital certificates](http://support.microsoft.com/kb/179380)
+- [Importing a PKCS #12 certificate (in Czech)](http://idoc.vsb.cz/xwiki/wiki/infra/view/uzivatel/outl-cert-imp)
Mozilla Thudnerbird
-* [Installing an SMIME certificate](http://kb.mozillazine.org/Installing_an_SMIME_certificate)
-* [Importing a PKCS #12 certificate (in Czech)](http://idoc.vsb.cz/xwiki/wiki/infra/view/uzivatel/moz-cert-imp)
+- [Installing an SMIME certificate](http://kb.mozillazine.org/Installing_an_SMIME_certificate)
+- [Importing a PKCS #12 certificate (in Czech)](http://idoc.vsb.cz/xwiki/wiki/infra/view/uzivatel/moz-cert-imp)
## End of User Account Lifecycle
@@ -162,8 +162,8 @@ User accounts are supported by membership in active Project(s) or by affiliation
User will get 3 automatically generated warning e-mail messages of the pending removal:.
-* First message will be sent 3 months before the removal
-* Second message will be sent 1 month before the removal
-* Third message will be sent 1 week before the removal.
+- First message will be sent 3 months before the removal
+- Second message will be sent 1 month before the removal
+- Third message will be sent 1 week before the removal.
The messages will inform about the projected removal date and will challenge the user to migrate her/his data
diff --git a/docs.it4i/index.md b/docs.it4i/index.md
index 2c45d7fdd23f25479ddcf9310d75bb921dc54116..3d1ab58521dd9e38367019ffa5591e7588937326 100644
--- a/docs.it4i/index.md
+++ b/docs.it4i/index.md
@@ -1,25 +1,21 @@
-Documentation
-=============
+# Documentation
Welcome to IT4Innovations documentation pages. The IT4Innovations national supercomputing center operates supercomputers [Salomon](/salomon/introduction/) and [Anselm](/anselm-cluster-documentation/introduction/). The supercomputers are [available](get-started-with-it4innovations/applying-for-resources/) to academic community within the Czech Republic and Europe and industrial community worldwide. The purpose of these pages is to provide a comprehensive documentation on hardware, software and usage of the computers.
-How to read the documentation
-------------------------------
+## How to read the documentation
-1. Read the list in the left column. Select the subject of interest. Alternatively, use the Search in the upper right corner.
-1. Scan for all the notes and reminders on the page.
-1. Read the details if still more information is needed. **Look for examples** illustrating the concepts.
+1. Read the list in the left column. Select the subject of interest. Alternatively, use the Search in the upper right corner.
+2. Scan for all the notes and reminders on the page.
+3. Read the details if still more information is needed. **Look for examples** illustrating the concepts.
-Getting Help and Support
-------------------------
+## Getting Help and Support
!!! note
- Contact [support[at]it4i.cz](mailto:support@it4i.cz) for help and support regarding the cluster technology at IT4Innovations. Please use **Czech**, **Slovak** or **English** language for communication with us. Follow the status of your request to IT4Innovations at [support.it4i.cz/rt](http://support.it4i.cz/rt).
+ Contact [support\[at\]it4i.cz](mailto:support@it4i.cz) for help and support regarding the cluster technology at IT4Innovations. Please use **Czech**, **Slovak** or **English** language for communication with us. Follow the status of your request to IT4Innovations at [support.it4i.cz/rt](http://support.it4i.cz/rt).
Use your IT4Innotations username and password to log in to the [support](http://support.it4i.cz/) portal.
-Required Proficiency
---------------------
+## Required Proficiency
!!! Note "Note"
You need basic proficiency in Linux environment.
@@ -31,23 +27,21 @@ In order to use the system for your calculations, you need basic proficiency in
In many cases, you will run your own code on the cluster. In order to fully exploit the cluster, you will need to carefully consider how to utilize all the cores available on the node and how to use multiple nodes at the same time. You need to **parallelize** your code. Proficieny in MPI, OpenMP, CUDA, UPC or GPI2 programming may be gained via the [training provided by IT4Innovations.](http://prace.it4i.cz)
-Terminology Frequently Used on These Pages
-------------------------------------------
+## Terminology Frequently Used on These Pages
-- **node:** a computer, interconnected by network to other computers - Computational nodes are powerful computers, designed and dedicated for executing demanding scientific computations.
-- **core:** processor core, a unit of processor, executing computations
-- **corehours:** wall clock hours of processor core time - Each node is equipped with **X** processor cores, provides **X** corehours per 1 wall clock hour.
-- **job:** a calculation running on the supercomputer - The job allocates and utilizes resources of the supercomputer for certain time.
-- **HPC:** High Performance Computing
-- **HPC (computational) resources:** corehours, storage capacity, software licences
-- **code:** a program
-- **primary investigator (PI):** a person responsible for execution of computational project and utilization of computational resources allocated to that project
-- **collaborator:** a person participating on execution of computational project and utilization of computational resources allocated to that project
-- **project:** a computational project under investigation by the PI - The project is identified by the project ID. The computational resources are allocated and charged per project.
-- **jobscript:** a script to be executed by the PBS Professional workload manager
+- **node:** a computer, interconnected by network to other computers - Computational nodes are powerful computers, designed and dedicated for executing demanding scientific computations.
+- **core:** processor core, a unit of processor, executing computations
+- **corehours:** wall clock hours of processor core time - Each node is equipped with **X** processor cores, provides **X** corehours per 1 wall clock hour.
+- **job:** a calculation running on the supercomputer - The job allocates and utilizes resources of the supercomputer for certain time.
+- **HPC:** High Performance Computing
+- **HPC (computational) resources:** corehours, storage capacity, software licences
+- **code:** a program
+- **primary investigator (PI):** a person responsible for execution of computational project and utilization of computational resources allocated to that project
+- **collaborator:** a person participating on execution of computational project and utilization of computational resources allocated to that project
+- **project:** a computational project under investigation by the PI - The project is identified by the project ID. The computational resources are allocated and charged per project.
+- **jobscript:** a script to be executed by the PBS Professional workload manager
-Conventions
------------
+## Conventions
In this documentation, you will find a number of pages containing examples. We use the following conventions:
@@ -63,7 +57,6 @@ Your local linux host command prompt
local $
```
-Errata
--------
+## Errata
-Although we have taken every care to ensure the accuracy of our content, mistakes do happen. If you find a mistake in the text or the code we would be grateful if you would report this to us. By doing so, you can save other readers from frustration and help us improve subsequent versions of this documentation. If you find any errata, please report them by visiting [http://support.it4i.cz/rt](http://support.it4i.cz/rt), creating a new ticket, and entering the details of your errata. Once your errata are verified, your submission will be accepted and the errata will be uploaded on our website.
\ No newline at end of file
+Although we have taken every care to ensure the accuracy of our content, mistakes do happen. If you find a mistake in the text or the code we would be grateful if you would report this to us. By doing so, you can save other readers from frustration and help us improve subsequent versions of this documentation. If you find any errata, please report them by visiting <http://support.it4i.cz/rt>, creating a new ticket, and entering the details of your errata. Once your errata are verified, your submission will be accepted and the errata will be uploaded on our website.
diff --git a/docs.it4i/modules-anselm.md b/docs.it4i/modules-anselm.md
index d65c3e72baf16323ead6357ec6455542e63da446..83d973c8615c952aeeccee0c497581777d9bf97f 100644
--- a/docs.it4i/modules-anselm.md
+++ b/docs.it4i/modules-anselm.md
@@ -2,429 +2,429 @@
## Core
-|Module|Description|Available versions|
-|--|--|--|
-|**lmod**| |<nobr>7.2.2.lua</nobr>|
-|**settarg**| |<nobr>7.2.2.lua</nobr>|
+| Module | Description | Available versions |
+| ----------- | ----------- | ---------------------- |
+| **lmod** | Â | <nobr>7.2.2.lua</nobr> |
+| **settarg** | Â | <nobr>7.2.2.lua</nobr> |
## Bio
-|Module|Description|Available versions|
-|--|--|--|
-|**[almost](http://www-almost.ch.cam.ac.uk/site)**|all atom molecular simulation toolkit - is a fast and flexible molecular modeling environment that provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations.|<nobr>2.1.0-foss-2015g</br>2.1.0-foss-2016a</nobr>|
-|**bowtie2**| |<nobr>2.2.3</nobr>|
-|**[GROMACS](http://www.gromacs.org)**|GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.|<nobr>5.1.2-intel-2015b-hybrid-single-cuda</br>5.1.2-intel-2016a-hybrid</br>5.1.2-intel-2015b-hybrid-single-CUDA-7.5-PLUMED-2.2.1</br>5.1.2-intel-2015b-hybrid-single-CUDA-7.5-PLUMED-2.2.1-test</nobr>|
-|**[PLUMED](http://www.plumed-code.org)**|PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.|<nobr>2.3b-foss-2016a</nobr>|
+| Module | Description | Available versions |
+| ------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[almost](http://www-almost.ch.cam.ac.uk/site)** | all atom molecular simulation toolkit - is a fast and flexible molecular modeling environment that provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations. | <nobr>2.1.0-foss-2015g</br>2.1.0-foss-2016a</nobr> |
+| **bowtie2** | Â | <nobr>2.2.3</nobr> |
+| **[GROMACS](http://www.gromacs.org)** | GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. | <nobr>5.1.2-intel-2015b-hybrid-single-cuda</br>5.1.2-intel-2016a-hybrid</br>5.1.2-intel-2015b-hybrid-single-CUDA-7.5-PLUMED-2.2.1</br>5.1.2-intel-2015b-hybrid-single-CUDA-7.5-PLUMED-2.2.1-test</nobr> |
+| **[PLUMED](http://www.plumed-code.org)** | PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. | <nobr>2.3b-foss-2016a</nobr> |
## Bullxde
-|Module|Description|Available versions|
-|--|--|--|
-|**bullxde**| |<nobr>2.0</nobr>|
+| Module | Description | Available versions |
+| ----------- | ----------- | ------------------ |
+| **bullxde** | Â | <nobr>2.0</nobr> |
## Bullxmpi
-|Module|Description|Available versions|
-|--|--|--|
-|**bullxmpi**| |<nobr>bullxmpi-1.2.4.3</nobr>|
+| Module | Description | Available versions |
+| ------------ | ----------- | ----------------------------- |
+| **bullxmpi** | Â | <nobr>bullxmpi-1.2.4.3</nobr> |
## Chem
-|Module|Description|Available versions|
-|--|--|--|
-|**abinit**| |<nobr>7.10.1-icc-impi</br>7.10.1-gcc-openmpi</br>7.6.2</nobr>|
-|**cp2k-mpi**| |<nobr>2.5.1-gcc</nobr>|
-|**lammps**| |<nobr>28Jun14</nobr>|
-|**molpro**| |<nobr>2010.1-p45-intel</nobr>|
-|**namd**| |<nobr>2.8</nobr>|
-|**nwchem**| |<nobr>6.1.1</br>6.3-rev2-patch1-openmpi</br>6.3-rev2-patch1-venus</br>6.3-rev2-patch1</nobr>|
-|**[ORCA](http://cec.mpg.de/forum/)**|ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.|<nobr>3_0_3-linux_x86-64</nobr>|
-|**[PLUMED](http://www.plumed-code.org)**|PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.|<nobr>2.2.1-intel-2015b</nobr>|
-|**[QuantumESPRESSO](http://www.pwscf.org/)**|Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).|<nobr>5.4.0-intel-2017.00</nobr>|
-|**[xdrfile](http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library)**|XTC library|<nobr>1.1.4-foss-2016a</br>1.1.4-foss-2015g</br>1.1.4-intel-2015b</nobr>|
+| Module | Description | Available versions |
+| ---------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------- |
+| **abinit** | Â | <nobr>7.10.1-icc-impi</br>7.10.1-gcc-openmpi</br>7.6.2</nobr> |
+| **cp2k-mpi** | Â | <nobr>2.5.1-gcc</nobr> |
+| **lammps** | Â | <nobr>28Jun14</nobr> |
+| **molpro** | Â | <nobr>2010.1-p45-intel</nobr> |
+| **namd** | Â | <nobr>2.8</nobr> |
+| **nwchem** | Â | <nobr>6.1.1</br>6.3-rev2-patch1-openmpi</br>6.3-rev2-patch1-venus</br>6.3-rev2-patch1</nobr> |
+| **[ORCA](http://cec.mpg.de/forum/)** | ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. | <nobr>3_0_3-linux_x86-64</nobr> |
+| **[PLUMED](http://www.plumed-code.org)** | PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. | <nobr>2.2.1-intel-2015b</nobr> |
+| **[QuantumESPRESSO](http://www.pwscf.org/)** | Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). | <nobr>5.4.0-intel-2017.00</nobr> |
+| **[xdrfile](http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library)** | XTC library | <nobr>1.1.4-foss-2016a</br>1.1.4-foss-2015g</br>1.1.4-intel-2015b</nobr> |
## Compilers
-|Module|Description|Available versions|
-|--|--|--|
-|**bupc**| |<nobr>2.16.2</nobr>|
-|**chicken**| |<nobr>4.8.0.6</nobr>|
-|**gcc**| |<nobr>4.9.0</br>5.4.0</br>4.8.1</nobr>|
-|**[GCC](http://gcc.gnu.org/)**|The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).|<nobr>4.9.3-binutils-2.25</br>5.1.0-binutils-2.25</br>5.3.0-2.26</br>4.9.3</br>4.9.3-2.25</br>5.3.0-binutils-2.25</nobr>|
-|**[GCCcore](http://gcc.gnu.org/)**|The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).|<nobr>5.3.0</br>4.9.3</br>5.4.0</nobr>|
-|**gupc**| |<nobr>4.8.0.3</nobr>|
-|**[icc](http://software.intel.com/en-us/intel-compilers/)**|C and C++ compiler from Intel|<nobr>2015.3.187-GNU-5.1.0-2.25</br>2017.0.098-GCC-5.4.0-2.26</br>2016.1.150-GCC-4.9.3-2.25</br>2015.3.187-GNU-4.9.3-2.25</nobr>|
-|**[ifort](http://software.intel.com/en-us/intel-compilers/)**|Fortran compiler from Intel|<nobr>2015.3.187-GNU-5.1.0-2.25</br>2017.0.098-GCC-5.4.0-2.26</br>2016.1.150-GCC-4.9.3-2.25</br>2015.3.187-GNU-4.9.3-2.25</nobr>|
-|**java**| |<nobr>1.7</nobr>|
-|**llvm**| |<nobr>3.6.0</nobr>|
+| Module | Description | Available versions |
+| ------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------- |
+| **bupc** | Â | <nobr>2.16.2</nobr> |
+| **chicken** | Â | <nobr>4.8.0.6</nobr> |
+| **gcc** | Â | <nobr>4.9.0</br>5.4.0</br>4.8.1</nobr> |
+| **[GCC](http://gcc.gnu.org/)** | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). | <nobr>4.9.3-binutils-2.25</br>5.1.0-binutils-2.25</br>5.3.0-2.26</br>4.9.3</br>4.9.3-2.25</br>5.3.0-binutils-2.25</nobr> |
+| **[GCCcore](http://gcc.gnu.org/)** | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). | <nobr>5.3.0</br>4.9.3</br>5.4.0</nobr> |
+| **gupc** | Â | <nobr>4.8.0.3</nobr> |
+| **[icc](http://software.intel.com/en-us/intel-compilers/)** | C and C++ compiler from Intel | <nobr>2015.3.187-GNU-5.1.0-2.25</br>2017.0.098-GCC-5.4.0-2.26</br>2016.1.150-GCC-4.9.3-2.25</br>2015.3.187-GNU-4.9.3-2.25</nobr> |
+| **[ifort](http://software.intel.com/en-us/intel-compilers/)** | Fortran compiler from Intel | <nobr>2015.3.187-GNU-5.1.0-2.25</br>2017.0.098-GCC-5.4.0-2.26</br>2016.1.150-GCC-4.9.3-2.25</br>2015.3.187-GNU-4.9.3-2.25</nobr> |
+| **java** | Â | <nobr>1.7</nobr> |
+| **llvm** | Â | <nobr>3.6.0</nobr> |
## Data
-|Module|Description|Available versions|
-|--|--|--|
-|**[GDAL](http://www.gdal.org/)**|GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.|<nobr>2.1.0-foss-2015g</br>1.9.2-foss-2015g</nobr>|
-|**[HDF5](http://www.hdfgroup.org/HDF5/)**|HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.|<nobr>1.8.16-foss-2016a</br>1.8.16-intel-2016.01</br>1.8.16-intel-2015b</nobr>|
+| Module | Description | Available versions |
+| ----------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------ |
+| **[GDAL](http://www.gdal.org/)** | GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. | <nobr>2.1.0-foss-2015g</br>1.9.2-foss-2015g</nobr> |
+| **[HDF5](http://www.hdfgroup.org/HDF5/)** | HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. | <nobr>1.8.16-foss-2016a</br>1.8.16-intel-2016.01</br>1.8.16-intel-2015b</nobr> |
## Debugger
-|Module|Description|Available versions|
-|--|--|--|
-|**[Forge](http://www.allinea.com/products/develop-allinea-forge)**|Allinea Forge is the complete toolsuite for software development - with everything needed to debug, profile, optimize, edit and build C, C++ and FORTRAN applications on Linux for high performance - from single threads through to complex parallel HPC codes with MPI, OpenMP, threads or CUDA.|<nobr>6.0.6</br>5.7</br>6.1.2.lua</br>6.0.5</br>5.1-43967</nobr>|
-|**[PerformanceReports](http://www.allinea.com/products/allinea-performance-reports)**|Allinea Performance Reports are the most effective way to characterize and understand the performance of HPC application runs. One single-page HTML report elegantly answers a range of vital questions for any HPC site. - Is this application well-optimized for the system and the processors it is running on? - Does it benefit from running at this scale? - Are there I/O, networking or threading bottlenecks affecting performance? - Which hardware, software or configuration changes can we make to improve performance further. - How much energy did this application use?|<nobr>6.0.6</nobr>|
+| Module | Description | Available versions |
+| ------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------- |
+| **[Forge](http://www.allinea.com/products/develop-allinea-forge)** | Allinea Forge is the complete toolsuite for software development - with everything needed to debug, profile, optimize, edit and build C, C++ and FORTRAN applications on Linux for high performance - from single threads through to complex parallel HPC codes with MPI, OpenMP, threads or CUDA. | <nobr>6.0.6</br>5.7</br>6.1.2.lua</br>6.0.5</br>5.1-43967</nobr> |
+| **[PerformanceReports](http://www.allinea.com/products/allinea-performance-reports)** | Allinea Performance Reports are the most effective way to characterize and understand the performance of HPC application runs. One single-page HTML report elegantly answers a range of vital questions for any HPC site. - Is this application well-optimized for the system and the processors it is running on? - Does it benefit from running at this scale? - Are there I/O, networking or threading bottlenecks affecting performance? - Which hardware, software or configuration changes can we make to improve performance further. - How much energy did this application use? | <nobr>6.0.6</nobr> |
## Devel
-|Module|Description|Available versions|
-|--|--|--|
-|**[Autoconf](http://www.gnu.org/software/autoconf/)**|Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.|<nobr>2.69</br>2.69-GNU-4.9.3-2.25</br>2.69-intel-2015b</br>2.69-intel-2017.00</br>2.69-foss-2016a</br>2.69-GNU-5.1.0-2.25</nobr>|
-|**[Automake](http://www.gnu.org/software/automake/automake.html)**|Automake: GNU Standards-compliant Makefile generator|<nobr>1.15-GNU-5.1.0-2.25</br>1.15-foss-2016a</br>1.15-GNU-4.9.3-2.25</br>1.15-intel-2015b</br>1.15</br>1.15-intel-2017.00</nobr>|
-|**[Autotools](http://autotools.io)**|This bundle collect the standard GNU build tools: Autoconf, Automake and libtool|<nobr>20150215-GNU-4.9.3-2.25</br>20150215-intel-2017.00</br>20150215-GNU-5.1.0-2.25</br>20150215-intel-2015b</br>20150215-foss-2016a</br>20150215</nobr>|
-|**[Boost](http://www.boost.org/)**|Boost provides free peer-reviewed portable C++ source libraries.|<nobr>1.58.0-foss-2015g-Python-2.7.9</br>1.60.0-intel-2016a</br>1.59.0-intel-2015b</br>1.60.0-foss-2015g-Python-2.7.9</br>1.61.0-foss-2016a-serial</br>1.60.0-foss-2015g-Python-2.7.9.lua</nobr>|
-|**[CMake](http://www.cmake.org)**|CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.|<nobr>3.5.2-intel-2016a</br>3.6.2.lua</br>3.4.1-foss-2016a</br>3.5.2-foss-2016a</br>3.3.1-GCC-4.9.3-2.25</br>eb-CMake-3.6.2-gc3pie-job-20165321-UTC-09-53-36.log</br>3.4.1-intel-2015b</br>3.3.1-foss-2016a</br>3.3.1-foss-2015g</br>3.5.2</nobr>|
-|**[Doxygen](http://www.doxygen.org)**|Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.|<nobr>1.8.11</nobr>|
-|**[fontsproto](http://www.freedesktop.org/wiki/Software/xlibs)**|X11 font extension wire protocol|<nobr>2.1.3</nobr>|
-|**[guile](http://www.gnu.org/software/guile)**|Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system.|<nobr>1.8.8</br>1.8.8-intel-2015b</br>1.8.8-foss-2016a</nobr>|
-|**[libSM](http://www.freedesktop.org/wiki/Software/xlibs)**|X11 Session Management library, which allows for applications to both manage sessions, and make use of session managers to save and restore their state for later use.|<nobr>1.2.2</nobr>|
-|**[M4](http://www.gnu.org/software/m4/m4.html)**|GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.|<nobr>1.4.17</br>1.4.17-GCCcore-5.3.0</br>1.4.17-GCC-4.9.3</br>1.4.17-GCC-4.9.3-binutils-2.25</br>1.4.17-GCCcore-5.4.0</br>1.4.17-foss-2016a</br>1.4.16-intel-2015b</br>1.4.17-GNU-4.9.3-2.25</br>1.4.17-GCCcore-4.9.3</br>1.4.17-GNU-5.1.0-2.25</br>1.4.17-intel-2015b</br>1.4.17-intel-2017.00</br>1.4.17-GCC-5.1.0-binutils-2.25</nobr>|
-|**[make](http://www.gnu.org/software/make/make.html)**|make-3.82: GNU version of make utility|<nobr>3.82</nobr>|
-|**[makedepend](http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html)**|The makedepend package contains a C-preprocessor like utility to determine build-time dependencies.|<nobr>1.0.4</nobr>|
-|**Maven**| |<nobr>3.3.9.lua</br>3.3.9</nobr>|
-|**[ncurses](http://www.gnu.org/software/ncurses/)**|The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.|<nobr>5.9-intel-2016.01</br>5.9-intel-2015b</br>.6.0</br>5.9-gimkl-2.11.5</br>6.0-foss-2016a</br>5.9-foss-2015g</br>5.9</br>.6.0-intel-2016a.lua</br>5.9-GCC-4.9.3-2.25</br>6.0-intel-2016a</br>6.0-intel-2017.00</br>6.0</br>5.9-GNU-4.9.3-2.25</nobr>|
-|**[PCRE](http://www.pcre.org/)**|The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.|<nobr>8.37</br>8.37-intel-2016.01</br>8.37-gimkl-2.11.5</br>8.37-foss-2015g</nobr>|
-|**[pkg-config](http://www.freedesktop.org/wiki/Software/pkg-config/)**|pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries).|<nobr>0.27.1</br>0.27.1-intel-2015b</br>0.29-foss-2016a</nobr>|
-|**[Qt](http://qt-project.org/)**|Qt is a comprehensive cross-platform C++ application framework.|<nobr>4.8.6</nobr>|
-|**[renderproto](http://www.freedesktop.org/wiki/Software/xlibs)**|Xrender protocol and ancillary headers|<nobr>0.11</nobr>|
-|**[SCons](http://www.scons.org/)**|SCons is a software construction tool.|<nobr>2.3.6-foss-2015g-Python-2.7.9</nobr>|
-|**[SQLite](http://www.sqlite.org/)**|SQLite: SQL Database Engine in a C Library|<nobr>3.8.8.1-intel-2015b</br>3.8.8.1-foss-2015g</br>3.8.8.1-foss-2016a</br>3.9.2-intel-2017.00</br>3.8.8.1</br>3.9.2-intel-2015b</br>3.8.8.1-intel-2016.01</br>3.9.2-foss-2016a</nobr>|
-|**[xbitmaps](http://www.freedesktop.org/wiki/Software/xlibs)**|provides bitmaps for x|<nobr>1.1.1</nobr>|
-|**[xcb-proto](http://xcb.freedesktop.org/)**|The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.|<nobr>1.11-Python-2.7.9</nobr>|
-|**[xextproto](http://www.freedesktop.org/wiki/Software/xlibs)**|XExtProto protocol headers.|<nobr>7.3.0</nobr>|
-|**[xineramaproto](http://www.freedesktop.org/wiki/Software/xlibs)**|X protocol and ancillary headers for xinerama|<nobr>1.2.1</nobr>|
-|**[xorg-macros](http://cgit.freedesktop.org/xorg/util/macros)**|X.org macros utilities.|<nobr>1.17</nobr>|
-|**[xproto](http://www.freedesktop.org/wiki/Software/xlibs)**|X protocol and ancillary headers|<nobr>7.0.26</nobr>|
-|**[xtrans](http://www.freedesktop.org/wiki/Software/xlibs)**|xtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet.|<nobr>1.3.5</br>1.3.4</nobr>|
+| Module | Description | Available versions |
+| --------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| **[Autoconf](http://www.gnu.org/software/autoconf/)** | Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls. | <nobr>2.69</br>2.69-GNU-4.9.3-2.25</br>2.69-intel-2015b</br>2.69-intel-2017.00</br>2.69-foss-2016a</br>2.69-GNU-5.1.0-2.25</nobr> |
+| **[Automake](http://www.gnu.org/software/automake/automake.html)** | Automake: GNU Standards-compliant Makefile generator | <nobr>1.15-GNU-5.1.0-2.25</br>1.15-foss-2016a</br>1.15-GNU-4.9.3-2.25</br>1.15-intel-2015b</br>1.15</br>1.15-intel-2017.00</nobr> |
+| **[Autotools](http://autotools.io)** | This bundle collect the standard GNU build tools: Autoconf, Automake and libtool | <nobr>20150215-GNU-4.9.3-2.25</br>20150215-intel-2017.00</br>20150215-GNU-5.1.0-2.25</br>20150215-intel-2015b</br>20150215-foss-2016a</br>20150215</nobr> |
+| **[Boost](http://www.boost.org/)** | Boost provides free peer-reviewed portable C++ source libraries. | <nobr>1.58.0-foss-2015g-Python-2.7.9</br>1.60.0-intel-2016a</br>1.59.0-intel-2015b</br>1.60.0-foss-2015g-Python-2.7.9</br>1.61.0-foss-2016a-serial</br>1.60.0-foss-2015g-Python-2.7.9.lua</nobr> |
+| **[CMake](http://www.cmake.org)** | CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. | <nobr>3.5.2-intel-2016a</br>3.6.2.lua</br>3.4.1-foss-2016a</br>3.5.2-foss-2016a</br>3.3.1-GCC-4.9.3-2.25</br>eb-CMake-3.6.2-gc3pie-job-20165321-UTC-09-53-36.log</br>3.4.1-intel-2015b</br>3.3.1-foss-2016a</br>3.3.1-foss-2015g</br>3.5.2</nobr> |
+| **[Doxygen](http://www.doxygen.org)** | Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. | <nobr>1.8.11</nobr> |
+| **[fontsproto](http://www.freedesktop.org/wiki/Software/xlibs)** | X11 font extension wire protocol | <nobr>2.1.3</nobr> |
+| **[guile](http://www.gnu.org/software/guile)** | Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system. | <nobr>1.8.8</br>1.8.8-intel-2015b</br>1.8.8-foss-2016a</nobr> |
+| **[libSM](http://www.freedesktop.org/wiki/Software/xlibs)** | X11 Session Management library, which allows for applications to both manage sessions, and make use of session managers to save and restore their state for later use. | <nobr>1.2.2</nobr> |
+| **[M4](http://www.gnu.org/software/m4/m4.html)** | GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. | <nobr>1.4.17</br>1.4.17-GCCcore-5.3.0</br>1.4.17-GCC-4.9.3</br>1.4.17-GCC-4.9.3-binutils-2.25</br>1.4.17-GCCcore-5.4.0</br>1.4.17-foss-2016a</br>1.4.16-intel-2015b</br>1.4.17-GNU-4.9.3-2.25</br>1.4.17-GCCcore-4.9.3</br>1.4.17-GNU-5.1.0-2.25</br>1.4.17-intel-2015b</br>1.4.17-intel-2017.00</br>1.4.17-GCC-5.1.0-binutils-2.25</nobr> |
+| **[make](http://www.gnu.org/software/make/make.html)** | make-3.82: GNU version of make utility | <nobr>3.82</nobr> |
+| **[makedepend](http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html)** | The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. | <nobr>1.0.4</nobr> |
+| **Maven** | Â | <nobr>3.3.9.lua</br>3.3.9</nobr> |
+| **[ncurses](http://www.gnu.org/software/ncurses/)** | The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. | <nobr>5.9-intel-2016.01</br>5.9-intel-2015b</br>.6.0</br>5.9-gimkl-2.11.5</br>6.0-foss-2016a</br>5.9-foss-2015g</br>5.9</br>.6.0-intel-2016a.lua</br>5.9-GCC-4.9.3-2.25</br>6.0-intel-2016a</br>6.0-intel-2017.00</br>6.0</br>5.9-GNU-4.9.3-2.25</nobr> |
+| **[PCRE](http://www.pcre.org/)** | The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. | <nobr>8.37</br>8.37-intel-2016.01</br>8.37-gimkl-2.11.5</br>8.37-foss-2015g</nobr> |
+| **[pkg-config](http://www.freedesktop.org/wiki/Software/pkg-config/)** | pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries). | <nobr>0.27.1</br>0.27.1-intel-2015b</br>0.29-foss-2016a</nobr> |
+| **[Qt](http://qt-project.org/)** | Qt is a comprehensive cross-platform C++ application framework. | <nobr>4.8.6</nobr> |
+| **[renderproto](http://www.freedesktop.org/wiki/Software/xlibs)** | Xrender protocol and ancillary headers | <nobr>0.11</nobr> |
+| **[SCons](http://www.scons.org/)** | SCons is a software construction tool. | <nobr>2.3.6-foss-2015g-Python-2.7.9</nobr> |
+| **[SQLite](http://www.sqlite.org/)** | SQLite: SQL Database Engine in a C Library | <nobr>3.8.8.1-intel-2015b</br>3.8.8.1-foss-2015g</br>3.8.8.1-foss-2016a</br>3.9.2-intel-2017.00</br>3.8.8.1</br>3.9.2-intel-2015b</br>3.8.8.1-intel-2016.01</br>3.9.2-foss-2016a</nobr> |
+| **[xbitmaps](http://www.freedesktop.org/wiki/Software/xlibs)** | provides bitmaps for x | <nobr>1.1.1</nobr> |
+| **[xcb-proto](http://xcb.freedesktop.org/)** | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. | <nobr>1.11-Python-2.7.9</nobr> |
+| **[xextproto](http://www.freedesktop.org/wiki/Software/xlibs)** | XExtProto protocol headers. | <nobr>7.3.0</nobr> |
+| **[xineramaproto](http://www.freedesktop.org/wiki/Software/xlibs)** | X protocol and ancillary headers for xinerama | <nobr>1.2.1</nobr> |
+| **[xorg-macros](http://cgit.freedesktop.org/xorg/util/macros)** | X.org macros utilities. | <nobr>1.17</nobr> |
+| **[xproto](http://www.freedesktop.org/wiki/Software/xlibs)** | X protocol and ancillary headers | <nobr>7.0.26</nobr> |
+| **[xtrans](http://www.freedesktop.org/wiki/Software/xlibs)** | xtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. | <nobr>1.3.5</br>1.3.4</nobr> |
## Engineering
-|Module|Description|Available versions|
-|--|--|--|
-|**adams**| |<nobr>2013.2</nobr>|
-|**ansys**| |<nobr>15.0.x</br>16.0.x</br>14.5.x</nobr>|
-|**beopest**| |<nobr>12.0.1</br>13.3</br>12.2</nobr>|
-|**blender**| |<nobr>2.71</nobr>|
-|**Code_Saturne**| |<nobr>3.0.5</nobr>|
-|**comsol**| |<nobr>43b-EDU</br>44-EDU</br>50-EDU</br>50-COM</br>44-COM</br>43b-COM</nobr>|
-|**digimat**| |<nobr>5.0.1</nobr>|
-|**Discovery_Studio**| |<nobr>4.0</nobr>|
-|**dytran**| |<nobr>2013.0.1</nobr>|
-|**fds**| |<nobr>5.5.3</br>6.svn</br>5.5.3-omp</nobr>|
-|**hypermesh**| |<nobr>12.0.110</nobr>|
-|**hyperworks**| |<nobr>13.0</nobr>|
-|**lsdyna**| |<nobr>7.x.x</nobr>|
-|**lsprepost**| |<nobr>4.2</nobr>|
-|**lux**| |<nobr>1.3.1</nobr>|
-|**marc**| |<nobr>2011</br>2013.1</nobr>|
-|**matlab**| |<nobr>R2014a-COM</br>R2013a-COM</br>R2013a-EDU</br>R2014a-EDU</nobr>|
-|**maxwell**| |<nobr>3.0</nobr>|
-|**modflow-2005**| |<nobr>1.11.00</nobr>|
-|**modflow-nwt**| |<nobr>1.0.9-aquaveo</br>1.0.9</nobr>|
-|**nastran**| |<nobr>2013.1.1</nobr>|
-|**openfoam**| |<nobr>2.2.1-icc-openmpi1.6.5-DP</br>2.2.1-gcc481-openmpi1.6.5-SP</br>2.2.1-gcc481-openmpi1.6.5-DP</br>2.2.2-icc-openmpi1.8.1-DP</br>2.2.1-icc-impi4.1.1.036-DP</nobr>|
-|**paraview**| |<nobr>4.0.1-gcc481-bullxmpi1.2.4.1-osmesa10.0</nobr>|
-|**pest**| |<nobr>13.0</nobr>|
-|**wien2k**| |<nobr>13.1</br>14.2</nobr>|
+| Module | Description | Available versions |
+| -------------------- | ----------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **adams** | Â | <nobr>2013.2</nobr> |
+| **ansys** | Â | <nobr>15.0.x</br>16.0.x</br>14.5.x</nobr> |
+| **beopest** | Â | <nobr>12.0.1</br>13.3</br>12.2</nobr> |
+| **blender** | Â | <nobr>2.71</nobr> |
+| **Code_Saturne** | Â | <nobr>3.0.5</nobr> |
+| **comsol** | Â | <nobr>43b-EDU</br>44-EDU</br>50-EDU</br>50-COM</br>44-COM</br>43b-COM</nobr> |
+| **digimat** | Â | <nobr>5.0.1</nobr> |
+| **Discovery_Studio** | Â | <nobr>4.0</nobr> |
+| **dytran** | Â | <nobr>2013.0.1</nobr> |
+| **fds** | Â | <nobr>5.5.3</br>6.svn</br>5.5.3-omp</nobr> |
+| **hypermesh** | Â | <nobr>12.0.110</nobr> |
+| **hyperworks** | Â | <nobr>13.0</nobr> |
+| **lsdyna** | Â | <nobr>7.x.x</nobr> |
+| **lsprepost** | Â | <nobr>4.2</nobr> |
+| **lux** | Â | <nobr>1.3.1</nobr> |
+| **marc** | Â | <nobr>2011</br>2013.1</nobr> |
+| **matlab** | Â | <nobr>R2014a-COM</br>R2013a-COM</br>R2013a-EDU</br>R2014a-EDU</nobr> |
+| **maxwell** | Â | <nobr>3.0</nobr> |
+| **modflow-2005** | Â | <nobr>1.11.00</nobr> |
+| **modflow-nwt** | Â | <nobr>1.0.9-aquaveo</br>1.0.9</nobr> |
+| **nastran** | Â | <nobr>2013.1.1</nobr> |
+| **openfoam** | Â | <nobr>2.2.1-icc-openmpi1.6.5-DP</br>2.2.1-gcc481-openmpi1.6.5-SP</br>2.2.1-gcc481-openmpi1.6.5-DP</br>2.2.2-icc-openmpi1.8.1-DP</br>2.2.1-icc-impi4.1.1.036-DP</nobr> |
+| **paraview** | Â | <nobr>4.0.1-gcc481-bullxmpi1.2.4.1-osmesa10.0</nobr> |
+| **pest** | Â | <nobr>13.0</nobr> |
+| **wien2k** | Â | <nobr>13.1</br>14.2</nobr> |
## Environments
-|Module|Description|Available versions|
-|--|--|--|
-|**bullxde**| |<nobr>2.0</nobr>|
-|**PrgEnv-gnu**| |<nobr>4.4.6</br>4.4.6-test</br>4.8.1</nobr>|
-|**PrgEnv-intel**| |<nobr>15.0.3</br>13.5.192</br>14.0.1</nobr>|
+| Module | Description | Available versions |
+| ---------------- | ----------- | ------------------------------------------- |
+| **bullxde** | Â | <nobr>2.0</nobr> |
+| **PrgEnv-gnu** | Â | <nobr>4.4.6</br>4.4.6-test</br>4.8.1</nobr> |
+| **PrgEnv-intel** | Â | <nobr>15.0.3</br>13.5.192</br>14.0.1</nobr> |
## Lang
-|Module|Description|Available versions|
-|--|--|--|
-|**[Bison](http://www.gnu.org/software/bison)**|Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.|<nobr>3.0.4-foss-2016a</br>3.0.4-GCC-4.9.3</br>3.0.4</br>2.7-foss-2015g</br>3.0.2</br>3.0.4-GCCcore-5.4.0</br>2.7</br>3.0.4-intel-2015b</br>2.5-intel-2015b</br>3.0.4-GCC-4.9.3-binutils-2.25</br>3.0.4-GCC-5.1.0-binutils-2.25</br>3.0.4-GCCcore-4.9.3</br>3.0.4-GCCcore-5.3.0</nobr>|
-|**[byacc](http://invisible-island.net/byacc/byacc.html)**|Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular compiler.|<nobr>20150711-intel-2015b</br>20120526</br>20120526-foss-2016a</br>20120526-foss-2015g</br>20120526-intel-2015b</nobr>|
-|**[flex](http://flex.sourceforge.net/)**|Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.|<nobr>2.5.39-foss-2015g</br>2.5.39-GCC-5.1.0-binutils-2.25</br>2.6.0</br>2.5.39-GCC-4.9.3-binutils-2.25</br>2.5.39-GCC-4.9.3</br>2.6.0-GCCcore-5.3.0</br>2.5.35-intel-2015b</br>2.6.0-GCCcore-5.4.0</br>2.5.39</br>2.5.39-foss-2016a</br>2.5.39-GCCcore-4.9.3</br>2.5.39-intel-2015b</nobr>|
-|**[Java](http://java.com/)**|Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.|<nobr>1.8.0_51</br>1.7.0_79.lua</br>1.7.0_79</nobr>|
-|**[libgdiplus](https://github.com/mono/libgdiplus)**|An Open Source implementation of the GDI+ API.|<nobr>3.12</nobr>|
-|**[Lua](http://www.lua.org/)**|Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.|<nobr>.5.1.4-8</br>5.1.4-8.lua</nobr>|
-|**[NASM](http://www.nasm.us/)**|NASM: General-purpose x86 assembler|<nobr>2.11.05</nobr>|
-|**Perl**| |<nobr>5.24.0-GCC-4.9.3-2.25-bare.lua</br>5.20.2-GNU-4.9.3-2.25-bare</nobr>|
-|**[Python](http://python.org/)**|Python is a programming language that lets you work more quickly and integrate your systems more effectively.|<nobr>3.5.2-foss-2016a</br>2.7.9-intel-2015b</br>2.7.9-foss-2015g</br>2.7.9-intel-2016.01</br>3.5.2-intel-2017.00</br>2.7.11-intel-2015b</br>2.7.9</nobr>|
-|**[Ruby](https://www.ruby-lang.org)**|Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.|<nobr>2.3.1</nobr>|
-|**[Tcl](http://www.tcl.tk/)**|Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.|<nobr>8.6.4</br>8.6.4-intel-2017.00</br>8.6.3-intel-2016.01</br>8.6.3-foss-2016a</br>8.6.3-intel-2015b</br>8.6.4-foss-2016a</br>8.6.4-intel-2015b</br>8.6.3</br>8.6.3-foss-2015g</br>8.5.12</nobr>|
+| Module | Description | Available versions |
+| --------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[Bison](http://www.gnu.org/software/bison)** | Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. | <nobr>3.0.4-foss-2016a</br>3.0.4-GCC-4.9.3</br>3.0.4</br>2.7-foss-2015g</br>3.0.2</br>3.0.4-GCCcore-5.4.0</br>2.7</br>3.0.4-intel-2015b</br>2.5-intel-2015b</br>3.0.4-GCC-4.9.3-binutils-2.25</br>3.0.4-GCC-5.1.0-binutils-2.25</br>3.0.4-GCCcore-4.9.3</br>3.0.4-GCCcore-5.3.0</nobr> |
+| **[byacc](http://invisible-island.net/byacc/byacc.html)** | Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular compiler. | <nobr>20150711-intel-2015b</br>20120526</br>20120526-foss-2016a</br>20120526-foss-2015g</br>20120526-intel-2015b</nobr> |
+| **[flex](http://flex.sourceforge.net/)** | Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. | <nobr>2.5.39-foss-2015g</br>2.5.39-GCC-5.1.0-binutils-2.25</br>2.6.0</br>2.5.39-GCC-4.9.3-binutils-2.25</br>2.5.39-GCC-4.9.3</br>2.6.0-GCCcore-5.3.0</br>2.5.35-intel-2015b</br>2.6.0-GCCcore-5.4.0</br>2.5.39</br>2.5.39-foss-2016a</br>2.5.39-GCCcore-4.9.3</br>2.5.39-intel-2015b</nobr> |
+| **[Java](http://java.com/)** | Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. | <nobr>1.8.0_51</br>1.7.0_79.lua</br>1.7.0_79</nobr> |
+| **[libgdiplus](https://github.com/mono/libgdiplus)** | An Open Source implementation of the GDI+ API. | <nobr>3.12</nobr> |
+| **[Lua](http://www.lua.org/)** | Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping. | <nobr>.5.1.4-8</br>5.1.4-8.lua</nobr> |
+| **[NASM](http://www.nasm.us/)** | NASM: General-purpose x86 assembler | <nobr>2.11.05</nobr> |
+| **Perl** | Â | <nobr>5.24.0-GCC-4.9.3-2.25-bare.lua</br>5.20.2-GNU-4.9.3-2.25-bare</nobr> |
+| **[Python](http://python.org/)** | Python is a programming language that lets you work more quickly and integrate your systems more effectively. | <nobr>3.5.2-foss-2016a</br>2.7.9-intel-2015b</br>2.7.9-foss-2015g</br>2.7.9-intel-2016.01</br>3.5.2-intel-2017.00</br>2.7.11-intel-2015b</br>2.7.9</nobr> |
+| **[Ruby](https://www.ruby-lang.org)** | Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. | <nobr>2.3.1</nobr> |
+| **[Tcl](http://www.tcl.tk/)** | Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. | <nobr>8.6.4</br>8.6.4-intel-2017.00</br>8.6.3-intel-2016.01</br>8.6.3-foss-2016a</br>8.6.3-intel-2015b</br>8.6.4-foss-2016a</br>8.6.4-intel-2015b</br>8.6.3</br>8.6.3-foss-2015g</br>8.5.12</nobr> |
## Lib
-|Module|Description|Available versions|
-|--|--|--|
-|**[libdrm](http://dri.freedesktop.org)**|Direct Rendering Manager runtime library.|<nobr>2.4.27</nobr>|
-|**[libffi](http://sourceware.org/libffi/)**|The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.|<nobr>3.2.1-foss-2016a</br>3.0.13</br>3.1-intel-2015b</br>3.0.13-intel-2015b</br>3.1-intel-2016.01</nobr>|
-|**[libfontenc](http://www.freedesktop.org/wiki/Software/xlibs/)**|X11 font encoding library|<nobr>1.1.3</nobr>|
-|**[libjpeg-turbo](http://sourceforge.net/projects/libjpeg-turbo/)**|libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.|<nobr>1.4.0</nobr>|
-|**[libmatheval](http://www.gnu.org/software/libmatheval/)**|GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.|<nobr>1.1.8</br>1.1.8-foss-2016a</br>1.1.8-intel-2015b</br>1.1.11-intel-2015b</nobr>|
-|**[libpng](http://www.libpng.org/pub/png/libpng.html)**|libpng is the official PNG reference library|<nobr>1.6.12</nobr>|
-|**[libpthread-stubs](http://xcb.freedesktop.org/)**|The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.|<nobr>0.3</nobr>|
-|**[libreadline](http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html)**|The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.|<nobr>.6.3</br>6.3-intel-2016.01</br>6.3-foss-2015g</br>6.3-foss-2016a</br>6.3-intel-2017.00</br>6.3-gimkl-2.11.5</br>6.3-intel-2015b</br>6.3</nobr>|
-|**[LibTIFF](http://www.remotesensing.org/libtiff/)**|tiff: Library and tools for reading and writing TIFF data files|<nobr>4.0.3</nobr>|
-|**[libtool](http://www.gnu.org/software/libtool)**|GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.|<nobr>2.4.2</br>2.4.6-foss-2016a</br>2.4.2-foss-2015g</br>2.4.6-intel-2017.00</br>2.4.6-intel-2015b</br>2.4.6-GNU-5.1.0-2.25</br>2.4.6</br>2.4.6-GNU-4.9.3-2.25</nobr>|
-|**[libunistring](http://www.gnu.org/software/libunistring/)**|This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.|<nobr>0.9.3</br>0.9.3-foss-2016a</br>0.9.3-intel-2015b</nobr>|
-|**[libxcb](http://xcb.freedesktop.org/)**|The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.|<nobr>1.11-Python-2.7.9</nobr>|
-|**[libxml2](http://xmlsoft.org/)**|Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).|<nobr>2.9.3-intel-2016a</br>2.9.3-foss-2016a</br>2.9.2-intel-2015b</nobr>|
-|**[SIONlib](http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html)**|SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version.|<nobr>1.6.1-tools</nobr>|
-|**[spGPU](https://github.com/davidebarbieri/spgpu)**|spGPU is a set of custom matrix storages and CUDA kernels for sparse linear algebra computing on GPU. It isn't a replacement for cuBLAS/cuSPARSE that should be used for a full featured linear algebra environment on GPU.|<nobr>master-GCC-4.9.3-2.25</nobr>|
-|**tbb**| |<nobr>4.4.2.152.lua</br>4.4.2.152</nobr>|
-|**zlib**| |<nobr>.1.2.8-foss-2015g.lua</br>1.2.8-intel-2015b</br>1.2.8-GCC-5.1.0-binutils-2.25</br>1.2.8-foss-2016a</br>1.2.8-intel-2017.00</br>1.2.8-GCC-4.9.3-binutils-2.25</br>1.2.8-GCCcore-4.9.3</br>1.2.8-foss-2015g</br>1.2.8</br>1.2.8-intel-2016a</br>1.2.8-intel-2016.01</br>1.2.8-GCC-4.9.3</br>1.2.8-GCCcore-5.3.0</br>1.2.8-GCCcore-5.4.0</nobr>|
+| Module | Description | Available versions |
+| ------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[libdrm](http://dri.freedesktop.org)** | Direct Rendering Manager runtime library. | <nobr>2.4.27</nobr> |
+| **[libffi](http://sourceware.org/libffi/)** | The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. | <nobr>3.2.1-foss-2016a</br>3.0.13</br>3.1-intel-2015b</br>3.0.13-intel-2015b</br>3.1-intel-2016.01</nobr> |
+| **[libfontenc](http://www.freedesktop.org/wiki/Software/xlibs/)** | X11 font encoding library | <nobr>1.1.3</nobr> |
+| **[libjpeg-turbo](http://sourceforge.net/projects/libjpeg-turbo/)** | libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. | <nobr>1.4.0</nobr> |
+| **[libmatheval](http://www.gnu.org/software/libmatheval/)** | GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. | <nobr>1.1.8</br>1.1.8-foss-2016a</br>1.1.8-intel-2015b</br>1.1.11-intel-2015b</nobr> |
+| **[libpng](http://www.libpng.org/pub/png/libpng.html)** | libpng is the official PNG reference library | <nobr>1.6.12</nobr> |
+| **[libpthread-stubs](http://xcb.freedesktop.org/)** | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. | <nobr>0.3</nobr> |
+| **[libreadline](http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html)** | The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands. | <nobr>.6.3</br>6.3-intel-2016.01</br>6.3-foss-2015g</br>6.3-foss-2016a</br>6.3-intel-2017.00</br>6.3-gimkl-2.11.5</br>6.3-intel-2015b</br>6.3</nobr> |
+| **[LibTIFF](http://www.remotesensing.org/libtiff/)** | tiff: Library and tools for reading and writing TIFF data files | <nobr>4.0.3</nobr> |
+| **[libtool](http://www.gnu.org/software/libtool)** | GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. | <nobr>2.4.2</br>2.4.6-foss-2016a</br>2.4.2-foss-2015g</br>2.4.6-intel-2017.00</br>2.4.6-intel-2015b</br>2.4.6-GNU-5.1.0-2.25</br>2.4.6</br>2.4.6-GNU-4.9.3-2.25</nobr> |
+| **[libunistring](http://www.gnu.org/software/libunistring/)** | This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard. | <nobr>0.9.3</br>0.9.3-foss-2016a</br>0.9.3-intel-2015b</nobr> |
+| **[libxcb](http://xcb.freedesktop.org/)** | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. | <nobr>1.11-Python-2.7.9</nobr> |
+| **[libxml2](http://xmlsoft.org/)** | Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). | <nobr>2.9.3-intel-2016a</br>2.9.3-foss-2016a</br>2.9.2-intel-2015b</nobr> |
+| **[SIONlib](http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html)** | SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version. | <nobr>1.6.1-tools</nobr> |
+| **[spGPU](https://github.com/davidebarbieri/spgpu)** | spGPU is a set of custom matrix storages and CUDA kernels for sparse linear algebra computing on GPU. It isn't a replacement for cuBLAS/cuSPARSE that should be used for a full featured linear algebra environment on GPU. | <nobr>master-GCC-4.9.3-2.25</nobr> |
+| **tbb** | Â | <nobr>4.4.2.152.lua</br>4.4.2.152</nobr> |
+| **zlib** | Â | <nobr>.1.2.8-foss-2015g.lua</br>1.2.8-intel-2015b</br>1.2.8-GCC-5.1.0-binutils-2.25</br>1.2.8-foss-2016a</br>1.2.8-intel-2017.00</br>1.2.8-GCC-4.9.3-binutils-2.25</br>1.2.8-GCCcore-4.9.3</br>1.2.8-foss-2015g</br>1.2.8</br>1.2.8-intel-2016a</br>1.2.8-intel-2016.01</br>1.2.8-GCC-4.9.3</br>1.2.8-GCCcore-5.3.0</br>1.2.8-GCCcore-5.4.0</nobr> |
## Libraries
-|Module|Description|Available versions|
-|--|--|--|
-|**adios**| |<nobr>1.8.0</nobr>|
-|**boost**| |<nobr>1.56-icc-impi</br>1.56-gcc-openmpi</nobr>|
-|**dataspaces**| |<nobr>1.4.0</nobr>|
-|**fftw2**| |<nobr>2.1.5-icc</br>2.1.5-gcc</nobr>|
-|**fftw2-mpi**| |<nobr>2.1.5-icc</br>2.1.5-gcc</nobr>|
-|**fftw3**| |<nobr>3.3.3-gcc</br>3.3.3-icc</nobr>|
-|**fftw3-mpi**| |<nobr>3.3.3-gcc</br>3.3.3-icc</nobr>|
-|**gpi2**| |<nobr>1.0.2</br>1.1.1</br>1.1.0</nobr>|
-|**gsl**| |<nobr>1.16-icc</br>1.16-gcc</nobr>|
-|**hdf5**| |<nobr>1.8.13</br>1.8.11</nobr>|
-|**hdf5-parallel**| |<nobr>1.8.11-gcc</br>1.8.13-gcc</br>1.8.13</br>1.8.13-gcc49</br>1.8.11</nobr>|
-|**ipp**| |<nobr>13.5.192</br>15.3.187</br>14.0.1</br>15.2.164</nobr>|
-|**libmesh**| |<nobr>0.9.3-petsc-3.4.4-icc-impi-mkl-dbg</br>0.9.3-petsc-3.4.4-icc-impi-mkl-dbg-2d</br>0.9.3-petsc-3.4.4-icc-impi-mkl-opt</nobr>|
-|**magma**| |<nobr>.common-mic</br>1.3.0-mic</br>1.1.0-mic</nobr>|
-|**mkl**| |<nobr>13.5.192</br>15.3.187</br>14.0.1</br>15.2.164</nobr>|
-|**mxml**| |<nobr>2.9</nobr>|
-|**netcdf**| |<nobr>4.2.1.1</br>4.3.0</nobr>|
-|**netcdf-cxx**| |<nobr>4.2</nobr>|
-|**netcdf-fortran**| |<nobr>4.2</nobr>|
-|**netcdf-parallel**| |<nobr>4.3.0</nobr>|
-|**opencl-rt**| |<nobr>4.5.0.8</nobr>|
-|**opencl-sdk**| |<nobr>4.6.0.92</nobr>|
-|**petsc**| |<nobr>3.5.3-icc15-impi-mkl-threads-dbg</br>3.5.3-icc15-impi-mkl-threads-opt</br>3.7.3-icc16-impi5-mkl-dbg</br>3.5.3-icc15-impi-mkl-opt</br>3.7.3-icc16-impi5-mkl-opt</br>3.5.3-icc15-impi-mkl-dbg</br>.common_help</br>.common_petsc_pre</br>.common_petsc_post</br>.common_functions</nobr>|
-|**plasma**| |<nobr>2.6.0</nobr>|
-|**slepc**| |<nobr>3.7.2-icc16-impi5-mkl-opt</br>3.7.2-icc16-impi5-mkl-dbg</br>3.4.4-icc15-impi-mkl-opt</br>3.4.4-icc15-impi-mkl-dbg</nobr>|
-|**szip**| |<nobr>2.1</nobr>|
-|**tbb**| |<nobr>13.5.192</br>15.3.187</br>14.0.1</br>15.2.164</nobr>|
-|**trilinos**| |<nobr>11.2.3-gcc-openmpi-mkl-dbg</br>11.2.3-icc</br>11.2.3-gcc-openmpi-mkl-opt</nobr>|
-|**zlib**| |<nobr>1.2.5</br>1.2.8</nobr>|
+| Module | Description | Available versions |
+| ------------------- | ----------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **adios** | Â | <nobr>1.8.0</nobr> |
+| **boost** | Â | <nobr>1.56-icc-impi</br>1.56-gcc-openmpi</nobr> |
+| **dataspaces** | Â | <nobr>1.4.0</nobr> |
+| **fftw2** | Â | <nobr>2.1.5-icc</br>2.1.5-gcc</nobr> |
+| **fftw2-mpi** | Â | <nobr>2.1.5-icc</br>2.1.5-gcc</nobr> |
+| **fftw3** | Â | <nobr>3.3.3-gcc</br>3.3.3-icc</nobr> |
+| **fftw3-mpi** | Â | <nobr>3.3.3-gcc</br>3.3.3-icc</nobr> |
+| **gpi2** | Â | <nobr>1.0.2</br>1.1.1</br>1.1.0</nobr> |
+| **gsl** | Â | <nobr>1.16-icc</br>1.16-gcc</nobr> |
+| **hdf5** | Â | <nobr>1.8.13</br>1.8.11</nobr> |
+| **hdf5-parallel** | Â | <nobr>1.8.11-gcc</br>1.8.13-gcc</br>1.8.13</br>1.8.13-gcc49</br>1.8.11</nobr> |
+| **ipp** | Â | <nobr>13.5.192</br>15.3.187</br>14.0.1</br>15.2.164</nobr> |
+| **libmesh** | Â | <nobr>0.9.3-petsc-3.4.4-icc-impi-mkl-dbg</br>0.9.3-petsc-3.4.4-icc-impi-mkl-dbg-2d</br>0.9.3-petsc-3.4.4-icc-impi-mkl-opt</nobr> |
+| **magma** | Â | <nobr>.common-mic</br>1.3.0-mic</br>1.1.0-mic</nobr> |
+| **mkl** | Â | <nobr>13.5.192</br>15.3.187</br>14.0.1</br>15.2.164</nobr> |
+| **mxml** | Â | <nobr>2.9</nobr> |
+| **netcdf** | Â | <nobr>4.2.1.1</br>4.3.0</nobr> |
+| **netcdf-cxx** | Â | <nobr>4.2</nobr> |
+| **netcdf-fortran** | Â | <nobr>4.2</nobr> |
+| **netcdf-parallel** | Â | <nobr>4.3.0</nobr> |
+| **opencl-rt** | Â | <nobr>4.5.0.8</nobr> |
+| **opencl-sdk** | Â | <nobr>4.6.0.92</nobr> |
+| **petsc** | Â | <nobr>3.5.3-icc15-impi-mkl-threads-dbg</br>3.5.3-icc15-impi-mkl-threads-opt</br>3.7.3-icc16-impi5-mkl-dbg</br>3.5.3-icc15-impi-mkl-opt</br>3.7.3-icc16-impi5-mkl-opt</br>3.5.3-icc15-impi-mkl-dbg</br>.common_help</br>.common_petsc_pre</br>.common_petsc_post</br>.common_functions</nobr> |
+| **plasma** | Â | <nobr>2.6.0</nobr> |
+| **slepc** | Â | <nobr>3.7.2-icc16-impi5-mkl-opt</br>3.7.2-icc16-impi5-mkl-dbg</br>3.4.4-icc15-impi-mkl-opt</br>3.4.4-icc15-impi-mkl-dbg</nobr> |
+| **szip** | Â | <nobr>2.1</nobr> |
+| **tbb** | Â | <nobr>13.5.192</br>15.3.187</br>14.0.1</br>15.2.164</nobr> |
+| **trilinos** | Â | <nobr>11.2.3-gcc-openmpi-mkl-dbg</br>11.2.3-icc</br>11.2.3-gcc-openmpi-mkl-opt</nobr> |
+| **zlib** | Â | <nobr>1.2.5</br>1.2.8</nobr> |
## Math
-|Module|Description|Available versions|
-|--|--|--|
-|**[GMP](http://gmplib.org/)**|GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.|<nobr>6.1.0-intel-2015b</br>5.0.5</br>6.1.0-foss-2016a</br>6.0.0a</br>6.0.0a-intel-2015b</br>6.1.0-intel-2017.00</br>5.0.5-foss-2015g</nobr>|
-|**[ISL](http://isl.gforge.inria.fr/)**|isl is a library for manipulating sets and relations of integer points bounded by linear constraints.|<nobr>0.15</nobr>|
-|**[MLD2P4](http://www.mld2p4.it)**|MLD2P4 (Multi-Level Domain Decomposition Parallel Preconditioners Package based on PSBLAS) is a package of parallel algebraic multi-level preconditioners. It implements various versions of one-level additive and of multi-level additive and hybrid Schwarz algorithms. In the multi-level case, a purely algebraic approach is applied to generate coarse-level corrections, so that no geometric background is needed concerning the matrix to be preconditioned. The matrix is assumed to be square, real or complex, with a symmetric sparsity pattern.|<nobr>2.0-rc4-GCC-4.9.3-2.25</nobr>|
-|**[numpy](http://www.numpy.org)**|NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.|<nobr>1.8.2-intel-2015b-Python-2.7.9</br>1.8.2-intel-2015b-Python-2.7.11</br>1.8.2-intel-2016.01-Python-2.7.9</nobr>|
-|**[Octave](http://www.gnu.org/software/octave/)**|GNU Octave is a high-level interpreted language, primarily intended for numerical computations.|<nobr>3.8.2-gimkl-2.11.5</br>4.0.0-foss-2015g</br>4.0.1-gimkl-2.11.5</nobr>|
-|**[PSBLAS](http://people.uniroma2.it/salvatore.filippone/psblas/)**|Most computationally intensive applications work on irregular and sparse domains that complicate their implementation on parallel machines. The major goal of the Parallel Sparse Basic Linear Algebra Subroutines (PSBLAS) project is to provide a framework to enable easy, efficient and portable implementations of iterative solvers for linear systems, while shielding the user from most details of their parallelization. The interface is designed keeping in view a Single Program Multiple Data programming model on distributed memory machines.|<nobr>3.3.4-3-GCC-4.9.3-2.25</nobr>|
-|**[PSBLAS-ext](http://people.uniroma2.it/salvatore.filippone/psblas/)**|PSBLAS - Extended formats and NVIDIA GPU support|<nobr>1.0-4-GCC-4.9.3-2.25</nobr>|
-|**[ScientificPython](https://sourcesup.cru.fr/projects/scientific-py/)**|ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization.|<nobr>2.9.4-intel-2016.01-Python-2.7.9</br>2.9.4-intel-2015b-Python-2.7.9</br>2.9.4-intel-2015b-Python-2.7.11</nobr>|
+| Module | Description | Available versions |
+| ------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[GMP](http://gmplib.org/)** | GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. | <nobr>6.1.0-intel-2015b</br>5.0.5</br>6.1.0-foss-2016a</br>6.0.0a</br>6.0.0a-intel-2015b</br>6.1.0-intel-2017.00</br>5.0.5-foss-2015g</nobr> |
+| **[ISL](http://isl.gforge.inria.fr/)** | isl is a library for manipulating sets and relations of integer points bounded by linear constraints. | <nobr>0.15</nobr> |
+| **[MLD2P4](http://www.mld2p4.it)** | MLD2P4 (Multi-Level Domain Decomposition Parallel Preconditioners Package based on PSBLAS) is a package of parallel algebraic multi-level preconditioners. It implements various versions of one-level additive and of multi-level additive and hybrid Schwarz algorithms. In the multi-level case, a purely algebraic approach is applied to generate coarse-level corrections, so that no geometric background is needed concerning the matrix to be preconditioned. The matrix is assumed to be square, real or complex, with a symmetric sparsity pattern. | <nobr>2.0-rc4-GCC-4.9.3-2.25</nobr> |
+| **[numpy](http://www.numpy.org)** | NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. | <nobr>1.8.2-intel-2015b-Python-2.7.9</br>1.8.2-intel-2015b-Python-2.7.11</br>1.8.2-intel-2016.01-Python-2.7.9</nobr> |
+| **[Octave](http://www.gnu.org/software/octave/)** | GNU Octave is a high-level interpreted language, primarily intended for numerical computations. | <nobr>3.8.2-gimkl-2.11.5</br>4.0.0-foss-2015g</br>4.0.1-gimkl-2.11.5</nobr> |
+| **[PSBLAS](http://people.uniroma2.it/salvatore.filippone/psblas/)** | Most computationally intensive applications work on irregular and sparse domains that complicate their implementation on parallel machines. The major goal of the Parallel Sparse Basic Linear Algebra Subroutines (PSBLAS) project is to provide a framework to enable easy, efficient and portable implementations of iterative solvers for linear systems, while shielding the user from most details of their parallelization. The interface is designed keeping in view a Single Program Multiple Data programming model on distributed memory machines. | <nobr>3.3.4-3-GCC-4.9.3-2.25</nobr> |
+| **[PSBLAS-ext](http://people.uniroma2.it/salvatore.filippone/psblas/)** | PSBLAS - Extended formats and NVIDIA GPU support | <nobr>1.0-4-GCC-4.9.3-2.25</nobr> |
+| **[ScientificPython](https://sourcesup.cru.fr/projects/scientific-py/)** | ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization. | <nobr>2.9.4-intel-2016.01-Python-2.7.9</br>2.9.4-intel-2015b-Python-2.7.9</br>2.9.4-intel-2015b-Python-2.7.11</nobr> |
## Mpi
-|Module|Description|Available versions|
-|--|--|--|
-|**bullxmpi**| |<nobr>bullxmpi_1.2.4.1</nobr>|
-|**[impi](http://software.intel.com/en-us/intel-mpi-library/)**|The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.|<nobr>2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26</br>5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25</br>5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25</br>5.0.3.048</br>4.1.1.036</br>5.0.3.048-GCC-4.9.3</nobr>|
-|**lam**| |<nobr>7.1.4-icc</nobr>|
-|**[MPICH](http://www.mpich.org/)**|MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).|<nobr>3.2-GCC-4.9.3-2.25</nobr>|
-|**mvapich2**| |<nobr>1.9-gcc46</br>1.9-icc</br>1.9-gcc</nobr>|
-|**[OpenMPI](http://www.open-mpi.org/)**|The Open MPI Project is an open source MPI-2 implementation.|<nobr>1.10.2-GCC-5.3.0-2.26</br>1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25</br>1.8.8-GNU-4.9.3-2.25</br>1.10.2-GCC-4.9.3-2.25</nobr>|
-|**openmpi**| |<nobr>1.8.1-gcc46</br>1.8.1-gcc49</br>1.6.5-gcc</br>1.8.1-gcc</br>1.6.5-icc</br>1.6.5-gcc46</br>1.8.1-icc</nobr>|
+| Module | Description | Available versions |
+| -------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **bullxmpi** | Â | <nobr>bullxmpi_1.2.4.1</nobr> |
+| **[impi](http://software.intel.com/en-us/intel-mpi-library/)** | The Intel(R) MPI Library for Linux\* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification. | <nobr>2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26</br>5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25</br>5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25</br>5.0.3.048</br>4.1.1.036</br>5.0.3.048-GCC-4.9.3</nobr> |
+| **lam** | Â | <nobr>7.1.4-icc</nobr> |
+| **[MPICH](http://www.mpich.org/)** | MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices). | <nobr>3.2-GCC-4.9.3-2.25</nobr> |
+| **mvapich2** | Â | <nobr>1.9-gcc46</br>1.9-icc</br>1.9-gcc</nobr> |
+| **[OpenMPI](http://www.open-mpi.org/)** | The Open MPI Project is an open source MPI-2 implementation. | <nobr>1.10.2-GCC-5.3.0-2.26</br>1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25</br>1.8.8-GNU-4.9.3-2.25</br>1.10.2-GCC-4.9.3-2.25</nobr> |
+| **openmpi** | Â | <nobr>1.8.1-gcc46</br>1.8.1-gcc49</br>1.6.5-gcc</br>1.8.1-gcc</br>1.6.5-icc</br>1.6.5-gcc46</br>1.8.1-icc</nobr> |
## Numlib
-|Module|Description|Available versions|
-|--|--|--|
-|**[Armadillo](http://arma.sourceforge.net/)**|Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.|<nobr>7.500.0-foss-2016a-Python-3.5.2</nobr>|
-|**[arpack-ng](http://forge.scilab.org/index.php/p/arpack-ng/)**|ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.|<nobr>3.3.0-foss-2016a</nobr>|
-|**[ATLAS](http://math-atlas.sourceforge.net)**|ATLAS (Automatically Tuned Linear Algebra Software) is the application of the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear algebra kernel library.|<nobr>3.10.1-GCC-4.9.3-2.25-LAPACK-3.4.2</nobr>|
-|**[FFTW](http://www.fftw.org)**|FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.|<nobr>3.3.4-intel-2015b</br>3.3.4-gompi-2016.04</br>3.3.4-gompi-2016a</br>3.3.5-intel-2017.00</br>3.3.4-gompi-2015g</nobr>|
-|**[GSL](http://www.gnu.org/software/gsl/)**|The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.|<nobr>2.1-intel-2015b</br>1.16-intel-2015b</br>1.16-intel-2016.01</nobr>|
-|**[imkl](http://software.intel.com/en-us/intel-mkl/)**|Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.|<nobr>11.2.3.187-gimpi-2.11.5</br>11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25</br>2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26</br>11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25</br>11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25</nobr>|
-|**[OpenBLAS](http://xianyi.github.com/OpenBLAS/)**|OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.|<nobr>0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0</br>0.2.15-GCC-5.1.0-binutils-2.25-LAPACK-3.6.0</br>0.2.15-GCC-5.1.0-binutils-2.25-LAPACK-3.6.0-gompi-2016a</br>0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0</br>0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0</br>0.2.14-GNU-5.1.0-2.25-LAPACK-3.5.0</nobr>|
-|**[ScaLAPACK](http://www.netlib.org/scalapack/)**|The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.|<nobr>2.0.2-gompi-2015g-OpenBLAS-0.2.14-LAPACK-3.5.0</br>2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0</br>2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0</nobr>|
+| Module | Description | Available versions |
+| --------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[Armadillo](http://arma.sourceforge.net/)** | Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. | <nobr>7.500.0-foss-2016a-Python-3.5.2</nobr> |
+| **[arpack-ng](http://forge.scilab.org/index.php/p/arpack-ng/)** | ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. | <nobr>3.3.0-foss-2016a</nobr> |
+| **[ATLAS](http://math-atlas.sourceforge.net)** | ATLAS (Automatically Tuned Linear Algebra Software) is the application of the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear algebra kernel library. | <nobr>3.10.1-GCC-4.9.3-2.25-LAPACK-3.4.2</nobr> |
+| **[FFTW](http://www.fftw.org)** | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. | <nobr>3.3.4-intel-2015b</br>3.3.4-gompi-2016.04</br>3.3.4-gompi-2016a</br>3.3.5-intel-2017.00</br>3.3.4-gompi-2015g</nobr> |
+| **[GSL](http://www.gnu.org/software/gsl/)** | The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. | <nobr>2.1-intel-2015b</br>1.16-intel-2015b</br>1.16-intel-2016.01</nobr> |
+| **[imkl](http://software.intel.com/en-us/intel-mkl/)** | Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. | <nobr>11.2.3.187-gimpi-2.11.5</br>11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25</br>2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26</br>11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25</br>11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25</nobr> |
+| **[OpenBLAS](http://xianyi.github.com/OpenBLAS/)** | OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. | <nobr>0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0</br>0.2.15-GCC-5.1.0-binutils-2.25-LAPACK-3.6.0</br>0.2.15-GCC-5.1.0-binutils-2.25-LAPACK-3.6.0-gompi-2016a</br>0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0</br>0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0</br>0.2.14-GNU-5.1.0-2.25-LAPACK-3.5.0</nobr> |
+| **[ScaLAPACK](http://www.netlib.org/scalapack/)** | The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. | <nobr>2.0.2-gompi-2015g-OpenBLAS-0.2.14-LAPACK-3.5.0</br>2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0</br>2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0</nobr> |
## Nvidia
-|Module|Description|Available versions|
-|--|--|--|
-|**cuda**| |<nobr>7.5</br>6.5.14</br>6.0.37</nobr>|
+| Module | Description | Available versions |
+| -------- | ----------- | -------------------------------------- |
+| **cuda** | Â | <nobr>7.5</br>6.5.14</br>6.0.37</nobr> |
## Omics
-|Module|Description|Available versions|
-|--|--|--|
-|**fastqc**| |<nobr>0.11.2</nobr>|
-|**gatk**| |<nobr>2.6-4</br>.2.6-4.swp</nobr>|
-|**hpg-aligner**| |<nobr>1.0.0</nobr>|
-|**hpg-fastq**| |<nobr>1.0.0</nobr>|
-|**hpg-variant**| |<nobr>1.0.0</nobr>|
-|**ngsPipeline**| |<nobr>.1.0.0.swp</br>1.0.0</nobr>|
-|**picard**| |<nobr>1.117</nobr>|
-|**samtools**| |<nobr>0.1.19</nobr>|
-|**snpEff**| |<nobr>3.6</nobr>|
+| Module | Description | Available versions |
+| --------------- | ----------- | --------------------------------- |
+| **fastqc** | Â | <nobr>0.11.2</nobr> |
+| **gatk** | Â | <nobr>2.6-4</br>.2.6-4.swp</nobr> |
+| **hpg-aligner** | Â | <nobr>1.0.0</nobr> |
+| **hpg-fastq** | Â | <nobr>1.0.0</nobr> |
+| **hpg-variant** | Â | <nobr>1.0.0</nobr> |
+| **ngsPipeline** | Â | <nobr>.1.0.0.swp</br>1.0.0</nobr> |
+| **picard** | Â | <nobr>1.117</nobr> |
+| **samtools** | Â | <nobr>0.1.19</nobr> |
+| **snpEff** | Â | <nobr>3.6</nobr> |
## Oscar-Modulefiles
-|Module|Description|Available versions|
-|--|--|--|
+| Module | Description | Available versions |
+| ------ | ----------- | ------------------ |
## Oscar-Modules
-|Module|Description|Available versions|
-|--|--|--|
-|**oscar-modules**| |<nobr>1.0.3</nobr>|
+| Module | Description | Available versions |
+| ----------------- | ----------- | ------------------ |
+| **oscar-modules** | Â | <nobr>1.0.3</nobr> |
## Perf
-|Module|Description|Available versions|
-|--|--|--|
-|**[OPARI2](http://www.score-p.org)**|OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface.|<nobr>2.0</nobr>|
-|**[OTF2](http://www.score-p.org)**|The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library. It is the new standard trace format for Scalasca, Vampir, and TAU and is open for other tools.|<nobr>2.0</nobr>|
-|**[PAPI](http://icl.cs.utk.edu/projects/papi/)**|PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack.|<nobr>5.4.3</nobr>|
-|**[Vampir](http://www.vampir.eu)**|The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.|<nobr>8.5.0</nobr>|
+| Module | Description | Available versions |
+| ------------------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------ |
+| **[OPARI2](http://www.score-p.org)** | OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface. | <nobr>2.0</nobr> |
+| **[OTF2](http://www.score-p.org)** | The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library. It is the new standard trace format for Scalasca, Vampir, and TAU and is open for other tools. | <nobr>2.0</nobr> |
+| **[PAPI](http://icl.cs.utk.edu/projects/papi/)** | PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack. | <nobr>5.4.3</nobr> |
+| **[Vampir](http://www.vampir.eu)** | The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data. | <nobr>8.5.0</nobr> |
## Phys
-|Module|Description|Available versions|
-|--|--|--|
-|**[phono3py](http://python.org/)**|Python is a programming language that lets you work more quickly and integrate your systems more effectively.|<nobr>1.11.7.8-intel-2015b-Python-2.7.11</nobr>|
-|**[phonopy](http://python.org/)**|Python is a programming language that lets you work more quickly and integrate your systems more effectively.|<nobr>1.11.6.7-intel-2015b-Python-2.7.11</nobr>|
-|**VASP**| |<nobr>5.4.1-intel-2015b-24Jun15</br>5.4.1-intel-2017.00-24Jun15</nobr>|
+| Module | Description | Available versions |
+| ---------------------------------- | ------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------- |
+| **[phono3py](http://python.org/)** | Python is a programming language that lets you work more quickly and integrate your systems more effectively. | <nobr>1.11.7.8-intel-2015b-Python-2.7.11</nobr> |
+| **[phonopy](http://python.org/)** | Python is a programming language that lets you work more quickly and integrate your systems more effectively. | <nobr>1.11.6.7-intel-2015b-Python-2.7.11</nobr> |
+| **VASP** | Â | <nobr>5.4.1-intel-2015b-24Jun15</br>5.4.1-intel-2017.00-24Jun15</nobr> |
## Prace
-|Module|Description|Available versions|
-|--|--|--|
-|**GLOBUS**| |<nobr>globus</nobr>|
-|**PRACE**| |<nobr>prace</nobr>|
+| Module | Description | Available versions |
+| ---------- | ----------- | ------------------- |
+| **GLOBUS** | Â | <nobr>globus</nobr> |
+| **PRACE** | Â | <nobr>prace</nobr> |
## System
-|Module|Description|Available versions|
-|--|--|--|
-|**[CUDA](https://developer.nvidia.com/cuda-toolkit)**|CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.|<nobr>7.5.18</nobr>|
-|**[hwloc](http://www.open-mpi.org/projects/hwloc/)**|The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.|<nobr>1.11.0</br>1.11.3-GCC-5.3.0-2.26</br>1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25</br>1.11.0-GNU-4.9.3-2.25</br>1.11.2-GCC-4.9.3-2.25</br>1.11.0-GNU-5.1.0-2.25</nobr>|
-|**[libpciaccess](http://cgit.freedesktop.org/xorg/lib/libpciaccess/)**|Generic PCI access library.|<nobr>0.13.1</nobr>|
+| Module | Description | Available versions |
+| ---------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[CUDA](https://developer.nvidia.com/cuda-toolkit)** | CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. | <nobr>7.5.18</nobr> |
+| **[hwloc](http://www.open-mpi.org/projects/hwloc/)** | The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. | <nobr>1.11.0</br>1.11.3-GCC-5.3.0-2.26</br>1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25</br>1.11.0-GNU-4.9.3-2.25</br>1.11.2-GCC-4.9.3-2.25</br>1.11.0-GNU-5.1.0-2.25</nobr> |
+| **[libpciaccess](http://cgit.freedesktop.org/xorg/lib/libpciaccess/)** | Generic PCI access library. | <nobr>0.13.1</nobr> |
## Toolchain
-|Module|Description|Available versions|
-|--|--|--|
-|**[foss]((none))**|GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.|<nobr>2016a</br>2016.04</br>2015g</nobr>|
-|**[gimkl]((none))**|GNU Compiler Collection (GCC) based compiler toolchain, next to Intel MPI and Intel MKL (BLAS, (Sca)LAPACK, FFTW).|<nobr>2.11.5</nobr>|
-|**[gimpi]((none))**|GNU Compiler Collection (GCC) based compiler toolchain, next to Intel MPI.|<nobr>2.11.5</nobr>|
-|**[GNU](http://www.gnu.org/software/)**|Compiler-only toolchain with GCC and binutils.|<nobr>4.9.3-2.25</br>5.1.0-2.25</nobr>|
-|**[gompi]((none))**|GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.|<nobr>2016a</br>2016.04</br>2015g</nobr>|
-|**[iccifort](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/)**|Intel C, C++ and Fortran compilers|<nobr>2015.3.187-GNU-5.1.0-2.25</br>2017.0.098-GCC-5.4.0-2.26</br>2016.1.150-GCC-4.9.3-2.25</br>2015.3.187-GNU-4.9.3-2.25</nobr>|
-|**[iimpi](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/)**|Intel C/C++ and Fortran compilers, alongside Intel MPI.|<nobr>8.1.5-GCC-4.9.3-2.25</br>7.3.5-GNU-5.1.0-2.25</br>2017.00-GCC-5.4.0-2.26</br>2016.01-GCC-4.9.3-2.25</nobr>|
-|**intel**| |<nobr>13.5.192</br>2017.00</br>2015b</br>2016.01</br>2016a</br>15.3.187</br>14.0.1</br>15.2.164</nobr>|
+| Module | Description | Available versions |
+| ------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------- |
+| **[foss]((none))** | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. | <nobr>2016a</br>2016.04</br>2015g</nobr> |
+| **[gimkl]((none))** | GNU Compiler Collection (GCC) based compiler toolchain, next to Intel MPI and Intel MKL (BLAS, (Sca)LAPACK, FFTW). | <nobr>2.11.5</nobr> |
+| **[gimpi]((none))** | GNU Compiler Collection (GCC) based compiler toolchain, next to Intel MPI. | <nobr>2.11.5</nobr> |
+| **[GNU](http://www.gnu.org/software/)** | Compiler-only toolchain with GCC and binutils. | <nobr>4.9.3-2.25</br>5.1.0-2.25</nobr> |
+| **[gompi]((none))** | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. | <nobr>2016a</br>2016.04</br>2015g</nobr> |
+| **[iccifort](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/)** | Intel C, C++ and Fortran compilers | <nobr>2015.3.187-GNU-5.1.0-2.25</br>2017.0.098-GCC-5.4.0-2.26</br>2016.1.150-GCC-4.9.3-2.25</br>2015.3.187-GNU-4.9.3-2.25</nobr> |
+| **[iimpi](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/)** | Intel C/C++ and Fortran compilers, alongside Intel MPI. | <nobr>8.1.5-GCC-4.9.3-2.25</br>7.3.5-GNU-5.1.0-2.25</br>2017.00-GCC-5.4.0-2.26</br>2016.01-GCC-4.9.3-2.25</nobr> |
+| **intel** | Â | <nobr>13.5.192</br>2017.00</br>2015b</br>2016.01</br>2016a</br>15.3.187</br>14.0.1</br>15.2.164</nobr> |
## Tools
-|Module|Description|Available versions|
-|--|--|--|
-|**advisor_xe**| |<nobr>2013.5</br>2015.1.10.380555</nobr>|
-|**[APR](http://apr.apache.org/)**|Apache Portable Runtime (APR) libraries.|<nobr>1.5.2-foss-2015g</br>1.5.2</nobr>|
-|**[APR-util](http://apr.apache.org/)**|Apache Portable Runtime (APR) util libraries.|<nobr>1.5.4</br>1.5.4-foss-2015g</nobr>|
-|**[Bash](http://www.gnu.org/software/bash)**|Bash is an sh-compatible command language interpreter that executes commands read from the standard input or from a file. Bash also incorporates useful features from the Korn and C shells (ksh and csh).|<nobr>4.3</nobr>|
-|**[binutils](http://directory.fsf.org/project/binutils/)**|binutils: GNU binary utilities|<nobr>2.25</br>2.26-GCCcore-5.4.0</br>2.26</br>2.25-GCC-5.1.0-binutils-2.25</br>2.25-GCCcore-4.9.3</br>2.26-GCCcore-5.3.0</br>2.25-GCC-4.9.3</br>2.25-GCC-4.9.3-binutils-2.25</nobr>|
-|**[bzip2](http://www.bzip.org/)**|bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.|<nobr>1.0.6-intel-2017.00</br>1.0.6-intel-2016.01</br>1.0.6</br>1.0.6-foss-2016a</br>1.0.6-intel-2016a</br>1.0.6-intel-2015b</br>.1.0.6-foss-2015g.lua</br>1.0.6-foss-2015g</nobr>|
-|**cmake**| |<nobr>2.8.11</br>2.8.11-mic</nobr>|
-|**cube**| |<nobr>4.2.3-gcc</br>4.2.3-icc</nobr>|
-|**[cURL](http://curl.haxx.se)**|libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.|<nobr>7.51.0</br>7.37.1-foss-2015g</br>7.37.1</nobr>|
-|**dhi-mike**| |<nobr>2016-SP2</br>2014</br>2016</br>default</nobr>|
-|**[EasyBuild](http://hpcugent.github.com/easybuild/)**|EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.|<nobr>2.6.0</br>2.8.1</br>3.0.0</br>2.7.0</br>3.0.2.lua</br>2.8.0</nobr>|
-|**elmer**| |<nobr>7.0-r6695-dbg</br>7.0-r6695-opt</nobr>|
-|**[expat](http://expat.sourceforge.net/)**|Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags)|<nobr>2.1.0-foss-2015g</br>2.1.0</nobr>|
-|**git**| |<nobr>2.11.0-GNU-4.9.3-2.25.lua</br>2.8.0-GNU-4.9.3-2.25</nobr>|
-|**gnuplot**| |<nobr>4.6.5</nobr>|
-|**grace**| |<nobr>5.1.23</nobr>|
-|**[gzip](http://www.gnu.org/software/gzip/)**|gzip (GNU zip) is a popular data compression program as a replacement for compress|<nobr>1.6-foss-2015g</br>1.6</br>1.6-foss-2016a</br>1.6-intel-2015b</nobr>|
-|**inspector_xe**| |<nobr>2015.1.2.379161</br>2013.5</nobr>|
-|**intelpcm**| |<nobr>2.6</nobr>|
-|**ipm**| |<nobr>0.983-icc-impi</nobr>|
-|**itac**| |<nobr>8.1.4.045</br>9.0.3.051</nobr>|
-|**[JOE](http://joe-editor.sourceforge.net)**|JOE is a full featured terminal-based screen editor which is distributed under the GNU General Public License (GPL)|<nobr>4.2</nobr>|
-|**likwid**| |<nobr>3.1.2-gcc</br>3.1.1-mic</br>3.1.2-icc</br>3.1.1-icc</br>3.1.2-mic</nobr>|
-|**Lmod**| |<nobr>7.2.2.lua</br>.7.0.6</br>.6.4.2</nobr>|
-|**MATLAB**| |<nobr>2015b-EDU</br>2015b-COM</nobr>|
-|**memoryscape**| |<nobr>3.4</nobr>|
-|**[Mercurial](http://mercurial.selenic.com/)**|Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface.|<nobr>3.7.3-foss-2015g-Python-2.7.9</nobr>|
-|**mercurial**| |<nobr>2.9.1</nobr>|
-|**MIKE**| |<nobr>2016-SP2</br>2014</br>2016</br>default</nobr>|
-|**mono**| |<nobr>3.12.1</br>3.2.3</nobr>|
-|**mpi.net**| |<nobr>1.0.0-mono-3.12.1</br>1.0.0-impi</br>1.0.0</nobr>|
-|**[numactl](http://oss.sgi.com/projects/libnuma/)**|The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.|<nobr>2.0.10-GNU-5.1.0-2.25</br>2.0.9</br>2.0.11-GCC-5.3.0-2.26</br>2.0.11-GCC-4.9.3-2.25</br>2.0.10-iccifort-2015.3.187-GNU-4.9.3-2.25</br>2.0.11</br>2.0.10-GNU-4.9.3-2.25</br>2.0.10</nobr>|
-|**octave**| |<nobr>.hg-20130730</br>.3.6.4</nobr>|
-|**opari2**| |<nobr>1.1.2-gcc</br>1.1.2-icc</nobr>|
-|**openssh-x509**| |<nobr>6.2p2</nobr>|
-|**oscar-modules**| |<nobr>1.0.3</nobr>|
-|**otf2**| |<nobr>1.4-icc</br>1.2.1-gcc</br>1.4-gcc</br>1.2.1-icc</nobr>|
-|**papi**| |<nobr>5.4.0-mic</br>5.3.0</br>5.3.2-mic</br>5.4.0</br>5.3.2</nobr>|
-|**parallel**| |<nobr>20141122</nobr>|
-|**python**| |<nobr>2.7.6</br>2.7.5</br>3.3.2</br>3.3.5</br>3.4.2</nobr>|
-|**R**| |<nobr>3.1.1</br>.old.3.0.1</br>3.0.1</nobr>|
-|**racket**| |<nobr>6.0.1</nobr>|
-|**relion**| |<nobr>1.3</br>1.2</nobr>|
-|**Rstudio**| |<nobr>0.97</nobr>|
-|**ruby**| |<nobr>2.0.0-p247</nobr>|
-|**scalasca2**| |<nobr>2.0-icc-impi</br>2.0-gcc-openmpi</nobr>|
-|**scite**| |<nobr>3.4.3</nobr>|
-|**scorep**| |<nobr>1.2.3-gcc-openmpi</br>1.2.3-icc-impi</nobr>|
-|**[Serf](http://serf.apache.org/)**|The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library|<nobr>1.3.8-foss-2015g</nobr>|
-|**[Subversion](http://subversion.apache.org/)**|Subversion is an open source version control system.|<nobr>1.8.16-foss-2015g</nobr>|
-|**[Szip](http://www.hdfgroup.org/doc_resource/SZIP/)**|Szip compression software, providing lossless compression of scientific data|<nobr>2.1-intel-2015b</br>2.1-intel-2016.01</br>2.1-foss-2016a</br>2.1</nobr>|
-|**tcl**| |<nobr>8.5.15</nobr>|
-|**[tcsh](http://www.tcsh.org)**|Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax.|<nobr>6.19.00</nobr>|
-|**tk**| |<nobr>8.5.15</nobr>|
-|**totalview**| |<nobr>8.13</br>8.12</nobr>|
-|**turbovnc**| |<nobr>1.2.2</nobr>|
-|**[util-linux](http://www.kernel.org/pub/linux/utils/util-linux)**|Set of Linux utilities|<nobr>2.26.1</br>2.28-intel-2016a.lua</nobr>|
-|**valgrind**| |<nobr>3.9.0-impi</nobr>|
-|**vampir**| |<nobr>8.2</nobr>|
-|**virtualgl**| |<nobr>2.4</nobr>|
-|**[VTune](http://software.intel.com/en-us/intel-vtune-amplifier-xe)**|Intel VTune Amplifier XE 2016 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.|<nobr>2016_update1</nobr>|
-|**vtune_xe**| |<nobr>2013.15</br>2015.3.0.403110</nobr>|
-|**[XZ](http://tukaani.org/xz/)**|xz: XZ utilities|<nobr>5.2.2-foss-2016a</br>5.2.2-intel-2017.00</br>5.2.2.lua</nobr>|
+| Module | Description | Available versions |
+| --------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **advisor_xe** | Â | <nobr>2013.5</br>2015.1.10.380555</nobr> |
+| **[APR](http://apr.apache.org/)** | Apache Portable Runtime (APR) libraries. | <nobr>1.5.2-foss-2015g</br>1.5.2</nobr> |
+| **[APR-util](http://apr.apache.org/)** | Apache Portable Runtime (APR) util libraries. | <nobr>1.5.4</br>1.5.4-foss-2015g</nobr> |
+| **[Bash](http://www.gnu.org/software/bash)** | Bash is an sh-compatible command language interpreter that executes commands read from the standard input or from a file. Bash also incorporates useful features from the Korn and C shells (ksh and csh). | <nobr>4.3</nobr> |
+| **[binutils](http://directory.fsf.org/project/binutils/)** | binutils: GNU binary utilities | <nobr>2.25</br>2.26-GCCcore-5.4.0</br>2.26</br>2.25-GCC-5.1.0-binutils-2.25</br>2.25-GCCcore-4.9.3</br>2.26-GCCcore-5.3.0</br>2.25-GCC-4.9.3</br>2.25-GCC-4.9.3-binutils-2.25</nobr> |
+| **[bzip2](http://www.bzip.org/)** | bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression. | <nobr>1.0.6-intel-2017.00</br>1.0.6-intel-2016.01</br>1.0.6</br>1.0.6-foss-2016a</br>1.0.6-intel-2016a</br>1.0.6-intel-2015b</br>.1.0.6-foss-2015g.lua</br>1.0.6-foss-2015g</nobr> |
+| **cmake** | Â | <nobr>2.8.11</br>2.8.11-mic</nobr> |
+| **cube** | Â | <nobr>4.2.3-gcc</br>4.2.3-icc</nobr> |
+| **[cURL](http://curl.haxx.se)** | libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more. | <nobr>7.51.0</br>7.37.1-foss-2015g</br>7.37.1</nobr> |
+| **dhi-mike** | Â | <nobr>2016-SP2</br>2014</br>2016</br>default</nobr> |
+| **[EasyBuild](http://hpcugent.github.com/easybuild/)** | EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. | <nobr>2.6.0</br>2.8.1</br>3.0.0</br>2.7.0</br>3.0.2.lua</br>2.8.0</nobr> |
+| **elmer** | Â | <nobr>7.0-r6695-dbg</br>7.0-r6695-opt</nobr> |
+| **[expat](http://expat.sourceforge.net/)** | Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) | <nobr>2.1.0-foss-2015g</br>2.1.0</nobr> |
+| **git** | Â | <nobr>2.11.0-GNU-4.9.3-2.25.lua</br>2.8.0-GNU-4.9.3-2.25</nobr> |
+| **gnuplot** | Â | <nobr>4.6.5</nobr> |
+| **grace** | Â | <nobr>5.1.23</nobr> |
+| **[gzip](http://www.gnu.org/software/gzip/)** | gzip (GNU zip) is a popular data compression program as a replacement for compress | <nobr>1.6-foss-2015g</br>1.6</br>1.6-foss-2016a</br>1.6-intel-2015b</nobr> |
+| **inspector_xe** | Â | <nobr>2015.1.2.379161</br>2013.5</nobr> |
+| **intelpcm** | Â | <nobr>2.6</nobr> |
+| **ipm** | Â | <nobr>0.983-icc-impi</nobr> |
+| **itac** | Â | <nobr>8.1.4.045</br>9.0.3.051</nobr> |
+| **[JOE](http://joe-editor.sourceforge.net)** | JOE is a full featured terminal-based screen editor which is distributed under the GNU General Public License (GPL) | <nobr>4.2</nobr> |
+| **likwid** | Â | <nobr>3.1.2-gcc</br>3.1.1-mic</br>3.1.2-icc</br>3.1.1-icc</br>3.1.2-mic</nobr> |
+| **Lmod** | Â | <nobr>7.2.2.lua</br>.7.0.6</br>.6.4.2</nobr> |
+| **MATLAB** | Â | <nobr>2015b-EDU</br>2015b-COM</nobr> |
+| **memoryscape** | Â | <nobr>3.4</nobr> |
+| **[Mercurial](http://mercurial.selenic.com/)** | Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. | <nobr>3.7.3-foss-2015g-Python-2.7.9</nobr> |
+| **mercurial** | Â | <nobr>2.9.1</nobr> |
+| **MIKE** | Â | <nobr>2016-SP2</br>2014</br>2016</br>default</nobr> |
+| **mono** | Â | <nobr>3.12.1</br>3.2.3</nobr> |
+| **mpi.net** | Â | <nobr>1.0.0-mono-3.12.1</br>1.0.0-impi</br>1.0.0</nobr> |
+| **[numactl](http://oss.sgi.com/projects/libnuma/)** | The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program. | <nobr>2.0.10-GNU-5.1.0-2.25</br>2.0.9</br>2.0.11-GCC-5.3.0-2.26</br>2.0.11-GCC-4.9.3-2.25</br>2.0.10-iccifort-2015.3.187-GNU-4.9.3-2.25</br>2.0.11</br>2.0.10-GNU-4.9.3-2.25</br>2.0.10</nobr> |
+| **octave** | Â | <nobr>.hg-20130730</br>.3.6.4</nobr> |
+| **opari2** | Â | <nobr>1.1.2-gcc</br>1.1.2-icc</nobr> |
+| **openssh-x509** | Â | <nobr>6.2p2</nobr> |
+| **oscar-modules** | Â | <nobr>1.0.3</nobr> |
+| **otf2** | Â | <nobr>1.4-icc</br>1.2.1-gcc</br>1.4-gcc</br>1.2.1-icc</nobr> |
+| **papi** | Â | <nobr>5.4.0-mic</br>5.3.0</br>5.3.2-mic</br>5.4.0</br>5.3.2</nobr> |
+| **parallel** | Â | <nobr>20141122</nobr> |
+| **python** | Â | <nobr>2.7.6</br>2.7.5</br>3.3.2</br>3.3.5</br>3.4.2</nobr> |
+| **R** | Â | <nobr>3.1.1</br>.old.3.0.1</br>3.0.1</nobr> |
+| **racket** | Â | <nobr>6.0.1</nobr> |
+| **relion** | Â | <nobr>1.3</br>1.2</nobr> |
+| **Rstudio** | Â | <nobr>0.97</nobr> |
+| **ruby** | Â | <nobr>2.0.0-p247</nobr> |
+| **scalasca2** | Â | <nobr>2.0-icc-impi</br>2.0-gcc-openmpi</nobr> |
+| **scite** | Â | <nobr>3.4.3</nobr> |
+| **scorep** | Â | <nobr>1.2.3-gcc-openmpi</br>1.2.3-icc-impi</nobr> |
+| **[Serf](http://serf.apache.org/)** | The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library | <nobr>1.3.8-foss-2015g</nobr> |
+| **[Subversion](http://subversion.apache.org/)** | Subversion is an open source version control system. | <nobr>1.8.16-foss-2015g</nobr> |
+| **[Szip](http://www.hdfgroup.org/doc_resource/SZIP/)** | Szip compression software, providing lossless compression of scientific data | <nobr>2.1-intel-2015b</br>2.1-intel-2016.01</br>2.1-foss-2016a</br>2.1</nobr> |
+| **tcl** | Â | <nobr>8.5.15</nobr> |
+| **[tcsh](http://www.tcsh.org)** | Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax. | <nobr>6.19.00</nobr> |
+| **tk** | Â | <nobr>8.5.15</nobr> |
+| **totalview** | Â | <nobr>8.13</br>8.12</nobr> |
+| **turbovnc** | Â | <nobr>1.2.2</nobr> |
+| **[util-linux](http://www.kernel.org/pub/linux/utils/util-linux)** | Set of Linux utilities | <nobr>2.26.1</br>2.28-intel-2016a.lua</nobr> |
+| **valgrind** | Â | <nobr>3.9.0-impi</nobr> |
+| **vampir** | Â | <nobr>8.2</nobr> |
+| **virtualgl** | Â | <nobr>2.4</nobr> |
+| **[VTune](http://software.intel.com/en-us/intel-vtune-amplifier-xe)** | Intel VTune Amplifier XE 2016 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java. | <nobr>2016_update1</nobr> |
+| **vtune_xe** | Â | <nobr>2013.15</br>2015.3.0.403110</nobr> |
+| **[XZ](http://tukaani.org/xz/)** | xz: XZ utilities | <nobr>5.2.2-foss-2016a</br>5.2.2-intel-2017.00</br>5.2.2.lua</nobr> |
## Virtualization
-|Module|Description|Available versions|
-|--|--|--|
-|**qemu**| |<nobr>2.1.2-vde2</br>2.1.2</br>2.1.0</br>2.1.0-vde2</nobr>|
-|**vde2**| |<nobr>2.3.2</nobr>|
-|**wine**| |<nobr>1.7.29</nobr>|
+| Module | Description | Available versions |
+| -------- | ----------- | ---------------------------------------------------------- |
+| **qemu** | Â | <nobr>2.1.2-vde2</br>2.1.2</br>2.1.0</br>2.1.0-vde2</nobr> |
+| **vde2** | Â | <nobr>2.3.2</nobr> |
+| **wine** | Â | <nobr>1.7.29</nobr> |
## Vis
-|Module|Description|Available versions|
-|--|--|--|
-|**[cairo](http://cairographics.org)**|Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB|<nobr>1.12.18</nobr>|
-|**[ffmpeg](https://www.ffmpeg.org/)**|A complete, cross-platform solution to record, convert and stream audio and video.|<nobr>2.4</nobr>|
-|**[fixesproto](http://www.freedesktop.org/wiki/Software/xlibs)**|X.org FixesProto protocol headers.|<nobr>5.0</nobr>|
-|**[FLTK](http://www.fltk.org)**|FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.|<nobr>1.3.2</nobr>|
-|**[fontconfig](http://www.freedesktop.org/software/fontconfig)**|Fontconfig is a library designed to provide system-wide font configuration, customization and application access.|<nobr>2.11.1</nobr>|
-|**[freetype](http://freetype.org)**|FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.|<nobr>2.5.3</nobr>|
-|**gettext**| |<nobr>.0.19.2.lua</br>0.19.6-intel-2017.00</br>0.19.6-foss-2016a</br>0.19.4.lua</br>0.19.2</br>0.19.2-foss-2015g</nobr>|
-|**[GLib](http://www.gtk.org/)**|GLib is one of the base libraries of the GTK+ project|<nobr>2.40.0</nobr>|
-|**[inputproto](http://www.freedesktop.org/wiki/Software/xlibs)**|X.org InputProto protocol headers.|<nobr>2.3</nobr>|
-|**[kbproto](http://www.freedesktop.org/wiki/Software/xlibs)**|X.org KBProto protocol headers.|<nobr>1.0.6</nobr>|
-|**[libICE](http://www.freedesktop.org/wiki/Software/xlibs)**|X Inter-Client Exchange library for freedesktop.org|<nobr>1.0.9</nobr>|
-|**[libX11](http://www.freedesktop.org/wiki/Software/xlibs)**|X11 client-side library|<nobr>1.6.2-Python-2.7.9</nobr>|
-|**[libXau](http://www.freedesktop.org/wiki/Software/xlibs)**|The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display.|<nobr>1.0.8</nobr>|
-|**[libXdmcp](http://www.freedesktop.org/wiki/Software/xlibs)**|The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is useful for allowing clients to interact with the X Display Manager.|<nobr>1.1.2</nobr>|
-|**[libXext](http://www.freedesktop.org/wiki/Software/xlibs)**|Common X Extensions library|<nobr>1.3.3</nobr>|
-|**[libXfixes](http://www.freedesktop.org/wiki/Software/xlibs)**|X Fixes extension library|<nobr>5.0.1</nobr>|
-|**[libXfont](http://www.freedesktop.org/wiki/Software/xlibs)**|X font libary|<nobr>1.5.1-Python-2.7.9</nobr>|
-|**[libXt](http://www.freedesktop.org/wiki/Software/xlibs)**|libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).|<nobr>1.1.4-libX11-1.6.2</nobr>|
-|**[pixman](http://www.pixman.org/)**|Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.|<nobr>0.32.6</nobr>|
-|**[Tk](http://www.tcl.tk/)**|Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.|<nobr>8.6.4-foss-2016a-no-X11</br>8.6.4-intel-2017.00-no-X11</br>8.6.4-intel-2015b-no-X11</br>8.6.4-no-X11</br>8.5.12</nobr>|
+| Module | Description | Available versions |
+| ---------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- |
+| **[cairo](http://cairographics.org)** | Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB | <nobr>1.12.18</nobr> |
+| **[ffmpeg](https://www.ffmpeg.org/)** | A complete, cross-platform solution to record, convert and stream audio and video. | <nobr>2.4</nobr> |
+| **[fixesproto](http://www.freedesktop.org/wiki/Software/xlibs)** | X.org FixesProto protocol headers. | <nobr>5.0</nobr> |
+| **[FLTK](http://www.fltk.org)** | FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation. | <nobr>1.3.2</nobr> |
+| **[fontconfig](http://www.freedesktop.org/software/fontconfig)** | Fontconfig is a library designed to provide system-wide font configuration, customization and application access. | <nobr>2.11.1</nobr> |
+| **[freetype](http://freetype.org)** | FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well. | <nobr>2.5.3</nobr> |
+| **gettext** | Â | <nobr>.0.19.2.lua</br>0.19.6-intel-2017.00</br>0.19.6-foss-2016a</br>0.19.4.lua</br>0.19.2</br>0.19.2-foss-2015g</nobr> |
+| **[GLib](http://www.gtk.org/)** | GLib is one of the base libraries of the GTK+ project | <nobr>2.40.0</nobr> |
+| **[inputproto](http://www.freedesktop.org/wiki/Software/xlibs)** | X.org InputProto protocol headers. | <nobr>2.3</nobr> |
+| **[kbproto](http://www.freedesktop.org/wiki/Software/xlibs)** | X.org KBProto protocol headers. | <nobr>1.0.6</nobr> |
+| **[libICE](http://www.freedesktop.org/wiki/Software/xlibs)** | X Inter-Client Exchange library for freedesktop.org | <nobr>1.0.9</nobr> |
+| **[libX11](http://www.freedesktop.org/wiki/Software/xlibs)** | X11 client-side library | <nobr>1.6.2-Python-2.7.9</nobr> |
+| **[libXau](http://www.freedesktop.org/wiki/Software/xlibs)** | The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display. | <nobr>1.0.8</nobr> |
+| **[libXdmcp](http://www.freedesktop.org/wiki/Software/xlibs)** | The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is useful for allowing clients to interact with the X Display Manager. | <nobr>1.1.2</nobr> |
+| **[libXext](http://www.freedesktop.org/wiki/Software/xlibs)** | Common X Extensions library | <nobr>1.3.3</nobr> |
+| **[libXfixes](http://www.freedesktop.org/wiki/Software/xlibs)** | X Fixes extension library | <nobr>5.0.1</nobr> |
+| **[libXfont](http://www.freedesktop.org/wiki/Software/xlibs)** | X font libary | <nobr>1.5.1-Python-2.7.9</nobr> |
+| **[libXt](http://www.freedesktop.org/wiki/Software/xlibs)** | libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation). | <nobr>1.1.4-libX11-1.6.2</nobr> |
+| **[pixman](http://www.pixman.org/)** | Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server. | <nobr>0.32.6</nobr> |
+| **[Tk](http://www.tcl.tk/)** | Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages. | <nobr>8.6.4-foss-2016a-no-X11</br>8.6.4-intel-2017.00-no-X11</br>8.6.4-intel-2015b-no-X11</br>8.6.4-no-X11</br>8.5.12</nobr> |
diff --git a/docs.it4i/modules-matrix.md b/docs.it4i/modules-matrix.md
index 28c7d9eba75cec4e169ec8f905dbe15f10e4f3ed..661e647953377f70a01c785e57622a79ebbc1baa 100644
--- a/docs.it4i/modules-matrix.md
+++ b/docs.it4i/modules-matrix.md
@@ -1,407 +1,407 @@
-| Module | Versions | Clusters |
-| ------ | -------- | -------- |
-| abinit | 7.10.1-gcc-openmpi</br>7.10.1-icc-impi</br>7.6.2 | `--A`</br>`--A`</br>`--A` |
-| ABINIT | 7.10.1-foss-2015b</br>7.10.1-intel-2015b | `US-`</br>`US-` |
-| adams | 2013.2 | `--A` |
-| Adams | 2013.2 | `-S-` |
-| adios | 1.8.0 | `--A` |
-| Advisor | 2016_update2</br>2017 | `-S-`</br>`-S-` |
-| advisor_xe | 2015.1.10.380555</br>2013.5 | `--A`</br>`--A` |
-| aislinn | 20160105-Python-2.7.9-gompi-2015e | `-S-` |
-| almost | 2.1.0-intel-2015b</br>2.1.0-foss-2015g</br>2.1.0-foss-2016a</br>2.1.0-foss-2015b | `-S-`</br>`-SA`</br>`--A`</br>`-S-` |
-| Amber | 14 | `-SA` |
-| ANSYS | 17.0</br>16.1 | `US-`</br>`US-` |
-| ansys | 14.5.x</br>15.0.x</br>16.0.x | `--A`</br>`--A`</br>`--A` |
-| ant | 1.9.3-Java-1.7.0_79 | `-S-` |
-| APR | 1.5.2-foss-2015g</br>1.5.2 | `-SA`</br>`-SA` |
-| APR-util | 1.5.4</br>1.5.4-foss-2015g | `-SA`</br>`-SA` |
-| Armadillo | 7.500.0-foss-2016a-Python-3.5.2 | `-SA` |
-| arpack-ng | 3.3.0-foss-2016a</br>3.3.0-intel-2017.00</br>3.4.0-intel-2017.00</br>3.3.0-intel-2015b | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
-| ATLAS | 3.10.1-GCC-4.9.3-2.25-LAPACK-3.4.2 | `--A` |
-| Autoconf | 2.69-foss-2015g</br>2.69-intel-2016a</br>2.69</br>2.69-GCC-4.9.3-2.25</br>2.69-foss-2016a</br>2.69-GNU-5.1.0-2.25</br>2.69-intel-2017.00</br>2.69-GNU-4.9.3-2.25</br>2.69-intel-2016.01</br>2.69-intel-2015b | `-S-`</br>`-S-`</br>`USA`</br>`-S-`</br>`USA`</br>`USA`</br>`USA`</br>`USA`</br>`-S-`</br>`-SA` |
-| Automake | 1.15</br>1.15-GNU-5.1.0-2.25</br>1.15-intel-2017.00</br>1.15-foss-2016a</br>1.15-GCC-4.9.3-2.25</br>1.15-GNU-4.9.3-2.25</br>1.15-intel-2016.01</br>1.15-foss-2015g</br>1.15-intel-2015b</br>1.15-intel-2016a | `USA`</br>`USA`</br>`USA`</br>`USA`</br>`-S-`</br>`USA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-` |
-| Autotools | 20150215-GNU-5.1.0-2.25</br>20150215</br>20150215-intel-2015b</br>20150215-intel-2016a</br>20150215-foss-2016a</br>20150215-intel-2016.01</br>20150215-intel-2017.00</br>20150215-GNU-4.9.3-2.25</br>20150215-GCC-4.9.3-2.25 | `USA`</br>`USA`</br>`-SA`</br>`-S-`</br>`USA`</br>`-S-`</br>`USA`</br>`USA`</br>`-S-` |
-| Bash | 4.2-intel-2015b</br>4.3 | `US-`</br>`-SA` |
-| BCFtools | 1.3-foss-2015g | `-S-` |
-| beopest | 12.2</br>13.3</br>12.0.1 | `--A`</br>`--A`</br>`--A` |
-| BerkeleyUPC | 2.16.2-gompi-2015b | `-S-` |
-| binutils | 2.25-GCC-4.9.3 | `--A` |
-| Bison | 3.0.4-intel-2015b</br>3.0.4-GCC-4.9.3 | `--A`</br>`--A` |
-| blender | 2.71 | `--A` |
-| boost | 1.56-gcc-openmpi</br>1.56-icc-impi | `--A`</br>`--A` |
-| Boost | 1.60.0-foss-2015g-Python-2.7.9</br>1.58.0-Python-2.7.9</br>1.58.0-ictce-7.3.5-Python-2.7.9</br>1.59.0-intel-2015b</br>1.59.0-intel-2015b-Python-2.7.11</br>1.59.0-intel-2016.01</br>1.60.0-intel-2015b-Python-2.7.11</br>1.61.0-foss-2016a-serial</br>1.58.0-foss-2015g-Python-2.7.9</br>1.58.0-intel-2015b-Python-2.7.9</br>1.60.0-intel-2016a</br>1.61.0-foss-2016a</br>1.58.0-intel-2016.01-Python-2.7.9</br>1.58.0-gompi-2015e-Python-2.7.9 | `USA`</br>`-S-`</br>`-S-`</br>`--A`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`US-`</br>`--A`</br>`-S-`</br>`-S-`</br>`-S-` |
-| bowtie2 | 2.2.3 | `--A` |
-| bullxde | 2.0 | `--A` |
-| bullxmpi | bullxmpi-1.2.4.3</br>bullxmpi_1.2.4.1 | `--A`</br>`--A` |
-| bupc | 2.16.2 | `--A` |
-| BWA | 0.7.5a-foss-2015g | `-S-` |
-| byacc | 20120526-intel-2015b</br>20120526-foss-2015b</br>20120526-foss-2016a</br>20120526</br>20120526-foss-2015g</br>20150711-intel-2015b | `-SA`</br>`-S-`</br>`--A`</br>`-SA`</br>`-SA`</br>`--A` |
-| cairo | 1.12.18-foss-2015b</br>1.12.18 | `-S-`</br>`-SA` |
-| chicken | 4.8.0.6 | `--A` |
-| Clang | 3.7.0-GNU-5.1.0-2.25 | `-S-` |
-| CMake | 3.4.1-intel-2015b</br>3.3.1-foss-2016a</br>3.6.2-intel-2017.00</br>3.0.0-foss-2015g</br>3.3.2-intel-2016.01</br>3.5.2-intel-2017.00</br>3.5.2-GCC-4.9.3-2.25</br>3.4.1-foss-2016a</br>3.3.1-GCC-5.3.0-2.25</br>3.3.1-foss-2015g</br>3.5.1-intel-2016a</br>3.3.1-intel-2016.01</br>3.3.1-GNU-5.1.0-2.25</br>3.3.1-GCC-4.9.3-2.25</br>3.3.1-GNU-4.9.3-2.25</br>3.3.2-GNU-4.9.3-2.25</br>3.4.1-GCCcore-4.9.3</br>3.3.1-GCC-5.3.1-snapshot-20160419-2.25</br>3.4.3-intel-2016a</br>3.4.1-foss-2015b</br>3.5.2</br>3.0.0-intel-2016.01</br>3.0.0-ictce-7.3.5</br>3.5.2-intel-2016a</br>3.6.2</br>3.5.2-foss-2016a</br>3.0.0-intel-2015b | `-SA`</br>`--A`</br>`U--`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`--A`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`--A`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`US-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`--A`</br>`USA`</br>`USA`</br>`US-` |
-| cmake | 2.8.11-mic</br>2.8.11 | `--A`</br>`--A` |
-| Code_Saturne | 3.0.5 | `--A` |
-| COMSOL | 51-COM</br>51-EDU | `-S-`</br>`-S-` |
-| comsol | 44-EDU</br>50-EDU</br>43b-EDU</br>43b-COM</br>50-COM</br>44-COM | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
-| CP2K | 2.6.0-intel-2015b | `-S-` |
-| cp2k-mpi | 2.5.1-gcc | `--A` |
-| cube | 4.2.3-icc</br>4.2.3-gcc | `--A`</br>`--A` |
-| Cube | 4.3.4-intel-2015b | `-S-` |
-| CUDA | 7.5.18 | `--A` |
-| cuda | 6.5.14</br>6.0.37</br>7.5 | `--A`</br>`--A`</br>`--A` |
-| cURL | 7.47.0-intel-2017.00</br>7.51.0</br>7.51.0-intel-2017.00</br>7.37.1</br>7.45.0-foss-2015b</br>7.37.1-intel-2016.01</br>7.37.1-foss-2015g</br>7.37.1-intel-2015b | `-S-`</br>`--A`</br>`US-`</br>`USA`</br>`US-`</br>`-S-`</br>`-SA`</br>`US-` |
-| dataspaces | 1.4.0 | `--A` |
-| DCW | 1.1.2 | `-S-` |
-| DDT | 5.0.1</br>4.2 | `-S-`</br>`-S-` |
-| dhi-mike | default</br>2014</br>2016</br>2016-SP2 | `--A`</br>`--A`</br>`--A`</br>`--A` |
-| digimat | 5.0.1 | `--A` |
-| Digimat | 5.0.1-COM</br>5.0.1-EDU | `-S-`</br>`-S-` |
-| Discovery_Studio | 4.0 | `--A` |
-| Doxygen | 1.8.7-foss-2015g</br>1.8.7-intel-2016.01</br>1.8.11-intel-2017.00</br>1.8.10-foss-2015b</br>1.8.10-intel-2017.00</br>1.8.7-intel-2015b</br>1.8.11 | `-S-`</br>`-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`US-`</br>`-SA` |
-| dytran | 2013.0.1 | `--A` |
-| EasyBuild | 2.9.0</br>3.0.2</br>3.0.0</br>3.0.1</br>2.8.1</br>2.8.0 | `-S-`</br>`USA`</br>`-SA`</br>`-S-`</br>`--A`</br>`-SA` |
-| elmer | 7.0-r6695-dbg</br>7.0-r6695-opt | `--A`</br>`--A` |
-| eudev | 3.1.5-foss-2016a</br>3.1.5-intel-2016a | `-S-`</br>`-S-` |
-| expat | 2.1.0-intel-2015b</br>2.1.0</br>2.1.0-foss-2015g</br>2.1.0-intel-2017.00</br>2.1.0-foss-2015b | `-S-`</br>`USA`</br>`-SA`</br>`US-`</br>`US-` |
-| FastQC | 0.11.3 | `US-` |
-| fastqc | 0.11.2 | `--A` |
-| fds | 5.5.3-omp</br>5.5.3</br>6.svn | `--A`</br>`--A`</br>`--A` |
-| ffmpeg | 2.4-foss-2015g</br>2.4-intel-2015b</br>2.4 | `-S-`</br>`-S-`</br>`-SA` |
-| FFTW | 3.3.4-gompi-2015b</br>3.3.5-intel-2017.00</br>3.3.4-intel-2015b</br>3.3.4-gompi-2015g</br>3.3.4-gompi-2015e</br>3.3.5-intel-2016.01</br>2.1.5-iimpi-7.3.5-GNU-5.1.0-2.25</br>2.1.5-gompi-2015b</br>3.3.5-intel-2016a</br>3.3.5-gompi-2016a</br>3.3.5-foss-2016a</br>3.3.4-intel-2016.01</br>3.3.4-gompi-2016.04</br>3.3.4-gompi-2016a | `US-`</br>`USA`</br>`USA`</br>`USA`</br>`US-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`-SA`</br>`USA` |
-| fftw2 | 2.1.5-gcc</br>2.1.5-icc | `--A`</br>`--A` |
-| fftw2-mpi | 2.1.5-gcc</br>2.1.5-icc | `--A`</br>`--A` |
-| fftw3 | 3.3.3-gcc</br>3.3.3-icc | `--A`</br>`--A` |
-| fftw3-mpi | 3.3.3-gcc</br>3.3.3-icc | `--A`</br>`--A` |
-| FIAT | 1.6.0-intel-2016.01-Python-2.7.9</br>1.6.0-intel-2015b-Python-2.7.9</br>1.6.0-intel-2015b-Python-2.7.11 | `-S-`</br>`-S-`</br>`-S-` |
-| fixesproto | 5.0</br>5.0-foss-2015g</br>5.0-intel-2016a</br>5.0-foss-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
-| flex | 2.5.39-GCC-4.9.3</br>2.5.39-foss-2016a | `--A`</br>`--A` |
-| FLTK | 1.3.2</br>1.3.2-intel-2015b | `-SA`</br>`-S-` |
-| fontconfig | 2.11.1-intel-2015b</br>2.11.94-intel-2017.00</br>2.11.1-foss-2015b</br>2.11.1 | `-S-`</br>`-S-`</br>`-S-`</br>`-SA` |
-| fontsproto | 2.1.3</br>2.1.3-intel-2016a</br>2.1.3-foss-2015g</br>2.1.3-foss-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
-| Forge | 6.0.6</br>6.1.2</br>5.1-43967</br>6.0.5</br>5.7 | `-SA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`--A` |
-| foss | 2016.04</br>2016a</br>2015b</br>2015e</br>2015g | `-SA`</br>`USA`</br>`US-`</br>`US-`</br>`USA` |
-| FOX | 1.6.51-foss-2015g | `-S-` |
-| FreeFem++ | 3.45-intel-2015b | `-S-` |
-| freetype | 2.6.2-intel-2016a</br>2.5.3-foss-2015g</br>2.5.3-foss-2015b</br>2.5.5-intel-2015b</br>2.6.3-intel-2016a</br>2.6.2-intel-2017.00</br>2.5.3-intel-2015b</br>2.6.3-foss-2016a</br>2.5.3 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA` |
-| gatk | 2.6-4 | `--A` |
-| GATK | 2.6-5-Java-1.7.0_79</br>3.5-Java-1.7.0_79 | `US-`</br>`-S-` |
-| gcc | 4.8.1</br>5.4.0</br>4.9.0 | `--A`</br>`--A`</br>`--A` |
-| GCC | 6.2.0-2.27</br>4.9.2-binutils-2.25</br>4.4.7-system</br>5.4.0-2.26</br>5.3.1-snapshot-20160419-2.25</br>5.3.0-binutils-2.25</br>5.2.0</br>5.3.0-2.26</br>4.9.3-2.25</br>5.3.0-2.25</br>4.7.4</br>4.8.3</br>5.1.0-binutils-2.25</br>4.9.3-binutils-2.25</br>4.9.2</br>4.9.3 | `US-`</br>`-S-`</br>`US-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-SA`</br>`USA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`USA`</br>`USA`</br>`-S-`</br>`USA` |
-| GCCcore | 5.3.1-snapshot-20160419</br>5.3.0</br>5.4.0</br>6.2.0</br>4.9.3 | `-S-`</br>`-SA`</br>`USA`</br>`US-`</br>`USA` |
-| GDAL | 2.1.0-intel-2015b</br>2.1.0-GNU-5.1.0-2.25-intel-2015b</br>2.1.0-foss-2015g</br>1.9.2-foss-2015g</br>2.1.0-GNU-5.1.0-2.25</br>2.0.1-foss-2015b</br>2.0.2-intel-2017.00 | `-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`-S-`</br>`US-`</br>`-S-` |
-| GEOS | 3.5.0-foss-2015g | `-S-` |
-| gettext | 0.19.4</br>0.19.4-GCC-4.4.7-system</br>0.19.6-intel-2017.00 | `--A`</br>`U--`</br>`--A` |
-| gimkl | 2.11.5 | `--A` |
-| gimpi | 2.11.5 | `--A` |
-| git | 2.9.2</br>2.9.0</br>2.8.0-GNU-4.9.3-2.25</br>2.11.0-intel-2017.00</br>2.11.0-GNU-4.9.3-2.25</br>2.11.0</br>2.8.0-intel-2017.00 | `-S-`</br>`-S-`</br>`-SA`</br>`U--`</br>`--A`</br>`-S-`</br>`US-` |
-| GLib | 2.40.0-GCC-4.4.7-system</br>2.40.0</br>2.40.0-foss-2015b</br>2.40.0-intel-2016.01</br>2.40.0-foss-2015g</br>2.40.0-intel-2015b | `U--`</br>`-SA`</br>`U--`</br>`-S-`</br>`-S-`</br>`US-` |
-| GLOBUS | globus | `--A` |
-| globus | globus | `-S-` |
-| glproto | 1.4.16-foss-2015g</br>1.4.17-intel-2016a</br>1.4.17-foss-2016a | `-S-`</br>`-S-`</br>`-S-` |
-| GMP | 6.1.0-intel-2017.00</br>6.1.0-intel-2016a</br>5.0.5</br>6.0.0a-GNU-5.1.0-2.25</br>6.0.0a-GNU-4.9.3-2.25</br>6.1.0-GCC-4.9.3-2.25</br>6.0.0a-intel-2015b</br>6.1.0-foss-2016a</br>6.1.1-intel-2017.00</br>5.0.5-foss-2015g</br>5.0.5-intel-2015b</br>6.0.0a</br>5.0.5-foss-2015b</br>6.0.0a-foss-2015b</br>6.1.0-intel-2015b</br>6.1.0-intel-2016.01 | `USA`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`--A`</br>`USA`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-` |
-| GMT | 5.2.1-foss-2015g | `-S-` |
-| GNU | 4.9.3-2.25</br>5.1.0-2.25</br>5.1.0-2.25-intel-2015b | `USA`</br>`USA`</br>`-S-` |
-| gnuplot | 4.6.5 | `--A` |
-| gompi | 2016.04</br>2016a</br>2015b</br>2015e</br>2015g | `-SA`</br>`USA`</br>`US-`</br>`US-`</br>`USA` |
-| gperf | 3.0.4-foss-2015g</br>3.0.4-foss-2016a</br>3.0.4-intel-2016a | `-S-`</br>`-S-`</br>`-S-` |
-| GPI-2 | 1.1.1-gompi-2015e-MPI</br>1.1.1-gompi-2015e | `-S-`</br>`-S-` |
-| gpi2 | 1.1.1</br>1.1.0</br>1.0.2 | `--A`</br>`--A`</br>`--A` |
-| grace | 5.1.23</br>5.1.25-intel-2015b | `--A`</br>`-S-` |
-| GROMACS | 5.1.2-intel-2016a-hybrid</br>5.0.4-ictce-7.3.5-hybrid-single</br>4.6.7-foss-2015g-hybrid-single-PLUMED</br>5.0.4-foss-2015e-hybrid-single-PLUMED</br>5.1.2-intel-2015b-hybrid-single-CUDA-7.5-PLUMED-2.2.1-test</br>5.1.2-intel-2015b-hybrid-single-cuda</br>5.1.2-foss-2015g-hybrid-single-PLUMED</br>5.1.2-intel-2015b-hybrid-single-CUDA-7.5-PLUMED-2.2.1</br>5.0.4-foss-2015g-hybrid-single</br>5.0.4-foss-2015g-hybrid-single-PLUMED | `--A`</br>`-S-`</br>`-S-`</br>`-S-`</br>`--A`</br>`--A`</br>`-S-`</br>`--A`</br>`-S-`</br>`-S-` |
-| gsl | 1.16-icc</br>1.16-gcc | `--A`</br>`--A` |
-| GSL | 1.16-intel-2016.01</br>2.1-intel-2015b</br>1.16-intel-2015b | `--A`</br>`--A`</br>`-SA` |
-| guile | 1.8.8-foss-2015b</br>1.8.8-foss-2016a</br>1.8.8</br>1.8.8-intel-2015b</br>1.8.8-foss-2015g | `-S-`</br>`--A`</br>`-SA`</br>`-SA`</br>`-S-` |
-| gupc | 4.8.0.3 | `--A` |
-| gzip | 1.6-intel-2015b</br>1.6</br>1.6-foss-2016a</br>1.6-foss-2015g | `-SA`</br>`-SA`</br>`--A`</br>`USA` |
-| h5py | 2.4.0-ictce-7.3.5-Python-2.7.9-serial | `-S-` |
-| Harminv | 1.4-intel-2015b | `-S-` |
-| HDF5 | 1.8.16-intel-2016.01</br>1.8.13-intel-2016.01</br>1.8.16-foss-2015g</br>1.8.13-foss-2015g</br>1.8.13-intel-2015b</br>1.8.16-intel-2017.00</br>1.8.14-ictce-7.3.5-serial</br>1.8.13-intel-2015b-no-mpi</br>1.8.16-foss-2016a</br>1.10.0-patch1-intel-2016.01-mic</br>1.8.16-intel-2015b</br>1.8.15-patch1-foss-2015b</br>1.8.16-intel-2015b-threadsafe | `--A`</br>`-S-`</br>`-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`USA`</br>`-S-`</br>`USA`</br>`US-`</br>`-S-` |
-| hdf5 | 1.8.13</br>1.8.11 | `--A`</br>`--A` |
-| hdf5-parallel | 1.8.13-gcc49</br>1.8.13-gcc</br>1.8.13</br>1.8.11-gcc</br>1.8.11 | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
-| hpg-aligner | 1.0.0 | `--A` |
-| hpg-fastq | 1.0.0 | `--A` |
-| hpg-variant | 1.0.0 | `--A` |
-| HPL | 2.1-intel-2015b</br>2.1-foss-2015b | `-S-`</br>`-S-` |
-| HTSlib | 1.3-foss-2015g | `-S-` |
-| hwloc | 1.11.0</br>1.5-GCC-4.4.7-system</br>1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25</br>1.11.2-GCC-4.9.3-2.25</br>1.11.0-GNU-5.1.0-2.25</br>1.11.3-GCC-5.3.0-2.26</br>1.11.0-GNU-4.9.3-2.25 | `-SA`</br>`-S-`</br>`-SA`</br>`USA`</br>`USA`</br>`-SA`</br>`USA` |
-| hypermesh | 12.0.110 | `--A` |
-| HyperWorks | 13.0 | `-S-` |
-| hyperworks | 13.0 | `--A` |
-| Hypre | 2.10.0b-intel-2015b</br>2.10.0b-intel-2016.01</br>2.10.1-intel-2015b | `-S-`</br>`-S-`</br>`-S-` |
-| icc | 2013.5.192-GCC-4.8.3</br>2013.5.192</br>2015.3.187-GNU-4.9.3-2.25</br>2016.3.210-GCC-5.3.0-2.26</br>2016.1.150-GCC-4.9.3</br>2015.3.187-GNU-5.1.0-2.25</br>2017.0.098-GCC-5.4.0-2.26</br>2016.1.150-GCC-4.9.3-2.25</br>2016.0.109-GCC-4.9.3</br>2016.1.150</br>2015.3.187 | `-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`USA`</br>`USA`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
-| iccifort | 2013.5.192-GCC-4.8.3</br>2013.5.192</br>2015.3.187-GNU-4.9.3-2.25</br>2016.3.210-GCC-5.3.0-2.26</br>2016.1.150-GCC-4.9.3</br>2015.3.187-GNU-5.1.0-2.25</br>2017.0.098-GCC-5.4.0-2.26</br>2016.1.150-GCC-4.9.3-2.25</br>2016.0.109-GCC-4.9.3</br>2016.1.150</br>2015.3.187 | `-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`USA`</br>`USA`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
-| ictce | 7.3.5</br>5.5.0</br>8.3.5 | `-S-`</br>`-S-`</br>`-S-` |
-| ifort | 2013.5.192-GCC-4.8.3</br>2013.5.192</br>2015.3.187-GNU-4.9.3-2.25</br>2016.3.210-GCC-5.3.0-2.26</br>2016.1.150-GCC-4.9.3</br>2015.3.187-GNU-5.1.0-2.25</br>2017.0.098-GCC-5.4.0-2.26</br>2016.1.150-GCC-4.9.3-2.25</br>2016.0.109-GCC-4.9.3</br>2016.1.150</br>2015.3.187 | `-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`USA`</br>`USA`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
-| iimpi | 5.5.0</br>8.1.5-GCC-4.9.3-2.25</br>5.5.0-GCC-4.8.3</br>7.3.5-GNU-5.1.0-2.25</br>8.3.5</br>2016.00-GCC-4.9.3</br>2016.01-GCC-4.9.3-2.25</br>2016.01-GCC-4.9.3</br>2017.00-GCC-5.4.0-2.26</br>7.3.5</br>2016.03-GCC-5.3.0-2.26 | `-S-`</br>`-SA`</br>`-S-`</br>`USA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`USA`</br>`-S-`</br>`-S-` |
-| imkl | 11.2.3.187</br>11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26</br>11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25</br>11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25</br>2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26</br>11.3.1.150-iimpi-8.3.5</br>11.0.5.192-iimpi-5.5.0</br>11.3.1.150-iimpi-2016.00-GCC-4.9.3</br>11.2.3.187-iimpi-7.3.5</br>11.3.0.109-iimpi-2016.00-GCC-4.9.3</br>11.2.3.187-iompi-2015.03</br>11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25</br>11.0.5.192-iimpi-5.5.0-GCC-4.8.3</br>11.2.3.187-gimpi-2.11.5 | `-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`USA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`USA`</br>`-S-`</br>`--A` |
-| impi | 4.1.1.036-iccifort-2013.5.192</br>5.0.3.048-iccifort-2015.3.187</br>4.1.1.036</br>5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25</br>4.1.1.036-iccifort-2013.5.192-GCC-4.8.3</br>2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26</br>5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26</br>5.0.3.048-GCC-4.9.3</br>5.1.2.150-iccifort-2016.1.150</br>5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25</br>5.1.2.150-iccifort-2016.1.150-GCC-4.9.3</br>2017-BETA.ENG</br>5.0.3.048</br>5.1.1.109-iccifort-2016.0.109-GCC-4.9.3 | `-S-`</br>`-S-`</br>`--A`</br>`-SA`</br>`-S-`</br>`USA`</br>`-S-`</br>`--A`</br>`-S-`</br>`USA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-` |
-| inputproto | 2.3</br>2.3-foss-2015g</br>2.3-intel-2015b</br>2.3.1-intel-2016a</br>2.3.1-foss-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
-| Inspector | 2016_update1 | `-S-` |
-| inspector_xe | 2013.5</br>2015.1.2.379161 | `--A`</br>`--A` |
-| intel | 2014.06</br>2017.00</br>2016.03-GCC-5.3</br>15.2.164</br>2016.00</br>2016.01</br>14.0.1</br>2015b</br>2016a</br>15.3.187</br>13.5.192</br>2015b-intel-2015b | `-S-`</br>`USA`</br>`-S-`</br>`--A`</br>`-S-`</br>`-SA`</br>`--A`</br>`USA`</br>`-SA`</br>`--A`</br>`--A`</br>`-S-` |
-| intelpcm | 2.6 | `--A` |
-| ipm | 0.983-icc-impi | `--A` |
-| ipp | 14.0.1</br>13.5.192</br>15.3.187</br>9.0.1.150</br>15.2.164 | `--A`</br>`--A`</br>`--A`</br>`-S-`</br>`--A` |
-| ISL | 0.15</br>0.15-GCC-4.9.3-2.25</br>0.14-GNU-5.1.0-2.25</br>0.15-GNU-4.9.3-2.25 | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
-| itac | 9.0.3.051</br>9.1.2.024</br>8.1.4.045 | `--A`</br>`-S-`</br>`--A` |
-| JasPer | 1.900.1-intel-2015b | `-S-` |
-| java | 1.7 | `--A` |
-| Java | 1.8.0_112</br>1.8.0_51</br>1.8.0_72</br>1.7.0_79 | `-S-`</br>`USA`</br>`US-`</br>`USA` |
-| JOE | 4.2 | `-SA` |
-| JUnit | 4.11-Java-1.7.0_79 | `-S-` |
-| kbproto | 1.0.6</br>1.0.6-foss-2015g</br>1.0.7-intel-2016a</br>1.0.7-foss-2016a</br>1.0.7</br>1.0.6-intel-2015b | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
-| lam | 7.1.4-icc | `--A` |
-| LAMMPS | 28Jun14-intel-2015b | `-S-` |
-| lammps | 28Jun14 | `--A` |
-| LAPACKE | 3.5.0-LAPACK-3.5.0 | `-S-` |
-| libctl | 3.2.2-intel-2015b | `-S-` |
-| libdrm | 2.4.68-intel-2016a</br>2.4.68-foss-2016a</br>2.4.27</br>2.4.27-foss-2015g</br>2.4.67-intel-2016a | `-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-` |
-| libffi | 3.1-GNU-5.1.0-2.25</br>3.1-intel-2016.01</br>3.1-foss-2015b</br>3.1-intel-2015b</br>3.0.13-intel-2015b</br>3.2.1-intel-2017.00</br>3.0.13-foss-2015b</br>3.2.1-GCC-4.4.7-system</br>3.0.13</br>3.0.13-foss-2015g</br>3.2.1-foss-2016a | `-S-`</br>`-SA`</br>`-S-`</br>`USA`</br>`-SA`</br>`-S-`</br>`US-`</br>`U--`</br>`-SA`</br>`-S-`</br>`--A` |
-| libfontenc | 1.1.3</br>1.1.3-foss-2015g</br>1.1.3-foss-2016a</br>1.1.3-intel-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
-| libgdiplus | 3.12</br>3.12-GCC-4.4.7-system</br>3.12-intel-2016.01</br>3.12-GNU-5.1.0-2.25 | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
-| libGLU | 9.0.0-foss-2015g | `-S-` |
-| libICE | 1.0.9-foss-2015g</br>1.0.9-intel-2015b</br>1.0.9 | `-S-`</br>`-S-`</br>`-SA` |
-| Libint | 1.1.4-gompi-2015b</br>1.1.4-intel-2015b</br>1.1.4-foss-2015b | `-S-`</br>`US-`</br>`-S-` |
-| libjpeg-turbo | 1.4.0</br>1.4.2-intel-2017.00</br>1.4.0-foss-2015g</br>1.3.1-intel-2015b</br>1.4.1-foss-2015b</br>1.4.0-intel-2015b</br>1.3.1-foss-2015b | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`-S-` |
-| libmatheval | 1.1.11-intel-2015b</br>1.1.8-foss-2016a</br>1.1.8</br>1.1.8-foss-2015b</br>1.1.8-foss-2015g</br>1.1.8-intel-2015b | `--A`</br>`--A`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-SA` |
-| libMesh | 0.9.5-intel-2016.01 | `-S-` |
-| libmesh | 0.9.3-petsc-3.4.4-icc-impi-mkl-dbg</br>0.9.3-petsc-3.4.4-icc-impi-mkl-dbg-2d</br>0.9.3-petsc-3.4.4-icc-impi-mkl-opt | `--A`</br>`--A`</br>`--A` |
-| libpciaccess | 0.13.1-foss-2015g</br>0.13.4-foss-2016a</br>0.13.4-intel-2016a</br>0.13.1 | `-S-`</br>`-S-`</br>`-S-`</br>`-SA` |
-| libpng | 1.6.16-intel-2015b | `-S-` |
-| libpthread-stubs | 0.3-intel-2015b</br>0.3</br>0.3-foss-2016a</br>0.3-intel-2016a</br>0.3-foss-2015g | `-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
-| libreadline | 6.3-gimkl-2.11.5 | `--A` |
-| libSM | 1.2.2-foss-2015g</br>1.2.2</br>1.2.2-intel-2015b | `-S-`</br>`-SA`</br>`-S-` |
-| LibTIFF | 4.0.3-intel-2015b</br>4.0.3 | `-S-`</br>`-SA` |
-| libunistring | 0.9.3-foss-2015b</br>0.9.3</br>0.9.3-foss-2015g</br>0.9.3-intel-2015b</br>0.9.3-foss-2016a | `-S-`</br>`-SA`</br>`-S-`</br>`-SA`</br>`--A` |
-| libunwind | 1.1-GCC-5.4.0-2.26 | `-S-` |
-| libX11 | 1.6.2-foss-2015g-Python-2.7.9</br>1.6.3-foss-2016a</br>1.6.3-intel-2016a</br>1.6.2-Python-2.7.8</br>1.6.2-Python-2.7.9</br>1.6.2-intel-2015b-Python-2.7.9 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-` |
-| libXau | 1.0.8-intel-2016a</br>1.0.8-foss-2015g</br>1.0.8-foss-2016a</br>1.0.8</br>1.0.8-intel-2015b | `-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-` |
-| libxc | 2.2.0-gompi-2015b</br>2.2.1-intel-2015b</br>2.2.0-foss-2015b | `-S-`</br>`US-`</br>`-S-` |
-| libxcb | 1.11.1-foss-2016a</br>1.11-foss-2015g-Python-2.7.9</br>1.11.1-intel-2016a</br>1.10-Python-2.7.8</br>1.11-Python-2.7.9</br>1.11-intel-2015b-Python-2.7.9 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-` |
-| libXdamage | 1.1.4-intel-2016a</br>1.1.4-foss-2016a</br>1.1.4-foss-2015g-Python-2.7.9 | `-S-`</br>`-S-`</br>`-S-` |
-| libXdmcp | 1.1.2-intel-2016a</br>1.1.2</br>1.1.2-foss-2015g</br>1.1.2-intel-2015b</br>1.1.2-foss-2016a | `-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
-| libXext | 1.3.3-intel-2016a</br>1.3.3-foss-2015g-Python-2.7.9</br>1.3.3-intel-2015b</br>1.3.2-Python-2.7.8</br>1.3.3-foss-2016a</br>1.3.3</br>1.3.3-foss-2015g | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-` |
-| libXfixes | 5.0.1</br>5.0.1-intel-2016a</br>5.0.1-foss-2015g</br>5.0.1-foss-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
-| libXfont | 1.5.1-Python-2.7.9</br>1.5.1-intel-2016a-freetype-2.6.3</br>1.5.1-intel-2016a</br>1.5.1-foss-2016a-freetype-2.6.3</br>1.5.1-foss-2015g-Python-2.7.9 | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
-| libXft | 2.3.2-intel-2015b | `-S-` |
-| libXinerama | 1.1.3-intel-2015b | `-S-` |
-| libxml2 | 2.9.2</br>2.9.2-GCC-4.4.7-system</br>2.9.2-foss-2015b</br>2.9.2-foss-2015g</br>2.9.3-foss-2016a</br>2.9.2-ictce-7.3.5</br>2.9.2-gompi-2015e</br>2.9.3-intel-2017.00</br>2.9.2-GNU-5.1.0-2.25</br>2.9.2-foss-2015g-Python-2.7.9</br>2.9.2-GCC-4.9.3-2.25</br>2.9.2-intel-2015b</br>2.9.2-GNU-4.9.3-2.25</br>2.9.3-intel-2016a | `-S-`</br>`U--`</br>`US-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-SA` |
-| libXrender | 0.9.8</br>0.9.8-intel-2015b | `-S-`</br>`-S-` |
-| libxslt | 1.1.28-intel-2015b | `-S-` |
-| libXt | 1.1.4-libX11-1.6.2</br>1.1.4-foss-2015g-libX11-1.6.2</br>1.1.4-intel-2015b-libX11-1.6.2</br>1.1.5-foss-2015g | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
-| libyaml | 0.1.6-intel-2015b | `-S-` |
-| likwid | 3.1.2-mic</br>3.1.2-gcc</br>3.1.1-icc</br>4.1.2-intel</br>4.1.2-gcc</br>3.1.1-mic</br>3.1.2-icc | `--A`</br>`--A`</br>`--A`</br>`-S-`</br>`-S-`</br>`--A`</br>`--A` |
-| LLVM | 3.8.0-foss-2016a</br>3.7.1-foss-2015g</br>3.8.0-intel-2016a</br>3.7.1-intel-2016a</br>3.9.0-intel-2017.00 | `US-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`US-` |
-| llvm | 3.6.0 | `--A` |
-| lmod | 7.2.2 | `USA` |
-| Lmod | 7.2.2</br>7.0.6</br>6.4.2 | `-SA`</br>`-SA`</br>`--A` |
-| lsdyna | 7.x.x | `--A` |
-| lsprepost | 4.2 | `--A` |
-| Lua | 5.1.4-8 | `USA` |
-| lux | 1.3.1 | `--A` |
-| lxml | 3.4.4-intel-2015b-Python-2.7.9 | `-S-` |
-| M4 | 1.4.17-intel-2016.01</br>1.4.17-foss-2015b</br>1.4.17-GNU-4.9.3-2.25</br>1.4.17-GCCcore-4.9.3</br>1.4.17-foss-2015g</br>1.4.17-GCC-4.9.3-2.25</br>1.4.17-foss-2016a</br>1.4.17-intel-2015b</br>1.4.17-GCCcore-5.4.0</br>1.4.17</br>1.4.17-GCC-5.1.0-binutils-2.25</br>1.4.17-GNU-5.1.0-2.25</br>1.4.17-GCCcore-5.3.0</br>1.4.17-intel-2016a</br>1.4.16-foss-2015g</br>1.4.16-intel-2015b</br>1.4.17-intel-2017.00</br>1.4.17-GCC-4.9.3</br>1.4.17-GCC-4.9.3-binutils-2.25</br>1.4.17-GCCcore-6.2.0</br>1.4.17-GCCcore-5.3.1-snapshot-20160419 | `-S-`</br>`US-`</br>`USA`</br>`USA`</br>`-S-`</br>`-S-`</br>`USA`</br>`USA`</br>`USA`</br>`USA`</br>`-SA`</br>`USA`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`USA`</br>`--A`</br>`USA`</br>`US-`</br>`-S-` |
-| magma | 1.3.0-mic</br>1.1.0-mic | `--A`</br>`--A` |
-| make | 3.82</br>3.82-intel-2015b | `-SA`</br>`US-` |
-| makedepend | 1.0.4</br>1.0.5-foss-2016a</br>1.0.4-foss-2015g</br>1.0.5-intel-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
-| MAP | 5.0.1</br>4.2 | `-S-`</br>`-S-` |
-| marc | 2011</br>2013.1 | `--A`</br>`--A` |
-| Marc | 2013.1.0 | `-S-` |
-| matlab | R2013a-EDU</br>R2014a-EDU</br>R2014a-COM</br>R2013a-COM | `--A`</br>`--A`</br>`--A`</br>`--A` |
-| MATLAB | 2015b-EDU</br>2015a-EDU</br>2015a-COM</br>2015b-COM | `-SA`</br>`USA`</br>`USA`</br>`-SA` |
-| matplotlib | 1.4.3-intel-2015b-Python-2.7.9 | `-S-` |
-| Maven | 3.3.9 | `USA` |
-| maxwell | 3.0 | `--A` |
-| Meep | 1.3-intel-2015b | `-S-` |
-| memoryscape | 3.4 | `--A` |
-| mercurial | 2.9.1 | `--A` |
-| Mercurial | 3.7.3-foss-2015g-Python-2.7.9</br>3.5-Python-2.7.9 | `USA`</br>`-S-` |
-| Mesa | 11.0.8-foss-2015g-Python-2.7.9</br>11.2.1-foss-2016a | `-S-`</br>`-S-` |
-| METIS | 5.1.0-intel-2017.00</br>5.1.0-intel-2016.01-32bitIDX</br>5.1.0-intel-2015b</br>5.1.0-intel-2016.01 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
-| MIKE | default</br>2014</br>2016</br>2016-SP2 | `--A`</br>`-SA`</br>`-SA`</br>`-SA` |
-| mkl | 14.0.1</br>13.5.192</br>15.3.187</br>15.2.164 | `--A`</br>`--A`</br>`--A`</br>`--A` |
-| MLD2P4 | 2.0-rc4-GCC-4.9.3-2.25 | `--A` |
-| modflow-2005 | 1.11.00 | `--A` |
-| modflow-nwt | 1.0.9-aquaveo</br>1.0.9 | `--A`</br>`--A` |
-| Molpro | 2010.1-patch-57-intel2015b | `-S-` |
-| molpro | 2010.1-p45-intel | `--A` |
-| mono | 3.12.1</br>3.2.3 | `--A`</br>`--A` |
-| Mono | 3.12.1-GCC-4.4.7-system</br>4.2.2.10-intel-2016.01</br>3.12.1</br>4.0.3.20-GNU-5.1.0-2.25 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
-| motif | 2.3.4-foss-2015g-libX11-1.6.2</br>2.3.4-intel-2015b-libX11-1.6.2 | `-S-`</br>`-S-` |
-| MPC | 1.0.2-intel-2017.00 | `-S-` |
-| MPFR | 3.1.5-intel-2017.00 | `-S-` |
-| mpi.net | 1.0.0-mono-3.12.1</br>1.0.0</br>1.0.0-impi | `--A`</br>`--A`</br>`--A` |
-| MPI_NET | 1.2.0-gompi-2015e</br>1.2.0-intel-2016.01 | `-S-`</br>`-S-` |
-| MPICH | 3.2-GCC-5.3.1-snapshot-20160419-2.25</br>3.2-GCC-5.3.0-2.25</br>3.2-GCC-4.9.3-2.25 | `-S-`</br>`-S-`</br>`--A` |
-| mpt | 2.12 | `-S-` |
-| mvapich2 | 1.9-icc</br>1.9-gcc</br>1.9-gcc46 | `--A`</br>`--A`</br>`--A` |
-| MVAPICH2 | 2.1-GNU-5.1.0-2.25</br>2.1-iccifort-2015.3.187-GNU-5.1.0-2.25</br>2.1-GCC-4.4.7-system | `-S-`</br>`-S-`</br>`-S-` |
-| mxml | 2.9 | `--A` |
-| namd | 2.8 | `--A` |
-| NAMD | 2.9-mpi | `-S-` |
-| NASM | 2.11.05</br>2.11.08-intel-2017.00</br>2.11.05-foss-2015g</br>2.11.05-foss-2015b</br>2.11.06-intel-2015b</br>2.11.05-intel-2015b</br>2.11.08-foss-2015b | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`US-` |
-| nastran | 2013.1.1 | `--A` |
-| ncurses | 5.9-GCC-4.9.3-2.25</br>5.9-gimkl-2.11.5 | `--A`</br>`--A` |
-| netcdf | 4.3.0</br>4.2.1.1 | `--A`</br>`--A` |
-| netCDF | 4.4.0-intel-2017.00</br>4.3.2-intel-2016.01</br>4.3.3.1-intel-2017.00</br>4.3.3.1-foss-2015b</br>4.3.2-foss-2015g</br>4.3.2-intel-2015b | `-S-`</br>`-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`US-` |
-| netcdf-cxx | 4.2 | `--A` |
-| netcdf-fortran | 4.2 | `--A` |
-| netCDF-Fortran | 4.4.0-intel-2016.01 | `-S-` |
-| netcdf-parallel | 4.3.0 | `--A` |
-| ngsPipeline | 1.0.0 | `--A` |
-| numactl | 2.0.9-GCC-4.4.7-system</br>2.0.10-iccifort-2015.3.187-GNU-4.9.3-2.25</br>2.0.11-GCC-5.3.0-2.26</br>2.0.9</br>2.0.10-GNU-4.9.3-2.25</br>2.0.11-GCC-4.9.3-2.25</br>2.0.10-GNU-5.1.0-2.25</br>2.0.11</br>2.0.10 | `-S-`</br>`-SA`</br>`-SA`</br>`--A`</br>`USA`</br>`USA`</br>`USA`</br>`-SA`</br>`-SA` |
-| numpy | 1.8.2-intel-2015b-Python-2.7.9</br>1.8.2-intel-2015b-Python-2.7.11</br>1.9.1-intel-2015b-Python-2.7.9</br>1.8.2-intel-2016.01-Python-2.7.9 | `-SA`</br>`-SA`</br>`-S-`</br>`-SA` |
-| NWChem | 6.3.revision2-2013-10-17-Python-2.7.8</br>6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.8 | `-S-`</br>`-S-` |
-| nwchem | 6.3-rev2-patch1</br>6.3-rev2-patch1-venus</br>6.3-rev2-patch1-openmpi</br>6.1.1 | `--A`</br>`--A`</br>`--A`</br>`--A` |
-| Octave | 3.8.2-gimkl-2.11.5</br>3.8.2-foss-2015g</br>4.0.1-gimkl-2.11.5</br>4.0.0-foss-2015g</br>3.8.2-intel-2015b | `--A`</br>`-S-`</br>`--A`</br>`-SA`</br>`-S-` |
-| opari2 | 1.1.2-gcc</br>1.1.2-icc | `--A`</br>`--A` |
-| OPARI2 | 1.1.4-intel-2015b</br>2.0 | `-S-`</br>`-SA` |
-| OpenBLAS | 0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0</br>0.2.14-GNU-5.1.0-2.25-LAPACK-3.5.0</br>0.2.14-gompi-2015e-LAPACK-3.5.0</br>0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0</br>0.2.19-GCC-5.4.0-2.26-LAPACK-3.6.0</br>0.2.15-GCC-5.1.0-binutils-2.25-LAPACK-3.6.0</br>0.2.14-LAPACK-3.5.0</br>0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0</br>0.2.15-GCC-5.1.0-binutils-2.25-LAPACK-3.6.0-gompi-2016a | `USA`</br>`USA`</br>`US-`</br>`-SA`</br>`-S-`</br>`--A`</br>`-S-`</br>`USA`</br>`--A` |
-| OpenCL-builder | 2015 | `-S-` |
-| opencl-rt | 4.5.0.8 | `--A` |
-| OpenCL-runtime | 15.1 | `-S-` |
-| opencl-sdk | 4.6.0.92 | `--A` |
-| OpenCoarrays | 1.4.0-GCC-5.3.0-2.25</br>1.0.1-GNU-5.1.0-2.25</br>1.4.0-GCC-5.3.1-snapshot-20160419-2.25</br>1.0.0-GNU-5.1.0-2.25 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
-| OpenCV | 2.4.9-intel-2015b</br>3.0.0-intel-2015b | `-S-`</br>`-S-` |
-| OpenDX | 4.4.4-foss-2015g | `-S-` |
-| openfoam | 2.2.1-gcc481-openmpi1.6.5-DP</br>2.2.2-icc-openmpi1.8.1-DP</br>2.2.1-icc-openmpi1.6.5-DP</br>2.2.1-gcc481-openmpi1.6.5-SP</br>2.2.1-icc-impi4.1.1.036-DP | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
-| OpenFOAM | 2.2.2-intel-2015b</br>2.3.0-intel-2015b</br>3.0.0-intel-2016.01 | `US-`</br>`US-`</br>`-S-` |
-| openmpi | 1.6.5-gcc46</br>1.8.1-gcc</br>1.6.5-gcc</br>1.6.5-icc</br>1.8.1-gcc49</br>1.8.1-icc</br>1.8.1-gcc46 | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
-| OpenMPI | 1.8.6-iccifort-2015.3.187-GNU-5.1.0-2.25</br>1.8.6-GCC-4.4.7-system</br>1.10.1-GNU-4.9.3-2.25</br>1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25</br>1.10.2-GCC-4.9.3-2.25</br>1.8.8-GNU-5.1.0-2.25</br>1.10.2-GCC-5.3.0-2.26</br>1.10.1-GCC-4.9.3-2.25</br>1.8.6-GNU-5.1.0-2.25</br>1.8.8-GNU-4.9.3-2.25 | `-S-`</br>`US-`</br>`US-`</br>`-SA`</br>`USA`</br>`-S-`</br>`-SA`</br>`-S-`</br>`US-`</br>`USA` |
-| openssh-x509 | 6.2p2 | `--A` |
-| ORCA | 3_0_3-linux_x86-64 | `-SA` |
-| oscar-modules | 1.0.3 | `--A` |
-| OSPRay | 0.9.1 | `-S-` |
-| OTF2 | 1.4-intel-2015b</br>2.0</br>2.0-intel-2015b-mic | `-S-`</br>`-SA`</br>`-S-` |
-| otf2 | 1.4-icc</br>1.2.1-gcc</br>1.4-gcc</br>1.2.1-icc | `--A`</br>`--A`</br>`--A`</br>`--A` |
-| p4vasp | 0.3.29-GNU-4.9.3-2.25 | `-S-` |
-| PAPI | 5.4.3-pic</br>5.4.3</br>5.4.0-p-mic</br>5.4.0-intel-2015b</br>5.4.3-intel-2015b-mic</br>5.4.0-mic | `-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
-| papi | 5.3.2-mic</br>5.4.0</br>5.3.2</br>5.4.0-mic</br>5.3.0 | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
-| parallel | 20150322-GNU-5.1.0-2.25</br>20141122</br>20150322 | `-S-`</br>`--A`</br>`-S-` |
-| ParaView | 5.0.0-binary</br>4.3-OSPRay | `-S-`</br>`-S-` |
-| paraview | 4.0.1-gcc481-bullxmpi1.2.4.1-osmesa10.0 | `--A` |
-| ParMETIS | 4.0.3-intel-2015b</br>4.0.3-intel-2016.01 | `-S-`</br>`-S-` |
-| PCRE | 8.37-foss-2015g</br>8.37-intel-2016.01</br>8.39-intel-2017.00</br>8.36-foss-2015g</br>8.36-intel-2015b</br>8.37</br>8.37-gimkl-2.11.5</br>8.36-intel-2016.01 | `-SA`</br>`--A`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`--A`</br>`-S-` |
-| PCRE2 | 10.22-intel-2017.00 | `-S-` |
-| perfboost | 1.0 | `-S-` |
-| perfcatcher | 1.0 | `-S-` |
-| PerformanceReports | 5.1-43967</br>6.0.6 | `-S-`</br>`-SA` |
-| PerfReports | 5.0.1 | `-S-` |
-| perfsuite | 1a5.3 | `-S-` |
-| Perl | 5.20.2-GNU-4.9.3-2.25-bare</br>5.22.2-intel-2017.00</br>5.20.2-bare</br>5.16.3-intel-2015b</br>5.24.0-GCC-4.9.3-2.25-bare | `-SA`</br>`US-`</br>`-S-`</br>`US-`</br>`--A` |
-| pest | 13.0 | `--A` |
-| petsc | 3.5.3-icc15-impi-mkl-threads-opt</br>3.7.3-icc16-impi5-mkl-opt</br>3.5.3-icc15-impi-mkl-threads-dbg</br>3.5.3-icc15-impi-mkl-dbg</br>3.5.3-icc15-impi-mkl-opt</br>3.7.3-icc16-impi5-mkl-dbg | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
-| PETSc | 3.6.1-intel-2015b-Python-2.7.9</br>3.6.1-intel-2016.01-Python-2.7.9</br>3.6.3-intel-2015b-Python-2.7.11 | `-S-`</br>`-S-`</br>`-S-` |
-| PGI | 16.10-GNU-4.9.3-2.25</br>15.7 | `-S-`</br>`-S-` |
-| phono3py | 1.11.7.8-intel-2015b-Python-2.7.9</br>1.11.7.8-intel-2015b-Python-2.7.11 | `-S-`</br>`--A` |
-| phonopy | 1.11.6.7-intel-2015b-Python-2.7.9</br>1.11.6.7-intel-2015b-Python-2.7.11 | `-S-`</br>`--A` |
-| picard | 2.1.0</br>1.117</br>1.119 | `-S-`</br>`--A`</br>`-S-` |
-| pigz | 2.3.3-GCC-6.2.0-2.27 | `US-` |
-| pixman | 0.32.6-intel-2015b</br>0.32.6-foss-2015b</br>0.32.6 | `-S-`</br>`-S-`</br>`-SA` |
-| pkg-config | 0.29.1-foss-2016a</br>0.29</br>0.27.1-foss-2015g</br>0.27.1-foss-2015b</br>0.29.1-intel-2016a</br>0.29-foss-2016a</br>0.27.1-intel-2015b</br>0.27.1</br>0.29-intel-2016a | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-S-` |
-| plasma | 2.6.0 | `--A` |
-| PLUMED | 2.3b-foss-2015g</br>2.2.1-intel-2015b</br>2.1.3-foss-2015g</br>2.3b-foss-2016a | `-S-`</br>`--A`</br>`-S-`</br>`--A` |
-| prace | 20160107-intel-2016.01 | `-S-` |
-| PRACE | prace</br>20150630-intel-2015b | `--A`</br>`US-` |
-| PrgEnv-gnu | 4.8.1</br>4.4.6</br>4.4.6-test | `--A`</br>`--A`</br>`--A` |
-| PrgEnv-intel | 14.0.1</br>13.5.192</br>15.0.3 | `--A`</br>`--A`</br>`--A` |
-| PROJ | 4.9.2-intel-2017.00</br>4.8.0-foss-2015b | `-S-`</br>`US-` |
-| PROJ_4 | 4.9.2-foss-2015g | `-S-` |
-| PSBLAS | 3.3.4-3-GCC-4.9.3-2.25 | `--A` |
-| PSBLAS-ext | 1.0-4-GCC-4.9.3-2.25 | `--A` |
-| PyQt | 4.11.3-foss-2015g-Python-2.7.9</br>4.11.4-foss-2015g-Python-2.7.9 | `-S-`</br>`-S-` |
-| python | 3.4.2</br>2.7.5</br>2.7.6</br>3.3.2</br>3.3.5 | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
-| Python | 2.7.11-intel-2015b</br>2.7.10-GNU-4.9.3-2.25-bare</br>2.7.8-intel-2015b</br>3.5.2</br>2.7.9-foss-2015g</br>2.7.9-foss-2015b</br>3.5.2-intel-2017.00</br>3.5.1-intel-2017.00</br>2.7.9-GNU-5.1.0-2.25</br>2.7.9-intel-2015b</br>3.4.3-intel-2015b</br>2.7.9-gompi-2015e</br>2.7.9-ictce-7.3.5</br>2.7.11-GCC-4.9.3-2.25-bare</br>2.7.8-intel-2016.01</br>2.7.11-intel-2016a</br>2.7.9</br>2.7.9-intel-2016.01</br>3.5.1</br>2.7.11-foss-2016a</br>3.5.2-foss-2016a</br>3.5.1-intel-2016.01</br>2.7.10-GCC-4.9.3-2.25-bare</br>2.7.11-intel-2017.00 | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`USA`</br>`US-`</br>`USA`</br>`-S-`</br>`-S-`</br>`USA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`-S-`</br>`US-`</br>`USA`</br>`-S-`</br>`-S-`</br>`-S-` |
-| python-meep | 1.4.2-intel-2015b-Python-2.7.9-Meep-1.3 | `-S-` |
-| PyYAML | 3.11-intel-2015b-Python-2.7.9 | `-S-` |
-| QCA | 2.1.0-foss-2015g | `-S-` |
-| QEMU | 2.1.2-foss-2015b</br>2.1.2-GCC-4.4.7-system</br>2.1.2-GCC-4.4.7-system-VDE2 | `U--`</br>`US-`</br>`US-` |
-| qemu | 2.1.2</br>2.1.0</br>2.1.2-vde2</br>2.1.0-vde2 | `--A`</br>`--A`</br>`--A`</br>`--A` |
-| QGIS | 2.12.3-foss-2015g | `-S-` |
-| Qt | 4.8.6-foss-2015g</br>4.8.6 | `-S-`</br>`-SA` |
-| QuantumESPRESSO | 5.4.0-intel-2017.00 | `-SA` |
-| Qwt | 6.1.2-foss-2015g | `-S-` |
-| R | 3.1.1-intel-2015b</br>3.1.1</br>3.2.3-intel-2016.01</br>3.2.3-foss-2015b</br>3.0.1 | `US-`</br>`--A`</br>`-S-`</br>`US-`</br>`--A` |
-| Racket | 6.1.1-GNU-5.1.0-2.25 | `-S-` |
-| racket | 6.0.1 | `--A` |
-| relion | 1.2</br>1.3 | `--A`</br>`--A` |
-| RELION | 1.3-intel-2015b | `-S-` |
-| renderproto | 0.11-intel-2015b</br>0.11 | `-S-`</br>`-SA` |
-| Rstudio | 0.97 | `--A` |
-| RStudio | 0.98.1103 | `-S-` |
-| ruby | 2.0.0-p247 | `--A` |
-| Ruby | 2.1.5-intel-2015b</br>2.3.1 | `-S-`</br>`-SA` |
-| S4MPLE | 1.0.0 | `-S-` |
-| samtools | 0.1.19 | `--A` |
-| SAMtools | 1.3-foss-2015g | `-S-` |
-| ScaLAPACK | 2.0.2-gompi-2015g-OpenBLAS-0.2.14-LAPACK-3.5.0</br>2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0</br>2.0.2-OpenBLAS-0.2.14-LAPACK-3.5.0</br>2.0.2-gompi-2015e-OpenBLAS-0.2.14-LAPACK-3.5.0</br>2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0</br>2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0 | `USA`</br>`USA`</br>`-S-`</br>`US-`</br>`US-`</br>`-SA` |
-| Scalasca | 2.3.1-intel-2015b | `-S-` |
-| scalasca2 | 2.0-icc-impi</br>2.0-gcc-openmpi | `--A`</br>`--A` |
-| ScientificPython | 2.9.4-intel-2015b-Python-2.7.9</br>2.9.4-intel-2015b-Python-2.7.11</br>2.9.4-intel-2016.01-Python-2.7.9 | `-SA`</br>`-SA`</br>`-SA` |
-| Scipion | 1.0.1-Java-8u112-intel-2017.00 | `-S-` |
-| scite | 3.4.3 | `--A` |
-| SCons | 2.3.6-foss-2015g-Python-2.7.9</br>2.3.6-Python-2.7.9 | `-SA`</br>`-S-` |
-| Score-P | 3.0-intel-2015b | `-S-` |
-| scorep | 1.2.3-gcc-openmpi</br>1.2.3-icc-impi | `--A`</br>`--A` |
-| SCOTCH | 5.1.12b_esmumps-foss-2015b</br>6.0.4-intel-2016.01</br>6.0.3-intel-2016.01</br>6.0.0_esmumps-intel-2015b</br>6.0.4-intel-2015b</br>6.0.3-intel-2015b | `-S-`</br>`-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`US-` |
-| SDE | 7.41.0 | `-S-` |
-| Serf | 1.3.8-foss-2015g | `-SA` |
-| settarg | 7.2.2 | `USA` |
-| Siesta | 4.1-b2-intel-2017.00 | `-S-` |
-| SIONlib | 1.6.1-intel-2015b-tools</br>1.6.1-tools | `-S-`</br>`-SA` |
-| SIP | 4.17-foss-2015g-Python-2.7.9</br>4.17-Python-2.7.9</br>4.16.4-foss-2015g-Python-2.7.9 | `-S-`</br>`-S-`</br>`-S-` |
-| slepc | 3.4.4-icc15-impi-mkl-dbg</br>3.4.4-icc15-impi-mkl-opt</br>3.7.2-icc16-impi5-mkl-dbg</br>3.7.2-icc16-impi5-mkl-opt | `--A`</br>`--A`</br>`--A`</br>`--A` |
-| snpEff | 3.6 | `--A` |
-| SnpEff | 4.1_G | `US-` |
-| SnuCL | 1.3.3-gompi-2015e | `-S-` |
-| Spark | 1.5.2 | `-S-` |
-| spatialindex | 1.8.5-foss-2015g | `-S-` |
-| SpatiaLite | 4.3.0a-foss-2015g | `-S-` |
-| spGPU | master-GCC-4.9.3-2.25 | `--A` |
-| SQLite | 3.8.8.1-foss-2016a | `--A` |
-| Subversion | 1.8.16-foss-2015g | `-SA` |
-| SuiteSparse | 4.4.6-intel-2015b-ParMETIS-4.0.3</br>4.5.3-intel-2017.00-METIS-5.1.0</br>4.4.5-intel-2015b-METIS-5.1.0</br>4.4.3-intel-2016.01-ParMETIS-4.0.3</br>4.4.3-intel-2015b-ParMETIS-4.0.3 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
-| SUMO | 0.27.1-foss-2015g</br>0.25.0-foss-2015g</br>0.26.0-foss-2015g | `-S-`</br>`-S-`</br>`-S-` |
-| SWIG | 2.0.12-intel-2015b-Python-2.7.9</br>2.0.12-Python-2.7.9</br>3.0.7-Python-2.7.9 | `-S-`</br>`-S-`</br>`-S-` |
-| sympy | 0.7.6.1-intel-2015b-Python-2.7.11</br>0.7.6-intel-2016.01-Python-2.7.9</br>0.7.6-intel-2015b-Python-2.7.9 | `-S-`</br>`-S-`</br>`-S-` |
-| Szip | 2.1-ictce-7.3.5</br>2.1-intel-2015b</br>2.1-intel-2017.00</br>2.1-intel-2016.01</br>2.1</br>2.1-foss-2016a</br>2.1-foss-2015b</br>2.1-foss-2015g | `-S-`</br>`USA`</br>`-S-`</br>`-SA`</br>`-SA`</br>`USA`</br>`US-`</br>`-S-` |
-| szip | 2.1 | `--A` |
-| tbb | 15.2.164</br>4.4.2.152</br>4.3.5.187</br>14.0.1</br>15.3.187</br>13.5.192 | `--A`</br>`USA`</br>`-S-`</br>`--A`</br>`--A`</br>`--A` |
-| Tcl | 8.6.3-foss-2016a | `--A` |
-| tcl | 8.5.15 | `--A` |
-| tcsh | 6.18.01-intel-2015b</br>6.19.00 | `US-`</br>`-SA` |
-| tk | 8.5.15 | `--A` |
-| Tk | 8.6.3-foss-2015b-no-X11 | `U--` |
-| totalview | 8.13</br>8.12 | `--A`</br>`--A` |
-| TotalView | 8.15.4-6-linux-x86-64 | `-S-` |
-| trilinos | 11.2.3-gcc-openmpi-mkl-opt</br>11.2.3-gcc-openmpi-mkl-dbg</br>11.2.3-icc | `--A`</br>`--A`</br>`--A` |
-| Trimmomatic | 0.35-Java-1.7.0_79 | `-S-` |
-| turbovnc | 1.2.2</br>1.2.3 | `--A`</br>`-S-` |
-| util-linux | 2.28-intel-2016a</br>2.26.1</br>2.26.1-foss-2015g | `--A`</br>`-SA`</br>`-S-` |
-| Valgrind | 3.11.0-foss-2015b</br>3.11.0-intel-2015b | `-S-`</br>`-S-` |
-| valgrind | 3.9.0-impi | `--A` |
-| Vampir | 9.0.0</br>8.5.0 | `-S-`</br>`-SA` |
-| vampir | 8.2 | `--A` |
-| VampirServer | 9.0.0-intel-2015b</br>8.5.0-intel-2015b | `-S-`</br>`-S-` |
-| VASP | 5.4.1-intel-2015b-24Jun15-UV</br>5.4.1-intel-2017.00-24Jun15</br>5.4.1-intel-2015b-24Jun15 | `U--`</br>`-SA`</br>`-SA` |
-| vde2 | 2.3.2 | `--A` |
-| VDE2 | 2.3.2-GCC-4.4.7-system | `US-` |
-| VirtualGL | 2.4.1 | `-S-` |
-| virtualgl | 2.4 | `--A` |
-| VisIt | 2.10.0 | `US-` |
-| VTune | 2016_update1 | `USA` |
-| vtune_xe | 2013.15</br>2015.3.0.403110 | `--A`</br>`--A` |
-| wien2k | 14.2</br>13.1 | `--A`</br>`--A` |
-| wine | 1.7.29 | `--A` |
-| Wine | 1.7.29-GNU-5.1.0-2.25</br>1.7.29-GCC-4.4.7-system | `-S-`</br>`-S-` |
-| xbitmaps | 1.1.1</br>1.1.1-intel-2015b</br>1.1.1-foss-2015g | `-SA`</br>`-S-`</br>`-S-` |
-| xcb-proto | 1.11-Python-2.7.9</br>1.11-foss-2015g-Python-2.7.9</br>1.10-Python-2.7.8</br>1.11-intel-2015b-Python-2.7.9</br>1.11 | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
-| xdrfile | 1.1.4-foss-2015g</br>1.1.4-intel-2015b</br>1.1.4-foss-2016a | `-SA`</br>`--A`</br>`--A` |
-| xextproto | 7.3.0-intel-2016a</br>7.3.0-foss-2015g</br>7.3.0-intel-2015b</br>7.3.0</br>7.3.0-foss-2016a | `-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-` |
-| xineramaproto | 1.2.1-intel-2015b</br>1.2.1 | `-S-`</br>`-SA` |
-| xorg-macros | 1.17</br>1.17-foss-2015g</br>1.19.0-intel-2016a</br>1.19.0-foss-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
-| xproto | 7.0.26-foss-2015g</br>7.0.28-foss-2016a</br>7.0.28-intel-2016a</br>7.0.28</br>7.0.26-intel-2015b</br>7.0.26 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA` |
-| xtrans | 1.3.5-foss-2016a</br>1.3.4-intel-2015b</br>1.3.5-intel-2015b</br>1.3.5-intel-2016a</br>1.3.5</br>1.3.4</br>1.3.5-foss-2015g | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`--A`</br>`-S-` |
-| XZ | 5.2.2</br>5.2.2-intel-2016.01</br>5.2.2-intel-2017.00</br>5.2.2-foss-2016a | `-SA`</br>`-S-`</br>`USA`</br>`USA` |
-| zlib | 1.2.5</br>1.2.8-GCC-4.9.3</br>1.2.8-GCC-4.4.7-system | `--A`</br>`--A`</br>`U--` |
+| Module | Versions | Clusters |
+| ------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| abinit | 7.10.1-gcc-openmpi</br>7.10.1-icc-impi</br>7.6.2 | `--A`</br>`--A`</br>`--A` |
+| ABINIT | 7.10.1-foss-2015b</br>7.10.1-intel-2015b | `US-`</br>`US-` |
+| adams | 2013.2 | `--A` |
+| Adams | 2013.2 | `-S-` |
+| adios | 1.8.0 | `--A` |
+| Advisor | 2016_update2</br>2017 | `-S-`</br>`-S-` |
+| advisor_xe | 2015.1.10.380555</br>2013.5 | `--A`</br>`--A` |
+| aislinn | 20160105-Python-2.7.9-gompi-2015e | `-S-` |
+| almost | 2.1.0-intel-2015b</br>2.1.0-foss-2015g</br>2.1.0-foss-2016a</br>2.1.0-foss-2015b | `-S-`</br>`-SA`</br>`--A`</br>`-S-` |
+| Amber | 14 | `-SA` |
+| ANSYS | 17.0</br>16.1 | `US-`</br>`US-` |
+| ansys | 14.5.x</br>15.0.x</br>16.0.x | `--A`</br>`--A`</br>`--A` |
+| ant | 1.9.3-Java-1.7.0_79 | `-S-` |
+| APR | 1.5.2-foss-2015g</br>1.5.2 | `-SA`</br>`-SA` |
+| APR-util | 1.5.4</br>1.5.4-foss-2015g | `-SA`</br>`-SA` |
+| Armadillo | 7.500.0-foss-2016a-Python-3.5.2 | `-SA` |
+| arpack-ng | 3.3.0-foss-2016a</br>3.3.0-intel-2017.00</br>3.4.0-intel-2017.00</br>3.3.0-intel-2015b | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
+| ATLAS | 3.10.1-GCC-4.9.3-2.25-LAPACK-3.4.2 | `--A` |
+| Autoconf | 2.69-foss-2015g</br>2.69-intel-2016a</br>2.69</br>2.69-GCC-4.9.3-2.25</br>2.69-foss-2016a</br>2.69-GNU-5.1.0-2.25</br>2.69-intel-2017.00</br>2.69-GNU-4.9.3-2.25</br>2.69-intel-2016.01</br>2.69-intel-2015b | `-S-`</br>`-S-`</br>`USA`</br>`-S-`</br>`USA`</br>`USA`</br>`USA`</br>`USA`</br>`-S-`</br>`-SA` |
+| Automake | 1.15</br>1.15-GNU-5.1.0-2.25</br>1.15-intel-2017.00</br>1.15-foss-2016a</br>1.15-GCC-4.9.3-2.25</br>1.15-GNU-4.9.3-2.25</br>1.15-intel-2016.01</br>1.15-foss-2015g</br>1.15-intel-2015b</br>1.15-intel-2016a | `USA`</br>`USA`</br>`USA`</br>`USA`</br>`-S-`</br>`USA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-` |
+| Autotools | 20150215-GNU-5.1.0-2.25</br>20150215</br>20150215-intel-2015b</br>20150215-intel-2016a</br>20150215-foss-2016a</br>20150215-intel-2016.01</br>20150215-intel-2017.00</br>20150215-GNU-4.9.3-2.25</br>20150215-GCC-4.9.3-2.25 | `USA`</br>`USA`</br>`-SA`</br>`-S-`</br>`USA`</br>`-S-`</br>`USA`</br>`USA`</br>`-S-` |
+| Bash | 4.2-intel-2015b</br>4.3 | `US-`</br>`-SA` |
+| BCFtools | 1.3-foss-2015g | `-S-` |
+| beopest | 12.2</br>13.3</br>12.0.1 | `--A`</br>`--A`</br>`--A` |
+| BerkeleyUPC | 2.16.2-gompi-2015b | `-S-` |
+| binutils | 2.25-GCC-4.9.3 | `--A` |
+| Bison | 3.0.4-intel-2015b</br>3.0.4-GCC-4.9.3 | `--A`</br>`--A` |
+| blender | 2.71 | `--A` |
+| boost | 1.56-gcc-openmpi</br>1.56-icc-impi | `--A`</br>`--A` |
+| Boost | 1.60.0-foss-2015g-Python-2.7.9</br>1.58.0-Python-2.7.9</br>1.58.0-ictce-7.3.5-Python-2.7.9</br>1.59.0-intel-2015b</br>1.59.0-intel-2015b-Python-2.7.11</br>1.59.0-intel-2016.01</br>1.60.0-intel-2015b-Python-2.7.11</br>1.61.0-foss-2016a-serial</br>1.58.0-foss-2015g-Python-2.7.9</br>1.58.0-intel-2015b-Python-2.7.9</br>1.60.0-intel-2016a</br>1.61.0-foss-2016a</br>1.58.0-intel-2016.01-Python-2.7.9</br>1.58.0-gompi-2015e-Python-2.7.9 | `USA`</br>`-S-`</br>`-S-`</br>`--A`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`US-`</br>`--A`</br>`-S-`</br>`-S-`</br>`-S-` |
+| bowtie2 | 2.2.3 | `--A` |
+| bullxde | 2.0 | `--A` |
+| bullxmpi | bullxmpi-1.2.4.3</br>bullxmpi_1.2.4.1 | `--A`</br>`--A` |
+| bupc | 2.16.2 | `--A` |
+| BWA | 0.7.5a-foss-2015g | `-S-` |
+| byacc | 20120526-intel-2015b</br>20120526-foss-2015b</br>20120526-foss-2016a</br>20120526</br>20120526-foss-2015g</br>20150711-intel-2015b | `-SA`</br>`-S-`</br>`--A`</br>`-SA`</br>`-SA`</br>`--A` |
+| cairo | 1.12.18-foss-2015b</br>1.12.18 | `-S-`</br>`-SA` |
+| chicken | 4.8.0.6 | `--A` |
+| Clang | 3.7.0-GNU-5.1.0-2.25 | `-S-` |
+| CMake | 3.4.1-intel-2015b</br>3.3.1-foss-2016a</br>3.6.2-intel-2017.00</br>3.0.0-foss-2015g</br>3.3.2-intel-2016.01</br>3.5.2-intel-2017.00</br>3.5.2-GCC-4.9.3-2.25</br>3.4.1-foss-2016a</br>3.3.1-GCC-5.3.0-2.25</br>3.3.1-foss-2015g</br>3.5.1-intel-2016a</br>3.3.1-intel-2016.01</br>3.3.1-GNU-5.1.0-2.25</br>3.3.1-GCC-4.9.3-2.25</br>3.3.1-GNU-4.9.3-2.25</br>3.3.2-GNU-4.9.3-2.25</br>3.4.1-GCCcore-4.9.3</br>3.3.1-GCC-5.3.1-snapshot-20160419-2.25</br>3.4.3-intel-2016a</br>3.4.1-foss-2015b</br>3.5.2</br>3.0.0-intel-2016.01</br>3.0.0-ictce-7.3.5</br>3.5.2-intel-2016a</br>3.6.2</br>3.5.2-foss-2016a</br>3.0.0-intel-2015b | `-SA`</br>`--A`</br>`U--`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`--A`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`--A`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`US-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`--A`</br>`USA`</br>`USA`</br>`US-` |
+| cmake | 2.8.11-mic</br>2.8.11 | `--A`</br>`--A` |
+| Code_Saturne | 3.0.5 | `--A` |
+| COMSOL | 51-COM</br>51-EDU | `-S-`</br>`-S-` |
+| comsol | 44-EDU</br>50-EDU</br>43b-EDU</br>43b-COM</br>50-COM</br>44-COM | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
+| CP2K | 2.6.0-intel-2015b | `-S-` |
+| cp2k-mpi | 2.5.1-gcc | `--A` |
+| cube | 4.2.3-icc</br>4.2.3-gcc | `--A`</br>`--A` |
+| Cube | 4.3.4-intel-2015b | `-S-` |
+| CUDA | 7.5.18 | `--A` |
+| cuda | 6.5.14</br>6.0.37</br>7.5 | `--A`</br>`--A`</br>`--A` |
+| cURL | 7.47.0-intel-2017.00</br>7.51.0</br>7.51.0-intel-2017.00</br>7.37.1</br>7.45.0-foss-2015b</br>7.37.1-intel-2016.01</br>7.37.1-foss-2015g</br>7.37.1-intel-2015b | `-S-`</br>`--A`</br>`US-`</br>`USA`</br>`US-`</br>`-S-`</br>`-SA`</br>`US-` |
+| dataspaces | 1.4.0 | `--A` |
+| DCW | 1.1.2 | `-S-` |
+| DDT | 5.0.1</br>4.2 | `-S-`</br>`-S-` |
+| dhi-mike | default</br>2014</br>2016</br>2016-SP2 | `--A`</br>`--A`</br>`--A`</br>`--A` |
+| digimat | 5.0.1 | `--A` |
+| Digimat | 5.0.1-COM</br>5.0.1-EDU | `-S-`</br>`-S-` |
+| Discovery_Studio | 4.0 | `--A` |
+| Doxygen | 1.8.7-foss-2015g</br>1.8.7-intel-2016.01</br>1.8.11-intel-2017.00</br>1.8.10-foss-2015b</br>1.8.10-intel-2017.00</br>1.8.7-intel-2015b</br>1.8.11 | `-S-`</br>`-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`US-`</br>`-SA` |
+| dytran | 2013.0.1 | `--A` |
+| EasyBuild | 2.9.0</br>3.0.2</br>3.0.0</br>3.0.1</br>2.8.1</br>2.8.0 | `-S-`</br>`USA`</br>`-SA`</br>`-S-`</br>`--A`</br>`-SA` |
+| elmer | 7.0-r6695-dbg</br>7.0-r6695-opt | `--A`</br>`--A` |
+| eudev | 3.1.5-foss-2016a</br>3.1.5-intel-2016a | `-S-`</br>`-S-` |
+| expat | 2.1.0-intel-2015b</br>2.1.0</br>2.1.0-foss-2015g</br>2.1.0-intel-2017.00</br>2.1.0-foss-2015b | `-S-`</br>`USA`</br>`-SA`</br>`US-`</br>`US-` |
+| FastQC | 0.11.3 | `US-` |
+| fastqc | 0.11.2 | `--A` |
+| fds | 5.5.3-omp</br>5.5.3</br>6.svn | `--A`</br>`--A`</br>`--A` |
+| ffmpeg | 2.4-foss-2015g</br>2.4-intel-2015b</br>2.4 | `-S-`</br>`-S-`</br>`-SA` |
+| FFTW | 3.3.4-gompi-2015b</br>3.3.5-intel-2017.00</br>3.3.4-intel-2015b</br>3.3.4-gompi-2015g</br>3.3.4-gompi-2015e</br>3.3.5-intel-2016.01</br>2.1.5-iimpi-7.3.5-GNU-5.1.0-2.25</br>2.1.5-gompi-2015b</br>3.3.5-intel-2016a</br>3.3.5-gompi-2016a</br>3.3.5-foss-2016a</br>3.3.4-intel-2016.01</br>3.3.4-gompi-2016.04</br>3.3.4-gompi-2016a | `US-`</br>`USA`</br>`USA`</br>`USA`</br>`US-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`-SA`</br>`USA` |
+| fftw2 | 2.1.5-gcc</br>2.1.5-icc | `--A`</br>`--A` |
+| fftw2-mpi | 2.1.5-gcc</br>2.1.5-icc | `--A`</br>`--A` |
+| fftw3 | 3.3.3-gcc</br>3.3.3-icc | `--A`</br>`--A` |
+| fftw3-mpi | 3.3.3-gcc</br>3.3.3-icc | `--A`</br>`--A` |
+| FIAT | 1.6.0-intel-2016.01-Python-2.7.9</br>1.6.0-intel-2015b-Python-2.7.9</br>1.6.0-intel-2015b-Python-2.7.11 | `-S-`</br>`-S-`</br>`-S-` |
+| fixesproto | 5.0</br>5.0-foss-2015g</br>5.0-intel-2016a</br>5.0-foss-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
+| flex | 2.5.39-GCC-4.9.3</br>2.5.39-foss-2016a | `--A`</br>`--A` |
+| FLTK | 1.3.2</br>1.3.2-intel-2015b | `-SA`</br>`-S-` |
+| fontconfig | 2.11.1-intel-2015b</br>2.11.94-intel-2017.00</br>2.11.1-foss-2015b</br>2.11.1 | `-S-`</br>`-S-`</br>`-S-`</br>`-SA` |
+| fontsproto | 2.1.3</br>2.1.3-intel-2016a</br>2.1.3-foss-2015g</br>2.1.3-foss-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
+| Forge | 6.0.6</br>6.1.2</br>5.1-43967</br>6.0.5</br>5.7 | `-SA`</br>`-SA`</br>`-SA`</br>`-SA`</br>`--A` |
+| foss | 2016.04</br>2016a</br>2015b</br>2015e</br>2015g | `-SA`</br>`USA`</br>`US-`</br>`US-`</br>`USA` |
+| FOX | 1.6.51-foss-2015g | `-S-` |
+| FreeFem++ | 3.45-intel-2015b | `-S-` |
+| freetype | 2.6.2-intel-2016a</br>2.5.3-foss-2015g</br>2.5.3-foss-2015b</br>2.5.5-intel-2015b</br>2.6.3-intel-2016a</br>2.6.2-intel-2017.00</br>2.5.3-intel-2015b</br>2.6.3-foss-2016a</br>2.5.3 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA` |
+| gatk | 2.6-4 | `--A` |
+| GATK | 2.6-5-Java-1.7.0_79</br>3.5-Java-1.7.0_79 | `US-`</br>`-S-` |
+| gcc | 4.8.1</br>5.4.0</br>4.9.0 | `--A`</br>`--A`</br>`--A` |
+| GCC | 6.2.0-2.27</br>4.9.2-binutils-2.25</br>4.4.7-system</br>5.4.0-2.26</br>5.3.1-snapshot-20160419-2.25</br>5.3.0-binutils-2.25</br>5.2.0</br>5.3.0-2.26</br>4.9.3-2.25</br>5.3.0-2.25</br>4.7.4</br>4.8.3</br>5.1.0-binutils-2.25</br>4.9.3-binutils-2.25</br>4.9.2</br>4.9.3 | `US-`</br>`-S-`</br>`US-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-SA`</br>`USA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`USA`</br>`USA`</br>`-S-`</br>`USA` |
+| GCCcore | 5.3.1-snapshot-20160419</br>5.3.0</br>5.4.0</br>6.2.0</br>4.9.3 | `-S-`</br>`-SA`</br>`USA`</br>`US-`</br>`USA` |
+| GDAL | 2.1.0-intel-2015b</br>2.1.0-GNU-5.1.0-2.25-intel-2015b</br>2.1.0-foss-2015g</br>1.9.2-foss-2015g</br>2.1.0-GNU-5.1.0-2.25</br>2.0.1-foss-2015b</br>2.0.2-intel-2017.00 | `-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`-S-`</br>`US-`</br>`-S-` |
+| GEOS | 3.5.0-foss-2015g | `-S-` |
+| gettext | 0.19.4</br>0.19.4-GCC-4.4.7-system</br>0.19.6-intel-2017.00 | `--A`</br>`U--`</br>`--A` |
+| gimkl | 2.11.5 | `--A` |
+| gimpi | 2.11.5 | `--A` |
+| git | 2.9.2</br>2.9.0</br>2.8.0-GNU-4.9.3-2.25</br>2.11.0-intel-2017.00</br>2.11.0-GNU-4.9.3-2.25</br>2.11.0</br>2.8.0-intel-2017.00 | `-S-`</br>`-S-`</br>`-SA`</br>`U--`</br>`--A`</br>`-S-`</br>`US-` |
+| GLib | 2.40.0-GCC-4.4.7-system</br>2.40.0</br>2.40.0-foss-2015b</br>2.40.0-intel-2016.01</br>2.40.0-foss-2015g</br>2.40.0-intel-2015b | `U--`</br>`-SA`</br>`U--`</br>`-S-`</br>`-S-`</br>`US-` |
+| GLOBUS | globus | `--A` |
+| globus | globus | `-S-` |
+| glproto | 1.4.16-foss-2015g</br>1.4.17-intel-2016a</br>1.4.17-foss-2016a | `-S-`</br>`-S-`</br>`-S-` |
+| GMP | 6.1.0-intel-2017.00</br>6.1.0-intel-2016a</br>5.0.5</br>6.0.0a-GNU-5.1.0-2.25</br>6.0.0a-GNU-4.9.3-2.25</br>6.1.0-GCC-4.9.3-2.25</br>6.0.0a-intel-2015b</br>6.1.0-foss-2016a</br>6.1.1-intel-2017.00</br>5.0.5-foss-2015g</br>5.0.5-intel-2015b</br>6.0.0a</br>5.0.5-foss-2015b</br>6.0.0a-foss-2015b</br>6.1.0-intel-2015b</br>6.1.0-intel-2016.01 | `USA`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`--A`</br>`USA`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-` |
+| GMT | 5.2.1-foss-2015g | `-S-` |
+| GNU | 4.9.3-2.25</br>5.1.0-2.25</br>5.1.0-2.25-intel-2015b | `USA`</br>`USA`</br>`-S-` |
+| gnuplot | 4.6.5 | `--A` |
+| gompi | 2016.04</br>2016a</br>2015b</br>2015e</br>2015g | `-SA`</br>`USA`</br>`US-`</br>`US-`</br>`USA` |
+| gperf | 3.0.4-foss-2015g</br>3.0.4-foss-2016a</br>3.0.4-intel-2016a | `-S-`</br>`-S-`</br>`-S-` |
+| GPI-2 | 1.1.1-gompi-2015e-MPI</br>1.1.1-gompi-2015e | `-S-`</br>`-S-` |
+| gpi2 | 1.1.1</br>1.1.0</br>1.0.2 | `--A`</br>`--A`</br>`--A` |
+| grace | 5.1.23</br>5.1.25-intel-2015b | `--A`</br>`-S-` |
+| GROMACS | 5.1.2-intel-2016a-hybrid</br>5.0.4-ictce-7.3.5-hybrid-single</br>4.6.7-foss-2015g-hybrid-single-PLUMED</br>5.0.4-foss-2015e-hybrid-single-PLUMED</br>5.1.2-intel-2015b-hybrid-single-CUDA-7.5-PLUMED-2.2.1-test</br>5.1.2-intel-2015b-hybrid-single-cuda</br>5.1.2-foss-2015g-hybrid-single-PLUMED</br>5.1.2-intel-2015b-hybrid-single-CUDA-7.5-PLUMED-2.2.1</br>5.0.4-foss-2015g-hybrid-single</br>5.0.4-foss-2015g-hybrid-single-PLUMED | `--A`</br>`-S-`</br>`-S-`</br>`-S-`</br>`--A`</br>`--A`</br>`-S-`</br>`--A`</br>`-S-`</br>`-S-` |
+| gsl | 1.16-icc</br>1.16-gcc | `--A`</br>`--A` |
+| GSL | 1.16-intel-2016.01</br>2.1-intel-2015b</br>1.16-intel-2015b | `--A`</br>`--A`</br>`-SA` |
+| guile | 1.8.8-foss-2015b</br>1.8.8-foss-2016a</br>1.8.8</br>1.8.8-intel-2015b</br>1.8.8-foss-2015g | `-S-`</br>`--A`</br>`-SA`</br>`-SA`</br>`-S-` |
+| gupc | 4.8.0.3 | `--A` |
+| gzip | 1.6-intel-2015b</br>1.6</br>1.6-foss-2016a</br>1.6-foss-2015g | `-SA`</br>`-SA`</br>`--A`</br>`USA` |
+| h5py | 2.4.0-ictce-7.3.5-Python-2.7.9-serial | `-S-` |
+| Harminv | 1.4-intel-2015b | `-S-` |
+| HDF5 | 1.8.16-intel-2016.01</br>1.8.13-intel-2016.01</br>1.8.16-foss-2015g</br>1.8.13-foss-2015g</br>1.8.13-intel-2015b</br>1.8.16-intel-2017.00</br>1.8.14-ictce-7.3.5-serial</br>1.8.13-intel-2015b-no-mpi</br>1.8.16-foss-2016a</br>1.10.0-patch1-intel-2016.01-mic</br>1.8.16-intel-2015b</br>1.8.15-patch1-foss-2015b</br>1.8.16-intel-2015b-threadsafe | `--A`</br>`-S-`</br>`-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`USA`</br>`-S-`</br>`USA`</br>`US-`</br>`-S-` |
+| hdf5 | 1.8.13</br>1.8.11 | `--A`</br>`--A` |
+| hdf5-parallel | 1.8.13-gcc49</br>1.8.13-gcc</br>1.8.13</br>1.8.11-gcc</br>1.8.11 | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
+| hpg-aligner | 1.0.0 | `--A` |
+| hpg-fastq | 1.0.0 | `--A` |
+| hpg-variant | 1.0.0 | `--A` |
+| HPL | 2.1-intel-2015b</br>2.1-foss-2015b | `-S-`</br>`-S-` |
+| HTSlib | 1.3-foss-2015g | `-S-` |
+| hwloc | 1.11.0</br>1.5-GCC-4.4.7-system</br>1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25</br>1.11.2-GCC-4.9.3-2.25</br>1.11.0-GNU-5.1.0-2.25</br>1.11.3-GCC-5.3.0-2.26</br>1.11.0-GNU-4.9.3-2.25 | `-SA`</br>`-S-`</br>`-SA`</br>`USA`</br>`USA`</br>`-SA`</br>`USA` |
+| hypermesh | 12.0.110 | `--A` |
+| HyperWorks | 13.0 | `-S-` |
+| hyperworks | 13.0 | `--A` |
+| Hypre | 2.10.0b-intel-2015b</br>2.10.0b-intel-2016.01</br>2.10.1-intel-2015b | `-S-`</br>`-S-`</br>`-S-` |
+| icc | 2013.5.192-GCC-4.8.3</br>2013.5.192</br>2015.3.187-GNU-4.9.3-2.25</br>2016.3.210-GCC-5.3.0-2.26</br>2016.1.150-GCC-4.9.3</br>2015.3.187-GNU-5.1.0-2.25</br>2017.0.098-GCC-5.4.0-2.26</br>2016.1.150-GCC-4.9.3-2.25</br>2016.0.109-GCC-4.9.3</br>2016.1.150</br>2015.3.187 | `-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`USA`</br>`USA`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
+| iccifort | 2013.5.192-GCC-4.8.3</br>2013.5.192</br>2015.3.187-GNU-4.9.3-2.25</br>2016.3.210-GCC-5.3.0-2.26</br>2016.1.150-GCC-4.9.3</br>2015.3.187-GNU-5.1.0-2.25</br>2017.0.098-GCC-5.4.0-2.26</br>2016.1.150-GCC-4.9.3-2.25</br>2016.0.109-GCC-4.9.3</br>2016.1.150</br>2015.3.187 | `-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`USA`</br>`USA`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
+| ictce | 7.3.5</br>5.5.0</br>8.3.5 | `-S-`</br>`-S-`</br>`-S-` |
+| ifort | 2013.5.192-GCC-4.8.3</br>2013.5.192</br>2015.3.187-GNU-4.9.3-2.25</br>2016.3.210-GCC-5.3.0-2.26</br>2016.1.150-GCC-4.9.3</br>2015.3.187-GNU-5.1.0-2.25</br>2017.0.098-GCC-5.4.0-2.26</br>2016.1.150-GCC-4.9.3-2.25</br>2016.0.109-GCC-4.9.3</br>2016.1.150</br>2015.3.187 | `-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`USA`</br>`USA`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
+| iimpi | 5.5.0</br>8.1.5-GCC-4.9.3-2.25</br>5.5.0-GCC-4.8.3</br>7.3.5-GNU-5.1.0-2.25</br>8.3.5</br>2016.00-GCC-4.9.3</br>2016.01-GCC-4.9.3-2.25</br>2016.01-GCC-4.9.3</br>2017.00-GCC-5.4.0-2.26</br>7.3.5</br>2016.03-GCC-5.3.0-2.26 | `-S-`</br>`-SA`</br>`-S-`</br>`USA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`USA`</br>`-S-`</br>`-S-` |
+| imkl | 11.2.3.187</br>11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26</br>11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25</br>11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25</br>2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26</br>11.3.1.150-iimpi-8.3.5</br>11.0.5.192-iimpi-5.5.0</br>11.3.1.150-iimpi-2016.00-GCC-4.9.3</br>11.2.3.187-iimpi-7.3.5</br>11.3.0.109-iimpi-2016.00-GCC-4.9.3</br>11.2.3.187-iompi-2015.03</br>11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25</br>11.0.5.192-iimpi-5.5.0-GCC-4.8.3</br>11.2.3.187-gimpi-2.11.5 | `-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`USA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`USA`</br>`-S-`</br>`--A` |
+| impi | 4.1.1.036-iccifort-2013.5.192</br>5.0.3.048-iccifort-2015.3.187</br>4.1.1.036</br>5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25</br>4.1.1.036-iccifort-2013.5.192-GCC-4.8.3</br>2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26</br>5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26</br>5.0.3.048-GCC-4.9.3</br>5.1.2.150-iccifort-2016.1.150</br>5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25</br>5.1.2.150-iccifort-2016.1.150-GCC-4.9.3</br>2017-BETA.ENG</br>5.0.3.048</br>5.1.1.109-iccifort-2016.0.109-GCC-4.9.3 | `-S-`</br>`-S-`</br>`--A`</br>`-SA`</br>`-S-`</br>`USA`</br>`-S-`</br>`--A`</br>`-S-`</br>`USA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-` |
+| inputproto | 2.3</br>2.3-foss-2015g</br>2.3-intel-2015b</br>2.3.1-intel-2016a</br>2.3.1-foss-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
+| Inspector | 2016_update1 | `-S-` |
+| inspector_xe | 2013.5</br>2015.1.2.379161 | `--A`</br>`--A` |
+| intel | 2014.06</br>2017.00</br>2016.03-GCC-5.3</br>15.2.164</br>2016.00</br>2016.01</br>14.0.1</br>2015b</br>2016a</br>15.3.187</br>13.5.192</br>2015b-intel-2015b | `-S-`</br>`USA`</br>`-S-`</br>`--A`</br>`-S-`</br>`-SA`</br>`--A`</br>`USA`</br>`-SA`</br>`--A`</br>`--A`</br>`-S-` |
+| intelpcm | 2.6 | `--A` |
+| ipm | 0.983-icc-impi | `--A` |
+| ipp | 14.0.1</br>13.5.192</br>15.3.187</br>9.0.1.150</br>15.2.164 | `--A`</br>`--A`</br>`--A`</br>`-S-`</br>`--A` |
+| ISL | 0.15</br>0.15-GCC-4.9.3-2.25</br>0.14-GNU-5.1.0-2.25</br>0.15-GNU-4.9.3-2.25 | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
+| itac | 9.0.3.051</br>9.1.2.024</br>8.1.4.045 | `--A`</br>`-S-`</br>`--A` |
+| JasPer | 1.900.1-intel-2015b | `-S-` |
+| java | 1.7 | `--A` |
+| Java | 1.8.0_112</br>1.8.0_51</br>1.8.0_72</br>1.7.0_79 | `-S-`</br>`USA`</br>`US-`</br>`USA` |
+| JOE | 4.2 | `-SA` |
+| JUnit | 4.11-Java-1.7.0_79 | `-S-` |
+| kbproto | 1.0.6</br>1.0.6-foss-2015g</br>1.0.7-intel-2016a</br>1.0.7-foss-2016a</br>1.0.7</br>1.0.6-intel-2015b | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
+| lam | 7.1.4-icc | `--A` |
+| LAMMPS | 28Jun14-intel-2015b | `-S-` |
+| lammps | 28Jun14 | `--A` |
+| LAPACKE | 3.5.0-LAPACK-3.5.0 | `-S-` |
+| libctl | 3.2.2-intel-2015b | `-S-` |
+| libdrm | 2.4.68-intel-2016a</br>2.4.68-foss-2016a</br>2.4.27</br>2.4.27-foss-2015g</br>2.4.67-intel-2016a | `-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-` |
+| libffi | 3.1-GNU-5.1.0-2.25</br>3.1-intel-2016.01</br>3.1-foss-2015b</br>3.1-intel-2015b</br>3.0.13-intel-2015b</br>3.2.1-intel-2017.00</br>3.0.13-foss-2015b</br>3.2.1-GCC-4.4.7-system</br>3.0.13</br>3.0.13-foss-2015g</br>3.2.1-foss-2016a | `-S-`</br>`-SA`</br>`-S-`</br>`USA`</br>`-SA`</br>`-S-`</br>`US-`</br>`U--`</br>`-SA`</br>`-S-`</br>`--A` |
+| libfontenc | 1.1.3</br>1.1.3-foss-2015g</br>1.1.3-foss-2016a</br>1.1.3-intel-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
+| libgdiplus | 3.12</br>3.12-GCC-4.4.7-system</br>3.12-intel-2016.01</br>3.12-GNU-5.1.0-2.25 | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
+| libGLU | 9.0.0-foss-2015g | `-S-` |
+| libICE | 1.0.9-foss-2015g</br>1.0.9-intel-2015b</br>1.0.9 | `-S-`</br>`-S-`</br>`-SA` |
+| Libint | 1.1.4-gompi-2015b</br>1.1.4-intel-2015b</br>1.1.4-foss-2015b | `-S-`</br>`US-`</br>`-S-` |
+| libjpeg-turbo | 1.4.0</br>1.4.2-intel-2017.00</br>1.4.0-foss-2015g</br>1.3.1-intel-2015b</br>1.4.1-foss-2015b</br>1.4.0-intel-2015b</br>1.3.1-foss-2015b | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`-S-` |
+| libmatheval | 1.1.11-intel-2015b</br>1.1.8-foss-2016a</br>1.1.8</br>1.1.8-foss-2015b</br>1.1.8-foss-2015g</br>1.1.8-intel-2015b | `--A`</br>`--A`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-SA` |
+| libMesh | 0.9.5-intel-2016.01 | `-S-` |
+| libmesh | 0.9.3-petsc-3.4.4-icc-impi-mkl-dbg</br>0.9.3-petsc-3.4.4-icc-impi-mkl-dbg-2d</br>0.9.3-petsc-3.4.4-icc-impi-mkl-opt | `--A`</br>`--A`</br>`--A` |
+| libpciaccess | 0.13.1-foss-2015g</br>0.13.4-foss-2016a</br>0.13.4-intel-2016a</br>0.13.1 | `-S-`</br>`-S-`</br>`-S-`</br>`-SA` |
+| libpng | 1.6.16-intel-2015b | `-S-` |
+| libpthread-stubs | 0.3-intel-2015b</br>0.3</br>0.3-foss-2016a</br>0.3-intel-2016a</br>0.3-foss-2015g | `-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
+| libreadline | 6.3-gimkl-2.11.5 | `--A` |
+| libSM | 1.2.2-foss-2015g</br>1.2.2</br>1.2.2-intel-2015b | `-S-`</br>`-SA`</br>`-S-` |
+| LibTIFF | 4.0.3-intel-2015b</br>4.0.3 | `-S-`</br>`-SA` |
+| libunistring | 0.9.3-foss-2015b</br>0.9.3</br>0.9.3-foss-2015g</br>0.9.3-intel-2015b</br>0.9.3-foss-2016a | `-S-`</br>`-SA`</br>`-S-`</br>`-SA`</br>`--A` |
+| libunwind | 1.1-GCC-5.4.0-2.26 | `-S-` |
+| libX11 | 1.6.2-foss-2015g-Python-2.7.9</br>1.6.3-foss-2016a</br>1.6.3-intel-2016a</br>1.6.2-Python-2.7.8</br>1.6.2-Python-2.7.9</br>1.6.2-intel-2015b-Python-2.7.9 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-` |
+| libXau | 1.0.8-intel-2016a</br>1.0.8-foss-2015g</br>1.0.8-foss-2016a</br>1.0.8</br>1.0.8-intel-2015b | `-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-` |
+| libxc | 2.2.0-gompi-2015b</br>2.2.1-intel-2015b</br>2.2.0-foss-2015b | `-S-`</br>`US-`</br>`-S-` |
+| libxcb | 1.11.1-foss-2016a</br>1.11-foss-2015g-Python-2.7.9</br>1.11.1-intel-2016a</br>1.10-Python-2.7.8</br>1.11-Python-2.7.9</br>1.11-intel-2015b-Python-2.7.9 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-` |
+| libXdamage | 1.1.4-intel-2016a</br>1.1.4-foss-2016a</br>1.1.4-foss-2015g-Python-2.7.9 | `-S-`</br>`-S-`</br>`-S-` |
+| libXdmcp | 1.1.2-intel-2016a</br>1.1.2</br>1.1.2-foss-2015g</br>1.1.2-intel-2015b</br>1.1.2-foss-2016a | `-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
+| libXext | 1.3.3-intel-2016a</br>1.3.3-foss-2015g-Python-2.7.9</br>1.3.3-intel-2015b</br>1.3.2-Python-2.7.8</br>1.3.3-foss-2016a</br>1.3.3</br>1.3.3-foss-2015g | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-` |
+| libXfixes | 5.0.1</br>5.0.1-intel-2016a</br>5.0.1-foss-2015g</br>5.0.1-foss-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
+| libXfont | 1.5.1-Python-2.7.9</br>1.5.1-intel-2016a-freetype-2.6.3</br>1.5.1-intel-2016a</br>1.5.1-foss-2016a-freetype-2.6.3</br>1.5.1-foss-2015g-Python-2.7.9 | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
+| libXft | 2.3.2-intel-2015b | `-S-` |
+| libXinerama | 1.1.3-intel-2015b | `-S-` |
+| libxml2 | 2.9.2</br>2.9.2-GCC-4.4.7-system</br>2.9.2-foss-2015b</br>2.9.2-foss-2015g</br>2.9.3-foss-2016a</br>2.9.2-ictce-7.3.5</br>2.9.2-gompi-2015e</br>2.9.3-intel-2017.00</br>2.9.2-GNU-5.1.0-2.25</br>2.9.2-foss-2015g-Python-2.7.9</br>2.9.2-GCC-4.9.3-2.25</br>2.9.2-intel-2015b</br>2.9.2-GNU-4.9.3-2.25</br>2.9.3-intel-2016a | `-S-`</br>`U--`</br>`US-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-`</br>`-SA` |
+| libXrender | 0.9.8</br>0.9.8-intel-2015b | `-S-`</br>`-S-` |
+| libxslt | 1.1.28-intel-2015b | `-S-` |
+| libXt | 1.1.4-libX11-1.6.2</br>1.1.4-foss-2015g-libX11-1.6.2</br>1.1.4-intel-2015b-libX11-1.6.2</br>1.1.5-foss-2015g | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
+| libyaml | 0.1.6-intel-2015b | `-S-` |
+| likwid | 3.1.2-mic</br>3.1.2-gcc</br>3.1.1-icc</br>4.1.2-intel</br>4.1.2-gcc</br>3.1.1-mic</br>3.1.2-icc | `--A`</br>`--A`</br>`--A`</br>`-S-`</br>`-S-`</br>`--A`</br>`--A` |
+| LLVM | 3.8.0-foss-2016a</br>3.7.1-foss-2015g</br>3.8.0-intel-2016a</br>3.7.1-intel-2016a</br>3.9.0-intel-2017.00 | `US-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`US-` |
+| llvm | 3.6.0 | `--A` |
+| lmod | 7.2.2 | `USA` |
+| Lmod | 7.2.2</br>7.0.6</br>6.4.2 | `-SA`</br>`-SA`</br>`--A` |
+| lsdyna | 7.x.x | `--A` |
+| lsprepost | 4.2 | `--A` |
+| Lua | 5.1.4-8 | `USA` |
+| lux | 1.3.1 | `--A` |
+| lxml | 3.4.4-intel-2015b-Python-2.7.9 | `-S-` |
+| M4 | 1.4.17-intel-2016.01</br>1.4.17-foss-2015b</br>1.4.17-GNU-4.9.3-2.25</br>1.4.17-GCCcore-4.9.3</br>1.4.17-foss-2015g</br>1.4.17-GCC-4.9.3-2.25</br>1.4.17-foss-2016a</br>1.4.17-intel-2015b</br>1.4.17-GCCcore-5.4.0</br>1.4.17</br>1.4.17-GCC-5.1.0-binutils-2.25</br>1.4.17-GNU-5.1.0-2.25</br>1.4.17-GCCcore-5.3.0</br>1.4.17-intel-2016a</br>1.4.16-foss-2015g</br>1.4.16-intel-2015b</br>1.4.17-intel-2017.00</br>1.4.17-GCC-4.9.3</br>1.4.17-GCC-4.9.3-binutils-2.25</br>1.4.17-GCCcore-6.2.0</br>1.4.17-GCCcore-5.3.1-snapshot-20160419 | `-S-`</br>`US-`</br>`USA`</br>`USA`</br>`-S-`</br>`-S-`</br>`USA`</br>`USA`</br>`USA`</br>`USA`</br>`-SA`</br>`USA`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-SA`</br>`USA`</br>`--A`</br>`USA`</br>`US-`</br>`-S-` |
+| magma | 1.3.0-mic</br>1.1.0-mic | `--A`</br>`--A` |
+| make | 3.82</br>3.82-intel-2015b | `-SA`</br>`US-` |
+| makedepend | 1.0.4</br>1.0.5-foss-2016a</br>1.0.4-foss-2015g</br>1.0.5-intel-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
+| MAP | 5.0.1</br>4.2 | `-S-`</br>`-S-` |
+| marc | 2011</br>2013.1 | `--A`</br>`--A` |
+| Marc | 2013.1.0 | `-S-` |
+| matlab | R2013a-EDU</br>R2014a-EDU</br>R2014a-COM</br>R2013a-COM | `--A`</br>`--A`</br>`--A`</br>`--A` |
+| MATLAB | 2015b-EDU</br>2015a-EDU</br>2015a-COM</br>2015b-COM | `-SA`</br>`USA`</br>`USA`</br>`-SA` |
+| matplotlib | 1.4.3-intel-2015b-Python-2.7.9 | `-S-` |
+| Maven | 3.3.9 | `USA` |
+| maxwell | 3.0 | `--A` |
+| Meep | 1.3-intel-2015b | `-S-` |
+| memoryscape | 3.4 | `--A` |
+| mercurial | 2.9.1 | `--A` |
+| Mercurial | 3.7.3-foss-2015g-Python-2.7.9</br>3.5-Python-2.7.9 | `USA`</br>`-S-` |
+| Mesa | 11.0.8-foss-2015g-Python-2.7.9</br>11.2.1-foss-2016a | `-S-`</br>`-S-` |
+| METIS | 5.1.0-intel-2017.00</br>5.1.0-intel-2016.01-32bitIDX</br>5.1.0-intel-2015b</br>5.1.0-intel-2016.01 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
+| MIKE | default</br>2014</br>2016</br>2016-SP2 | `--A`</br>`-SA`</br>`-SA`</br>`-SA` |
+| mkl | 14.0.1</br>13.5.192</br>15.3.187</br>15.2.164 | `--A`</br>`--A`</br>`--A`</br>`--A` |
+| MLD2P4 | 2.0-rc4-GCC-4.9.3-2.25 | `--A` |
+| modflow-2005 | 1.11.00 | `--A` |
+| modflow-nwt | 1.0.9-aquaveo</br>1.0.9 | `--A`</br>`--A` |
+| Molpro | 2010.1-patch-57-intel2015b | `-S-` |
+| molpro | 2010.1-p45-intel | `--A` |
+| mono | 3.12.1</br>3.2.3 | `--A`</br>`--A` |
+| Mono | 3.12.1-GCC-4.4.7-system</br>4.2.2.10-intel-2016.01</br>3.12.1</br>4.0.3.20-GNU-5.1.0-2.25 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
+| motif | 2.3.4-foss-2015g-libX11-1.6.2</br>2.3.4-intel-2015b-libX11-1.6.2 | `-S-`</br>`-S-` |
+| MPC | 1.0.2-intel-2017.00 | `-S-` |
+| MPFR | 3.1.5-intel-2017.00 | `-S-` |
+| mpi.net | 1.0.0-mono-3.12.1</br>1.0.0</br>1.0.0-impi | `--A`</br>`--A`</br>`--A` |
+| MPI_NET | 1.2.0-gompi-2015e</br>1.2.0-intel-2016.01 | `-S-`</br>`-S-` |
+| MPICH | 3.2-GCC-5.3.1-snapshot-20160419-2.25</br>3.2-GCC-5.3.0-2.25</br>3.2-GCC-4.9.3-2.25 | `-S-`</br>`-S-`</br>`--A` |
+| mpt | 2.12 | `-S-` |
+| mvapich2 | 1.9-icc</br>1.9-gcc</br>1.9-gcc46 | `--A`</br>`--A`</br>`--A` |
+| MVAPICH2 | 2.1-GNU-5.1.0-2.25</br>2.1-iccifort-2015.3.187-GNU-5.1.0-2.25</br>2.1-GCC-4.4.7-system | `-S-`</br>`-S-`</br>`-S-` |
+| mxml | 2.9 | `--A` |
+| namd | 2.8 | `--A` |
+| NAMD | 2.9-mpi | `-S-` |
+| NASM | 2.11.05</br>2.11.08-intel-2017.00</br>2.11.05-foss-2015g</br>2.11.05-foss-2015b</br>2.11.06-intel-2015b</br>2.11.05-intel-2015b</br>2.11.08-foss-2015b | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`US-` |
+| nastran | 2013.1.1 | `--A` |
+| ncurses | 5.9-GCC-4.9.3-2.25</br>5.9-gimkl-2.11.5 | `--A`</br>`--A` |
+| netcdf | 4.3.0</br>4.2.1.1 | `--A`</br>`--A` |
+| netCDF | 4.4.0-intel-2017.00</br>4.3.2-intel-2016.01</br>4.3.3.1-intel-2017.00</br>4.3.3.1-foss-2015b</br>4.3.2-foss-2015g</br>4.3.2-intel-2015b | `-S-`</br>`-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`US-` |
+| netcdf-cxx | 4.2 | `--A` |
+| netcdf-fortran | 4.2 | `--A` |
+| netCDF-Fortran | 4.4.0-intel-2016.01 | `-S-` |
+| netcdf-parallel | 4.3.0 | `--A` |
+| ngsPipeline | 1.0.0 | `--A` |
+| numactl | 2.0.9-GCC-4.4.7-system</br>2.0.10-iccifort-2015.3.187-GNU-4.9.3-2.25</br>2.0.11-GCC-5.3.0-2.26</br>2.0.9</br>2.0.10-GNU-4.9.3-2.25</br>2.0.11-GCC-4.9.3-2.25</br>2.0.10-GNU-5.1.0-2.25</br>2.0.11</br>2.0.10 | `-S-`</br>`-SA`</br>`-SA`</br>`--A`</br>`USA`</br>`USA`</br>`USA`</br>`-SA`</br>`-SA` |
+| numpy | 1.8.2-intel-2015b-Python-2.7.9</br>1.8.2-intel-2015b-Python-2.7.11</br>1.9.1-intel-2015b-Python-2.7.9</br>1.8.2-intel-2016.01-Python-2.7.9 | `-SA`</br>`-SA`</br>`-S-`</br>`-SA` |
+| NWChem | 6.3.revision2-2013-10-17-Python-2.7.8</br>6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.8 | `-S-`</br>`-S-` |
+| nwchem | 6.3-rev2-patch1</br>6.3-rev2-patch1-venus</br>6.3-rev2-patch1-openmpi</br>6.1.1 | `--A`</br>`--A`</br>`--A`</br>`--A` |
+| Octave | 3.8.2-gimkl-2.11.5</br>3.8.2-foss-2015g</br>4.0.1-gimkl-2.11.5</br>4.0.0-foss-2015g</br>3.8.2-intel-2015b | `--A`</br>`-S-`</br>`--A`</br>`-SA`</br>`-S-` |
+| opari2 | 1.1.2-gcc</br>1.1.2-icc | `--A`</br>`--A` |
+| OPARI2 | 1.1.4-intel-2015b</br>2.0 | `-S-`</br>`-SA` |
+| OpenBLAS | 0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0</br>0.2.14-GNU-5.1.0-2.25-LAPACK-3.5.0</br>0.2.14-gompi-2015e-LAPACK-3.5.0</br>0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0</br>0.2.19-GCC-5.4.0-2.26-LAPACK-3.6.0</br>0.2.15-GCC-5.1.0-binutils-2.25-LAPACK-3.6.0</br>0.2.14-LAPACK-3.5.0</br>0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0</br>0.2.15-GCC-5.1.0-binutils-2.25-LAPACK-3.6.0-gompi-2016a | `USA`</br>`USA`</br>`US-`</br>`-SA`</br>`-S-`</br>`--A`</br>`-S-`</br>`USA`</br>`--A` |
+| OpenCL-builder | 2015 | `-S-` |
+| opencl-rt | 4.5.0.8 | `--A` |
+| OpenCL-runtime | 15.1 | `-S-` |
+| opencl-sdk | 4.6.0.92 | `--A` |
+| OpenCoarrays | 1.4.0-GCC-5.3.0-2.25</br>1.0.1-GNU-5.1.0-2.25</br>1.4.0-GCC-5.3.1-snapshot-20160419-2.25</br>1.0.0-GNU-5.1.0-2.25 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
+| OpenCV | 2.4.9-intel-2015b</br>3.0.0-intel-2015b | `-S-`</br>`-S-` |
+| OpenDX | 4.4.4-foss-2015g | `-S-` |
+| openfoam | 2.2.1-gcc481-openmpi1.6.5-DP</br>2.2.2-icc-openmpi1.8.1-DP</br>2.2.1-icc-openmpi1.6.5-DP</br>2.2.1-gcc481-openmpi1.6.5-SP</br>2.2.1-icc-impi4.1.1.036-DP | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
+| OpenFOAM | 2.2.2-intel-2015b</br>2.3.0-intel-2015b</br>3.0.0-intel-2016.01 | `US-`</br>`US-`</br>`-S-` |
+| openmpi | 1.6.5-gcc46</br>1.8.1-gcc</br>1.6.5-gcc</br>1.6.5-icc</br>1.8.1-gcc49</br>1.8.1-icc</br>1.8.1-gcc46 | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
+| OpenMPI | 1.8.6-iccifort-2015.3.187-GNU-5.1.0-2.25</br>1.8.6-GCC-4.4.7-system</br>1.10.1-GNU-4.9.3-2.25</br>1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25</br>1.10.2-GCC-4.9.3-2.25</br>1.8.8-GNU-5.1.0-2.25</br>1.10.2-GCC-5.3.0-2.26</br>1.10.1-GCC-4.9.3-2.25</br>1.8.6-GNU-5.1.0-2.25</br>1.8.8-GNU-4.9.3-2.25 | `-S-`</br>`US-`</br>`US-`</br>`-SA`</br>`USA`</br>`-S-`</br>`-SA`</br>`-S-`</br>`US-`</br>`USA` |
+| openssh-x509 | 6.2p2 | `--A` |
+| ORCA | 3_0_3-linux_x86-64 | `-SA` |
+| oscar-modules | 1.0.3 | `--A` |
+| OSPRay | 0.9.1 | `-S-` |
+| OTF2 | 1.4-intel-2015b</br>2.0</br>2.0-intel-2015b-mic | `-S-`</br>`-SA`</br>`-S-` |
+| otf2 | 1.4-icc</br>1.2.1-gcc</br>1.4-gcc</br>1.2.1-icc | `--A`</br>`--A`</br>`--A`</br>`--A` |
+| p4vasp | 0.3.29-GNU-4.9.3-2.25 | `-S-` |
+| PAPI | 5.4.3-pic</br>5.4.3</br>5.4.0-p-mic</br>5.4.0-intel-2015b</br>5.4.3-intel-2015b-mic</br>5.4.0-mic | `-S-`</br>`-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
+| papi | 5.3.2-mic</br>5.4.0</br>5.3.2</br>5.4.0-mic</br>5.3.0 | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
+| parallel | 20150322-GNU-5.1.0-2.25</br>20141122</br>20150322 | `-S-`</br>`--A`</br>`-S-` |
+| ParaView | 5.0.0-binary</br>4.3-OSPRay | `-S-`</br>`-S-` |
+| paraview | 4.0.1-gcc481-bullxmpi1.2.4.1-osmesa10.0 | `--A` |
+| ParMETIS | 4.0.3-intel-2015b</br>4.0.3-intel-2016.01 | `-S-`</br>`-S-` |
+| PCRE | 8.37-foss-2015g</br>8.37-intel-2016.01</br>8.39-intel-2017.00</br>8.36-foss-2015g</br>8.36-intel-2015b</br>8.37</br>8.37-gimkl-2.11.5</br>8.36-intel-2016.01 | `-SA`</br>`--A`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`--A`</br>`-S-` |
+| PCRE2 | 10.22-intel-2017.00 | `-S-` |
+| perfboost | 1.0 | `-S-` |
+| perfcatcher | 1.0 | `-S-` |
+| PerformanceReports | 5.1-43967</br>6.0.6 | `-S-`</br>`-SA` |
+| PerfReports | 5.0.1 | `-S-` |
+| perfsuite | 1a5.3 | `-S-` |
+| Perl | 5.20.2-GNU-4.9.3-2.25-bare</br>5.22.2-intel-2017.00</br>5.20.2-bare</br>5.16.3-intel-2015b</br>5.24.0-GCC-4.9.3-2.25-bare | `-SA`</br>`US-`</br>`-S-`</br>`US-`</br>`--A` |
+| pest | 13.0 | `--A` |
+| petsc | 3.5.3-icc15-impi-mkl-threads-opt</br>3.7.3-icc16-impi5-mkl-opt</br>3.5.3-icc15-impi-mkl-threads-dbg</br>3.5.3-icc15-impi-mkl-dbg</br>3.5.3-icc15-impi-mkl-opt</br>3.7.3-icc16-impi5-mkl-dbg | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
+| PETSc | 3.6.1-intel-2015b-Python-2.7.9</br>3.6.1-intel-2016.01-Python-2.7.9</br>3.6.3-intel-2015b-Python-2.7.11 | `-S-`</br>`-S-`</br>`-S-` |
+| PGI | 16.10-GNU-4.9.3-2.25</br>15.7 | `-S-`</br>`-S-` |
+| phono3py | 1.11.7.8-intel-2015b-Python-2.7.9</br>1.11.7.8-intel-2015b-Python-2.7.11 | `-S-`</br>`--A` |
+| phonopy | 1.11.6.7-intel-2015b-Python-2.7.9</br>1.11.6.7-intel-2015b-Python-2.7.11 | `-S-`</br>`--A` |
+| picard | 2.1.0</br>1.117</br>1.119 | `-S-`</br>`--A`</br>`-S-` |
+| pigz | 2.3.3-GCC-6.2.0-2.27 | `US-` |
+| pixman | 0.32.6-intel-2015b</br>0.32.6-foss-2015b</br>0.32.6 | `-S-`</br>`-S-`</br>`-SA` |
+| pkg-config | 0.29.1-foss-2016a</br>0.29</br>0.27.1-foss-2015g</br>0.27.1-foss-2015b</br>0.29.1-intel-2016a</br>0.29-foss-2016a</br>0.27.1-intel-2015b</br>0.27.1</br>0.29-intel-2016a | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`-SA`</br>`-S-` |
+| plasma | 2.6.0 | `--A` |
+| PLUMED | 2.3b-foss-2015g</br>2.2.1-intel-2015b</br>2.1.3-foss-2015g</br>2.3b-foss-2016a | `-S-`</br>`--A`</br>`-S-`</br>`--A` |
+| prace | 20160107-intel-2016.01 | `-S-` |
+| PRACE | prace</br>20150630-intel-2015b | `--A`</br>`US-` |
+| PrgEnv-gnu | 4.8.1</br>4.4.6</br>4.4.6-test | `--A`</br>`--A`</br>`--A` |
+| PrgEnv-intel | 14.0.1</br>13.5.192</br>15.0.3 | `--A`</br>`--A`</br>`--A` |
+| PROJ | 4.9.2-intel-2017.00</br>4.8.0-foss-2015b | `-S-`</br>`US-` |
+| PROJ_4 | 4.9.2-foss-2015g | `-S-` |
+| PSBLAS | 3.3.4-3-GCC-4.9.3-2.25 | `--A` |
+| PSBLAS-ext | 1.0-4-GCC-4.9.3-2.25 | `--A` |
+| PyQt | 4.11.3-foss-2015g-Python-2.7.9</br>4.11.4-foss-2015g-Python-2.7.9 | `-S-`</br>`-S-` |
+| python | 3.4.2</br>2.7.5</br>2.7.6</br>3.3.2</br>3.3.5 | `--A`</br>`--A`</br>`--A`</br>`--A`</br>`--A` |
+| Python | 2.7.11-intel-2015b</br>2.7.10-GNU-4.9.3-2.25-bare</br>2.7.8-intel-2015b</br>3.5.2</br>2.7.9-foss-2015g</br>2.7.9-foss-2015b</br>3.5.2-intel-2017.00</br>3.5.1-intel-2017.00</br>2.7.9-GNU-5.1.0-2.25</br>2.7.9-intel-2015b</br>3.4.3-intel-2015b</br>2.7.9-gompi-2015e</br>2.7.9-ictce-7.3.5</br>2.7.11-GCC-4.9.3-2.25-bare</br>2.7.8-intel-2016.01</br>2.7.11-intel-2016a</br>2.7.9</br>2.7.9-intel-2016.01</br>3.5.1</br>2.7.11-foss-2016a</br>3.5.2-foss-2016a</br>3.5.1-intel-2016.01</br>2.7.10-GCC-4.9.3-2.25-bare</br>2.7.11-intel-2017.00 | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`USA`</br>`US-`</br>`USA`</br>`-S-`</br>`-S-`</br>`USA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-SA`</br>`-S-`</br>`US-`</br>`USA`</br>`-S-`</br>`-S-`</br>`-S-` |
+| python-meep | 1.4.2-intel-2015b-Python-2.7.9-Meep-1.3 | `-S-` |
+| PyYAML | 3.11-intel-2015b-Python-2.7.9 | `-S-` |
+| QCA | 2.1.0-foss-2015g | `-S-` |
+| QEMU | 2.1.2-foss-2015b</br>2.1.2-GCC-4.4.7-system</br>2.1.2-GCC-4.4.7-system-VDE2 | `U--`</br>`US-`</br>`US-` |
+| qemu | 2.1.2</br>2.1.0</br>2.1.2-vde2</br>2.1.0-vde2 | `--A`</br>`--A`</br>`--A`</br>`--A` |
+| QGIS | 2.12.3-foss-2015g | `-S-` |
+| Qt | 4.8.6-foss-2015g</br>4.8.6 | `-S-`</br>`-SA` |
+| QuantumESPRESSO | 5.4.0-intel-2017.00 | `-SA` |
+| Qwt | 6.1.2-foss-2015g | `-S-` |
+| R | 3.1.1-intel-2015b</br>3.1.1</br>3.2.3-intel-2016.01</br>3.2.3-foss-2015b</br>3.0.1 | `US-`</br>`--A`</br>`-S-`</br>`US-`</br>`--A` |
+| Racket | 6.1.1-GNU-5.1.0-2.25 | `-S-` |
+| racket | 6.0.1 | `--A` |
+| relion | 1.2</br>1.3 | `--A`</br>`--A` |
+| RELION | 1.3-intel-2015b | `-S-` |
+| renderproto | 0.11-intel-2015b</br>0.11 | `-S-`</br>`-SA` |
+| Rstudio | 0.97 | `--A` |
+| RStudio | 0.98.1103 | `-S-` |
+| ruby | 2.0.0-p247 | `--A` |
+| Ruby | 2.1.5-intel-2015b</br>2.3.1 | `-S-`</br>`-SA` |
+| S4MPLE | 1.0.0 | `-S-` |
+| samtools | 0.1.19 | `--A` |
+| SAMtools | 1.3-foss-2015g | `-S-` |
+| ScaLAPACK | 2.0.2-gompi-2015g-OpenBLAS-0.2.14-LAPACK-3.5.0</br>2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0</br>2.0.2-OpenBLAS-0.2.14-LAPACK-3.5.0</br>2.0.2-gompi-2015e-OpenBLAS-0.2.14-LAPACK-3.5.0</br>2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0</br>2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0 | `USA`</br>`USA`</br>`-S-`</br>`US-`</br>`US-`</br>`-SA` |
+| Scalasca | 2.3.1-intel-2015b | `-S-` |
+| scalasca2 | 2.0-icc-impi</br>2.0-gcc-openmpi | `--A`</br>`--A` |
+| ScientificPython | 2.9.4-intel-2015b-Python-2.7.9</br>2.9.4-intel-2015b-Python-2.7.11</br>2.9.4-intel-2016.01-Python-2.7.9 | `-SA`</br>`-SA`</br>`-SA` |
+| Scipion | 1.0.1-Java-8u112-intel-2017.00 | `-S-` |
+| scite | 3.4.3 | `--A` |
+| SCons | 2.3.6-foss-2015g-Python-2.7.9</br>2.3.6-Python-2.7.9 | `-SA`</br>`-S-` |
+| Score-P | 3.0-intel-2015b | `-S-` |
+| scorep | 1.2.3-gcc-openmpi</br>1.2.3-icc-impi | `--A`</br>`--A` |
+| SCOTCH | 5.1.12b_esmumps-foss-2015b</br>6.0.4-intel-2016.01</br>6.0.3-intel-2016.01</br>6.0.0_esmumps-intel-2015b</br>6.0.4-intel-2015b</br>6.0.3-intel-2015b | `-S-`</br>`-S-`</br>`-S-`</br>`US-`</br>`-S-`</br>`US-` |
+| SDE | 7.41.0 | `-S-` |
+| Serf | 1.3.8-foss-2015g | `-SA` |
+| settarg | 7.2.2 | `USA` |
+| Siesta | 4.1-b2-intel-2017.00 | `-S-` |
+| SIONlib | 1.6.1-intel-2015b-tools</br>1.6.1-tools | `-S-`</br>`-SA` |
+| SIP | 4.17-foss-2015g-Python-2.7.9</br>4.17-Python-2.7.9</br>4.16.4-foss-2015g-Python-2.7.9 | `-S-`</br>`-S-`</br>`-S-` |
+| slepc | 3.4.4-icc15-impi-mkl-dbg</br>3.4.4-icc15-impi-mkl-opt</br>3.7.2-icc16-impi5-mkl-dbg</br>3.7.2-icc16-impi5-mkl-opt | `--A`</br>`--A`</br>`--A`</br>`--A` |
+| snpEff | 3.6 | `--A` |
+| SnpEff | 4.1_G | `US-` |
+| SnuCL | 1.3.3-gompi-2015e | `-S-` |
+| Spark | 1.5.2 | `-S-` |
+| spatialindex | 1.8.5-foss-2015g | `-S-` |
+| SpatiaLite | 4.3.0a-foss-2015g | `-S-` |
+| spGPU | master-GCC-4.9.3-2.25 | `--A` |
+| SQLite | 3.8.8.1-foss-2016a | `--A` |
+| Subversion | 1.8.16-foss-2015g | `-SA` |
+| SuiteSparse | 4.4.6-intel-2015b-ParMETIS-4.0.3</br>4.5.3-intel-2017.00-METIS-5.1.0</br>4.4.5-intel-2015b-METIS-5.1.0</br>4.4.3-intel-2016.01-ParMETIS-4.0.3</br>4.4.3-intel-2015b-ParMETIS-4.0.3 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
+| SUMO | 0.27.1-foss-2015g</br>0.25.0-foss-2015g</br>0.26.0-foss-2015g | `-S-`</br>`-S-`</br>`-S-` |
+| SWIG | 2.0.12-intel-2015b-Python-2.7.9</br>2.0.12-Python-2.7.9</br>3.0.7-Python-2.7.9 | `-S-`</br>`-S-`</br>`-S-` |
+| sympy | 0.7.6.1-intel-2015b-Python-2.7.11</br>0.7.6-intel-2016.01-Python-2.7.9</br>0.7.6-intel-2015b-Python-2.7.9 | `-S-`</br>`-S-`</br>`-S-` |
+| Szip | 2.1-ictce-7.3.5</br>2.1-intel-2015b</br>2.1-intel-2017.00</br>2.1-intel-2016.01</br>2.1</br>2.1-foss-2016a</br>2.1-foss-2015b</br>2.1-foss-2015g | `-S-`</br>`USA`</br>`-S-`</br>`-SA`</br>`-SA`</br>`USA`</br>`US-`</br>`-S-` |
+| szip | 2.1 | `--A` |
+| tbb | 15.2.164</br>4.4.2.152</br>4.3.5.187</br>14.0.1</br>15.3.187</br>13.5.192 | `--A`</br>`USA`</br>`-S-`</br>`--A`</br>`--A`</br>`--A` |
+| Tcl | 8.6.3-foss-2016a | `--A` |
+| tcl | 8.5.15 | `--A` |
+| tcsh | 6.18.01-intel-2015b</br>6.19.00 | `US-`</br>`-SA` |
+| tk | 8.5.15 | `--A` |
+| Tk | 8.6.3-foss-2015b-no-X11 | `U--` |
+| totalview | 8.13</br>8.12 | `--A`</br>`--A` |
+| TotalView | 8.15.4-6-linux-x86-64 | `-S-` |
+| trilinos | 11.2.3-gcc-openmpi-mkl-opt</br>11.2.3-gcc-openmpi-mkl-dbg</br>11.2.3-icc | `--A`</br>`--A`</br>`--A` |
+| Trimmomatic | 0.35-Java-1.7.0_79 | `-S-` |
+| turbovnc | 1.2.2</br>1.2.3 | `--A`</br>`-S-` |
+| util-linux | 2.28-intel-2016a</br>2.26.1</br>2.26.1-foss-2015g | `--A`</br>`-SA`</br>`-S-` |
+| Valgrind | 3.11.0-foss-2015b</br>3.11.0-intel-2015b | `-S-`</br>`-S-` |
+| valgrind | 3.9.0-impi | `--A` |
+| Vampir | 9.0.0</br>8.5.0 | `-S-`</br>`-SA` |
+| vampir | 8.2 | `--A` |
+| VampirServer | 9.0.0-intel-2015b</br>8.5.0-intel-2015b | `-S-`</br>`-S-` |
+| VASP | 5.4.1-intel-2015b-24Jun15-UV</br>5.4.1-intel-2017.00-24Jun15</br>5.4.1-intel-2015b-24Jun15 | `U--`</br>`-SA`</br>`-SA` |
+| vde2 | 2.3.2 | `--A` |
+| VDE2 | 2.3.2-GCC-4.4.7-system | `US-` |
+| VirtualGL | 2.4.1 | `-S-` |
+| virtualgl | 2.4 | `--A` |
+| VisIt | 2.10.0 | `US-` |
+| VTune | 2016_update1 | `USA` |
+| vtune_xe | 2013.15</br>2015.3.0.403110 | `--A`</br>`--A` |
+| wien2k | 14.2</br>13.1 | `--A`</br>`--A` |
+| wine | 1.7.29 | `--A` |
+| Wine | 1.7.29-GNU-5.1.0-2.25</br>1.7.29-GCC-4.4.7-system | `-S-`</br>`-S-` |
+| xbitmaps | 1.1.1</br>1.1.1-intel-2015b</br>1.1.1-foss-2015g | `-SA`</br>`-S-`</br>`-S-` |
+| xcb-proto | 1.11-Python-2.7.9</br>1.11-foss-2015g-Python-2.7.9</br>1.10-Python-2.7.8</br>1.11-intel-2015b-Python-2.7.9</br>1.11 | `-SA`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-` |
+| xdrfile | 1.1.4-foss-2015g</br>1.1.4-intel-2015b</br>1.1.4-foss-2016a | `-SA`</br>`--A`</br>`--A` |
+| xextproto | 7.3.0-intel-2016a</br>7.3.0-foss-2015g</br>7.3.0-intel-2015b</br>7.3.0</br>7.3.0-foss-2016a | `-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`-S-` |
+| xineramaproto | 1.2.1-intel-2015b</br>1.2.1 | `-S-`</br>`-SA` |
+| xorg-macros | 1.17</br>1.17-foss-2015g</br>1.19.0-intel-2016a</br>1.19.0-foss-2016a | `-SA`</br>`-S-`</br>`-S-`</br>`-S-` |
+| xproto | 7.0.26-foss-2015g</br>7.0.28-foss-2016a</br>7.0.28-intel-2016a</br>7.0.28</br>7.0.26-intel-2015b</br>7.0.26 | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA` |
+| xtrans | 1.3.5-foss-2016a</br>1.3.4-intel-2015b</br>1.3.5-intel-2015b</br>1.3.5-intel-2016a</br>1.3.5</br>1.3.4</br>1.3.5-foss-2015g | `-S-`</br>`-S-`</br>`-S-`</br>`-S-`</br>`-SA`</br>`--A`</br>`-S-` |
+| XZ | 5.2.2</br>5.2.2-intel-2016.01</br>5.2.2-intel-2017.00</br>5.2.2-foss-2016a | `-SA`</br>`-S-`</br>`USA`</br>`USA` |
+| zlib | 1.2.5</br>1.2.8-GCC-4.9.3</br>1.2.8-GCC-4.4.7-system | `--A`</br>`--A`</br>`U--` |
diff --git a/docs.it4i/modules-salomon-uv.md b/docs.it4i/modules-salomon-uv.md
index 1391cefaf1e12d4023f416e4034484e3c73397aa..1ce81e07568cd84cf29d319647d9d25d10316f8a 100644
--- a/docs.it4i/modules-salomon-uv.md
+++ b/docs.it4i/modules-salomon-uv.md
@@ -2,164 +2,164 @@
## Bio
-|Module|Description|
-|--|--|
-|**[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/download.html)**|A quality control application for high throughput sequence data|
-|**[GATK](http://www.broadinstitute.org/gatk/)**|The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.|
-|**[SnpEff](http://snpeff.sourceforge.net/)**|Genetic variant annotation and effect prediction toolbox.|
+| Module | Description |
+| ----------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/download.html)** | A quality control application for high throughput sequence data |
+| **[GATK](http://www.broadinstitute.org/gatk/)** | The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. |
+| **[SnpEff](http://snpeff.sourceforge.net/)** | Genetic variant annotation and effect prediction toolbox. |
## Cae
-|Module|Description|
-|--|--|
-|**ANSYS**| |
-|**[OpenFOAM](http://www.openfoam.com/)**|OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.|
+| Module | Description |
+| ---------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| **ANSYS** | Â |
+| **[OpenFOAM](http://www.openfoam.com/)** | OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. |
## Chem
-|Module|Description|
-|--|--|
-|**[ABINIT](http://www.abinit.org/)**|Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.|
-|**[Libint](https://sourceforge.net/p/libint/)**|Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.|
-|**[libxc](http://www.tddft.org/programs/octopus/wiki/index.php/Libxc)**|Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.|
+| Module | Description |
+| ----------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| **[ABINIT](http://www.abinit.org/)** | Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT. |
+| **[Libint](https://sourceforge.net/p/libint/)** | Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. |
+| **[libxc](http://www.tddft.org/programs/octopus/wiki/index.php/Libxc)** | Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. |
## Compiler
-|Module|Description|
-|--|--|
-|**[GCC](http://gcc.gnu.org/)**|The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).|
-|**GCCcore**| |
-|**[icc](http://software.intel.com/en-us/intel-compilers/)**|C and C++ compiler from Intel|
-|**[ifort](http://software.intel.com/en-us/intel-compilers/)**|Fortran compiler from Intel|
-|**LLVM**| |
+| Module | Description |
+| ------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| **[GCC](http://gcc.gnu.org/)** | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). |
+| **GCCcore** | Â |
+| **[icc](http://software.intel.com/en-us/intel-compilers/)** | C and C++ compiler from Intel |
+| **[ifort](http://software.intel.com/en-us/intel-compilers/)** | Fortran compiler from Intel |
+| **LLVM** | Â |
## Data
-|Module|Description|
-|--|--|
-|**[GDAL](http://www.gdal.org/)**|GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.|
-|**[HDF5](http://www.hdfgroup.org/HDF5/)**|HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.|
-|**[netCDF](http://www.unidata.ucar.edu/software/netcdf/)**|NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.|
+| Module | Description |
+| ---------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[GDAL](http://www.gdal.org/)** | GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. |
+| **[HDF5](http://www.hdfgroup.org/HDF5/)** | HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. |
+| **[netCDF](http://www.unidata.ucar.edu/software/netcdf/)** | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. |
## Devel
-|Module|Description|
-|--|--|
-|**[Autoconf](http://www.gnu.org/software/autoconf/)**|Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.|
-|**[Automake](http://www.gnu.org/software/automake/automake.html)**|Automake: GNU Standards-compliant Makefile generator|
-|**[Autotools](http://autotools.io)**|This bundle collect the standard GNU build tools: Autoconf, Automake and libtool|
-|**[Boost](http://www.boost.org/)**|Boost provides free peer-reviewed portable C++ source libraries.|
-|**[CMake](http://www.cmake.org)**|CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.|
-|**[Doxygen](http://www.doxygen.org)**|Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.|
-|**[M4](http://www.gnu.org/software/m4/m4.html)**|GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.|
-|**[make](http://www.gnu.org/software/make/make.html)**|make-3.82: GNU version of make utility|
-|**[Maven](http://maven.apache.org/index.html)**|Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information.|
-|**[ncurses](http://www.gnu.org/software/ncurses/)**|The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.|
-|**[SQLite](http://www.sqlite.org/)**|SQLite: SQL Database Engine in a C Library|
+| Module | Description |
+| ------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[Autoconf](http://www.gnu.org/software/autoconf/)** | Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls. |
+| **[Automake](http://www.gnu.org/software/automake/automake.html)** | Automake: GNU Standards-compliant Makefile generator |
+| **[Autotools](http://autotools.io)** | This bundle collect the standard GNU build tools: Autoconf, Automake and libtool |
+| **[Boost](http://www.boost.org/)** | Boost provides free peer-reviewed portable C++ source libraries. |
+| **[CMake](http://www.cmake.org)** | CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. |
+| **[Doxygen](http://www.doxygen.org)** | Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. |
+| **[M4](http://www.gnu.org/software/m4/m4.html)** | GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. |
+| **[make](http://www.gnu.org/software/make/make.html)** | make-3.82: GNU version of make utility |
+| **[Maven](http://maven.apache.org/index.html)** | Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. |
+| **[ncurses](http://www.gnu.org/software/ncurses/)** | The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. |
+| **[SQLite](http://www.sqlite.org/)** | SQLite: SQL Database Engine in a C Library |
## Lang
-|Module|Description|
-|--|--|
-|**[Bison](http://www.gnu.org/software/bison)**|Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.|
-|**[flex](http://flex.sourceforge.net/)**|Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.|
-|**[Java](http://java.com/)**|Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.|
-|**[Lua](http://www.lua.org/)**|Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.|
-|**[NASM](http://www.nasm.us/)**|NASM: General-purpose x86 assembler|
-|**[Perl](http://www.perl.org/)**|Larry Wall's Practical Extraction and Report Language|
-|**[Python](http://python.org/)**|Python is a programming language that lets you work more quickly and integrate your systems more effectively.|
-|**[R](http://www.r-project.org/)**|R is a free software environment for statistical computing and graphics.|
-|**[Tcl](http://www.tcl.tk/)**|Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.|
+| Module | Description |
+| ---------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| **[Bison](http://www.gnu.org/software/bison)** | Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. |
+| **[flex](http://flex.sourceforge.net/)** | Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. |
+| **[Java](http://java.com/)** | Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. |
+| **[Lua](http://www.lua.org/)** | Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping. |
+| **[NASM](http://www.nasm.us/)** | NASM: General-purpose x86 assembler |
+| **[Perl](http://www.perl.org/)** | Larry Wall's Practical Extraction and Report Language |
+| **[Python](http://python.org/)** | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
+| **[R](http://www.r-project.org/)** | R is a free software environment for statistical computing and graphics. |
+| **[Tcl](http://www.tcl.tk/)** | Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. |
## Lib
-|Module|Description|
-|--|--|
-|**[libffi](http://sourceware.org/libffi/)**|The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.|
-|**[libjpeg-turbo](http://sourceforge.net/libjpeg-turbo/)**|libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.|
-|**[libpng](http://www.libpng.org/pub/png/libpng.html)**|libpng is the official PNG reference library|
-|**[libreadline](http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html)**|The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.|
-|**[libtool](http://www.gnu.org/software/libtool)**|GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.|
-|**[libxml2](http://xmlsoft.org/)**|Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).|
-|**[PROJ](http://trac.osgeo.org/proj/)**|Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates|
-|**[tbb](http://software.intel.com/en-us/articles/intel-tbb/)**|Intel Threading Building Blocks 4.0 (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms.|
-|**[zlib](http://www.zlib.net/)**|zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.|
+| Module | Description |
+| -------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[libffi](http://sourceware.org/libffi/)** | The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. |
+| **[libjpeg-turbo](http://sourceforge.net/libjpeg-turbo/)** | libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. |
+| **[libpng](http://www.libpng.org/pub/png/libpng.html)** | libpng is the official PNG reference library |
+| **[libreadline](http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html)** | The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands. |
+| **[libtool](http://www.gnu.org/software/libtool)** | GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. |
+| **[libxml2](http://xmlsoft.org/)** | Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). |
+| **[PROJ](http://trac.osgeo.org/proj/)** | Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates |
+| **[tbb](http://software.intel.com/en-us/articles/intel-tbb/)** | Intel Threading Building Blocks 4.0 (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms. |
+| **[zlib](http://www.zlib.net/)** | zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. |
## Math
-|Module|Description|
-|--|--|
-|**GMP**| |
-|**[SCOTCH](http://gforge.inria.fr/projects/scotch/)**|Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.|
+| Module | Description |
+| ----------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **GMP** | Â |
+| **[SCOTCH](http://gforge.inria.fr/projects/scotch/)** | Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. |
## Mpi
-|Module|Description|
-|--|--|
-|**[impi](http://software.intel.com/en-us/intel-mpi-library/)**|The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.|
-|**[OpenMPI](http://www.open-mpi.org/)**|The Open MPI Project is an open source MPI-2 implementation.|
+| Module | Description |
+| -------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[impi](http://software.intel.com/en-us/intel-mpi-library/)** | The Intel(R) MPI Library for Linux\* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification. |
+| **[OpenMPI](http://www.open-mpi.org/)** | The Open MPI Project is an open source MPI-2 implementation. |
## Numlib
-|Module|Description|
-|--|--|
-|**[FFTW](http://www.fftw.org)**|FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.|
-|**[imkl](http://software.intel.com/en-us/intel-mkl/)**|Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.|
-|**[OpenBLAS](http://xianyi.github.com/OpenBLAS/)**|OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.|
-|**[ScaLAPACK](http://www.netlib.org/scalapack/)**|The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.|
+| Module | Description |
+| ------------------------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[FFTW](http://www.fftw.org)** | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. |
+| **[imkl](http://software.intel.com/en-us/intel-mkl/)** | Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. |
+| **[OpenBLAS](http://xianyi.github.com/OpenBLAS/)** | OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. |
+| **[ScaLAPACK](http://www.netlib.org/scalapack/)** | The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. |
## Phys
-|Module|Description|
-|--|--|
-|**[VASP](http://www.vasp.at)**|The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.|
+| Module | Description |
+| ------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[VASP](http://www.vasp.at)** | The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. |
## System
-|Module|Description|
-|--|--|
-|**[hwloc](http://www.open-mpi.org/projects/hwloc/)**|The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.|
+| Module | Description |
+| ---------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[hwloc](http://www.open-mpi.org/projects/hwloc/)** | The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. |
## Toolchain
-|Module|Description|
-|--|--|
-|**[foss]((none))**|GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.|
-|**[GNU](http://www.gnu.org/software/)**|Compiler-only toolchain with GCC and binutils.|
-|**[gompi]((none))**|GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.|
-|**[iccifort](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/)**|Intel C, C++ and Fortran compilers|
-|**[iimpi](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/)**|Intel C/C++ and Fortran compilers, alongside Intel MPI.|
-|**[intel](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/)**|Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.|
-|**[PRACE](http://www.prace-ri.eu/PRACE-Common-Production)**|The PRACE Common Production Environment (PCPE) is a set of software tools and libraries that are planned to be available on all PRACE execution sites. The PCPE also defines a set of environment variables that try to make compilation on all sites as homogeneous and simple as possible.|
+| Module | Description |
+| ------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[foss]((none))** | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. |
+| **[GNU](http://www.gnu.org/software/)** | Compiler-only toolchain with GCC and binutils. |
+| **[gompi]((none))** | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. |
+| **[iccifort](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/)** | Intel C, C++ and Fortran compilers |
+| **[iimpi](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/)** | Intel C/C++ and Fortran compilers, alongside Intel MPI. |
+| **[intel](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/)** | Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL. |
+| **[PRACE](http://www.prace-ri.eu/PRACE-Common-Production)** | The PRACE Common Production Environment (PCPE) is a set of software tools and libraries that are planned to be available on all PRACE execution sites. The PCPE also defines a set of environment variables that try to make compilation on all sites as homogeneous and simple as possible. |
## Tools
-|Module|Description|
-|--|--|
-|**[Bash](http://www.gnu.org/software/bash)**|Bash is an sh-compatible command language interpreter that executes commands read from the standard input or from a file. Bash also incorporates useful features from the Korn and C shells (ksh and csh).|
-|**[binutils](http://directory.fsf.org/project/binutils/)**|binutils: GNU binary utilities|
-|**[bzip2](http://www.bzip.org/)**|bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.|
-|**[cURL](http://curl.haxx.se)**|libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.|
-|**[EasyBuild](http://hpcugent.github.com/easybuild/)**|EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.|
-|**[expat](http://expat.sourceforge.net/)**|Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags)|
-|**git**| |
-|**[gzip](http://www.gnu.org/software/gzip/)**|gzip (GNU zip) is a popular data compression program as a replacement for compress|
-|**MATLAB**| |
-|**[Mercurial](http://mercurial.selenic.com/)**|Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface.|
-|**[numactl](http://oss.sgi.com/projects/libnuma/)**|The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.|
-|**pigz**| |
-|**[QEMU](http://wiki.qemu.org/Main_Page)**|QEMU is a generic and open source machine emulator and virtualizer.|
-|**[Szip](http://www.hdfgroup.org/doc_resource/SZIP/)**|Szip compression software, providing lossless compression of scientific data|
-|**[tcsh](http://www.tcsh.org)**|Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax.|
-|**[VDE2](http://vde.sourceforge.net)**|VDE is an ethernet compliant virtual network that can be spawned over a set of physical computer over the Internet. VDE is part of virtualsquare project.|
-|**[VTune](http://software.intel.com/en-us/intel-vtune-amplifier-xe)**|Intel VTune Amplifier XE 2016 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.|
-|**XZ**| |
+| Module | Description |
+| --------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[Bash](http://www.gnu.org/software/bash)** | Bash is an sh-compatible command language interpreter that executes commands read from the standard input or from a file. Bash also incorporates useful features from the Korn and C shells (ksh and csh). |
+| **[binutils](http://directory.fsf.org/project/binutils/)** | binutils: GNU binary utilities |
+| **[bzip2](http://www.bzip.org/)** | bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression. |
+| **[cURL](http://curl.haxx.se)** | libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more. |
+| **[EasyBuild](http://hpcugent.github.com/easybuild/)** | EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. |
+| **[expat](http://expat.sourceforge.net/)** | Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) |
+| **git** | Â |
+| **[gzip](http://www.gnu.org/software/gzip/)** | gzip (GNU zip) is a popular data compression program as a replacement for compress |
+| **MATLAB** | Â |
+| **[Mercurial](http://mercurial.selenic.com/)** | Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. |
+| **[numactl](http://oss.sgi.com/projects/libnuma/)** | The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program. |
+| **pigz** | Â |
+| **[QEMU](http://wiki.qemu.org/Main_Page)** | QEMU is a generic and open source machine emulator and virtualizer. |
+| **[Szip](http://www.hdfgroup.org/doc_resource/SZIP/)** | Szip compression software, providing lossless compression of scientific data |
+| **[tcsh](http://www.tcsh.org)** | Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax. |
+| **[VDE2](http://vde.sourceforge.net)** | VDE is an ethernet compliant virtual network that can be spawned over a set of physical computer over the Internet. VDE is part of virtualsquare project. |
+| **[VTune](http://software.intel.com/en-us/intel-vtune-amplifier-xe)** | Intel VTune Amplifier XE 2016 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java. |
+| **XZ** | Â |
## Vis
-|Module|Description|
-|--|--|
-|**[gettext](http://www.gnu.org/software/gettext/)**|GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation|
-|**[GLib](http://www.gtk.org/)**|GLib is one of the base libraries of the GTK+ project|
-|**[Tk](http://www.tcl.tk/)**|Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.|
-|**[VisIt](https://wci.llnl.gov/simulation/computer-codes/visit)**|VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool|
+| Module | Description |
+| ----------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| **[gettext](http://www.gnu.org/software/gettext/)** | GNU \`gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation |
+| **[GLib](http://www.gtk.org/)** | GLib is one of the base libraries of the GTK+ project |
+| **[Tk](http://www.tcl.tk/)** | Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages. |
+| **[VisIt](https://wci.llnl.gov/simulation/computer-codes/visit)** | VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool |
diff --git a/docs.it4i/modules-salomon.md b/docs.it4i/modules-salomon.md
index 99b6d5e85aec6a23ad1531e43d1926917cc2e9d0..7ef6398e700ca885e1e969d5fd4051f2eecb883f 100644
--- a/docs.it4i/modules-salomon.md
+++ b/docs.it4i/modules-salomon.md
@@ -2,384 +2,384 @@
## Core
-|Module|Description|
-|--|--|
-|**lmod**| |
-|**settarg**| |
+| Module | Description |
+| ----------- | ----------- |
+| **lmod** | Â |
+| **settarg** | Â |
## Bio
-|Module|Description|
-|--|--|
-|**[almost](http://www-almost.ch.cam.ac.uk/site)**|all atom molecular simulation toolkit - is a fast and flexible molecular modeling environment that provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations.|
-|**[Amber](http://ambermd.org)**|A set of molecular mechanical force fields for the simulation of biomolecules|
-|**[BCFtools](http://www.htslib.org/)**|Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants|
-|**[BWA](http://bio-bwa.sourceforge.net/)**|Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.|
-|**[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)**|FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.|
-|**[GATK](http://www.broadinstitute.org/gatk/)**|The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.|
-|**[GROMACS](http://www.gromacs.org)**|GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.|
-|**[HTSlib](http://www.htslib.org/)**|A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix|
-|**[picard](http://sourceforge.net/projects/picard)**|A set of tools (in Java) for working with next generation sequencing data in the BAM format.|
-|**[PLUMED](http://www.plumed-code.org)**|PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.|
-|**[RELION](http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page)**|RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).|
-|**[SAMtools](http://www.htslib.org/)**|SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.|
-|**[SnpEff](http://snpeff.sourceforge.net/)**|Genetic variant annotation and effect prediction toolbox.|
-|**[Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic)**|Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.|
+| Module | Description |
+| ----------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| **[almost](http://www-almost.ch.cam.ac.uk/site)** | all atom molecular simulation toolkit - is a fast and flexible molecular modeling environment that provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations. |
+| **[Amber](http://ambermd.org)** | A set of molecular mechanical force fields for the simulation of biomolecules |
+| **[BCFtools](http://www.htslib.org/)** | Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants |
+| **[BWA](http://bio-bwa.sourceforge.net/)** | Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. |
+| **[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)** | FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline. |
+| **[GATK](http://www.broadinstitute.org/gatk/)** | The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. |
+| **[GROMACS](http://www.gromacs.org)** | GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. |
+| **[HTSlib](http://www.htslib.org/)** | A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix |
+| **[picard](http://sourceforge.net/projects/picard)** | A set of tools (in Java) for working with next generation sequencing data in the BAM format. |
+| **[PLUMED](http://www.plumed-code.org)** | PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. |
+| **[RELION](http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page)** | RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). |
+| **[SAMtools](http://www.htslib.org/)** | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. |
+| **[SnpEff](http://snpeff.sourceforge.net/)** | Genetic variant annotation and effect prediction toolbox. |
+| **[Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic)** | Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. |
## Cae
-|Module|Description|
-|--|--|
-|**Adams**| |
-|**ANSYS**| |
-|**COMSOL**| |
-|**Digimat**| |
-|**[FreeFem++](http://www.freefem.org)**|FreeFem++ is a partial differential equation solver. It has its own language. freefem scripts can solve multiphysics non linear systems in 2D and 3D. Problems involving PDE (2d, 3d) from several branches of physics such as fluid-structure interactions require interpolations of data on several meshes and their manipulation within one program. FreeFem++ includes a fast 2^d-tree-based interpolation algorithm and a language for the manipulation of data on multiple meshes (as a follow up of bamg (now a part of FreeFem++ ). FreeFem++ is written in C++ and the FreeFem++ language is a C++ idiom. It runs on Macs, Windows, Unix machines. FreeFem++ replaces the older freefem and freefem+.|
-|**HyperWorks**| |
-|**Marc**| |
-|**[OpenFOAM](http://www.openfoam.com/)**|OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.|
+| Module | Description |
+| ---------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **Adams** | Â |
+| **ANSYS** | Â |
+| **COMSOL** | Â |
+| **Digimat** | Â |
+| **[FreeFem++](http://www.freefem.org)** | FreeFem++ is a partial differential equation solver. It has its own language. freefem scripts can solve multiphysics non linear systems in 2D and 3D. Problems involving PDE (2d, 3d) from several branches of physics such as fluid-structure interactions require interpolations of data on several meshes and their manipulation within one program. FreeFem++ includes a fast 2^d-tree-based interpolation algorithm and a language for the manipulation of data on multiple meshes (as a follow up of bamg (now a part of FreeFem++ ). FreeFem++ is written in C++ and the FreeFem++ language is a C++ idiom. It runs on Macs, Windows, Unix machines. FreeFem++ replaces the older freefem and freefem+. |
+| **HyperWorks** | Â |
+| **Marc** | Â |
+| **[OpenFOAM](http://www.openfoam.com/)** | OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. |
## Chem
-|Module|Description|
-|--|--|
-|**[ABINIT](http://www.abinit.org/)**|Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.|
-|**[CP2K](http://www.cp2k.org/)**|CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.|
-|**[LAMMPS](http://lammps.sandia.gov)**|LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. Has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.|
-|**[libctl](http://ab-initio.mit.edu/libctl)**|libctl is a free Guile-based library implementing flexible control files for scientific simulations.|
-|**[Libint](https://sourceforge.net/p/libint/)**|Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.|
-|**[libxc](http://www.tddft.org/programs/octopus/wiki/index.php/Libxc)**|Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.|
-|**Molpro**| |
-|**[NAMD](http://www.ks.uiuc.edu/Research/namd/)**|NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.|
-|**[NWChem](http://www.nwchem-sw.org)**|NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity.|
-|**[ORCA](http://cec.mpg.de/forum/)**|ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.|
-|**[QuantumESPRESSO](http://www.pwscf.org/)**|Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).|
-|**[S4MPLE](http://infochim.u-strasbg.fr/spip.php?rubrique152)**|S4MPLE (Sampler For Multiple Protein-Ligand Entities) is a flexible molecular modeling tool, supporting empirical force field-driven conformational sampling and geometry optimization heuristics using a hybrid genetic algorithm (GA).|
-|**Scipion**| |
-|**[xdrfile](http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library)**|XTC library|
+| Module | Description |
+| ---------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[ABINIT](http://www.abinit.org/)** | Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT. |
+| **[CP2K](http://www.cp2k.org/)** | CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. |
+| **[LAMMPS](http://lammps.sandia.gov)** | LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. Has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. |
+| **[libctl](http://ab-initio.mit.edu/libctl)** | libctl is a free Guile-based library implementing flexible control files for scientific simulations. |
+| **[Libint](https://sourceforge.net/p/libint/)** | Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. |
+| **[libxc](http://www.tddft.org/programs/octopus/wiki/index.php/Libxc)** | Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. |
+| **Molpro** | Â |
+| **[NAMD](http://www.ks.uiuc.edu/Research/namd/)** | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. |
+| **[NWChem](http://www.nwchem-sw.org)** | NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. |
+| **[ORCA](http://cec.mpg.de/forum/)** | ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. |
+| **[QuantumESPRESSO](http://www.pwscf.org/)** | Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). |
+| **[S4MPLE](http://infochim.u-strasbg.fr/spip.php?rubrique152)** | S4MPLE (Sampler For Multiple Protein-Ligand Entities) is a flexible molecular modeling tool, supporting empirical force field-driven conformational sampling and geometry optimization heuristics using a hybrid genetic algorithm (GA). |
+| **Scipion** | Â |
+| **[xdrfile](http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library)** | XTC library |
## Compiler
-|Module|Description|
-|--|--|
-|**[BerkeleyUPC](http://upc.lbl.gov)**|The goal of the Berkeley UPC compiler group is to develop a portable, high performance implementation of UPC for large-scale multiprocessors, PC clusters, and clusters of shared memory multiprocessors.|
-|**[Clang](http://clang.llvm.org/)**|C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.|
-|**[GCC](http://gcc.gnu.org/)**|The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).|
-|**[GCCcore](http://gcc.gnu.org/)**|The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).|
-|**[icc](http://software.intel.com/en-us/intel-compilers/)**|C and C++ compiler from Intel|
-|**[ifort](http://software.intel.com/en-us/intel-compilers/)**|Fortran compiler from Intel|
-|**[LLVM](http://llvm.org/)**|The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator.|
-|**[OpenCoarrays](http://www.opencoarrays.org/)**|A transport layer for coarray Fortran compilers.|
-|**PGI**| |
+| Module | Description |
+| ------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[BerkeleyUPC](http://upc.lbl.gov)** | The goal of the Berkeley UPC compiler group is to develop a portable, high performance implementation of UPC for large-scale multiprocessors, PC clusters, and clusters of shared memory multiprocessors. |
+| **[Clang](http://clang.llvm.org/)** | C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. |
+| **[GCC](http://gcc.gnu.org/)** | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). |
+| **[GCCcore](http://gcc.gnu.org/)** | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). |
+| **[icc](http://software.intel.com/en-us/intel-compilers/)** | C and C++ compiler from Intel |
+| **[ifort](http://software.intel.com/en-us/intel-compilers/)** | Fortran compiler from Intel |
+| **[LLVM](http://llvm.org/)** | The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. |
+| **[OpenCoarrays](http://www.opencoarrays.org/)** | A transport layer for coarray Fortran compilers. |
+| **PGI** | Â |
## Data
-|Module|Description|
-|--|--|
-|**[GDAL](http://www.gdal.org/)**|GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.|
-|**[h5py](http://www.h5py.org/)**|HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.|
-|**[HDF5](http://www.hdfgroup.org/HDF5/)**|HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.|
-|**[netCDF](http://www.unidata.ucar.edu/software/netcdf/)**|NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.|
-|**[netCDF-Fortran](http://www.unidata.ucar.edu/software/netcdf/)**|NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.|
+| Module | Description |
+| ------------------------------------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[GDAL](http://www.gdal.org/)** | GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. |
+| **[h5py](http://www.h5py.org/)** | HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data. |
+| **[HDF5](http://www.hdfgroup.org/HDF5/)** | HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. |
+| **[netCDF](http://www.unidata.ucar.edu/software/netcdf/)** | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. |
+| **[netCDF-Fortran](http://www.unidata.ucar.edu/software/netcdf/)** | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. |
## Debugger
-|Module|Description|
-|--|--|
-|**aislinn**| |
-|**DDT**| |
-|**[Forge](http://www.allinea.com/products/develop-allinea-forge)**|Allinea Forge is the complete toolsuite for software development - with everything needed to debug, profile, optimize, edit and build C, C++ and FORTRAN applications on Linux for high performance - from single threads through to complex parallel HPC codes with MPI, OpenMP, threads or CUDA.|
-|**[PerformanceReports](http://www.allinea.com/products/allinea-performance-reports)**|Allinea Performance Reports are the most effective way to characterize and understand the performance of HPC application runs. One single-page HTML report elegantly answers a range of vital questions for any HPC site. - Is this application well-optimized for the system and the processors it is running on? - Does it benefit from running at this scale? - Are there I/O, networking or threading bottlenecks affecting performance? - Which hardware, software or configuration changes can we make to improve performance further. - How much energy did this application use?|
-|**TotalView**| |
-|**[Valgrind](http://valgrind.org/downloads/)**|Valgrind: Debugging and profiling tools|
+| Module | Description |
+| ------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **aislinn** | Â |
+| **DDT** | Â |
+| **[Forge](http://www.allinea.com/products/develop-allinea-forge)** | Allinea Forge is the complete toolsuite for software development - with everything needed to debug, profile, optimize, edit and build C, C++ and FORTRAN applications on Linux for high performance - from single threads through to complex parallel HPC codes with MPI, OpenMP, threads or CUDA. |
+| **[PerformanceReports](http://www.allinea.com/products/allinea-performance-reports)** | Allinea Performance Reports are the most effective way to characterize and understand the performance of HPC application runs. One single-page HTML report elegantly answers a range of vital questions for any HPC site. - Is this application well-optimized for the system and the processors it is running on? - Does it benefit from running at this scale? - Are there I/O, networking or threading bottlenecks affecting performance? - Which hardware, software or configuration changes can we make to improve performance further. - How much energy did this application use? |
+| **TotalView** | Â |
+| **[Valgrind](http://valgrind.org/downloads/)** | Valgrind: Debugging and profiling tools |
## Devel
-|Module|Description|
-|--|--|
-|**[ant](http://ant.apache.org/)**|Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.|
-|**[Autoconf](http://www.gnu.org/software/autoconf/)**|Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.|
-|**[Automake](http://www.gnu.org/software/automake/automake.html)**|Automake: GNU Standards-compliant Makefile generator|
-|**[Autotools](http://autotools.io)**|This bundle collect the standard GNU build tools: Autoconf, Automake and libtool|
-|**[Boost](http://www.boost.org/)**|Boost provides free peer-reviewed portable C++ source libraries.|
-|**[CMake](http://www.cmake.org)**|CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.|
-|**[Doxygen](http://www.doxygen.org)**|Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.|
-|**[fontsproto](http://www.freedesktop.org/wiki/Software/xlibs)**|X11 font extension wire protocol|
-|**[glproto](http://www.freedesktop.org/wiki/Software/xlibs)**|X protocol and ancillary headers|
-|**[gperf](http://www.gnu.org/software/gperf/)**|GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.|
-|**[guile](http://www.gnu.org/software/guile)**|Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system.|
-|**[JUnit](http://sourceforge.net/projects/junit)**|A programmer-oriented testing framework for Java.|
-|**[libSM](http://www.freedesktop.org/wiki/Software/xlibs)**|X11 Session Management library, which allows for applications to both manage sessions, and make use of session managers to save and restore their state for later use.|
-|**[M4](http://www.gnu.org/software/m4/m4.html)**|GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.|
-|**[make](http://www.gnu.org/software/make/make.html)**|make-3.82: GNU version of make utility|
-|**[makedepend](http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html)**|The makedepend package contains a C-preprocessor like utility to determine build-time dependencies.|
-|**[Maven](http://maven.apache.org/index.html)**|Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information.|
-|**[ncurses](http://www.gnu.org/software/ncurses/)**|The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.|
-|**[PCRE](http://www.pcre.org/)**|The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.|
-|**[PCRE2](http://www.pcre.org/)**|The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.|
-|**[pkg-config](http://www.freedesktop.org/wiki/Software/pkg-config/)**|pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries).|
-|**[python-meep](https://code.launchpad.net/python-meep)**|Python wrapper for the Meep FDTD solver.|
-|**[Qt](http://qt-project.org/)**|Qt is a comprehensive cross-platform C++ application framework.|
-|**[renderproto](http://www.freedesktop.org/wiki/Software/xlibs)**|Xrender protocol and ancillary headers|
-|**[SCons](http://www.scons.org/)**|SCons is a software construction tool.|
-|**[Spark](http://spark.apache.org)**|Spark is Hadoop MapReduce done in memory|
-|**[SQLite](http://www.sqlite.org/)**|SQLite: SQL Database Engine in a C Library|
-|**[SWIG](http://www.swig.org/)**|SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.|
-|**[xbitmaps](http://www.freedesktop.org/wiki/Software/xlibs)**|provides bitmaps for x|
-|**[xcb-proto](http://xcb.freedesktop.org/)**|The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.|
-|**[xextproto](http://www.freedesktop.org/wiki/Software/xlibs)**|XExtProto protocol headers.|
-|**[xineramaproto](http://www.freedesktop.org/wiki/Software/xlibs)**|X protocol and ancillary headers for xinerama|
-|**[xorg-macros](http://cgit.freedesktop.org/xorg/util/macros)**|X.org macros utilities.|
-|**[xproto](http://www.freedesktop.org/wiki/Software/xlibs)**|X protocol and ancillary headers|
-|**[xtrans](http://www.freedesktop.org/wiki/Software/xlibs)**|xtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet.|
+| Module | Description |
+| --------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[ant](http://ant.apache.org/)** | Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. |
+| **[Autoconf](http://www.gnu.org/software/autoconf/)** | Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls. |
+| **[Automake](http://www.gnu.org/software/automake/automake.html)** | Automake: GNU Standards-compliant Makefile generator |
+| **[Autotools](http://autotools.io)** | This bundle collect the standard GNU build tools: Autoconf, Automake and libtool |
+| **[Boost](http://www.boost.org/)** | Boost provides free peer-reviewed portable C++ source libraries. |
+| **[CMake](http://www.cmake.org)** | CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. |
+| **[Doxygen](http://www.doxygen.org)** | Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. |
+| **[fontsproto](http://www.freedesktop.org/wiki/Software/xlibs)** | X11 font extension wire protocol |
+| **[glproto](http://www.freedesktop.org/wiki/Software/xlibs)** | X protocol and ancillary headers |
+| **[gperf](http://www.gnu.org/software/gperf/)** | GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only. |
+| **[guile](http://www.gnu.org/software/guile)** | Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system. |
+| **[JUnit](http://sourceforge.net/projects/junit)** | A programmer-oriented testing framework for Java. |
+| **[libSM](http://www.freedesktop.org/wiki/Software/xlibs)** | X11 Session Management library, which allows for applications to both manage sessions, and make use of session managers to save and restore their state for later use. |
+| **[M4](http://www.gnu.org/software/m4/m4.html)** | GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. |
+| **[make](http://www.gnu.org/software/make/make.html)** | make-3.82: GNU version of make utility |
+| **[makedepend](http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html)** | The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. |
+| **[Maven](http://maven.apache.org/index.html)** | Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. |
+| **[ncurses](http://www.gnu.org/software/ncurses/)** | The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. |
+| **[PCRE](http://www.pcre.org/)** | The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. |
+| **[PCRE2](http://www.pcre.org/)** | The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. |
+| **[pkg-config](http://www.freedesktop.org/wiki/Software/pkg-config/)** | pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries). |
+| **[python-meep](https://code.launchpad.net/python-meep)** | Python wrapper for the Meep FDTD solver. |
+| **[Qt](http://qt-project.org/)** | Qt is a comprehensive cross-platform C++ application framework. |
+| **[renderproto](http://www.freedesktop.org/wiki/Software/xlibs)** | Xrender protocol and ancillary headers |
+| **[SCons](http://www.scons.org/)** | SCons is a software construction tool. |
+| **[Spark](http://spark.apache.org)** | Spark is Hadoop MapReduce done in memory |
+| **[SQLite](http://www.sqlite.org/)** | SQLite: SQL Database Engine in a C Library |
+| **[SWIG](http://www.swig.org/)** | SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. |
+| **[xbitmaps](http://www.freedesktop.org/wiki/Software/xlibs)** | provides bitmaps for x |
+| **[xcb-proto](http://xcb.freedesktop.org/)** | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. |
+| **[xextproto](http://www.freedesktop.org/wiki/Software/xlibs)** | XExtProto protocol headers. |
+| **[xineramaproto](http://www.freedesktop.org/wiki/Software/xlibs)** | X protocol and ancillary headers for xinerama |
+| **[xorg-macros](http://cgit.freedesktop.org/xorg/util/macros)** | X.org macros utilities. |
+| **[xproto](http://www.freedesktop.org/wiki/Software/xlibs)** | X protocol and ancillary headers |
+| **[xtrans](http://www.freedesktop.org/wiki/Software/xlibs)** | xtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. |
## Geo
-|Module|Description|
-|--|--|
-|**[DCW](http://gmt.soest.hawaii.edu/projects/gmt)**|country polygons for GMT|
-|**[GMT](http://gmt.soest.hawaii.edu/)**|GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools.|
-|**[PROJ_4](http://proj.osgeo.org)**|PROJ.4 - Cartographic Projections Library originally written by Gerald Evenden then of the USGS.|
+| Module | Description |
+| --------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[DCW](http://gmt.soest.hawaii.edu/projects/gmt)** | country polygons for GMT |
+| **[GMT](http://gmt.soest.hawaii.edu/)** | GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools. |
+| **[PROJ_4](http://proj.osgeo.org)** | PROJ.4 - Cartographic Projections Library originally written by Gerald Evenden then of the USGS. |
## Lang
-|Module|Description|
-|--|--|
-|**[Bison](http://www.gnu.org/software/bison)**|Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.|
-|**[byacc](http://invisible-island.net/byacc/byacc.html)**|Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular compiler.|
-|**[flex](http://flex.sourceforge.net/)**|Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.|
-|**[Java](http://java.com/)**|Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.|
-|**[libgdiplus](https://github.com/mono/libgdiplus)**|An Open Source implementation of the GDI+ API.|
-|**[Lua](http://www.lua.org/)**|Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.|
-|**[Mono](http://www.mono-project.com)**|Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.|
-|**[NASM](http://www.nasm.us/)**|NASM: General-purpose x86 assembler|
-|**[OpenCL-builder](https://software.intel.com/en-us/intel-opencl)**|OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software. This is builder (formerly runtime) package.|
-|**[OpenCL-runtime](https://software.intel.com/en-us/intel-opencl)**|OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software.|
-|**[Perl](http://www.perl.org/)**|Larry Wall's Practical Extraction and Report Language|
-|**[Python](http://python.org/)**|Python is a programming language that lets you work more quickly and integrate your systems more effectively.|
-|**[R](http://www.r-project.org/)**|R is a free software environment for statistical computing and graphics.|
-|**[Racket](http://racket-lang.org)**|Racket is a full-spectrum programming language. It goes beyond Lisp and Scheme with dialects that support objects, types, laziness, and more.|
-|**[Ruby](https://www.ruby-lang.org)**|Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.|
-|**[SIP](http://www.riverbankcomputing.com/software/sip/)**|SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.|
-|**[SnuCL](http://snucl.snu.ac.kr)**|An OpenCL Framework for Heterogeneous Clusters|
-|**[Tcl](http://www.tcl.tk/)**|Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.|
+| Module | Description |
+| ------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| **[Bison](http://www.gnu.org/software/bison)** | Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. |
+| **[byacc](http://invisible-island.net/byacc/byacc.html)** | Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular compiler. |
+| **[flex](http://flex.sourceforge.net/)** | Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. |
+| **[Java](http://java.com/)** | Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. |
+| **[libgdiplus](https://github.com/mono/libgdiplus)** | An Open Source implementation of the GDI+ API. |
+| **[Lua](http://www.lua.org/)** | Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping. |
+| **[Mono](http://www.mono-project.com)** | Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime. |
+| **[NASM](http://www.nasm.us/)** | NASM: General-purpose x86 assembler |
+| **[OpenCL-builder](https://software.intel.com/en-us/intel-opencl)** | OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software. This is builder (formerly runtime) package. |
+| **[OpenCL-runtime](https://software.intel.com/en-us/intel-opencl)** | OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software. |
+| **[Perl](http://www.perl.org/)** | Larry Wall's Practical Extraction and Report Language |
+| **[Python](http://python.org/)** | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
+| **[R](http://www.r-project.org/)** | R is a free software environment for statistical computing and graphics. |
+| **[Racket](http://racket-lang.org)** | Racket is a full-spectrum programming language. It goes beyond Lisp and Scheme with dialects that support objects, types, laziness, and more. |
+| **[Ruby](https://www.ruby-lang.org)** | Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. |
+| **[SIP](http://www.riverbankcomputing.com/software/sip/)** | SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries. |
+| **[SnuCL](http://snucl.snu.ac.kr)** | An OpenCL Framework for Heterogeneous Clusters |
+| **[Tcl](http://www.tcl.tk/)** | Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. |
## Lib
-|Module|Description|
-|--|--|
-|**[FOX](http://fox-toolkit.org)**|FOX is a C++ based Toolkit for developing Graphical User Interfaces easily and effectively. It offers a wide, and growing, collection of Controls, and provides state of the art facilities such as drag and drop, selection, as well as OpenGL widgets for 3D graphical manipulation.|
-|**[libdrm](http://dri.freedesktop.org)**|Direct Rendering Manager runtime library.|
-|**[libffi](http://sourceware.org/libffi/)**|The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.|
-|**[libfontenc](http://www.freedesktop.org/wiki/Software/xlibs/)**|X11 font encoding library|
-|**[libjpeg-turbo](http://sourceforge.net/libjpeg-turbo/)**|libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.|
-|**[libmatheval](http://www.gnu.org/software/libmatheval/)**|GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.|
-|**[libMesh](http://libmesh.github.io/)**|The libMesh library provides a framework for the numerical simulation of partial differential equations using arbitrary unstructured discretizations on serial and parallel platforms. A major goal of the library is to provide support for adaptive mesh refinement (AMR) computations in parallel while allowing a research scientist to focus on the physics they are modeling.|
-|**[libpng](http://www.libpng.org/pub/png/libpng.html)**|libpng is the official PNG reference library|
-|**[libpthread-stubs](http://xcb.freedesktop.org/)**|The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.|
-|**[libreadline](http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html)**|The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.|
-|**[LibTIFF](http://www.remotesensing.org/libtiff/)**|tiff: Library and tools for reading and writing TIFF data files|
-|**[libtool](http://www.gnu.org/software/libtool)**|GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.|
-|**[libunistring](http://www.gnu.org/software/libunistring/)**|This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.|
-|**[libunwind](http://www.nongnu.org/libunwind/)**|The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications|
-|**[libxcb](http://xcb.freedesktop.org/)**|The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.|
-|**[libxml2](http://xmlsoft.org/)**|Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).|
-|**libxslt**| |
-|**libyaml**| |
-|**lxml**| |
-|**[OpenCoarrays](http://www.opencoarrays.org)**|OpenCoarrays is an open-source software project for developing, porting and tuning transport layers that support coarray Fortran compilers.|
-|**[PROJ](http://trac.osgeo.org/proj/)**|Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates|
-|**PyYAML**| |
-|**[QCA](http://delta.affinix.com/qca/)**|QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers|
-|**[QGIS](http://www.qgis.org)**|A Free and Open Source Geographic Information System|
-|**[Qwt](http://qwt.sourceforge.net/index.html)**|The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Beside a framework for 2D plots it provides scales, sliders, dials, compasses, thermometers, wheels and knobs to control or display values, arrays, or ranges of type double.|
-|**[SIONlib](http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html)**|SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version.|
-|**[spatialindex](https://libspatialindex.github.io/index.html)**|The purpose of this library is to provide: * An extensible framework that will support robust spatial indexing methods. * Support for sophisticated spatial queries. Range, point location, nearest neighbor and k-nearest neighbor as well as parametric queries (defined by spatial constraints) should be easy to deploy and run. * Easy to use interfaces for inserting, deleting and updating information.|
-|**[SpatiaLite](https://www.gaia-gis.it/fossil/libspatialite/index)**|SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities.|
-|**[tbb](http://software.intel.com/en-us/articles/intel-tbb/)**|Intel Threading Building Blocks 4.0 (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms.|
-|**[zlib](http://www.zlib.net/)**|zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.|
+| Module | Description |
+| ------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[FOX](http://fox-toolkit.org)** | FOX is a C++ based Toolkit for developing Graphical User Interfaces easily and effectively. It offers a wide, and growing, collection of Controls, and provides state of the art facilities such as drag and drop, selection, as well as OpenGL widgets for 3D graphical manipulation. |
+| **[libdrm](http://dri.freedesktop.org)** | Direct Rendering Manager runtime library. |
+| **[libffi](http://sourceware.org/libffi/)** | The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. |
+| **[libfontenc](http://www.freedesktop.org/wiki/Software/xlibs/)** | X11 font encoding library |
+| **[libjpeg-turbo](http://sourceforge.net/libjpeg-turbo/)** | libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. |
+| **[libmatheval](http://www.gnu.org/software/libmatheval/)** | GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. |
+| **[libMesh](http://libmesh.github.io/)** | The libMesh library provides a framework for the numerical simulation of partial differential equations using arbitrary unstructured discretizations on serial and parallel platforms. A major goal of the library is to provide support for adaptive mesh refinement (AMR) computations in parallel while allowing a research scientist to focus on the physics they are modeling. |
+| **[libpng](http://www.libpng.org/pub/png/libpng.html)** | libpng is the official PNG reference library |
+| **[libpthread-stubs](http://xcb.freedesktop.org/)** | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. |
+| **[libreadline](http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html)** | The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands. |
+| **[LibTIFF](http://www.remotesensing.org/libtiff/)** | tiff: Library and tools for reading and writing TIFF data files |
+| **[libtool](http://www.gnu.org/software/libtool)** | GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. |
+| **[libunistring](http://www.gnu.org/software/libunistring/)** | This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard. |
+| **[libunwind](http://www.nongnu.org/libunwind/)** | The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications |
+| **[libxcb](http://xcb.freedesktop.org/)** | The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. |
+| **[libxml2](http://xmlsoft.org/)** | Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). |
+| **libxslt** | Â |
+| **libyaml** | Â |
+| **lxml** | Â |
+| **[OpenCoarrays](http://www.opencoarrays.org)** | OpenCoarrays is an open-source software project for developing, porting and tuning transport layers that support coarray Fortran compilers. |
+| **[PROJ](http://trac.osgeo.org/proj/)** | Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates |
+| **PyYAML** | Â |
+| **[QCA](http://delta.affinix.com/qca/)** | QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers |
+| **[QGIS](http://www.qgis.org)** | A Free and Open Source Geographic Information System |
+| **[Qwt](http://qwt.sourceforge.net/index.html)** | The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Beside a framework for 2D plots it provides scales, sliders, dials, compasses, thermometers, wheels and knobs to control or display values, arrays, or ranges of type double. |
+| **[SIONlib](http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html)** | SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version. |
+| **[spatialindex](https://libspatialindex.github.io/index.html)** | The purpose of this library is to provide: _ An extensible framework that will support robust spatial indexing methods. _ Support for sophisticated spatial queries. Range, point location, nearest neighbor and k-nearest neighbor as well as parametric queries (defined by spatial constraints) should be easy to deploy and run. \* Easy to use interfaces for inserting, deleting and updating information. |
+| **[SpatiaLite](https://www.gaia-gis.it/fossil/libspatialite/index)** | SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities. |
+| **[tbb](http://software.intel.com/en-us/articles/intel-tbb/)** | Intel Threading Building Blocks 4.0 (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms. |
+| **[zlib](http://www.zlib.net/)** | zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. |
## Math
-|Module|Description|
-|--|--|
-|**[FIAT](https://bitbucket.org/fenics-project/fiat)**|The FInite element Automatic Tabulator FIAT supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.|
-|**[GEOS](http://trac.osgeo.org/geos)**|GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)|
-|**[GMP](http://gmplib.org/)**|GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.|
-|**[Harminv](http://ab-initio.mit.edu/wiki/index.php/Harminv)**|Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.|
-|**[ISL](http://isl.gforge.inria.fr/)**|isl is a library for manipulating sets and relations of integer points bounded by linear constraints.|
-|**[METIS](http://glaros.dtc.umn.edu/gkhome/metis/metis/overview)**|METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.|
-|**MPC**| |
-|**[MPFR](http://www.mpfr.org)**|The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.|
-|**[numpy](http://www.numpy.org)**|NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.|
-|**[Octave](http://www.gnu.org/software/octave/)**|GNU Octave is a high-level interpreted language, primarily intended for numerical computations.|
-|**[ParMETIS](http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview)**|ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.|
-|**[ScientificPython](https://sourcesup.cru.fr/projects/scientific-py/)**|ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization.|
-|**[SCOTCH](http://gforge.inria.fr/projects/scotch/)**|Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.|
-|**[sympy](http://sympy.org/)**|SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries.|
+| Module | Description |
+| ------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[FIAT](https://bitbucket.org/fenics-project/fiat)** | The FInite element Automatic Tabulator FIAT supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes. |
+| **[GEOS](http://trac.osgeo.org/geos)** | GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) |
+| **[GMP](http://gmplib.org/)** | GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. |
+| **[Harminv](http://ab-initio.mit.edu/wiki/index.php/Harminv)** | Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids. |
+| **[ISL](http://isl.gforge.inria.fr/)** | isl is a library for manipulating sets and relations of integer points bounded by linear constraints. |
+| **[METIS](http://glaros.dtc.umn.edu/gkhome/metis/metis/overview)** | METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. |
+| **MPC** | Â |
+| **[MPFR](http://www.mpfr.org)** | The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. |
+| **[numpy](http://www.numpy.org)** | NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. |
+| **[Octave](http://www.gnu.org/software/octave/)** | GNU Octave is a high-level interpreted language, primarily intended for numerical computations. |
+| **[ParMETIS](http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview)** | ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. |
+| **[ScientificPython](https://sourcesup.cru.fr/projects/scientific-py/)** | ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization. |
+| **[SCOTCH](http://gforge.inria.fr/projects/scotch/)** | Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. |
+| **[sympy](http://sympy.org/)** | SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries. |
## Mpi
-|Module|Description|
-|--|--|
-|**[impi](http://software.intel.com/en-us/intel-mpi-library/)**|The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.|
-|**[MPI_NET](http://www.osl.iu.edu/research/mpi.net/)**|MPI.NET is a high-performance, easy-to-use implementation of the Message Passing Interface (MPI) for Microsoft's .NET environment|
-|**[MPICH](http://www.mpich.org/)**|MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).|
-|**mpt**| |
-|**[MVAPICH2](http://mvapich.cse.ohio-state.edu/overview/mvapich2/)**|This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH.|
-|**[OpenMPI](http://www.open-mpi.org/)**|The Open MPI Project is an open source MPI-2 implementation.|
+| Module | Description |
+| -------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[impi](http://software.intel.com/en-us/intel-mpi-library/)** | The Intel(R) MPI Library for Linux\* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification. |
+| **[MPI_NET](http://www.osl.iu.edu/research/mpi.net/)** | MPI.NET is a high-performance, easy-to-use implementation of the Message Passing Interface (MPI) for Microsoft's .NET environment |
+| **[MPICH](http://www.mpich.org/)** | MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices). |
+| **mpt** | Â |
+| **[MVAPICH2](http://mvapich.cse.ohio-state.edu/overview/mvapich2/)** | This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH. |
+| **[OpenMPI](http://www.open-mpi.org/)** | The Open MPI Project is an open source MPI-2 implementation. |
## Numlib
-|Module|Description|
-|--|--|
-|**[Armadillo](http://arma.sourceforge.net/)**|Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.|
-|**[arpack-ng](http://forge.scilab.org/index.php/p/arpack-ng/)**|ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.|
-|**[FFTW](http://www.fftw.org)**|FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.|
-|**[GSL](http://www.gnu.org/software/gsl/)**|The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.|
-|**[Hypre](https://computation.llnl.gov/casc/linear_solvers/sls_hypre.html)**|Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.|
-|**[imkl](http://software.intel.com/en-us/intel-mkl/)**|Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.|
-|**[LAPACKE](http://www.netlib.org/lapack/lapacke.html)**|LAPACKE C Interface to LAPACK header files and library|
-|**[OpenBLAS](http://xianyi.github.com/OpenBLAS/)**|OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.|
-|**[PETSc](http://www.mcs.anl.gov/petsc)**|PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.|
-|**[ScaLAPACK](http://www.netlib.org/scalapack/)**|The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.|
-|**[SuiteSparse](http://www.cise.ufl.edu/research/sparse/SuiteSparse/)**|SuiteSparse is a collection of libraries manipulate sparse matrices.|
+| Module | Description |
+| ---------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[Armadillo](http://arma.sourceforge.net/)** | Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. |
+| **[arpack-ng](http://forge.scilab.org/index.php/p/arpack-ng/)** | ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. |
+| **[FFTW](http://www.fftw.org)** | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. |
+| **[GSL](http://www.gnu.org/software/gsl/)** | The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. |
+| **[Hypre](https://computation.llnl.gov/casc/linear_solvers/sls_hypre.html)** | Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences. |
+| **[imkl](http://software.intel.com/en-us/intel-mkl/)** | Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. |
+| **[LAPACKE](http://www.netlib.org/lapack/lapacke.html)** | LAPACKE C Interface to LAPACK header files and library |
+| **[OpenBLAS](http://xianyi.github.com/OpenBLAS/)** | OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. |
+| **[PETSc](http://www.mcs.anl.gov/petsc)** | PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. |
+| **[ScaLAPACK](http://www.netlib.org/scalapack/)** | The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. |
+| **[SuiteSparse](http://www.cise.ufl.edu/research/sparse/SuiteSparse/)** | SuiteSparse is a collection of libraries manipulate sparse matrices. |
## Perf
-|Module|Description|
-|--|--|
-|**[Advisor](https://software.intel.com/intel-advisor-xe)**|Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance “dies” - Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain|
-|**[Cube](http://www.scalasca.org/software/cube-4.x/download.html)**|Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity.|
-|**[ipp](http://software.intel.com/en-us/articles/intel-ipp/)**|Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms.|
-|**MAP**| |
-|**[OPARI2](http://www.score-p.org)**|OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface.|
-|**[OTF2](http://www.score-p.org)**|The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library. It will become the new standard trace format for Scalasca, Vampir, and Tau and is open for other tools.|
-|**[PAPI](http://icl.cs.utk.edu/projects/papi/)**|PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack.|
-|**perfboost**| |
-|**perfcatcher**| |
-|**PerfReports**| |
-|**perfsuite**| |
-|**[Vampir](http://www.vampir.eu)**|The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.|
-|**[VampirServer](http://www.vampir.eu)**|The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.|
+| Module | Description |
+| ------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[Advisor](https://software.intel.com/intel-advisor-xe)** | Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance “dies” - Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain |
+| **[Cube](http://www.scalasca.org/software/cube-4.x/download.html)** | Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. |
+| **[ipp](http://software.intel.com/en-us/articles/intel-ipp/)** | Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms. |
+| **MAP** | Â |
+| **[OPARI2](http://www.score-p.org)** | OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface. |
+| **[OTF2](http://www.score-p.org)** | The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library. It will become the new standard trace format for Scalasca, Vampir, and Tau and is open for other tools. |
+| **[PAPI](http://icl.cs.utk.edu/projects/papi/)** | PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack. |
+| **perfboost** | Â |
+| **perfcatcher** | Â |
+| **PerfReports** | Â |
+| **perfsuite** | Â |
+| **[Vampir](http://www.vampir.eu)** | The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data. |
+| **[VampirServer](http://www.vampir.eu)** | The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data. |
## Phys
-|Module|Description|
-|--|--|
-|**[Meep](http://ab-initio.mit.edu/wiki/index.php/Meep)**|Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems.|
-|**[phono3py](http://python.org/)**|Python is a programming language that lets you work more quickly and integrate your systems more effectively.|
-|**[phonopy](http://python.org/)**|Python is a programming language that lets you work more quickly and integrate your systems more effectively.|
-|**Siesta**| |
-|**VASP**| |
+| Module | Description |
+| -------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[Meep](http://ab-initio.mit.edu/wiki/index.php/Meep)** | Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems. |
+| **[phono3py](http://python.org/)** | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
+| **[phonopy](http://python.org/)** | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
+| **Siesta** | Â |
+| **VASP** | Â |
## System
-|Module|Description|
-|--|--|
-|**[eudev](https://wiki.gentoo.org/wiki/Project:Eudev)**|eudev is a fork of systemd-udev with the goal of obtaining better compatibility with existing software such as OpenRC and Upstart, older kernels, various toolchains and anything else required by users and various distributions.|
-|**[hwloc](http://www.open-mpi.org/projects/hwloc/)**|The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.|
-|**[libpciaccess](http://cgit.freedesktop.org/xorg/lib/libpciaccess/)**|Generic PCI access library.|
+| Module | Description |
+| ---------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[eudev](https://wiki.gentoo.org/wiki/Project:Eudev)** | eudev is a fork of systemd-udev with the goal of obtaining better compatibility with existing software such as OpenRC and Upstart, older kernels, various toolchains and anything else required by users and various distributions. |
+| **[hwloc](http://www.open-mpi.org/projects/hwloc/)** | The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. |
+| **[libpciaccess](http://cgit.freedesktop.org/xorg/lib/libpciaccess/)** | Generic PCI access library. |
## Toolchain
-|Module|Description|
-|--|--|
-|**[foss]((none))**|GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.|
-|**[GNU](http://www.gnu.org/software/)**|Compiler-only toolchain with GCC and binutils.|
-|**[gompi]((none))**|GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.|
-|**[iccifort](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/)**|Intel C, C++ and Fortran compilers|
-|**[ictce](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/)**|Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.|
-|**[iimpi](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/)**|Intel C/C++ and Fortran compilers, alongside Intel MPI.|
-|**[intel](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/)**|Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.|
-|**[PRACE](http://www.prace-ri.eu/PRACE-Common-Production)**|The PRACE Common Production Environment (PCPE) is a set of software tools and libraries that are planned to be available on all PRACE execution sites. The PCPE also defines a set of environment variables that try to make compilation on all sites as homogeneous and simple as possible.|
-|**[prace](http://www.prace-ri.eu/PRACE-Common-Production)**|**** PRACE Common Production Environment (PCPE) **** Initialisation of the PRACE common production environment. This allows you to assume that the following tools/libraries are available by default in your PATH/environment. * Fortran, C, C++ Compilers * MPI * BLAS, LAPACK, BLACS, ScaLAPACK * FFTW * HDF5, NetCDF The compiler commands on are: * mpif90 - Fortran compiler * mpicc - C compiler * mpicxx - C++ compiler For more information on the PCPE please see the documentation at: http://www.prace-ri.eu/PRACE-Common-Production For help using this system, please see Local User Guide available at: http://prace-ri.eu/Best-Practice-Guide-Anselm-HTML|
+| Module | Description |
+| ------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[foss]((none))** | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. |
+| **[GNU](http://www.gnu.org/software/)** | Compiler-only toolchain with GCC and binutils. |
+| **[gompi]((none))** | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. |
+| **[iccifort](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/)** | Intel C, C++ and Fortran compilers |
+| **[ictce](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/)** | Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL. |
+| **[iimpi](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/)** | Intel C/C++ and Fortran compilers, alongside Intel MPI. |
+| **[intel](http://software.intel.com/en-us/intel-cluster-toolkit-compiler/)** | Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL. |
+| **[PRACE](http://www.prace-ri.eu/PRACE-Common-Production)** | The PRACE Common Production Environment (PCPE) is a set of software tools and libraries that are planned to be available on all PRACE execution sites. The PCPE also defines a set of environment variables that try to make compilation on all sites as homogeneous and simple as possible. |
+| **[prace](http://www.prace-ri.eu/PRACE-Common-Production)** | \***\* PRACE Common Production Environment (PCPE) \*\*** Initialisation of the PRACE common production environment. This allows you to assume that the following tools/libraries are available by default in your PATH/environment. _ Fortran, C, C++ Compilers _ MPI _ BLAS, LAPACK, BLACS, ScaLAPACK _ FFTW _ HDF5, NetCDF The compiler commands on are: _ mpif90 - Fortran compiler _ mpicc - C compiler _ mpicxx - C++ compiler For more information on the PCPE please see the documentation at: <http://www.prace-ri.eu/PRACE-Common-Production> For help using this system, please see Local User Guide available at: <http://prace-ri.eu/Best-Practice-Guide-Anselm-HTML> |
## Tools
-|Module|Description|
-|--|--|
-|**[APR](http://apr.apache.org/)**|Apache Portable Runtime (APR) libraries.|
-|**[APR-util](http://apr.apache.org/)**|Apache Portable Runtime (APR) util libraries.|
-|**[Bash](http://www.gnu.org/software/bash)**|Bash is an sh-compatible command language interpreter that executes commands read from the standard input or from a file. Bash also incorporates useful features from the Korn and C shells (ksh and csh).|
-|**[binutils](http://directory.fsf.org/project/binutils/)**|binutils: GNU binary utilities|
-|**[bzip2](http://www.bzip.org/)**|bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.|
-|**[cURL](http://curl.haxx.se)**|libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.|
-|**[EasyBuild](http://hpcugent.github.com/easybuild/)**|EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.|
-|**[expat](http://expat.sourceforge.net/)**|Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags)|
-|**[git](http://git-scm.com/)**|Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.|
-|**globus**| |
-|**[gzip](http://www.gnu.org/software/gzip/)**|gzip (GNU zip) is a popular data compression program as a replacement for compress|
-|**[HPL](http://www.netlib.org/benchmark/hpl/)**|HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.|
-|**[Inspector](http://software.intel.com/en-us/intel-inspector-xe)**|Intel Inspector XE 2013 is an easy to use memory error checker and thread checker for serial and parallel applications|
-|**[itac](http://software.intel.com/en-us/intel-trace-analyzer/)**|The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays.|
-|**[JOE](http://joe-editor.sourceforge.net)**|JOE is a full featured terminal-based screen editor which is distributed under the GNU General Public License (GPL)|
-|**[likwid](https://github.com/RRZE-HPC/likwid)**|Toolsuite of command line applications for performance oriented programmers|
-|**[Lmod](http://sourceforge.net/projects/lmod/)**|Lmod is a Lua based module system. Modules allow for dynamic modification of a user's environment under Unix systems. See www.tacc.utexas.edu/tacc-projects/lmod for a complete description. Lmod is a new implementation that easily handles the MODULEPATH Hierarchical problem. It is drop-in replacement for TCL/C modules and reads TCL modulefiles directly.|
-|**MATLAB**| |
-|**[Mercurial](http://mercurial.selenic.com/)**|Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface.|
-|**[MIKE](http://www.mikepoweredbydhi.com)**|MIKE Powered by DHI is a part of DHI, the global organisation dedicated to solving challenges in water environments worldwide.|
-|**[numactl](http://oss.sgi.com/projects/libnuma/)**|The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.|
-|**[PAPI](http://icl.cs.utk.edu/projects/papi/)**|PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack.|
-|**[parallel](http://savannah.gnu.org/projects/parallel/)**|parallel: Build and execute shell commands in parallel|
-|**pigz**| |
-|**[QEMU](http://wiki.qemu.org/Main_Page)**|QEMU is a generic and open source machine emulator and virtualizer.|
-|**[RStudio](https://www.rstudio.com)**|RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.|
-|**Scalasca**| |
-|**Score-P**| |
-|**[SDE](https://software.intel.com/en-us/articles/intel-software-development-emulator)**|Intel Software Development Emulator is a pintool that enables the development of applications using instruction set extensions that are not currently implemented in hardware.|
-|**[Serf](http://serf.apache.org/)**|The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library|
-|**[Subversion](http://subversion.apache.org/)**|Subversion is an open source version control system.|
-|**[Szip](http://www.hdfgroup.org/doc_resource/SZIP/)**|Szip compression software, providing lossless compression of scientific data|
-|**[tcsh](http://www.tcsh.org)**|Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax.|
-|**[turbovnc](http://www.turbovnc.org)**|TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide peak performance for 3D and video workloads.|
-|**[util-linux](http://www.kernel.org/pub/linux/utils/util-linux)**|Set of Linux utilities|
-|**[VDE2](http://vde.sourceforge.net)**|VDE is an ethernet compliant virtual network that can be spawned over a set of physical computer over the Internet. VDE is part of virtualsquare project.|
-|**[VirtualGL](http://www.virtualgl.org)**|VirtualGL is an open source toolkit that gives any Unix or Linux remote display software the ability to run OpenGL applications with full 3D hardware acceleration.|
-|**[VTune](http://software.intel.com/en-us/intel-vtune-amplifier-xe)**|Intel VTune Amplifier XE 2016 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.|
-|**[Wine](https://www.winehq.org)**|Wine (originally an acronym for "Wine Is Not an Emulator") is a compatibility layer capable of running Windows applications on several POSIX-compliant operating systems, such as Linux, Mac OSX, & BSD.|
-|**[XZ](http://tukaani.org/xz/)**|xz: XZ utilities|
+| Module | Description |
+| ---------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[APR](http://apr.apache.org/)** | Apache Portable Runtime (APR) libraries. |
+| **[APR-util](http://apr.apache.org/)** | Apache Portable Runtime (APR) util libraries. |
+| **[Bash](http://www.gnu.org/software/bash)** | Bash is an sh-compatible command language interpreter that executes commands read from the standard input or from a file. Bash also incorporates useful features from the Korn and C shells (ksh and csh). |
+| **[binutils](http://directory.fsf.org/project/binutils/)** | binutils: GNU binary utilities |
+| **[bzip2](http://www.bzip.org/)** | bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression. |
+| **[cURL](http://curl.haxx.se)** | libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more. |
+| **[EasyBuild](http://hpcugent.github.com/easybuild/)** | EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. |
+| **[expat](http://expat.sourceforge.net/)** | Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) |
+| **[git](http://git-scm.com/)** | Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. |
+| **globus** | Â |
+| **[gzip](http://www.gnu.org/software/gzip/)** | gzip (GNU zip) is a popular data compression program as a replacement for compress |
+| **[HPL](http://www.netlib.org/benchmark/hpl/)** | HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark. |
+| **[Inspector](http://software.intel.com/en-us/intel-inspector-xe)** | Intel Inspector XE 2013 is an easy to use memory error checker and thread checker for serial and parallel applications |
+| **[itac](http://software.intel.com/en-us/intel-trace-analyzer/)** | The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. |
+| **[JOE](http://joe-editor.sourceforge.net)** | JOE is a full featured terminal-based screen editor which is distributed under the GNU General Public License (GPL) |
+| **[likwid](https://github.com/RRZE-HPC/likwid)** | Toolsuite of command line applications for performance oriented programmers |
+| **[Lmod](http://sourceforge.net/projects/lmod/)** | Lmod is a Lua based module system. Modules allow for dynamic modification of a user's environment under Unix systems. See www.tacc.utexas.edu/tacc-projects/lmod for a complete description. Lmod is a new implementation that easily handles the MODULEPATH Hierarchical problem. It is drop-in replacement for TCL/C modules and reads TCL modulefiles directly. |
+| **MATLAB** | Â |
+| **[Mercurial](http://mercurial.selenic.com/)** | Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. |
+| **[MIKE](http://www.mikepoweredbydhi.com)** | MIKE Powered by DHI is a part of DHI, the global organisation dedicated to solving challenges in water environments worldwide. |
+| **[numactl](http://oss.sgi.com/projects/libnuma/)** | The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program. |
+| **[PAPI](http://icl.cs.utk.edu/projects/papi/)** | PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack. |
+| **[parallel](http://savannah.gnu.org/projects/parallel/)** | parallel: Build and execute shell commands in parallel |
+| **pigz** | Â |
+| **[QEMU](http://wiki.qemu.org/Main_Page)** | QEMU is a generic and open source machine emulator and virtualizer. |
+| **[RStudio](https://www.rstudio.com)** | RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. |
+| **Scalasca** | Â |
+| **Score-P** | Â |
+| **[SDE](https://software.intel.com/en-us/articles/intel-software-development-emulator)** | Intel Software Development Emulator is a pintool that enables the development of applications using instruction set extensions that are not currently implemented in hardware. |
+| **[Serf](http://serf.apache.org/)** | The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library |
+| **[Subversion](http://subversion.apache.org/)** | Subversion is an open source version control system. |
+| **[Szip](http://www.hdfgroup.org/doc_resource/SZIP/)** | Szip compression software, providing lossless compression of scientific data |
+| **[tcsh](http://www.tcsh.org)** | Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax. |
+| **[turbovnc](http://www.turbovnc.org)** | TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide peak performance for 3D and video workloads. |
+| **[util-linux](http://www.kernel.org/pub/linux/utils/util-linux)** | Set of Linux utilities |
+| **[VDE2](http://vde.sourceforge.net)** | VDE is an ethernet compliant virtual network that can be spawned over a set of physical computer over the Internet. VDE is part of virtualsquare project. |
+| **[VirtualGL](http://www.virtualgl.org)** | VirtualGL is an open source toolkit that gives any Unix or Linux remote display software the ability to run OpenGL applications with full 3D hardware acceleration. |
+| **[VTune](http://software.intel.com/en-us/intel-vtune-amplifier-xe)** | Intel VTune Amplifier XE 2016 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java. |
+| **[Wine](https://www.winehq.org)** | Wine (originally an acronym for "Wine Is Not an Emulator") is a compatibility layer capable of running Windows applications on several POSIX-compliant operating systems, such as Linux, Mac OSX, & BSD. |
+| **[XZ](http://tukaani.org/xz/)** | xz: XZ utilities |
## Vis
-|Module|Description|
-|--|--|
-|**[cairo](http://cairographics.org)**|Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB|
-|**[ffmpeg](https://www.ffmpeg.org/)**|A complete, cross-platform solution to record, convert and stream audio and video.|
-|**[fixesproto](http://www.freedesktop.org/wiki/Software/xlibs)**|X.org FixesProto protocol headers.|
-|**[FLTK](http://www.fltk.org)**|FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.|
-|**[fontconfig](http://www.freedesktop.org/software/fontconfig)**|Fontconfig is a library designed to provide system-wide font configuration, customization and application access.|
-|**[freetype](http://freetype.org)**|FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.|
-|**[gettext](http://www.gnu.org/software/gettext/)**|GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation|
-|**[GLib](http://www.gtk.org/)**|GLib is one of the base libraries of the GTK+ project|
-|**[GPI-2](http://www.gpi-site.com/gpi2/)**|GPI-2 is an API for the development of scalable, asynchronous and fault tolerant parallel applications.|
-|**[grace](http://freecode.com/projects/grace)**|Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.|
-|**[inputproto](http://www.freedesktop.org/wiki/Software/xlibs)**|X.org InputProto protocol headers.|
-|**[JasPer](http://www.ece.uvic.ca/~frodo/jasper/)**|The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.|
-|**[kbproto](http://www.freedesktop.org/wiki/Software/xlibs)**|X.org KBProto protocol headers.|
-|**[libGLU](ftp://ftp.freedesktop.org/pub/mesa/glu/)**|The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.|
-|**[libICE](http://www.freedesktop.org/wiki/Software/xlibs)**|X Inter-Client Exchange library for freedesktop.org|
-|**[libX11](http://www.freedesktop.org/wiki/Software/xlibs)**|X11 client-side library|
-|**[libXau](http://www.freedesktop.org/wiki/Software/xlibs)**|The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display.|
-|**[libXdamage](http://www.freedesktop.org/wiki/Software/xlibs)**|X Damage extension library|
-|**[libXdmcp](http://www.freedesktop.org/wiki/Software/xlibs)**|The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is useful for allowing clients to interact with the X Display Manager.|
-|**[libXext](http://www.freedesktop.org/wiki/Software/xlibs)**|Common X Extensions library|
-|**[libXfixes](http://www.freedesktop.org/wiki/Software/xlibs)**|X Fixes extension library|
-|**[libXfont](http://www.freedesktop.org/wiki/Software/xlibs)**|X font libary|
-|**[libXft](http://www.freedesktop.org/wiki/Software/xlibs)**|X11 client-side library|
-|**[libXinerama](http://www.freedesktop.org/wiki/Software/xlibs)**|Xinerama multiple monitor library|
-|**[libXrender](http://www.freedesktop.org/wiki/Software/xlibs)**|X11 client-side library|
-|**[libXt](http://www.freedesktop.org/wiki/Software/xlibs)**|libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).|
-|**matplotlib**| |
-|**[Mesa](http://www.mesa3d.org/)**|Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.|
-|**[motif](http://motif.ics.com/)**|Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix.|
-|**[OpenCV](http://opencv.org/)**|OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products.|
-|**[OpenDX](http://www.opendx.org)**|Open source visualization software package based on IBM's Visualization Data Explorer.|
-|**[OSPRay](http://www.ospray.org)**|A Ray Tracing Based Rendering Engine for High-Fidelity Visualization|
-|**[p4vasp](http://www.p4vasp.at)**|p4vasp is a visualization suite for the Vienna Ab-initio Simulation Package (VASP). It contains an extensible GUI framework, that can be used to view material structure, density of states, band-structure and more.|
-|**[ParaView](http://www.paraview.org)**|ParaView is a scientific parallel visualizer.|
-|**[pixman](http://www.pixman.org/)**|Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.|
-|**[PyQt](http://www.riverbankcomputing.co.uk/software/pyqt)**|PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.|
-|**[SUMO](http://www.sumo.dlr.de/wiki/Main_Page)**|Simulation of Urban MObility (SUMO) is an open source, highly portable, microscopic and continuous road traffic simulation package designed to handle large road networks.|
-|**[Tk](http://www.tcl.tk/)**|Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.|
-|**[VisIt](https://wci.llnl.gov/simulation/computer-codes/visit)**|VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool|
+| Module | Description |
+| ----------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **[cairo](http://cairographics.org)** | Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB |
+| **[ffmpeg](https://www.ffmpeg.org/)** | A complete, cross-platform solution to record, convert and stream audio and video. |
+| **[fixesproto](http://www.freedesktop.org/wiki/Software/xlibs)** | X.org FixesProto protocol headers. |
+| **[FLTK](http://www.fltk.org)** | FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation. |
+| **[fontconfig](http://www.freedesktop.org/software/fontconfig)** | Fontconfig is a library designed to provide system-wide font configuration, customization and application access. |
+| **[freetype](http://freetype.org)** | FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well. |
+| **[gettext](http://www.gnu.org/software/gettext/)** | GNU \`gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation |
+| **[GLib](http://www.gtk.org/)** | GLib is one of the base libraries of the GTK+ project |
+| **[GPI-2](http://www.gpi-site.com/gpi2/)** | GPI-2 is an API for the development of scalable, asynchronous and fault tolerant parallel applications. |
+| **[grace](http://freecode.com/projects/grace)** | Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. |
+| **[inputproto](http://www.freedesktop.org/wiki/Software/xlibs)** | X.org InputProto protocol headers. |
+| **[JasPer](http://www.ece.uvic.ca/~frodo/jasper/)** | The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard. |
+| **[kbproto](http://www.freedesktop.org/wiki/Software/xlibs)** | X.org KBProto protocol headers. |
+| **[libGLU](ftp://ftp.freedesktop.org/pub/mesa/glu/)** | The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. |
+| **[libICE](http://www.freedesktop.org/wiki/Software/xlibs)** | X Inter-Client Exchange library for freedesktop.org |
+| **[libX11](http://www.freedesktop.org/wiki/Software/xlibs)** | X11 client-side library |
+| **[libXau](http://www.freedesktop.org/wiki/Software/xlibs)** | The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display. |
+| **[libXdamage](http://www.freedesktop.org/wiki/Software/xlibs)** | X Damage extension library |
+| **[libXdmcp](http://www.freedesktop.org/wiki/Software/xlibs)** | The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is useful for allowing clients to interact with the X Display Manager. |
+| **[libXext](http://www.freedesktop.org/wiki/Software/xlibs)** | Common X Extensions library |
+| **[libXfixes](http://www.freedesktop.org/wiki/Software/xlibs)** | X Fixes extension library |
+| **[libXfont](http://www.freedesktop.org/wiki/Software/xlibs)** | X font libary |
+| **[libXft](http://www.freedesktop.org/wiki/Software/xlibs)** | X11 client-side library |
+| **[libXinerama](http://www.freedesktop.org/wiki/Software/xlibs)** | Xinerama multiple monitor library |
+| **[libXrender](http://www.freedesktop.org/wiki/Software/xlibs)** | X11 client-side library |
+| **[libXt](http://www.freedesktop.org/wiki/Software/xlibs)** | libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation). |
+| **matplotlib** | Â |
+| **[Mesa](http://www.mesa3d.org/)** | Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. |
+| **[motif](http://motif.ics.com/)** | Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix. |
+| **[OpenCV](http://opencv.org/)** | OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. |
+| **[OpenDX](http://www.opendx.org)** | Open source visualization software package based on IBM's Visualization Data Explorer. |
+| **[OSPRay](http://www.ospray.org)** | A Ray Tracing Based Rendering Engine for High-Fidelity Visualization |
+| **[p4vasp](http://www.p4vasp.at)** | p4vasp is a visualization suite for the Vienna Ab-initio Simulation Package (VASP). It contains an extensible GUI framework, that can be used to view material structure, density of states, band-structure and more. |
+| **[ParaView](http://www.paraview.org)** | ParaView is a scientific parallel visualizer. |
+| **[pixman](http://www.pixman.org/)** | Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server. |
+| **[PyQt](http://www.riverbankcomputing.co.uk/software/pyqt)** | PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework. |
+| **[SUMO](http://www.sumo.dlr.de/wiki/Main_Page)** | Simulation of Urban MObility (SUMO) is an open source, highly portable, microscopic and continuous road traffic simulation package designed to handle large road networks. |
+| **[Tk](http://www.tcl.tk/)** | Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages. |
+| **[VisIt](https://wci.llnl.gov/simulation/computer-codes/visit)** | VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool |
diff --git a/docs.it4i/pbspro.md b/docs.it4i/pbspro.md
index 72f5c3dd33b2946d0399ffe3c16c7cab8613a5b8..9dd4ccdab63753ad2fe475a90a857e9c50cdd4df 100644
--- a/docs.it4i/pbspro.md
+++ b/docs.it4i/pbspro.md
@@ -1,4 +1,4 @@
-* [PBS Pro Programmer's Guide](http://www.pbsworks.com/pdfs/PBSProgramGuide13.0.pdf)
-* [PBS Pro Quick Start Guide](http://www.pbsworks.com/pdfs/PBSQuickStartGuide13.0.pdf)
-* [PBS Pro Reference Guide](http://www.pbsworks.com/pdfs/PBSReferenceGuide13.0.pdf)
-* [PBS Pro User's Guide](http://www.pbsworks.com/pdfs/PBSUserGuide13.0.pdf)
+- [PBS Pro Programmer's Guide](http://www.pbsworks.com/pdfs/PBSProgramGuide13.0.pdf)
+- [PBS Pro Quick Start Guide](http://www.pbsworks.com/pdfs/PBSQuickStartGuide13.0.pdf)
+- [PBS Pro Reference Guide](http://www.pbsworks.com/pdfs/PBSReferenceGuide13.0.pdf)
+- [PBS Pro User's Guide](http://www.pbsworks.com/pdfs/PBSUserGuide13.0.pdf)
diff --git a/docs.it4i/salomon/7d-enhanced-hypercube.md b/docs.it4i/salomon/7d-enhanced-hypercube.md
index ec11ddb1145823a67c2b8b72fae0f80c42a8c00e..1c3d4fafb26e7d53d3d1226979f021d776730ca6 100644
--- a/docs.it4i/salomon/7d-enhanced-hypercube.md
+++ b/docs.it4i/salomon/7d-enhanced-hypercube.md
@@ -1,16 +1,14 @@
-7D Enhanced Hypercube
-=====================
+# 7D Enhanced Hypercube
### 7D Enhanced Hypercube {#d-enhanced-hypercube}
-|Node type|Count|Short name|Long name|Rack|
-|---|---|---|---|---|
-|M-Cell compute nodes w/o accelerator|576|cns1 -cns576|r1i0n0 - r4i7n17|1-4|
-|compute nodes MIC accelerated|432|cns577 - cns1008|r21u01n577 - r37u31n1008|21-38|
+| Node type | Count | Short name | Long name | Rack |
+| ------------------------------------ | ----- | ---------------- | ------------------------ | ----- |
+| M-Cell compute nodes w/o accelerator | 576 | cns1 -cns576 | r1i0n0 - r4i7n17 | 1-4 |
+| compute nodes MIC accelerated | 432 | cns577 - cns1008 | r21u01n577 - r37u31n1008 | 21-38 |
-### IB Topology
+### IB Topology
-
diff --git a/docs.it4i/salomon/capacity-computing.md b/docs.it4i/salomon/capacity-computing.md
index ec853f41fae7632a55859d54533f49f792294850..9ad9f94d2b466fc9525fd96434eb8a84a62318a0 100644
--- a/docs.it4i/salomon/capacity-computing.md
+++ b/docs.it4i/salomon/capacity-computing.md
@@ -1,8 +1,6 @@
-Capacity computing
-==================
+# Capacity computing
-Introduction
-------------
+## Introduction
In many cases, it is useful to submit huge (100+) number of computational jobs into the PBS queue system. Huge number of (small) jobs is one of the most effective ways to execute embarrassingly parallel calculations, achieving best runtime, throughput and computer utilization.
@@ -15,14 +13,12 @@ However, executing huge number of jobs via the PBS queue may strain the system.
- Use [GNU parallel](capacity-computing/#gnu-parallel) when running single core jobs
- Combine [GNU parallel with Job arrays](capacity-computing/#job-arrays-and-gnu-parallel) when running huge number of single core jobs
-Policy
-------
+## Policy
1. A user is allowed to submit at most 100 jobs. Each job may be [a job array](capacity-computing/#job-arrays).
2. The array size is at most 1000 subjobs.
-Job arrays
---------------
+## Job arrays
!!! Note "Note"
Huge number of jobs may be easily submitted and managed as a job array.
@@ -153,8 +149,7 @@ $ qstat -u $USER -tJ
Read more on job arrays in the [PBSPro Users guide](../../pbspro-documentation/).
-GNU parallel
-----------------
+## GNU parallel
!!! Note "Note"
Use GNU parallel to run many single core tasks on one node.
@@ -225,8 +220,7 @@ In this example, we submit a job of 101 tasks. 24 input files will be processed
Please note the #PBS directives in the beginning of the jobscript file, dont' forget to set your valid PROJECT_ID and desired queue.
-Job arrays and GNU parallel
--------------------------------
+## Job arrays and GNU parallel
!!! Note "Note"
Combine the Job arrays and GNU parallel for best throughput of single core jobs
@@ -293,7 +287,7 @@ In this example, the jobscript executes in multiple instances in parallel, on al
When deciding this values, think about following guiding rules :
-1. Let n=N/24. Inequality (n+1) * T < W should hold. The N is number of tasks per subjob, T is expected single task walltime and W is subjob walltime. Short subjob walltime improves scheduling and job throughput.
+1. Let n=N/24. Inequality (n+1) \* T < W should hold. The N is number of tasks per subjob, T is expected single task walltime and W is subjob walltime. Short subjob walltime improves scheduling and job throughput.
2. Number of tasks should be modulo 24.
3. These rules are valid only when all tasks have similar task walltimes T.
@@ -310,8 +304,7 @@ In this example, we submit a job array of 31 subjobs. Note the -J 1-992:**48**,
Please note the #PBS directives in the beginning of the jobscript file, dont' forget to set your valid PROJECT_ID and desired queue.
-Examples
---------
+## Examples
Download the examples in [capacity.zip](capacity.zip), illustrating the above listed ways to run huge number of jobs. We recommend to try out the examples, before using this for running production jobs.
diff --git a/docs.it4i/salomon/compute-nodes.md b/docs.it4i/salomon/compute-nodes.md
index af6b9708691b33a03103e8926076ab5637057b9d..910ac9611c43c519283272f69baa09a5bc462428 100644
--- a/docs.it4i/salomon/compute-nodes.md
+++ b/docs.it4i/salomon/compute-nodes.md
@@ -1,14 +1,13 @@
-Compute Nodes
-=============
+# Compute Nodes
+
+## Nodes Configuration
-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](ib-single-plane-topology/).
-###Compute Nodes Without Accelerator
+\###Compute Nodes Without Accelerator
- codename "grafton"
- 576 nodes
@@ -18,7 +17,7 @@ Compute nodes with MIC accelerator **contains two Intel Xeon Phi 7120P accelerat
-###Compute Nodes With MIC Accelerator
+\###Compute Nodes With MIC Accelerator
- codename "perrin"
- 432 nodes
@@ -46,14 +45,13 @@ Compute nodes with MIC accelerator **contains two Intel Xeon Phi 7120P accelerat
### Compute Nodes Summary
- |Node type |Count |Memory |Cores |
- | --- | --- | --- | --- |
- |Nodes without accelerator |576 |128 GB |24 @ 2.5Ghz |
- |Nodes with MIC accelerator |432 |128 GB<p>32GB\ |<p>24 @ 2.5Ghz<p>61 @ 1.238 GHz\ |
- |UV2000 SMP node |1 |3328GB\ |<p>112 @ 3.3GHz\ |
+| Node type | Count | Memory | Cores |
+| -------------------------- | ----- | ---------------- | ----------------------------------- |
+| Nodes without accelerator | 576 | 128 GB | 24 @ 2.5Ghz |
+| Nodes with MIC accelerator | 432 | 128 GB<p>32GB\\ | <p>24 @ 2.5Ghz<p>61 @ 1.238 GHz\\ |
+| UV2000 SMP node | 1 | 3328GB\\ | <p>112 @ 3.3GHz\\ |
-Processor Architecture
-----------------------
+## 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.
@@ -63,7 +61,7 @@ Salomon is equipped with Intel Xeon processors Intel Xeon E5-2680v3. Processors
- 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
+ - Intel® Smart Cache: 30 MB
- memory bandwidth at the level of the processor: 68 GB/s
### MIC Accelerator Intel Xeon Phi 7120P Processor
@@ -76,8 +74,8 @@ Salomon is equipped with Intel Xeon processors Intel Xeon E5-2680v3. Processors
- L2: 30.5 MB
- memory bandwidth at the level of the processor: 352 GB/s
-Memory Architecture
--------------------
+## 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
diff --git a/docs.it4i/salomon/environment-and-modules.md b/docs.it4i/salomon/environment-and-modules.md
index e5e33007f53f259da21f29ac2f1de8386fc0dedf..48b3f4932c5b11bc1cebfeb13926da1ecf11e27a 100644
--- a/docs.it4i/salomon/environment-and-modules.md
+++ b/docs.it4i/salomon/environment-and-modules.md
@@ -1,5 +1,4 @@
-Environment and Modules
-=======================
+# Environment and Modules
### Environment Customization
@@ -28,7 +27,7 @@ fi
Do not run commands outputting to standard output (echo, module list, etc) in .bashrc for non-interactive SSH sessions. It breaks fundamental functionality (scp, PBS) of your account! Take care for SSH session interactivity for such commands as stated in the previous example.
How to using modules in examples:
-<tty-player controls src=/src/salomon/modules_salomon.ttyrec></tty-player>
+<tty-player controls src=/src/salomon/modules_salomon.ttyrec></tty-player>
### Application Modules
@@ -117,12 +116,12 @@ Recent releases of EasyBuild include out-of-the-box toolchain support for:
On Salomon, we have currently following toolchains installed:
- |Toolchain|Module(s)|
- |---|----|
- |GCC|GCC|
- |ictce|icc, ifort, imkl, impi|
- |intel|GCC, icc, ifort, imkl, impi|
- |gompi|GCC, OpenMPI|
- |goolf|BLACS, FFTW, GCC, OpenBLAS, OpenMPI, ScaLAPACK|
- |iompi|OpenMPI, icc, ifort|
- |iccifort|icc, ifort|
+| Toolchain | Module(s) |
+| --------- | ---------------------------------------------- |
+| GCC | GCC |
+| ictce | icc, ifort, imkl, impi |
+| intel | GCC, icc, ifort, imkl, impi |
+| gompi | GCC, OpenMPI |
+| goolf | BLACS, FFTW, GCC, OpenBLAS, OpenMPI, ScaLAPACK |
+| iompi | OpenMPI, icc, ifort |
+| iccifort | icc, ifort |
diff --git a/docs.it4i/salomon/hardware-overview.md b/docs.it4i/salomon/hardware-overview.md
index a7465b809e8664fd968b187502dfcbe1ebb47da9..d888d314a4fb585fea9862273a5412b8b46e376e 100644
--- a/docs.it4i/salomon/hardware-overview.md
+++ b/docs.it4i/salomon/hardware-overview.md
@@ -1,8 +1,7 @@
-Hardware Overview
-=================
+# Hardware Overview
+
+## Introduction
-Introduction
-------------
The Salomon cluster consists of 1008 computational nodes of which 576 are regular compute nodes and 432 accelerated nodes. Each node is a powerful x86-64 computer, equipped with 24 cores (two twelve-core Intel Xeon processors) and 128 GB RAM. The nodes are interlinked by high speed InfiniBand and Ethernet networks. All nodes share 0.5 PB /home NFS disk storage to store the user files. Users may use a DDN Lustre shared storage with capacity of 1.69 PB which is available for the scratch project data. The user access to the Salomon cluster is provided by four login nodes.
[More about schematic representation of the Salomon cluster compute nodes IB topology](ib-single-plane-topology/).
@@ -11,50 +10,48 @@ The Salomon cluster consists of 1008 computational nodes of which 576 are regula
The parameters are summarized in the following tables:
-General information
--------------------
-
-|**In general**||
-|---|---|
-|Primary purpose|High Performance Computing|
-|Architecture of compute nodes|x86-64|
-|Operating system|CentOS 6.x Linux|
-|[**Compute nodes**](compute-nodes/)||
-|Totally|1008|
-|Processor|2 x Intel Xeon E5-2680v3, 2.5 GHz, 12 cores|
-|RAM|128GB, 5.3 GB per core, DDR4@2133 MHz|
-|Local disk drive|no|
-|Compute network / Topology|InfiniBand FDR56 / 7D Enhanced hypercube|
-|w/o accelerator|576|
-|MIC accelerated|432|
-|**In total**||
-|Total theoretical peak performance (Rpeak)|2011 TFLOP/s|
-|Total amount of RAM|129.024 TB|
-
-Compute nodes
--------------
-
-|Node|Count|Processor|Cores|Memory|Accelerator|
-|---|---|---|---|---|---|
-|w/o accelerator|576|2 x Intel Xeon E5-2680v3, 2.5 GHz|24|128 GB|-|
-|MIC accelerated|432|2 x Intel Xeon E5-2680v3, 2.5 GHz|24|128 GB|2 x Intel Xeon Phi 7120P, 61 cores, 16 GB RAM|
+## General information
+
+| **In general** | |
+| ------------------------------------------- | ------------------------------------------- |
+| Primary purpose | High Performance Computing |
+| Architecture of compute nodes | x86-64 |
+| Operating system | CentOS 6.x Linux |
+| [**Compute nodes**](compute-nodes/) | |
+| Totally | 1008 |
+| Processor | 2 x Intel Xeon E5-2680v3, 2.5 GHz, 12 cores |
+| RAM | 128GB, 5.3 GB per core, DDR4@2133 MHz |
+| Local disk drive | no |
+| Compute network / Topology | InfiniBand FDR56 / 7D Enhanced hypercube |
+| w/o accelerator | 576 |
+| MIC accelerated | 432 |
+| **In total** | |
+| Total theoretical peak performance (Rpeak) | 2011 TFLOP/s |
+| Total amount of RAM | 129.024 TB |
+
+## Compute nodes
+
+| Node | Count | Processor | Cores | Memory | Accelerator |
+| --------------- | ----- | --------------------------------- | ----- | ------ | --------------------------------------------- |
+| w/o accelerator | 576 | 2 x Intel Xeon E5-2680v3, 2.5 GHz | 24 | 128 GB | - |
+| MIC accelerated | 432 | 2 x Intel Xeon E5-2680v3, 2.5 GHz | 24 | 128 GB | 2 x Intel Xeon Phi 7120P, 61 cores, 16 GB RAM |
For more details please refer to the [Compute nodes](compute-nodes/).
-Remote visualization nodes
---------------------------
+## Remote visualization nodes
+
For remote visualization two nodes with NICE DCV software are available each configured:
-|Node|Count|Processor|Cores|Memory|GPU Accelerator|
-|---|---|---|---|---|---|
-|visualization|2|2 x Intel Xeon E5-2695v3, 2.3 GHz|28|512 GB|NVIDIA QUADRO K5000, 4 GB RAM|
+| Node | Count | Processor | Cores | Memory | GPU Accelerator |
+| ------------- | ----- | --------------------------------- | ----- | ------ | ----------------------------- |
+| visualization | 2 | 2 x Intel Xeon E5-2695v3, 2.3 GHz | 28 | 512 GB | NVIDIA QUADRO K5000, 4 GB RAM |
+
+## SGI UV 2000
-SGI UV 2000
------------
For large memory computations a special SMP/NUMA SGI UV 2000 server is available:
-|Node |Count |Processor |Cores|Memory|Extra HW |
-| --- | --- | --- | --- | --- | --- |
-|UV2000 |1 |14 x Intel Xeon E5-4627v2, 3.3 GHz, 8 cores |112 |3328 GB DDR3@1866 MHz |2 x 400GB local SSD</br>1x NVIDIA GM200 (GeForce GTX TITAN X), 12 GB RAM |
+| Node | Count | Processor | Cores | Memory | Extra HW |
+| ------ | ----- | ------------------------------------------- | ----- | --------------------- | ------------------------------------------------------------------------ |
+| UV2000 | 1 | 14 x Intel Xeon E5-4627v2, 3.3 GHz, 8 cores | 112 | 3328 GB DDR3@1866 MHz | 2 x 400GB local SSD</br>1x NVIDIA GM200 (GeForce GTX TITAN X), 12 GB RAM |
diff --git a/docs.it4i/salomon/ib-single-plane-topology.md b/docs.it4i/salomon/ib-single-plane-topology.md
index 8bb8d0d0229c83612e3dad13ff1cd39955628486..e37cdf4b3f2f2a7a869a0ce101284269a65c23ba 100644
--- a/docs.it4i/salomon/ib-single-plane-topology.md
+++ b/docs.it4i/salomon/ib-single-plane-topology.md
@@ -1,5 +1,4 @@
-IB single-plane topology
-========================
+# IB single-plane topology
A complete M-Cell assembly consists of four compute racks. Each rack contains 4 x physical IRUs - Independent rack units. Using one dual socket node per one blade slot leads to 8 logical IRUs. Each rack contains 4 x 2 SGI ICE X IB Premium Blades.
@@ -9,11 +8,11 @@ The SGI ICE X IB Premium Blade provides the first level of interconnection via d
- 3 ports on each chip provide connectivity between the chips
- 24 ports from each switch chip connect to the external bulkhead, for a total of 48
-###IB single-plane topology - ICEX M-Cell
+\###IB single-plane topology - ICEX M-Cell
Each color in each physical IRU represents one dual-switch ASIC switch.
-[IB single-plane topology - ICEX Mcell.pdf](../src/IB single-plane topology - ICEX Mcell.pdf)
+[IB single-plane topology - ICEX Mcell.pdf](<../src/IB single-plane topology - ICEX Mcell.pdf>)
@@ -27,6 +26,6 @@ As shown in a diagram 
- Racks 27, 28, 29, 30, 31, 32 are equivalent to one M-Cell rack.
- Racks 33, 34, 35, 36, 37, 38 are equivalent to one M-Cell rack.
-[IB single-plane topology - Accelerated nodes.pdf](../src/IB single-plane topology - Accelerated nodes.pdf)
+[IB single-plane topology - Accelerated nodes.pdf](<../src/IB single-plane topology - Accelerated nodes.pdf>)
diff --git a/docs.it4i/salomon/introduction.md b/docs.it4i/salomon/introduction.md
index 87950f42243c3eb1829edd44122cea8d15c1e721..1563518906866ae72937039dd6dc2ddb29126c15 100644
--- a/docs.it4i/salomon/introduction.md
+++ b/docs.it4i/salomon/introduction.md
@@ -1,5 +1,4 @@
-Introduction
-============
+# Introduction
Welcome to Salomon supercomputer cluster. The Salomon cluster consists of 1008 compute nodes, totaling 24192 compute cores with 129 TB RAM and giving over 2 Pflop/s theoretical peak performance. Each node is a powerful x86-64 computer, equipped with 24 cores, at least 128 GB RAM. Nodes are interconnected by 7D Enhanced hypercube InfiniBand network and equipped with Intel Xeon E5-2680v3 processors. The Salomon cluster consists of 576 nodes without accelerators and 432 nodes equipped with Intel Xeon Phi MIC accelerators. Read more in [Hardware Overview](hardware-overview/).
diff --git a/docs.it4i/salomon/job-priority.md b/docs.it4i/salomon/job-priority.md
index 97bc6968c4bd537521d1a2e9700454456fff80ab..c6c97a5e9e59dde966ad173936208152f7ddd4c6 100644
--- a/docs.it4i/salomon/job-priority.md
+++ b/docs.it4i/salomon/job-priority.md
@@ -1,8 +1,7 @@
-Job scheduling
-==============
+# Job scheduling
+
+## Job execution priority
-Job execution priority
-----------------------
Scheduler gives each job an execution priority and then uses this job execution priority to select which job(s) to run.
Job execution priority is determined by these job properties (in order of importance):
@@ -30,19 +29,19 @@ Fair-share priority is calculated as
where MAX_FAIRSHARE has value 1E6,
-usage*Project* is cumulated usage by all members of selected project,
-usage*Total* is total usage by all users, by all projects.
+usage_Project_ is cumulated usage by all members of selected project,
+usage_Total_ is total usage by all users, by all projects.
Usage counts allocated core-hours (`ncpus x walltime`). Usage is decayed, or cut in half periodically, at the interval 168 hours (one week).
-Jobs queued in queue qexp are not calculated to project's usage.
-=======
+
+# Jobs queued in queue qexp are not calculated to project's usage.
!!! Note "Note"
Calculated usage and fair-share priority can be seen at <https://extranet.it4i.cz/rsweb/salomon/projects>.
Calculated fair-share priority can be also seen as Resource_List.fairshare attribute of a job.
-###Eligible time
+\###Eligible time
Eligible time is amount (in seconds) of eligible time job accrued while waiting to run. Jobs with higher eligible time gains higher priority.
diff --git a/docs.it4i/salomon/job-submission-and-execution.md b/docs.it4i/salomon/job-submission-and-execution.md
index 23f97bb9bae22abde7943c8fb9bc42fa708a3748..83e7c6f9d5a4db2a7c256c2f86635e665ec9a857 100644
--- a/docs.it4i/salomon/job-submission-and-execution.md
+++ b/docs.it4i/salomon/job-submission-and-execution.md
@@ -1,8 +1,7 @@
-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)
@@ -105,8 +104,7 @@ 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
@@ -133,7 +131,6 @@ Network location of allocated nodes in the [Infiniband network](network/) influe
For communication intensive jobs it is possible to set stricter requirement - to require nodes directly connected to the same Infiniband switch or to require nodes located in the same dimension group of the Infiniband network.
-
### Placement by Infiniband switch
Nodes directly connected to the same Infiniband switch can communicate most efficiently. Using the same switch prevents hops in the network and provides for unbiased, most efficient network communication. There are 9 nodes directly connected to every Infiniband switch.
@@ -154,12 +151,10 @@ $ qsub -A OPEN-0-0 -q qprod -l select=9:ncpus=24 -l place=group=switch ./myjob
!!! Note "Note"
Not useful for ordinary computing, suitable for testing and management tasks.
-
-Nodes directly connected to the specific Infiniband switch can be selected using the PBS resource attribute *switch*.
+Nodes directly connected to the specific Infiniband switch can be selected using the PBS resource attribute _switch_.
In this example, we request all 9 nodes directly connected to r4i1s0sw1 switch.
-
```bash
$ qsub -A OPEN-0-0 -q qprod -l select=9:ncpus=24:switch=r4i1s0sw1 ./myjob
```
@@ -178,6 +173,7 @@ r1i2s0sw0
```
List of all all nodes directly connected to the specific Infiniband switch:
+
```bash
$ qmgr -c 'p n @d' | grep 'switch = r36sw3' | awk '{print $3}' | sort
r36u31n964
@@ -193,19 +189,20 @@ r37u34n972
### Placement by Hypercube dimension
-Nodes located in the same dimension group may be allocated using node grouping on PBS resource attribute ehc_[1-7]d .
+Nodes located in the same dimension group may be allocated using node grouping on PBS resource attribute ehc\_[1-7]d .
-|Hypercube dimension|node_group_key|#nodes per group|
-|---|---|---|
-|1D|ehc_1d|18|
-|2D|ehc_2d|36|
-|3D|ehc_3d|72|
-|4D|ehc_4d|144|
-|5D|ehc_5d|144,288|
-|6D|ehc_6d|432,576|
-|7D|ehc_7d|all|
+| Hypercube dimension | node_group_key | #nodes per group |
+| ------------------- | -------------- | ---------------- |
+| 1D | ehc_1d | 18 |
+| 2D | ehc_2d | 36 |
+| 3D | ehc_3d | 72 |
+| 4D | ehc_4d | 144 |
+| 5D | ehc_5d | 144,288 |
+| 6D | ehc_6d | 432,576 |
+| 7D | ehc_7d | all |
In this example, we allocate 16 nodes in the same [hypercube dimension](7d-enhanced-hypercube/) 1 group.
+
```bash
$ qsub -A OPEN-0-0 -q qprod -l select=16:ncpus=24 -l place=group=ehc_1d -I
```
@@ -224,6 +221,7 @@ $ qmgr -c 'p n @d' | grep ehc_1d | awk '{print $6}' | sort |uniq -c
```
List of all all nodes in specific dimension 1 group:
+
```bash
$ $ qmgr -c 'p n @d' | grep 'ehc_1d = r1i0' | awk '{print $3}' | sort
r1i0n0
@@ -233,8 +231,7 @@ r1i0n11
...
```
-Job Management
---------------
+## Job Management
!!! Note "Note"
Check status of your jobs using the **qstat** and **check-pbs-jobs** commands
@@ -260,7 +257,7 @@ Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
16547.isrv5 user2 qprod job3x 13516 2 32 -- 48:00 R 00:58
```
-In this example user1 and user2 are running jobs named job1, job2 and job3x. The jobs job1 and job2 are using 4 nodes, 16 cores per node each. The job1 already runs for 38 hours and 25 minutes, job2 for 17 hours 44 minutes. The job1 already consumed 64*38.41 = 2458.6 core hours. The job3x already consumed 0.96*32 = 30.93 core hours. These consumed core hours will be accounted on the respective project accounts, regardless of whether the allocated cores were actually used for computations.
+In this example user1 and user2 are running jobs named job1, job2 and job3x. The jobs job1 and job2 are using 4 nodes, 16 cores per node each. The job1 already runs for 38 hours and 25 minutes, job2 for 17 hours 44 minutes. The job1 already consumed 64_38.41 = 2458.6 core hours. The job3x already consumed 0.96_32 = 30.93 core hours. These consumed core hours will be accounted on the respective project accounts, regardless of whether the allocated cores were actually used for computations.
Check status of your jobs using check-pbs-jobs command. Check presence of user's PBS jobs' processes on execution hosts. Display load, processes. Display job standard and error output. Continuously display (tail -f) job standard or error output.
@@ -336,8 +333,7 @@ Learn more by reading the pbs man page
$ man pbs_professional
```
-Job Execution
--------------
+## Job Execution
### Jobscript
diff --git a/docs.it4i/salomon/network.md b/docs.it4i/salomon/network.md
index 9fbf17d255c2a5c542cb881dba1f689c6c68baff..005e6d6600147d5b7ff344017c377368338d295f 100644
--- a/docs.it4i/salomon/network.md
+++ b/docs.it4i/salomon/network.md
@@ -1,11 +1,10 @@
-Network
-=======
+# Network
All compute and login nodes of Salomon are interconnected by 7D Enhanced hypercube [InfiniBand](http://en.wikipedia.org/wiki/InfiniBand) network and by Gigabit [Ethernet](http://en.wikipedia.org/wiki/Ethernet)
network. Only [InfiniBand](http://en.wikipedia.org/wiki/InfiniBand) network may be used to transfer user data.
-InfiniBand Network
-------------------
+## InfiniBand Network
+
All compute and login nodes of Salomon are interconnected by 7D Enhanced hypercube [Infiniband](http://en.wikipedia.org/wiki/InfiniBand) network (56 Gbps). The network topology is a [7D Enhanced hypercube](7d-enhanced-hypercube/).
Read more about schematic representation of the Salomon cluster [IB single-plain topology](ib-single-plane-topology/)
@@ -15,8 +14,7 @@ The compute nodes may be accessed via the Infiniband network using ib0 network i
The network provides **2170MB/s** transfer rates via the TCP connection (single stream) and up to **3600MB/s** via native Infiniband protocol.
-Example
--------
+## Example
```bash
$ qsub -q qexp -l select=4:ncpus=16 -N Name0 ./myjob
diff --git a/docs.it4i/salomon/prace.md b/docs.it4i/salomon/prace.md
index facda414a0c72b7ebe6e0a43a2c1590f8723c06a..fd56e39a7ecd5cc5899976bdee399484cc8797bf 100644
--- a/docs.it4i/salomon/prace.md
+++ b/docs.it4i/salomon/prace.md
@@ -1,26 +1,24 @@
-PRACE User Support
-==================
+# PRACE User Support
+
+## Intro
-Intro
------
PRACE users coming to Salomon as to TIER-1 system offered through the DECI calls are in general treated as standard users and so most of the 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 Salomon cluster, the user needs to obtain the login credentials. The procedure is the same as for general users of the cluster, so please see the corresponding [section of the general documentation here](../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials/).
-Accessing the cluster
----------------------
+## Accessing the cluster
### Access with GSI-SSH
@@ -54,13 +52,13 @@ To access Salomon cluster, two login nodes running GSI SSH service are available
It is recommended to use the single DNS name salomon-prace.it4i.cz which is distributed between the two login nodes. If needed, user can login directly to one of the login nodes. The addresses are:
-|Login address|Port|Protocol|Login node|
-|---|---|---|---|
-|salomon-prace.it4i.cz|2222|gsissh|login1, login2, login3 or login4|
-|login1-prace.salomon.it4i.cz|2222|gsissh|login1|
-|login2-prace.salomon.it4i.cz|2222|gsissh|login2|
-|login3-prace.salomon.it4i.cz|2222|gsissh|login3|
-|login4-prace.salomon.it4i.cz|2222|gsissh|login4|
+| Login address | Port | Protocol | Login node |
+| ---------------------------- | ---- | -------- | -------------------------------- |
+| salomon-prace.it4i.cz | 2222 | gsissh | login1, login2, login3 or login4 |
+| login1-prace.salomon.it4i.cz | 2222 | gsissh | login1 |
+| login2-prace.salomon.it4i.cz | 2222 | gsissh | login2 |
+| login3-prace.salomon.it4i.cz | 2222 | gsissh | login3 |
+| login4-prace.salomon.it4i.cz | 2222 | gsissh | login4 |
```bash
$ gsissh -p 2222 salomon-prace.it4i.cz
@@ -76,13 +74,13 @@ When logging from other PRACE system, the prace_service script can be used:
It is recommended to use the single DNS name salomon.it4i.cz which is distributed between the two login nodes. If needed, user can login directly to one of the login nodes. The addresses are:
-|Login address|Port|Protocol|Login node|
-|---|---|---|---|
-|salomon.it4i.cz|2222|gsissh|login1, login2, login3 or login4|
-|login1.salomon.it4i.cz|2222|gsissh|login1|
-|login2-prace.salomon.it4i.cz|2222|gsissh|login2|
-|login3-prace.salomon.it4i.cz|2222|gsissh|login3|
-|login4-prace.salomon.it4i.cz|2222|gsissh|login4|
+| Login address | Port | Protocol | Login node |
+| ---------------------------- | ---- | -------- | -------------------------------- |
+| salomon.it4i.cz | 2222 | gsissh | login1, login2, login3 or login4 |
+| login1.salomon.it4i.cz | 2222 | gsissh | login1 |
+| login2-prace.salomon.it4i.cz | 2222 | gsissh | login2 |
+| login3-prace.salomon.it4i.cz | 2222 | gsissh | login3 |
+| login4-prace.salomon.it4i.cz | 2222 | gsissh | login4 |
```bash
$ gsissh -p 2222 salomon.it4i.cz
@@ -121,8 +119,8 @@ 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](shell-and-data-access/).
-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](shell-and-data-access/).
Apart from the standard mechanisms, for PRACE users to transfer data to/from Salomon cluster, a GridFTP server running Globus Toolkit GridFTP service is available. The service is available from public Internet as well as from the internal PRACE network (accessible only from other PRACE partners).
@@ -131,12 +129,12 @@ There's one control server and three backend servers for striping and/or backup
**Access from PRACE network:**
-|Login address|Port|Node role|
-|---|---|---|
-|gridftp-prace.salomon.it4i.cz|2812|Front end /control server|
-|lgw1-prace.salomon.it4i.cz|2813|Backend / data mover server|
-|lgw2-prace.salomon.it4i.cz|2813|Backend / data mover server|
-|lgw3-prace.salomon.it4i.cz|2813|Backend / data mover server|
+| Login address | Port | Node role |
+| ----------------------------- | ---- | --------------------------- |
+| gridftp-prace.salomon.it4i.cz | 2812 | Front end /control server |
+| lgw1-prace.salomon.it4i.cz | 2813 | Backend / data mover server |
+| lgw2-prace.salomon.it4i.cz | 2813 | Backend / data mover server |
+| lgw3-prace.salomon.it4i.cz | 2813 | Backend / data mover server |
Copy files **to** Salomon by running the following commands on your local machine:
@@ -164,12 +162,12 @@ Or by using prace_service script:
**Access from public Internet:**
-|Login address|Port|Node role|
-|---|---|---|---|
-|gridftp.salomon.it4i.cz|2812|Front end /control server|
-|lgw1.salomon.it4i.cz|2813|Backend / data mover server|
-|lgw2.salomon.it4i.cz|2813|Backend / data mover server|
-|lgw3.salomon.it4i.cz|2813|Backend / data mover server|
+| Login address | Port | Node role |
+| ----------------------- | ---- | --------------------------- |
+| gridftp.salomon.it4i.cz | 2812 | Front end /control server |
+| lgw1.salomon.it4i.cz | 2813 | Backend / data mover server |
+| lgw2.salomon.it4i.cz | 2813 | Backend / data mover server |
+| lgw3.salomon.it4i.cz | 2813 | Backend / data mover server |
Copy files **to** Salomon by running the following commands on your local machine:
@@ -197,22 +195,22 @@ Or by using prace_service script:
Generally both shared file systems are available through GridFTP:
-|File system mount point|Filesystem|Comment|
-|---|---|---|
-|/home|Lustre|Default HOME directories of users in format /home/prace/login/|
-|/scratch|Lustre|Shared SCRATCH mounted on the whole cluster|
+| File system mount point | Filesystem | Comment |
+| ----------------------- | ---------- | -------------------------------------------------------------- |
+| /home | Lustre | Default HOME directories of users in format /home/prace/login/ |
+| /scratch | Lustre | Shared SCRATCH mounted on the whole cluster |
More information about the shared file systems is available [here](storage/).
Please note, that for PRACE users a "prace" directory is used also on the SCRATCH file system.
-|Data type|Default path|
-|---|---|
-|large project files|/scratch/work/user/prace/login/|
-|large scratch/temporary data|/scratch/temp/|
+| Data type | Default path |
+| ---------------------------- | ------------------------------- |
+| large project files | /scratch/work/user/prace/login/ |
+| large scratch/temporary data | /scratch/temp/ |
+
+## Usage of the cluster
-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. The available file systems are described [here](storage/).
@@ -233,12 +231,11 @@ General information about the resource allocation, job queuing and job execution
For PRACE users, the default production run queue is "qprace". PRACE users can also use two other queues "qexp" and "qfree".
- |queue|Active project|Project resources|Nodes|priority|authorization|walltime |
- |---|---|---|---|---|---|---|
- |**qexp** Express queue|no|none required|32 nodes, max 8 per user|150|no|1 / 1 h|
- |**qprace** Production queue|yes|>0|1006 nodes, max 86 per job|0|no|24 / 48 h|
- |**qfree** Free resource queue|yes|none required|752 nodes, max 86 per job|-1024|no|12 / 12 h|
-
+| queue | Active project | Project resources | Nodes | priority | authorization | walltime |
+| ----------------------------- | -------------- | ----------------- | -------------------------- | -------- | ------------- | --------- |
+| **qexp** Express queue | no | none required | 32 nodes, max 8 per user | 150 | no | 1 / 1 h |
+| **qprace** Production queue | yes | >0 | 1006 nodes, max 86 per job | 0 | no | 24 / 48 h |
+| **qfree** Free resource queue | yes | none required | 752 nodes, max 86 per job | -1024 | 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 48 hours. If the job needs longer time, it must use checkpoint/restart functionality.
diff --git a/docs.it4i/salomon/resource-allocation-and-job-execution.md b/docs.it4i/salomon/resource-allocation-and-job-execution.md
index 283ae774617c28048f6f8d9e892bd2dbfe8ae73b..d9c10ba524669e235cde4d8aaee22730307f7fdb 100644
--- a/docs.it4i/salomon/resource-allocation-and-job-execution.md
+++ b/docs.it4i/salomon/resource-allocation-and-job-execution.md
@@ -1,26 +1,25 @@
-Resource Allocation and Job Execution
-=====================================
+# Resource Allocation and Job Execution
To run a [job](job-submission-and-execution/), [computational resources](resources-allocation-policy/) for this particular job must be allocated. This is done via the PBS Pro job workload manager software, which efficiently distributes workloads across the supercomputer. Extensive information about PBS Pro can be found in the [official documentation here](../pbspro-documentation/pbspro/), especially in the PBS Pro User's Guide.
-Resources Allocation Policy
----------------------------
+## 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](job-priority/) at Salomon ensures that individual users may consume approximately equal amount of resources per week. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following queues are available to Anselm users:
-- **qexp**, the Express queue
-- **qprod**, the Production queue
-- **qlong**, the Long queue
-- **qmpp**, the Massively parallel queue
-- **qfat**, the queue to access SMP UV2000 machine
-- **qfree**, the Free resource utilization queue
+- **qexp**, the Express queue
+- **qprod**, the Production queue
+- **qlong**, the Long queue
+- **qmpp**, the Massively parallel queue
+- **qfat**, the queue to access SMP UV2000 machine
+- **qfree**, the Free resource utilization queue
!!! Note "Note"
Check the queue status at <https://extranet.it4i.cz/rsweb/salomon/>
Read more on the [Resource Allocation Policy](resources-allocation-policy/) page.
-Job submission and execution
-----------------------------
+## Job submission and execution
+
!!! Note "Note"
Use the **qsub** command to submit your jobs.
diff --git a/docs.it4i/salomon/resources-allocation-policy.md b/docs.it4i/salomon/resources-allocation-policy.md
index dd5f736adbecf56de562d1ef09974a73a0c15b87..fa86f8439653f5f9e5cab8df1714c5e794d1e49c 100644
--- a/docs.it4i/salomon/resources-allocation-policy.md
+++ b/docs.it4i/salomon/resources-allocation-policy.md
@@ -1,33 +1,32 @@
-Resources Allocation Policy
-===========================
+# Resources Allocation Policy
+
+## Resources Allocation Policy
-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/rsweb/salomon/
-
- |queue |active project |project resources |nodes|min ncpus |priority|authorization|walltime |
- | --- | --- |--- |--- |--- |--- |--- |--- |
- |**qexe** Express queue|no |none required |32 nodes, max 8 per user |24 |150 |no |1 / 1h |
- |**qprod** Production queue|yes |> 0 |1006 nodes, max 86 per job |24 |0 |no |24 / 48h |
- |**qlong** Long queue |yes |> 0 |256 nodes, max 40 per job, only non-accelerated nodes allowed |24 |0 |no |72 / 144h |
- |**qmpp** Massive parallel queue |yes |> 0 |1006 nodes |24 |0 |yes |2 / 4h |
- |**qfat** UV2000 queue |yes |> 0 |1 (uv1) |8 |0 |yes |24 / 48h |
- |**qfree** Free resource queue|yes |none required |752 nodes, max 86 per job |24 |-1024 |no |12 / 12h |
- |**qviz** Visualization queue |yes |none required |2 (with NVIDIA Quadro K5000) |4 |150 |no |1 / 8h |
+ Check the queue status at <https://extranet.it4i.cz/rsweb/salomon/>
+
+| queue | active project | project resources | nodes | min ncpus | priority | authorization | walltime |
+| ------------------------------- | -------------- | ----------------- | ------------------------------------------------------------- | --------- | -------- | ------------- | --------- |
+| **qexe** Express queue | no | none required | 32 nodes, max 8 per user | 24 | 150 | no | 1 / 1h |
+| **qprod** Production queue | yes | > 0 | 1006 nodes, max 86 per job | 24 | 0 | no | 24 / 48h |
+| **qlong** Long queue | yes | > 0 | 256 nodes, max 40 per job, only non-accelerated nodes allowed | 24 | 0 | no | 72 / 144h |
+| **qmpp** Massive parallel queue | yes | > 0 | 1006 nodes | 24 | 0 | yes | 2 / 4h |
+| **qfat** UV2000 queue | yes | > 0 | 1 (uv1) | 8 | 0 | yes | 24 / 48h |
+| **qfree** Free resource queue | yes | none required | 752 nodes, max 86 per job | 24 | -1024 | no | 12 / 12h |
+| **qviz** Visualization queue | yes | none required | 2 (with NVIDIA Quadro K5000) | 4 | 150 | no | 1 / 8h |
!!! Note "Note"
**The qfree queue is not free of charge**. [Normal accounting](resources-allocation-policy/#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.
-- **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. 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, however only 86 per job. Full nodes, 24 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qprod is 48 hours.
-- **qlong**, the Long queue: This queue is intended for long production runs. It is required that active project with nonzero remaining resources is specified to enter the qlong. Only 336 nodes without acceleration may be accessed via the qlong queue. Full nodes, 24 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qlong is 144 hours (three times of the standard qprod time - 3 * 48 h)
-- **qmpp**, the massively parallel queue. This queue is intended for massively parallel runs. It is required that active project with nonzero remaining resources is specified to enter the qmpp. All nodes may be accessed via the qmpp queue. Full nodes, 24 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qmpp is 4 hours. An PI needs explicitly ask support for authorization to enter the queue for all users associated to her/his Project.
-- **qfat**, the UV2000 queue. This queue is dedicated to access the fat SGI UV2000 SMP machine. The machine (uv1) has 112 Intel IvyBridge cores at 3.3GHz and 3.25TB RAM. An PI needs explicitly ask support for authorization to enter the queue 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, 24 cores per node are allocated. The queue runs with very low priority and no special authorization is required to use it. The maximum runtime in qfree is 12 hours.
-- **qviz**, the Visualization queue: Intended for pre-/post-processing using OpenGL accelerated graphics. Currently when accessing the node, each user gets 4 cores of a CPU allocated, thus approximately 73 GB of RAM and 1/7 of the GPU capacity (default "chunk"). If more GPU power or RAM is required, it is recommended to allocate more chunks (with 4 cores each) up to one whole node per user, so that all 28 cores, 512 GB RAM and whole GPU is exclusive. This is currently also the maximum allowed allocation per one user. One hour of work is allocated by default, the user may ask for 2 hours maximum.
+- **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. 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, however only 86 per job. Full nodes, 24 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qprod is 48 hours.
+- **qlong**, the Long queue: This queue is intended for long production runs. It is required that active project with nonzero remaining resources is specified to enter the qlong. Only 336 nodes without acceleration may be accessed via the qlong queue. Full nodes, 24 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qlong is 144 hours (three times of the standard qprod time - 3 \* 48 h)
+- **qmpp**, the massively parallel queue. This queue is intended for massively parallel runs. It is required that active project with nonzero remaining resources is specified to enter the qmpp. All nodes may be accessed via the qmpp queue. Full nodes, 24 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qmpp is 4 hours. An PI needs explicitly ask support for authorization to enter the queue for all users associated to her/his Project.
+- **qfat**, the UV2000 queue. This queue is dedicated to access the fat SGI UV2000 SMP machine. The machine (uv1) has 112 Intel IvyBridge cores at 3.3GHz and 3.25TB RAM. An PI needs explicitly ask support for authorization to enter the queue 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, 24 cores per node are allocated. The queue runs with very low priority and no special authorization is required to use it. The maximum runtime in qfree is 12 hours.
+- **qviz**, the Visualization queue: Intended for pre-/post-processing using OpenGL accelerated graphics. Currently when accessing the node, each user gets 4 cores of a CPU allocated, thus approximately 73 GB of RAM and 1/7 of the GPU capacity (default "chunk"). If more GPU power or RAM is required, it is recommended to allocate more chunks (with 4 cores each) up to one whole node per user, so that all 28 cores, 512 GB RAM and whole GPU is exclusive. This is currently also the maximum allowed allocation per one user. One hour of work is allocated by default, the user may ask for 2 hours maximum.
!!! Note "Note"
To access node with Xeon Phi co-processor user needs to specify that in [job submission select statement](job-submission-and-execution/).
@@ -112,8 +111,7 @@ Options:
--incl-finished Include finished jobs
```
-Resources Accounting Policy
--------------------------------
+## Resources Accounting Policy
### The Core-Hour
diff --git a/docs.it4i/salomon/shell-and-data-access.md b/docs.it4i/salomon/shell-and-data-access.md
index a779c8697062b30056e3a0a49c873eb8c3e681d5..94da50a462261ea8fe571a8fa159a5489a6c4c23 100644
--- a/docs.it4i/salomon/shell-and-data-access.md
+++ b/docs.it4i/salomon/shell-and-data-access.md
@@ -1,20 +1,19 @@
-Accessing the Cluster
-==============================
+# Accessing the Cluster
+
+## Shell Access
-Shell Access
------------------
The Salomon cluster is accessed by SSH protocol via login nodes login1, login2, login3 and login4 at address salomon.it4i.cz. The login nodes may be addressed specifically, by prepending the login node name to the address.
!!! Note "Note"
The alias salomon.it4i.cz is currently not available through VPN connection. Please use loginX.salomon.it4i.cz when connected to VPN.
- |Login address|Port|Protocol|Login node|
- |---|---|---|---|
- |salomon.it4i.cz|22|ssh|round-robin DNS record for login[1-4]|
- |login1.salomon.it4i.cz|22|ssh|login1|
- |login1.salomon.it4i.cz|22|ssh|login1|
- |login1.salomon.it4i.cz|22|ssh|login1|
- |login1.salomon.it4i.cz|22|ssh|login1|
+| Login address | Port | Protocol | Login node |
+| ---------------------- | ---- | -------- | ------------------------------------- |
+| salomon.it4i.cz | 22 | ssh | round-robin DNS record for login[1-4] |
+| login1.salomon.it4i.cz | 22 | ssh | login1 |
+| login1.salomon.it4i.cz | 22 | ssh | login1 |
+| login1.salomon.it4i.cz | 22 | ssh | login1 |
+| login1.salomon.it4i.cz | 22 | ssh | login1 |
The authentication is by the [private key](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/)
@@ -60,17 +59,17 @@ Last login: Tue Jul 9 15:57:38 2013 from your-host.example.com
!!! Note "Note"
The environment is **not** shared between login nodes, except for [shared filesystems](storage/).
-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.
- |Address|Port|Protocol|
- |---|---|---|
- |salomon.it4i.cz|22|scp, sftp|
- |login1.salomon.it4i.cz|22|scp, sftp|
- |login2.salomon.it4i.cz|22|scp, sftp|
- |login3.salomon.it4i.cz|22|scp, sftp|
- |login4.salomon.it4i.cz|22|scp, sftp|
+| Address | Port | Protocol |
+| ---------------------- | ---- | --------- |
+| salomon.it4i.cz | 22 | scp, sftp |
+| login1.salomon.it4i.cz | 22 | scp, sftp |
+| login2.salomon.it4i.cz | 22 | scp, sftp |
+| login3.salomon.it4i.cz | 22 | scp, sftp |
+| login4.salomon.it4i.cz | 22 | scp, sftp |
The authentication is by the [private key](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/)
@@ -110,24 +109,23 @@ 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 Salomon Cluster login nodes to the outside world, are restricted to following ports:
-|Port|Protocol|
-|---|---|
-|22|ssh|
-|80|http|
-|443|https|
-|9418|git|
+| Port | Protocol |
+| ---- | -------- |
+| 22 | ssh |
+| 80 | http |
+| 443 | https |
+| 9418 | git |
!!! Note "Note"
Please use **ssh port forwarding** and proxy servers to connect from Salomon to all other remote ports.
Outgoing connections, from Salomon 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
@@ -144,7 +142,7 @@ local $ ssh -R 6000:remote.host.com:1234 salomon.it4i.cz
In this example, we establish port forwarding between port 6000 on Salomon and port 1234 on the remote.host.com. By accessing localhost:6000 on Salomon, an application will see response of remote.host.com:1234. The traffic will run via users local workstation.
-Port forwarding may be done **using PuTTY** as well. On the PuTTY Configuration screen, load your Salomon configuration first. Then go to Connection->SSH->Tunnels to set up the port forwarding. Click Remote radio button. Insert 6000 to Source port textbox. Insert remote.host.com:1234. Click Add button, then Open.
+Port forwarding may be done **using PuTTY** as well. On the PuTTY Configuration screen, load your Salomon configuration first. Then go to Connection->SSH->Tunnels to set up the port forwarding. Click Remote radio button. Insert 6000 to Source port textbox. Insert remote.host.com:1234. Click Add button, then Open.
Port forwarding may be established directly to the remote host. However, this requires that user has ssh access to remote.host.com
@@ -191,13 +189,11 @@ local $ ssh -R 6000:localhost:1080 salomon.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).
-VPN Access
-----------
+## VPN Access
- Access to IT4Innovations internal resources via [VPN](../get-started-with-it4innovations/accessing-the-clusters/vpn-access/).
diff --git a/docs.it4i/salomon/software/ansys/ansys-cfx.md b/docs.it4i/salomon/software/ansys/ansys-cfx.md
index d1b8ade6ec1bf50d430d9f34d790609111fd283c..741e565503fa19b82b6ef41c36eec69ed9c21128 100644
--- a/docs.it4i/salomon/software/ansys/ansys-cfx.md
+++ b/docs.it4i/salomon/software/ansys/ansys-cfx.md
@@ -1,5 +1,4 @@
-ANSYS CFX
-=========
+# ANSYS CFX
[ANSYS CFX](http://www.ansys.com/products/fluids/ansys-cfx) software is a high-performance, general purpose fluid dynamics program that has been applied to solve wide-ranging fluid flow problems for over 20 years. At the heart of ANSYS CFX is its advanced solver technology, the key to achieving reliable and accurate solutions quickly and robustly. The modern, highly parallelized solver is the foundation for an abundant choice of physical models to capture virtually any type of phenomena related to fluid flow. The solver and its many physical models are wrapped in a modern, intuitive, and flexible GUI and user environment, with extensive capabilities for customization and automation using session files, scripting and a powerful expression language.
diff --git a/docs.it4i/salomon/software/ansys/ansys-fluent.md b/docs.it4i/salomon/software/ansys/ansys-fluent.md
index 0ebec531d8ef8dfe30eceedf6045d2d80916c719..c9c2a8020d09ff4b8e4503252480f6a7a5687599 100644
--- a/docs.it4i/salomon/software/ansys/ansys-fluent.md
+++ b/docs.it4i/salomon/software/ansys/ansys-fluent.md
@@ -1,11 +1,12 @@
-ANSYS Fluent
-============
+# ANSYS Fluent
[ANSYS Fluent](http://www.ansys.com/products/fluids/ansys-fluent)
software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants. Special models that give the software the ability to model in-cylinder combustion, aeroacoustics, turbomachinery, and multiphase systems have served to broaden its reach.
-1. Common way to run Fluent over pbs file
-------------------------------------------------------
+1. Common way to run Fluent over pbs file
+
+* * *
+
To run ANSYS Fluent in batch mode you can utilize/modify the default fluent.pbs script and execute it via the qsub command.
```bash
@@ -57,17 +58,20 @@ Journal file with definition of the input geometry and boundary conditions and d
The appropriate dimension of the problem has to be set by parameter (2d/3d).
-2. Fast way to run Fluent from command line
---------------------------------------------------------
+2. Fast way to run Fluent from command line
+
+* * *
```bash
fluent solver_version [FLUENT_options] -i journal_file -pbs
```
-This syntax will start the ANSYS FLUENT job under PBS Professional using the qsub command in a batch manner. When resources are available, PBS Professional will start the job and return a job ID, usually in the form of *job_ID.hostname*. This job ID can then be used to query, control, or stop the job using standard PBS Professional commands, such as qstat or qdel. The job will be run out of the current working directory, and all output will be written to the file fluent.o *job_ID*.
+This syntax will start the ANSYS FLUENT job under PBS Professional using the qsub command in a batch manner. When resources are available, PBS Professional will start the job and return a job ID, usually in the form of _job_ID.hostname_. This job ID can then be used to query, control, or stop the job using standard PBS Professional commands, such as qstat or qdel. The job will be run out of the current working directory, and all output will be written to the file fluent.o _job_ID_.
+
+3. Running Fluent via user's config file
+
+* * *
-3. Running Fluent via user's config file
-----------------------------------------
The sample script uses a configuration file called pbs_fluent.conf if no command line arguments are present. This configuration file should be present in the directory from which the jobs are submitted (which is also the directory in which the jobs are executed). The following is an example of what the content of pbs_fluent.conf can be:
```bash
@@ -143,8 +147,10 @@ To run ANSYS Fluent in batch mode with user's config file you can utilize/modify
It runs the jobs out of the directory from which they are submitted (PBS_O_WORKDIR).
-4. Running Fluent in parralel
------------------------------
+4. Running Fluent in parralel
+
+* * *
+
Fluent could be run in parallel only under Academic Research license. To do so this ANSYS Academic Research license must be placed before ANSYS CFD license in user preferences. To make this change anslic_admin utility should be run
```bash
diff --git a/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md b/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md
index 9284e151c7d723d883c55eabf0a38c133ba9e613..65423033146af8c27fe47a513aad0e51543128c3 100644
--- a/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md
+++ b/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md
@@ -1,5 +1,4 @@
-ANSYS LS-DYNA
-=============
+# ANSYS LS-DYNA
**[ANSYSLS-DYNA](http://www.ansys.com/products/structures/ansys-ls-dyna)** software provides convenient and easy-to-use access to the technology-rich, time-tested explicit solver without the need to contend with the complex input requirements of this sophisticated program. Introduced in 1996, ANSYS LS-DYNA capabilities have helped customers in numerous industries to resolve highly intricate design issues. ANSYS Mechanical users have been able take advantage of complex explicit solutions for a long time utilizing the traditional ANSYS Parametric Design Language (APDL) environment. These explicit capabilities are available to ANSYS Workbench users as well. The Workbench platform is a powerful, comprehensive, easy-to-use environment for engineering simulation. CAD import from all sources, geometry cleanup, automatic meshing, solution, parametric optimization, result visualization and comprehensive report generation are all available within a single fully interactive modern graphical user environment.
diff --git a/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md b/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md
index 9c05b279128303104d281a508f02cd5202471570..70448b8903b0ab067691d3d7d4442f141b7a084e 100644
--- a/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md
+++ b/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md
@@ -1,5 +1,4 @@
-ANSYS MAPDL
-===========
+# ANSYS MAPDL
**[ANSYS Multiphysics](http://www.ansys.com/products/multiphysics)**
software offers a comprehensive product solution for both multiphysics and single-physics analysis. The product includes structural, thermal, fluid and both high- and low-frequency electromagnetic analysis. The product also contains solutions for both direct and sequentially coupled physics problems including direct coupled-field elements and the ANSYS multi-field solver.
diff --git a/docs.it4i/salomon/software/ansys/ansys.md b/docs.it4i/salomon/software/ansys/ansys.md
index 093bcf9567db939e38673fc9dd5373b1f3d14c37..c72e964629ed098f6413c5ccc491ef5920220363 100644
--- a/docs.it4i/salomon/software/ansys/ansys.md
+++ b/docs.it4i/salomon/software/ansys/ansys.md
@@ -1,9 +1,8 @@
-Overview of ANSYS Products
-==========================
+# Overview of ANSYS Products
**[SVS FEM](http://www.svsfem.cz/)** as **[ANSYS Channel partner](http://www.ansys.com/)** for Czech Republic provided all ANSYS licenses for ANSELM cluster and supports of all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent, Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging to problem of ANSYS functionality contact please [hotline@svsfem.cz](mailto:hotline@svsfem.cz?subject=Ostrava%20-%20ANSELM)
-Anselm provides as commercial as academic variants. Academic variants are distinguished by "**Academic...**" word in the name of license or by two letter preposition "**aa_**" in the license feature name. Change of license is realized on command line respectively directly in user's pbs file (see individual products). [ More about licensing here](licensing/)
+Anselm provides as commercial as academic variants. Academic variants are distinguished by "**Academic...**" word in the name of license or by two letter preposition "**aa\_**" in the license feature name. Change of license is realized on command line respectively directly in user's pbs file (see individual products). [ More about licensing here](licensing/)
To load the latest version of any ANSYS product (Mechanical, Fluent, CFX, MAPDL,...) load the module:
@@ -14,4 +13,3 @@ To load the latest version of any ANSYS product (Mechanical, Fluent, CFX, MAPDL,
ANSYS supports interactive regime, but due to assumed solution of extremely difficult tasks it is not recommended.
If user needs to work in interactive regime we recommend to configure the RSM service on the client machine which allows to forward the solution to the Anselm directly from the client's Workbench project (see ANSYS RSM service).
-
diff --git a/docs.it4i/salomon/software/ansys/licensing.md b/docs.it4i/salomon/software/ansys/licensing.md
index 63842ea29dc85a0480bb5d34d8812d633f45844d..c69480c6ae8dd17148b5588993dc228c405e548f 100644
--- a/docs.it4i/salomon/software/ansys/licensing.md
+++ b/docs.it4i/salomon/software/ansys/licensing.md
@@ -1,25 +1,24 @@
-Licensing and Available Versions
-================================
+# Licensing and Available Versions
-ANSYS licence can be used by:
------------------------------
-- all persons in the carrying out of the CE IT4Innovations Project (In addition to the primary licensee, which is VSB - Technical University of Ostrava, users are CE IT4Innovations third parties - CE IT4Innovations project partners, particularly the University of Ostrava, the Brno University of Technology - Faculty of Informatics, the Silesian University in Opava, Institute of Geonics AS CR.)
-- all persons who have a valid license
-- students of the Technical University
+## ANSYS licence can be used by:
+
+- all persons in the carrying out of the CE IT4Innovations Project (In addition to the primary licensee, which is VSB - Technical University of Ostrava, users are CE IT4Innovations third parties - CE IT4Innovations project partners, particularly the University of Ostrava, the Brno University of Technology - Faculty of Informatics, the Silesian University in Opava, Institute of Geonics AS CR.)
+- all persons who have a valid license
+- students of the Technical University
+
+## ANSYS Academic Research
-ANSYS Academic Research
------------------------
The licence intended to be used for science and research, publications, students’ projects (academic licence).
-ANSYS COM
----------
+## ANSYS COM
+
The licence intended to be used for science and research, publications, students’ projects, commercial research with no commercial use restrictions.
-Available Versions
-------------------
+## Available Versions
+
- 16.1
- 17.0
-License Preferences
--------------------
+## License Preferences
+
Please [see this page to set license preferences](setting-license-preferences/).
diff --git a/docs.it4i/salomon/software/ansys/setting-license-preferences.md b/docs.it4i/salomon/software/ansys/setting-license-preferences.md
index 44e0b8bde968c4336d5d7e8cb7e1625ff348cda3..f3dfad8e2daa5212d4620b5b17155e60b5aadad7 100644
--- a/docs.it4i/salomon/software/ansys/setting-license-preferences.md
+++ b/docs.it4i/salomon/software/ansys/setting-license-preferences.md
@@ -1,5 +1,4 @@
-Setting license preferences
-===========================
+# Setting license preferences
Some ANSYS tools allow you to explicitly specify usage of academic or commercial licenses in the command line (eg. ansys161 -p aa_r to select Academic Research license). However, we have observed that not all tools obey this option and choose commercial license.
@@ -21,4 +20,4 @@ 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
+
diff --git a/docs.it4i/salomon/software/ansys/workbench.md b/docs.it4i/salomon/software/ansys/workbench.md
index af5c9f9ff002efff830d1ce687e961e03c92dac7..8bc1edb4dd7348d27fcdf57937f04e237e3cba83 100644
--- a/docs.it4i/salomon/software/ansys/workbench.md
+++ b/docs.it4i/salomon/software/ansys/workbench.md
@@ -1,8 +1,7 @@
-Workbench
-=========
+# Workbench
+
+## Workbench Batch Mode
-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 ...
@@ -13,7 +12,7 @@ Enable Distribute Solution checkbox and enter number of cores (eg. 48 to run on
-mpifile /path/to/my/job/mpifile.txt
```
-Where /path/to/my/job is the directory where your project is saved. We will create the file mpifile.txt programatically later in the batch script. For more information, refer to *ANSYS Mechanical APDL Parallel Processing* *Guide*.
+Where /path/to/my/job is the directory where your project is saved. We will create the file mpifile.txt programatically later in the batch script. For more information, refer to _ANSYS Mechanical APDL Parallel Processing_ _Guide_.
Now, save the project and close Workbench. We will use this script to launch the job:
diff --git a/docs.it4i/salomon/software/chemistry/molpro.md b/docs.it4i/salomon/software/chemistry/molpro.md
index 787f86054873db8961e5f7fd6798b564a79eda84..2b8ead8136c81f35a434fb421f0a48f802485994 100644
--- a/docs.it4i/salomon/software/chemistry/molpro.md
+++ b/docs.it4i/salomon/software/chemistry/molpro.md
@@ -1,36 +1,35 @@
-Molpro
-======
+# Molpro
Molpro is a complete system of ab initio programs for molecular electronic structure calculations.
-About Molpro
-------------
+## About Molpro
+
Molpro is a software package used for accurate ab-initio quantum chemistry calculations. More information can be found at the [official webpage](http://www.molpro.net/).
-License
--------
+## License
+
Molpro software package is available only to users that have a valid license. Please contact support to enable access to Molpro if you have a valid license appropriate for running on our cluster (eg. academic research group licence, parallel execution).
To run Molpro, you need to have a valid license token present in " $HOME/.molpro/token". You can download the token from [Molpro website](https://www.molpro.net/licensee/?portal=licensee).
-Installed version
------------------
+## Installed version
+
Currently on Anselm is installed version 2010.1, patch level 45, parallel version compiled with Intel compilers and Intel MPI.
Compilation parameters are default:
-|Parameter|Value|
-|---|---|
-|max number of atoms|200|
-|max number of valence orbitals|300|
-|max number of basis functions|4095|
-|max number of states per symmmetry|20|
-|max number of state symmetries|16|
-|max number of records|200|
-|max number of primitives|maxbfn x [2]|
-
-Running
-------
+| Parameter | Value |
+| ---------------------------------- | ------------ |
+| max number of atoms | 200 |
+| max number of valence orbitals | 300 |
+| max number of basis functions | 4095 |
+| max number of states per symmmetry | 20 |
+| max number of state symmetries | 16 |
+| max number of records | 200 |
+| max number of primitives | maxbfn x [2] |
+
+## Running
+
Molpro is compiled for parallel execution using MPI and OpenMP. By default, Molpro reads the number of allocated nodes from PBS and launches a data server on one node. On the remaining allocated nodes, compute processes are launched, one process per node, each with 16 threads. You can modify this behavior by using -n, -t and helper-server options. Please refer to the [Molpro documentation](http://www.molpro.net/info/2010.1/doc/manual/node9.html) for more details.
!!! Note "Note"
diff --git a/docs.it4i/salomon/software/chemistry/nwchem.md b/docs.it4i/salomon/software/chemistry/nwchem.md
index 3db648754f6ad50e0ae89758ae825c4cb20956d7..2feebda57f3928c89ed55a7c836eee8d8d3d672f 100644
--- a/docs.it4i/salomon/software/chemistry/nwchem.md
+++ b/docs.it4i/salomon/software/chemistry/nwchem.md
@@ -1,16 +1,14 @@
-NWChem
-======
+# NWChem
**High-Performance Computational Chemistry**
-Introduction
--------------------------
+## Introduction
+
NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.
[Homepage](http://www.nwchem-sw.org/index.php/Main_Page)
-Installed versions
-------------------
+## Installed versions
The following versions are currently installed:
@@ -25,8 +23,8 @@ For a current list of installed versions, execute:
The recommend to use version 6.5. Version 6.3 fails on Salomon nodes with accelerator, because it attempts to communicate over scif0 interface. In 6.5 this is avoided by setting ARMCI_OPENIB_DEVICE=mlx4_0, this setting is included in the module.
-Running
--------
+## Running
+
NWChem is compiled for parallel MPI execution. Normal procedure for MPI jobs applies. Sample jobscript :
```bash
@@ -39,8 +37,8 @@ Running
mpirun nwchem h2o.nw
```
-Options
---------------------
+## Options
+
Please refer to [the documentation](http://www.nwchem-sw.org/index.php/Release62:Top-level) and in the input file set the following directives :
- MEMORY : controls the amount of memory NWChem will use
diff --git a/docs.it4i/salomon/software/chemistry/phono3py.md b/docs.it4i/salomon/software/chemistry/phono3py.md
index 5d5487f97eea389aacba3e57566e0ebf865fba13..970eb3019284426b8ce4ac3b24cc5b7859adfc82 100644
--- a/docs.it4i/salomon/software/chemistry/phono3py.md
+++ b/docs.it4i/salomon/software/chemistry/phono3py.md
@@ -1,9 +1,8 @@
-Phono3py
-========
+# Phono3py
-Introduction
--------------
-This GPL software calculates phonon-phonon interactions via the third order force constants. It allows to obtain lattice thermal conductivity, phonon lifetime/linewidth, imaginary part of self energy at the lowest order, joint density of states (JDOS) and weighted-JDOS. For details see Phys. Rev. B 91, 094306 (2015) and [http://atztogo.github.io/phono3py/index.html](http://atztogo.github.io/phono3py/index.html)
+## Introduction
+
+This GPL software calculates phonon-phonon interactions via the third order force constants. It allows to obtain lattice thermal conductivity, phonon lifetime/linewidth, imaginary part of self energy at the lowest order, joint density of states (JDOS) and weighted-JDOS. For details see Phys. Rev. B 91, 094306 (2015) and <http://atztogo.github.io/phono3py/index.html>
!!! Note "Note"
Load the phono3py/0.9.14-ictce-7.3.5-Python-2.7.9 module
@@ -12,8 +11,7 @@ This GPL software calculates phonon-phonon interactions via the third order forc
$ module load phono3py/0.9.14-ictce-7.3.5-Python-2.7.9
```
-Example of calculating thermal conductivity of Si using VASP code.
-------------------------------------------------------------------
+## Example of calculating thermal conductivity of Si using VASP code.
### Calculating force constants
@@ -81,8 +79,8 @@ Taylor your run.sh script to fit into your project and other needs and submit al
$ ./submit.sh
```
-Collecting results and post-processing with phono3py
----------------------------------------------------------------------------
+## Collecting results and post-processing with phono3py
+
Once all jobs are finished and vasprun.xml is created in each disp-XXXXX directory the collection is done by
```bash
@@ -105,7 +103,7 @@ The phonon lifetime calculations takes some time, however is independent on grid
$ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" --sigma 0.1 --wgp
```
-### Inspecting ir_grid_points.yaml
+### Inspecting ir_grid_points.yaml
```bash
$ grep grid_point ir_grid_points.yaml
diff --git a/docs.it4i/salomon/software/compilers.md b/docs.it4i/salomon/software/compilers.md
index b14287af39e8f1f05176f7938bd11c6097e74c1a..ca8a0f747c0e0a70ac41696b46f977b98958715c 100644
--- a/docs.it4i/salomon/software/compilers.md
+++ b/docs.it4i/salomon/software/compilers.md
@@ -1,5 +1,4 @@
-Compilers
-=========
+# Compilers
Available compilers, including GNU, INTEL and UPC compilers
@@ -22,13 +21,11 @@ Commercial licenses:
- Intel
- PGI
-Intel Compilers
----------------
+## Intel Compilers
For information about the usage of Intel Compilers and other Intel products, please read the [Intel Parallel studio](intel-suite/) page.
-PGI Compilers
--------------
+## PGI Compilers
The Portland Group Cluster Development Kit (PGI CDK) is available.
@@ -55,8 +52,8 @@ PGDBG OpenMP/MPI debugger and PGPROF OpenMP/MPI profiler are available
For more information, see the [PGI page](http://www.pgroup.com/products/pgicdk.htm).
-GNU
----
+## GNU
+
For compatibility reasons there are still available the original (old 4.4.7-11) versions of GNU compilers as part of the OS. These are accessible in the search path by default.
It is strongly recommended to use the up to date version which comes with the module GCC:
@@ -80,8 +77,8 @@ With the module loaded two environment variables are predefined. One for maximum
For more information about the possibilities of the compilers, please see the man pages.
-Unified Parallel C
-------------------
+## Unified Parallel C
+
UPC is supported by two compiler/runtime implementations:
- GNU - SMP/multi-threading support only
@@ -184,10 +181,10 @@ To run the example on two compute nodes using all 48 cores, with 48 threads, iss
For more information 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/).
diff --git a/docs.it4i/salomon/software/comsol/comsol-multiphysics.md b/docs.it4i/salomon/software/comsol/comsol-multiphysics.md
index a9f06a44239e9da93ec0df0e72ab79a38cc1cbe0..007e17ad1d4a8cf7b039235a3d9a6c8ae0d02b73 100644
--- a/docs.it4i/salomon/software/comsol/comsol-multiphysics.md
+++ b/docs.it4i/salomon/software/comsol/comsol-multiphysics.md
@@ -1,8 +1,7 @@
-COMSOL Multiphysics®
-====================
+# COMSOL Multiphysics®
+
+## Introduction
-Introduction
--------------------------
[COMSOL](http://www.comsol.com) is a powerful environment for modelling and solving various engineering and scientific problems based on partial differential equations. COMSOL is designed to solve coupled or multiphysics phenomena. For many standard engineering problems COMSOL provides add-on products such as electrical, mechanical, fluid flow, and chemical applications.
- [Structural Mechanics Module](http://www.comsol.com/structural-mechanics-module),
@@ -13,8 +12,7 @@ Introduction
COMSOL also allows an interface support for equation-based modelling of partial differential equations.
-Execution
-----------------------
+## Execution
On the clusters COMSOL is available in the latest stable version. There are two variants of the release:
@@ -72,8 +70,8 @@ comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tm
Working directory has to be created before sending the (comsol.pbs) job script into the queue. Input file (name_input_f.mph) has to be in working directory or full path to input file has to be specified. The appropriate path to the temp directory of the job has to be set by command option (-tmpdir).
-LiveLink™* *for MATLAB®
--------------------------
+## LiveLink™\* \*for MATLAB®
+
COMSOL is the software package for the numerical solution of the partial differential equations. LiveLink for MATLAB allows connection to the COMSOL®API (Application Programming Interface) with the benefits of the programming language and computing environment of the MATLAB.
LiveLink for MATLAB is available in both **EDU** and **COM** **variant** of the COMSOL release. On the clusters 1 commercial (**COM**) license and the 5 educational (**EDU**) licenses of LiveLink for MATLAB (please see the [ISV Licenses](../isv_licenses/)) are available. Following example shows how to start COMSOL model from MATLAB via LiveLink in the interactive mode.
diff --git a/docs.it4i/salomon/software/comsol/licensing-and-available-versions.md b/docs.it4i/salomon/software/comsol/licensing-and-available-versions.md
index e3a4950a772e6942dbd4caeabc2e5d6d885b3a9e..b27b36a28b1afba257cb1f620c823106db34535f 100644
--- a/docs.it4i/salomon/software/comsol/licensing-and-available-versions.md
+++ b/docs.it4i/salomon/software/comsol/licensing-and-available-versions.md
@@ -1,23 +1,19 @@
-Licensing and Available Versions
-================================
+# Licensing and Available Versions
-Comsol licence can be used by:
-------------------------------
+## Comsol licence can be used by:
-- all persons in the carrying out of the CE IT4Innovations Project (In addition to the primary licensee, which is VSB - Technical University of Ostrava, users are CE IT4Innovations third parties - CE IT4Innovations project partners, particularly the University of Ostrava, the Brno University of Technology - Faculty of Informatics, the Silesian University in Opava, Institute of Geonics AS CR.)
-- all persons who have a valid license
-- students of the Technical University
+- all persons in the carrying out of the CE IT4Innovations Project (In addition to the primary licensee, which is VSB - Technical University of Ostrava, users are CE IT4Innovations third parties - CE IT4Innovations project partners, particularly the University of Ostrava, the Brno University of Technology - Faculty of Informatics, the Silesian University in Opava, Institute of Geonics AS CR.)
+- all persons who have a valid license
+- students of the Technical University
-Comsol EDU Network Licence
---------------------------
+## Comsol EDU Network Licence
The licence intended to be used for science and research, publications, students’ projects, teaching (academic licence).
-Comsol COM Network Licence
---------------------------
+## Comsol COM Network Licence
The licence intended to be used for science and research, publications, students’ projects, commercial research with no commercial use restrictions. Enables the solution of at least one job by one user in one program start.
-Available Versions
-------------------
-- ver. 51
\ No newline at end of file
+## Available Versions
+
+- ver. 51
diff --git a/docs.it4i/salomon/software/debuggers/Introduction.md b/docs.it4i/salomon/software/debuggers/Introduction.md
index c85157da67777964414ed2133e82df75fc1a797d..3b9f18ba1d7656d10c1021cbd3460b22f0c3bf07 100644
--- a/docs.it4i/salomon/software/debuggers/Introduction.md
+++ b/docs.it4i/salomon/software/debuggers/Introduction.md
@@ -1,13 +1,10 @@
-Debuggers and profilers summary
-===============================
+# Debuggers and profilers summary
-Introduction
-------------
+## Introduction
We provide state of the art programms and tools to develop, profile and debug HPC codes at IT4Innovations. On these pages, we provide an overview of the profiling and debugging tools available on Anslem at IT4I.
-Intel debugger
---------------
+## Intel debugger
Intel debugger is no longer available since Parallel Studio version 2015
@@ -20,8 +17,8 @@ The intel debugger version 13.0 is available, via module intel. The debugger wor
Read more at the [Intel Debugger](../intel-suite/intel-debugger/) page.
-Allinea Forge (DDT/MAP)
------------------------
+## Allinea Forge (DDT/MAP)
+
Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel Xeon Phi accelerators. DDT provides all the standard debugging features (stack trace, breakpoints, watches, view variables, threads etc.) for every thread running as part of your program, or for every process - even if these processes are distributed across a cluster using an MPI implementation.
```bash
@@ -31,8 +28,8 @@ Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or Op
Read more at the [Allinea DDT](allinea-ddt/) page.
-Allinea Performance Reports
----------------------------
+## Allinea Performance Reports
+
Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs. Our license is limited to 64 MPI processes.
```bash
@@ -42,8 +39,8 @@ Allinea Performance Reports characterize the performance of HPC application runs
Read more at the [Allinea Performance Reports](allinea-performance-reports/) page.
-RougeWave Totalview
--------------------
+## RougeWave Totalview
+
TotalView is a source- and machine-level debugger for multi-process, multi-threaded programs. Its wide range of tools provides ways to analyze, organize, and test programs, making it easy to isolate and identify problems in individual threads and processes in programs of great complexity.
```bash
@@ -53,8 +50,8 @@ TotalView is a source- and machine-level debugger for multi-process, multi-threa
Read more at the [Totalview](total-view/) page.
-Vampir trace analyzer
----------------------
+## Vampir trace analyzer
+
Vampir is a GUI trace analyzer for traces in OTF format.
```bash
diff --git a/docs.it4i/salomon/software/debuggers/aislinn.md b/docs.it4i/salomon/software/debuggers/aislinn.md
index c2a9982448b0bee936940655f406615075d60301..cf3c57b62db4975663eefb539a14436c55886773 100644
--- a/docs.it4i/salomon/software/debuggers/aislinn.md
+++ b/docs.it4i/salomon/software/debuggers/aislinn.md
@@ -1,5 +1,4 @@
-Aislinn
-=======
+# Aislinn
- Aislinn is a dynamic verifier for MPI programs. For a fixed input it covers all possible runs with respect to nondeterminism introduced by MPI. It allows to detect bugs (for sure) that occurs very rare in normal runs.
- Aislinn detects problems like invalid memory accesses, deadlocks, misuse of MPI, and resource leaks.
@@ -7,7 +6,7 @@ Aislinn
- Web page of the project: <http://verif.cs.vsb.cz/aislinn/>
!!! Note "Note"
- Aislinn is software developed at IT4Innovations and some parts are still considered experimental. If you have any questions or experienced any problems, please contact the author: <stanislav.bohm@vsb.cz>.
+ Aislinn is software developed at IT4Innovations and some parts are still considered experimental. If you have any questions or experienced any problems, please contact the author: <mailto:stanislav.bohm@vsb.cz>.
### Usage
@@ -83,20 +82,21 @@ At the beginning of the report there are some basic summaries of the verificatio
It shows us:
- - Error occurs in process 0 in test.cpp on line 16.
- - Stdout and stderr streams are empty. (The program does not write anything).
- - The last part shows MPI calls for each process that occurs in the invalid run. The more detailed information about each call can be obtained by mouse cursor.
+
+- Error occurs in process 0 in test.cpp on line 16.
+- Stdout and stderr streams are empty. (The program does not write anything).
+- The last part shows MPI calls for each process that occurs in the invalid run. The more detailed information about each call can be obtained by mouse cursor.
### Limitations
Since the verification is a non-trivial process there are some of limitations.
-- The verified process has to terminate in all runs, i.e. we cannot answer the halting problem.
-- The verification is a computationally and memory demanding process. We put an effort to make it efficient and it is an important point for further research. However covering all runs will be always more demanding than techniques that examines only a single run. The good practise is to start with small instances and when it is feasible, make them bigger. The Aislinn is good to find bugs that are hard to find because they occur very rarely (only in a rare scheduling). Such bugs often do not need big instances.
-- Aislinn expects that your program is a "standard MPI" program, i.e. processes communicate only through MPI, the verified program does not interacts with the system in some unusual ways (e.g. opening sockets).
+- The verified process has to terminate in all runs, i.e. we cannot answer the halting problem.
+- The verification is a computationally and memory demanding process. We put an effort to make it efficient and it is an important point for further research. However covering all runs will be always more demanding than techniques that examines only a single run. The good practise is to start with small instances and when it is feasible, make them bigger. The Aislinn is good to find bugs that are hard to find because they occur very rarely (only in a rare scheduling). Such bugs often do not need big instances.
+- Aislinn expects that your program is a "standard MPI" program, i.e. processes communicate only through MPI, the verified program does not interacts with the system in some unusual ways (e.g. opening sockets).
There are also some limitations bounded to the current version and they will be removed in the future:
-- All files containing MPI calls have to be recompiled by MPI implementation provided by Aislinn. The files that does not contain MPI calls, they do not have to recompiled. Aislinn MPI implementation supports many commonly used calls from MPI-2 and MPI-3 related to point-to-point communication, collective communication, and communicator management. Unfortunately, MPI-IO and one-side communication is not implemented yet.
-- Each MPI can use only one thread (if you use OpenMP, set OMP_NUM_THREADS to 1).
-- There are some limitations for using files, but if the program just reads inputs and writes results, it is ok.
+- All files containing MPI calls have to be recompiled by MPI implementation provided by Aislinn. The files that does not contain MPI calls, they do not have to recompiled. Aislinn MPI implementation supports many commonly used calls from MPI-2 and MPI-3 related to point-to-point communication, collective communication, and communicator management. Unfortunately, MPI-IO and one-side communication is not implemented yet.
+- Each MPI can use only one thread (if you use OpenMP, set OMP_NUM_THREADS to 1).
+- There are some limitations for using files, but if the program just reads inputs and writes results, it is ok.
diff --git a/docs.it4i/salomon/software/debuggers/allinea-ddt.md b/docs.it4i/salomon/software/debuggers/allinea-ddt.md
index 4badb0582736df26d3128dd160c2c9617cb799fe..c119f40a8d48d8b97a8608ead54c8f2e225fea56 100644
--- a/docs.it4i/salomon/software/debuggers/allinea-ddt.md
+++ b/docs.it4i/salomon/software/debuggers/allinea-ddt.md
@@ -1,5 +1,4 @@
-Allinea Forge (DDT,MAP)
-=======================
+# Allinea Forge (DDT,MAP)
Allinea Forge consist of two tools - debugger DDT and profiler MAP.
@@ -7,8 +6,8 @@ Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or Op
Allinea MAP is a profiler for C/C++/Fortran HPC codes. It is designed for profiling parallel code, which uses pthreads, OpenMP or MPI.
-License and Limitations for Anselm Users
-----------------------------------------
+## License and Limitations for Anselm Users
+
On Anselm users can debug OpenMP or MPI code that runs up to 64 parallel processes. In case of debugging GPU or Xeon Phi accelerated codes the limit is 8 accelerators. These limitation means that:
- 1 user can debug up 64 processes, or
@@ -19,8 +18,7 @@ In case of debugging on accelerators:
- 1 user can debug on up to 8 accelerators, or
- 8 users can debug on single accelerator.
-Compiling Code to run with DDT
-------------------------------
+## Compiling Code to run with DDT
### Modules
@@ -50,12 +48,12 @@ $ mpif90 -g -O0 -o test_debug test.f
Before debugging, you need to compile your code with theses flags:
!!! Note "Note"
- - **g** : Generates extra debugging information usable by GDB. -g3 includes even more debugging information. This option is available for GNU and INTEL C/C++ and Fortran compilers.
+ \- **g** : Generates extra debugging information usable by GDB. -g3 includes even more debugging information. This option is available for GNU and INTEL C/C++ and Fortran compilers.
+
+ - - **O0** : Suppress all optimizations.
- - - **O0** : Suppress all optimizations.
+## Starting a Job with DDT
-Starting a Job with DDT
------------------------
Be sure to log in with an X window forwarding enabled. This could mean using the -X in the ssh:
```bash
@@ -86,8 +84,8 @@ To start the debugging directly without the submission window, user can specify
ddt -start -np 4 ./hello_debug_impi
```
-Documentation
--------------
+## Documentation
+
Users can find original User Guide after loading the DDT module:
```bash
diff --git a/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md b/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md
index 6ab49b2d779ee27eef400e8ecbf227d58d01aa68..ec39904bb166d31f8f181aa8a66c738d02359ad3 100644
--- a/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md
+++ b/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md
@@ -1,17 +1,15 @@
-Allinea Performance Reports
-===========================
+# Allinea Performance Reports
+## Introduction
-Introduction
-------------
Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs.
The Allinea Performance Reports is most useful in profiling MPI rograms.
Our license is limited to 64 MPI processes.
-Modules
--------
+## Modules
+
Allinea Performance Reports version 6.0 is available
```bash
@@ -20,8 +18,7 @@ Allinea Performance Reports version 6.0 is available
The module sets up environment variables, required for using the Allinea Performance Reports.
-Usage
------
+## Usage
Use the the perf-report wrapper on your (MPI) program.
@@ -31,10 +28,10 @@ Instead of [running your MPI program the usual way](../mpi/mpi/), use the the pe
$ perf-report mpirun ./mympiprog.x
```
-The mpi program will run as usual. The perf-report creates two additional files, in *.txt and *.html format, containing the performance report. Note that demanding MPI codes should be run within [ the queue system](../../resource-allocation-and-job-execution/job-submission-and-execution/).
+The mpi program will run as usual. The perf-report creates two additional files, in _.txt and _.html format, containing the performance report. Note that demanding MPI codes should be run within [ the queue system](../../resource-allocation-and-job-execution/job-submission-and-execution/).
+
+## Example
-Example
--------
In this example, we will be profiling the mympiprog.x MPI program, using Allinea performance reports. Assume that the code is compiled with intel compilers and linked against intel MPI library:
First, we allocate some nodes via the express queue:
@@ -58,4 +55,4 @@ Now lets profile the code:
$ perf-report mpirun ./mympiprog.x
```
-Performance report files [mympiprog_32p*.txt](mympiprog_32p_2014-10-15_16-56.txt) and [mympiprog_32p*.html](mympiprog_32p_2014-10-15_16-56.html) were created. We can see that the code is very efficient on MPI and is CPU bounded.
+Performance report files [mympiprog_32p\*.txt](mympiprog_32p_2014-10-15_16-56.txt) and [mympiprog_32p\*.html](mympiprog_32p_2014-10-15_16-56.html) were created. We can see that the code is very efficient on MPI and is CPU bounded.
diff --git a/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md b/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md
index 332601743958bf114e417f1ab2ce98d21034fa62..3007857498d13233c3d9b0d229ab62c4f30cc40f 100644
--- a/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md
+++ b/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md
@@ -1,9 +1,8 @@
-Intel VTune Amplifier XE
-========================
+# Intel VTune Amplifier XE
-Introduction
-------------
-Intel*® *VTune™ Amplifier, part of Intel Parallel studio, is a GUI profiling tool designed for Intel processors. It offers a graphical performance analysis of single core and multithreaded applications. A highlight of the features:
+## Introduction
+
+Intel_® _VTune™ Amplifier, part of Intel Parallel studio, is a GUI profiling tool designed for Intel processors. It offers a graphical performance analysis of single core and multithreaded applications. A highlight of the features:
- Hotspot analysis
- Locks and waits analysis
@@ -12,15 +11,15 @@ Intel*® *VTune™ Amplifier, part of Intel Parallel studio, is a GUI profiling
-Usage
------
+## Usage
+
To profile an application with VTune Amplifier, special kernel modules need to be loaded. The modules are not loaded on the login nodes, thus direct profiling on login nodes is not possible. By default, the kernel modules ale not loaded on compute nodes neither. In order to have the modules loaded, you need to specify vtune=version PBS resource at job submit. The version is the same as for environment module. For example to use VTune/2016_update1:
```bash
$ qsub -q qexp -A OPEN-0-0 -I -l select=1,vtune=2016_update1
```
-After that, you can verify the modules sep*, pax and vtsspp are present in the kernel :
+After that, you can verify the modules sep\*, pax and vtsspp are present in the kernel :
```bash
$ lsmod | grep -e sep -e pax -e vtsspp
@@ -34,6 +33,7 @@ To launch the GUI, first load the module:
```bash
$ module add VTune/2016_update1
```
+
and launch the GUI :
```bash
@@ -44,8 +44,7 @@ The GUI will open in new window. Click on "New Project..." to create a new proje
To run a new analysis, click "New analysis...". You will see a list of possible analysis. Some of them will not be possible on the current CPU (eg. Intel Atom analysis is not possible on Sandy bridge CPU), the GUI will show an error box if you select the wrong analysis. For example, select "Advanced Hotspots". Clicking on Start will start profiling of the application.
-Remote Analysis
----------------
+## Remote Analysis
VTune Amplifier also allows a form of remote analysis. In this mode, data for analysis is collected from the command line without GUI, and the results are then loaded to GUI on another machine. This allows profiling without interactive graphical jobs. To perform a remote analysis, launch a GUI somewhere, open the new analysis window and then click the button "Command line" in bottom right corner. It will show the command line needed to perform the selected analysis.
@@ -57,17 +56,17 @@ The command line will look like this:
Copy the line to clipboard and then you can paste it in your jobscript or in command line. After the collection is run, open the GUI once again, click the menu button in the upper right corner, and select "Open > Result...". The GUI will load the results from the run.
-Xeon Phi
---------
+## Xeon Phi
+
It is possible to analyze both native and offloaded Xeon Phi applications.
### Native mode
-This mode is useful for native Xeon Phi applications launched directly on the card. In *Analysis Target* window, select *Intel Xeon Phi coprocessor (native), *choose path to the binary and MIC card to run on.
+This mode is useful for native Xeon Phi applications launched directly on the card. In _Analysis Target_ window, select _Intel Xeon Phi coprocessor (native), _choose path to the binary and MIC card to run on.
### Offload mode
-This mode is useful for applications that are launched from the host and use offload, OpenCL or mpirun. In *Analysis Target* window, select *Intel Xeon Phi coprocessor (native), *choose path to the binaryand MIC card to run on.
+This mode is useful for applications that are launched from the host and use offload, OpenCL or mpirun. In _Analysis Target_ window, select _Intel Xeon Phi coprocessor (native), _choose path to the binaryand MIC card to run on.
!!! Note "Note"
If the analysis is interrupted or aborted, further analysis on the card might be impossible and you will get errors like "ERROR connecting to MIC card". In this case please contact our support to reboot the MIC card.
@@ -88,8 +87,8 @@ Host launch:
You can obtain this command line by pressing the "Command line..." button on Analysis Type screen.
-References
-----------
+## References
+
1. <https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf> Performance Tuning for Intel® Xeon Phi™ Coprocessors
2. <https://software.intel.com/en-us/intel-vtune-amplifier-xe-support/documentation> >Intel® VTune™ Amplifier Support
3. <https://software.intel.com/en-us/amplifier_help_linux>
diff --git a/docs.it4i/salomon/software/debuggers/total-view.md b/docs.it4i/salomon/software/debuggers/total-view.md
index 7781ab41042c06cef7484f78c22a4d877bff4af4..27cd6c56f30db92de764d6812f328d84b98772b0 100644
--- a/docs.it4i/salomon/software/debuggers/total-view.md
+++ b/docs.it4i/salomon/software/debuggers/total-view.md
@@ -1,10 +1,9 @@
-Total View
-==========
+# Total View
TotalView is a GUI-based source code multi-process, multi-thread debugger.
-License and Limitations for cluster Users
------------------------------------------
+## License and Limitations for cluster Users
+
On the cluster users can debug OpenMP or MPI code that runs up to 64 parallel processes. These limitation means that:
```bash
@@ -16,8 +15,7 @@ Debugging of GPU accelerated codes is also supported.
You can check the status of the licenses [here](https://extranet.it4i.cz/rsweb/anselm/license/totalview).
-Compiling Code to run with TotalView
-------------------------------------
+## Compiling Code to run with TotalView
### Modules
@@ -50,10 +48,10 @@ Before debugging, you need to compile your code with theses flags:
!!! Note "Note"
**-g** : Generates extra debugging information usable by GDB. -g3 includes even more debugging information. This option is available for GNU and INTEL C/C++ and Fortran compilers.
- **-O0** : Suppress all optimizations.
+ **-O0** : Suppress all optimizations.
+
+## Starting a Job with TotalView
-Starting a Job with TotalView
------------------------------
Be sure to log in with an X window forwarding enabled. This could mean using the -X in the ssh:
```bash
@@ -148,7 +146,6 @@ After running previous command you will see the same window as shown in the scre
More information regarding the command line parameters of the TotalView can be found TotalView Reference Guide, Chapter 7: TotalView Command Syntax.
-Documentation
--------------
+## Documentation
[1] The [TotalView documentation](http://www.roguewave.com/support/product-documentation/totalview-family.aspx#totalview) web page is a good resource for learning more about some of the advanced TotalView features.
diff --git a/docs.it4i/salomon/software/debuggers/valgrind.md b/docs.it4i/salomon/software/debuggers/valgrind.md
index df3bda344fc9a0d41599a573e6405632ce2b6983..fd9615bc83015b0609bed2e13ed97f957d5fd760 100644
--- a/docs.it4i/salomon/software/debuggers/valgrind.md
+++ b/docs.it4i/salomon/software/debuggers/valgrind.md
@@ -1,8 +1,7 @@
-Valgrind
-========
+# Valgrind
+
+## About Valgrind
-About Valgrind
---------------
Valgrind is an open-source tool, used mainly for debuggig memory-related problems, such as memory leaks, use of uninitalized memory etc. in C/C++ applications. The toolchain was however extended over time with more functionality, such as debugging of threaded applications, cache profiling, not limited only to C/C++.
Valgind is an extremely useful tool for debugging memory errors such as [off-by-one](http://en.wikipedia.org/wiki/Off-by-one_error). Valgrind uses a virtual machine and dynamic recompilation of binary code, because of that, you can expect that programs being debugged by Valgrind run 5-100 times slower.
@@ -16,16 +15,16 @@ The main tools available in Valgrind are :
- **Callgrind**, a callgraph analyzer.
- For a full list and detailed documentation, please refer to the [official Valgrind documentation](http://valgrind.org/docs/).
-Installed versions
-------------------
+## Installed versions
+
There are two versions of Valgrind available on the cluster.
-- Version 3.8.1, installed by operating system vendor in /usr/bin/valgrind. This version is available by default, without the need to load any module. This version however does not provide additional MPI support. Also, it does not support AVX2 instructions, debugging of an AVX2-enabled executable with this version will fail
-- Version 3.11.0 built by ICC with support for Intel MPI, available in module Valgrind/3.11.0-intel-2015b. After loading the module, this version replaces the default valgrind.
-- Version 3.11.0 built by GCC with support for Open MPI, module Valgrind/3.11.0-foss-2015b
+- Version 3.8.1, installed by operating system vendor in /usr/bin/valgrind. This version is available by default, without the need to load any module. This version however does not provide additional MPI support. Also, it does not support AVX2 instructions, debugging of an AVX2-enabled executable with this version will fail
+- Version 3.11.0 built by ICC with support for Intel MPI, available in module Valgrind/3.11.0-intel-2015b. After loading the module, this version replaces the default valgrind.
+- Version 3.11.0 built by GCC with support for Open MPI, module Valgrind/3.11.0-foss-2015b
+
+## Usage
-Usage
------
Compile the application which you want to debug as usual. It is advisable to add compilation flags -g (to add debugging information to the binary so that you will see original source code lines in the output) and -O0 (to disable compiler optimizations).
For example, lets look at this C code, which has two problems:
@@ -55,7 +54,7 @@ Now, compile it with Intel compiler:
Now, lets run it with Valgrind. The syntax is:
-valgrind [valgrind options] <your program binary> [your program options]
+valgrind [valgrind options] <your program binary> [your program options]
If no Valgrind options are specified, Valgrind defaults to running Memcheck tool. Please refer to the Valgrind documentation for a full description of command line options.
@@ -131,8 +130,8 @@ In the output we can see that Valgrind has detected both errors - the off-by-one
Now we can see that the memory leak is due to the malloc() at line 6.
-Usage with MPI
----------------------------
+## Usage with MPI
+
Although Valgrind is not primarily a parallel debugger, it can be used to debug parallel applications as well. When launching your parallel applications, prepend the valgrind command. For example:
```bash
diff --git a/docs.it4i/salomon/software/debuggers/vampir.md b/docs.it4i/salomon/software/debuggers/vampir.md
index c19f105f006d40733b80443f42b11b119db6a626..ad4e97cf55b02254012b728f724e55bbb00fe9a4 100644
--- a/docs.it4i/salomon/software/debuggers/vampir.md
+++ b/docs.it4i/salomon/software/debuggers/vampir.md
@@ -1,12 +1,11 @@
-Vampir
-======
+# 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
-------------------
+## Installed versions
+
Version 8.5.0 is currently installed as module Vampir/8.5.0 :
```bash
@@ -14,11 +13,10 @@ Version 8.5.0 is currently installed as module Vampir/8.5.0 :
$ vampir &
```
-User manual
------------
+## User manual
+
You can find the detailed user manual in PDF format in $EBROOTVAMPIR/doc/vampir-manual.pdf
-References
-----------
-1. <https://www.vampir.eu>
+## References
+1. <https://www.vampir.eu>
diff --git a/docs.it4i/salomon/software/index.md b/docs.it4i/salomon/software/index.md
index da0befc72109dad8ce4f5c764a6eb40a79237bd2..cebebebfeac0e20cc3679a03176f77e03c72af11 100644
--- a/docs.it4i/salomon/software/index.md
+++ b/docs.it4i/salomon/software/index.md
@@ -1,64 +1,64 @@
-Salomon Cluster Software
-===
+# Salomon Cluster Software
## [Modules](../../modules-salomon)
-* List of Available Modules
-## [Compilers](compilers)
-* Available compilers, including GNU, INTEL and UPC compilers
-## [Intel Xeon Phi](intel-xeon-phi)
-* A guide to Intel Xeon Phi usage
-## [Java](java)
-* Java on the cluster
-## [Operating System](operating-system)
-* The operating system, deployed on Salomon cluster
-## Intel Suite
-* The Intel Parallel Studio XE
-### [Introduction](intel-suite/intel-parallel-studio-introduction)
-### [Intel MKL](intel-suite/intel-mkl)
-### [Intel Compilers](intel-suite/intel-compilers)
-### [Intel IPP](intel-suite/intel-integrated-performance-primitives)
-### [Intel TBB](intel-suite/intel-tbb)
-### [Intel Debugger](intel-suite/intel-debugger)
-### [Intel Inspector](intel-suite/intel-inspector)
-### [Intel Trace Analyzer and Collector](intel-suite/intel-trace-analyzer-and-collector)
-### [Intel Advisor](intel-suite/intel-advisor)
-## MPI
-* Message Passing Interface libraries
-### [Introduction](mpi/mpi)
-### [MPI4Py (MPI for Python)](mpi/mpi4py-mpi-for-python)
-### [Running Open MPI](mpi/Running_OpenMPI)
-## Debuggers
-* A collection of development tools
-### [Introduction](debuggers/Introduction)
-### [Valgrind](debuggers/valgrind)
-### [Allinea Forge (DDT,MAP)](debuggers/allinea-ddt)
-### [Total View](debuggers/total-view)
-### [Intel VTune Amplifier XE](debuggers/intel-vtune-amplifier)
-### [Aislinn](debuggers/aislinn)
-### [Allinea Performance Reports](debuggers/allinea-performance-reports)
-### [Vampir](debuggers/vampir)
-## Numerical Languages
-* Interpreted languages for numerical computations
-### [Introduction](numerical-languages/introduction)
-### [R](numerical-languages/r)
-### [MATLAB](numerical-languages/matlab)
-### [Octave](numerical-languages/octave)
-## Chemistry
-* Tools for computational chemistry
-### [Molpro](chemistry/molpro)
-### [Phono3py](chemistry/phono3py)
-### [NWChem](chemistry/nwchem)
-## COMSOL
-* A finite element analysis, solver and Simulation software
-### [COMSOL](comsol/comsol-multiphysics)
-### [Licensing and Available Versions](comsol/licensing-and-available-versions)
-## ANSYS
-* An engineering simulation software
-### [Introduction](ansys/ansys)
-### [Workbench](ansys/workbench)
-### [ANSYS CFX](ansys/ansys-cfx)
-### [ANSYS LS-DYNA](ansys/ansys-ls-dyna)
-### [ANSYS MAPDL](ansys/ansys-mechanical-apdl)
-### [ANSYS Fluent](ansys/ansys-fluent)
-### [Setting license preferences](ansys/licensing)
-### [Licensing and Available Versions](ansys/setting-license-preferences)
+
+- List of Available Modules
+ ## [Compilers](compilers)
+- Available compilers, including GNU, INTEL and UPC compilers
+ ## [Intel Xeon Phi](intel-xeon-phi)
+- A guide to Intel Xeon Phi usage
+ ## [Java](java)
+- Java on the cluster
+ ## [Operating System](operating-system)
+- The operating system, deployed on Salomon cluster
+ ## Intel Suite
+- The Intel Parallel Studio XE
+ ### [Introduction](intel-suite/intel-parallel-studio-introduction)
+ ### [Intel MKL](intel-suite/intel-mkl)
+ ### [Intel Compilers](intel-suite/intel-compilers)
+ ### [Intel IPP](intel-suite/intel-integrated-performance-primitives)
+ ### [Intel TBB](intel-suite/intel-tbb)
+ ### [Intel Debugger](intel-suite/intel-debugger)
+ ### [Intel Inspector](intel-suite/intel-inspector)
+ ### [Intel Trace Analyzer and Collector](intel-suite/intel-trace-analyzer-and-collector)
+ ### [Intel Advisor](intel-suite/intel-advisor)
+ ## MPI
+- Message Passing Interface libraries
+ ### [Introduction](mpi/mpi)
+ ### [MPI4Py (MPI for Python)](mpi/mpi4py-mpi-for-python)
+ ### [Running Open MPI](mpi/Running_OpenMPI)
+ ## Debuggers
+- A collection of development tools
+ ### [Introduction](debuggers/Introduction)
+ ### [Valgrind](debuggers/valgrind)
+ ### [Allinea Forge (DDT,MAP)](debuggers/allinea-ddt)
+ ### [Total View](debuggers/total-view)
+ ### [Intel VTune Amplifier XE](debuggers/intel-vtune-amplifier)
+ ### [Aislinn](debuggers/aislinn)
+ ### [Allinea Performance Reports](debuggers/allinea-performance-reports)
+ ### [Vampir](debuggers/vampir)
+ ## Numerical Languages
+- Interpreted languages for numerical computations
+ ### [Introduction](numerical-languages/introduction)
+ ### [R](numerical-languages/r)
+ ### [MATLAB](numerical-languages/matlab)
+ ### [Octave](numerical-languages/octave)
+ ## Chemistry
+- Tools for computational chemistry
+ ### [Molpro](chemistry/molpro)
+ ### [Phono3py](chemistry/phono3py)
+ ### [NWChem](chemistry/nwchem)
+ ## COMSOL
+- A finite element analysis, solver and Simulation software
+ ### [COMSOL](comsol/comsol-multiphysics)
+ ### [Licensing and Available Versions](comsol/licensing-and-available-versions)
+ ## ANSYS
+- An engineering simulation software
+ ### [Introduction](ansys/ansys)
+ ### [Workbench](ansys/workbench)
+ ### [ANSYS CFX](ansys/ansys-cfx)
+ ### [ANSYS LS-DYNA](ansys/ansys-ls-dyna)
+ ### [ANSYS MAPDL](ansys/ansys-mechanical-apdl)
+ ### [ANSYS Fluent](ansys/ansys-fluent)
+ ### [Setting license preferences](ansys/licensing)
+ ### [Licensing and Available Versions](ansys/setting-license-preferences)
diff --git a/docs.it4i/salomon/software/intel-suite/intel-advisor.md b/docs.it4i/salomon/software/intel-suite/intel-advisor.md
index 3d074032a5709b27148738c992fe991341ec79c7..484c781d67a614d090244f53b0d8e715936f0b0f 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-advisor.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-advisor.md
@@ -1,16 +1,15 @@
-Intel Advisor
-=============
+# Intel Advisor
is tool aiming to assist you in vectorization and threading of your code. You can use it to profile your application and identify loops, that could benefit from vectorization and/or threading parallelism.
-Installed versions
-------------------
+## Installed versions
+
The following versions are currently available on Salomon as modules:
2016 Update 2 - Advisor/2016_update2
-Usage
------
+## Usage
+
Your program should be compiled with -g switch to include symbol names. You should compile with -O2 or higher to see code that is already vectorized by the compiler.
Profiling is possible either directly from the GUI, or from command line.
@@ -21,12 +20,12 @@ To profile from GUI, launch Advisor:
$ advixe-gui
```
-Then select menu File -> New -> Project. Choose a directory to save project data to. After clicking OK, Project properties window will appear, where you can configure path to your binary, launch arguments, working directory etc. After clicking OK, the project is ready.
+Then select menu File -> New -> Project. Choose a directory to save project data to. After clicking OK, Project properties window will appear, where you can configure path to your binary, launch arguments, working directory etc. After clicking OK, the project is ready.
In the left pane, you can switch between Vectorization and Threading workflows. Each has several possible steps which you can execute by clicking Collect button. Alternatively, you can click on Command Line, to see the command line required to run the analysis directly from command line.
-References
-----------
+## References
+
1. [Intel® Advisor 2015 Tutorial: Find Where to Add Parallelism - C++ Sample](https://software.intel.com/en-us/intel-advisor-tutorial-vectorization-windows-cplusplus)
2. [Product page](https://software.intel.com/en-us/intel-advisor-xe)
3. [Documentation](https://software.intel.com/en-us/intel-advisor-2016-user-guide-linux)
diff --git a/docs.it4i/salomon/software/intel-suite/intel-compilers.md b/docs.it4i/salomon/software/intel-suite/intel-compilers.md
index 0b61d00afc3b7ecc7122d56994313bfa8dafdc6d..1157d602d8f2fb486e440010e6f5d5baa917b80c 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-compilers.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-compilers.md
@@ -1,5 +1,4 @@
-Intel Compilers
-===============
+# Intel Compilers
The Intel compilers in multiple versions are available, via module intel. The compilers include the icc C and C++ compiler and the ifort fortran 77/90/95 compiler.
@@ -29,8 +28,8 @@ The compiler recognizes the omp, simd, vector and ivdep pragmas for OpenMP paral
Read more at <https://software.intel.com/en-us/intel-cplusplus-compiler-16.0-user-and-reference-guide>
-Sandy Bridge/Ivy Bridge/Haswell binary compatibility
-----------------------------------------------------
+## Sandy Bridge/Ivy Bridge/Haswell binary compatibility
+
Anselm nodes are currently equipped with Sandy Bridge CPUs, while Salomon compute nodes are equipped with Haswell based architecture. The UV1 SMP compute server has Ivy Bridge CPUs, which are equivalent to Sandy Bridge (only smaller manufacturing technology). The new processors are backward compatible with the Sandy Bridge nodes, so all programs that ran on the Sandy Bridge processors, should also run on the new Haswell nodes. To get optimal performance out of the Haswell processors a program should make use of the special AVX2 instructions for this processor. One can do this by recompiling codes with the compiler flags designated to invoke these instructions. For the Intel compiler suite, there are two ways of doing this:
- Using compiler flag (both for Fortran and C): -xCORE-AVX2. This will create a binary with AVX2 instructions, specifically for the Haswell processors. Note that the executable will not run on Sandy Bridge/Ivy Bridge nodes.
diff --git a/docs.it4i/salomon/software/intel-suite/intel-debugger.md b/docs.it4i/salomon/software/intel-suite/intel-debugger.md
index 7452cbb501860d8117a480bc0d6e524c73e49311..5be127bbf5e539e0670ec876a882289e29c3ff50 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-debugger.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-debugger.md
@@ -1,10 +1,9 @@
-Intel Debugger
-==============
+# Intel Debugger
IDB is no longer available since Intel Parallel Studio 2015
-Debugging serial applications
------------------------------
+## Debugging serial applications
+
The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use [X display](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/) for running the GUI.
```bash
@@ -36,8 +35,8 @@ Example:
In this example, we allocate 1 full compute node, compile program myprog.c with debugging options -O0 -g and run the idb debugger interactively on the myprog.x executable. The GUI access is via X11 port forwarding provided by the PBS workload manager.
-Debugging parallel applications
--------------------------------
+## Debugging parallel applications
+
Intel debugger is capable of debugging multithreaded and MPI parallel programs as well.
### Small number of MPI ranks
@@ -72,6 +71,6 @@ Run the idb debugger from within the MPI debug option. This will cause the debug
Run the idb debugger in GUI mode. The menu Parallel contains number of tools for debugging multiple threads. One of the most useful tools is the **Serialize Execution** tool, which serializes execution of concurrent threads for easy orientation and identification of concurrency related bugs.
-Further information
--------------------
+## Further information
+
Exhaustive manual on idb features and usage is published at Intel website, <https://software.intel.com/sites/products/documentation/doclib/iss/2013/compiler/cpp-lin/>
diff --git a/docs.it4i/salomon/software/intel-suite/intel-inspector.md b/docs.it4i/salomon/software/intel-suite/intel-inspector.md
index 992b7bd15450d1d523b2f149d1fd1e0c2f99b206..94ad54776417204210a68f4c70ed4edc1eed0345 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-inspector.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-inspector.md
@@ -1,16 +1,15 @@
-Intel Inspector
-===============
+# Intel Inspector
Intel Inspector is a dynamic memory and threading error checking tool for C/C++/Fortran applications. It can detect issues such as memory leaks, invalid memory references, uninitalized variables, race conditions, deadlocks etc.
-Installed versions
-------------------
+## Installed versions
+
The following versions are currently available on Salomon as modules:
2016 Update 1 - Inspector/2016_update1
-Usage
------
+## Usage
+
Your program should be compiled with -g switch to include symbol names. Optimizations can be turned on.
Debugging is possible either directly from the GUI, or from command line.
@@ -23,7 +22,7 @@ To debug from GUI, launch Inspector:
$ inspxe-gui &
```
-Then select menu File -> New -> Project. Choose a directory to save project data to. After clicking OK, Project properties window will appear, where you can configure path to your binary, launch arguments, working directory etc. After clicking OK, the project is ready.
+Then select menu File -> New -> Project. Choose a directory to save project data to. After clicking OK, Project properties window will appear, where you can configure path to your binary, launch arguments, working directory etc. After clicking OK, the project is ready.
In the main pane, you can start a predefined analysis type or define your own. Click Start to start the analysis. Alternatively, you can click on Command Line, to see the command line required to run the analysis directly from command line.
@@ -31,10 +30,10 @@ In the main pane, you can start a predefined analysis type or define your own. C
Analysis can be also run from command line in batch mode. Batch mode analysis is run with command inspxe-cl. To obtain the required parameters, either consult the documentation or you can configure the analysis in the GUI and then click "Command Line" button in the lower right corner to the respective command line.
-Results obtained from batch mode can be then viewed in the GUI by selecting File -> Open -> Result...
+Results obtained from batch mode can be then viewed in the GUI by selecting File -> Open -> Result...
+
+## References
-References
-----------
1. [Product page](https://software.intel.com/en-us/intel-inspector-xe)
2. [Documentation and Release Notes](https://software.intel.com/en-us/intel-inspector-xe-support/documentation)
3. [Tutorials](https://software.intel.com/en-us/articles/inspectorxe-tutorials)
diff --git a/docs.it4i/salomon/software/intel-suite/intel-integrated-performance-primitives.md b/docs.it4i/salomon/software/intel-suite/intel-integrated-performance-primitives.md
index b324e2339143e63a43e6de72a86cd0d83682b9db..fb040dd18c6330c3fe2bcf943c2963cf8125ed2a 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-integrated-performance-primitives.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-integrated-performance-primitives.md
@@ -1,8 +1,7 @@
-Intel IPP
-=========
+# Intel IPP
+
+## Intel Integrated Performance Primitives
-Intel Integrated Performance Primitives
---------------------------------------
Intel Integrated Performance Primitives, version 9.0.1, compiled for AVX2 vector instructions is available, via module ipp. The IPP is a very rich library of highly optimized algorithmic building blocks for media and data applications. This includes signal, image and frame processing algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax, as well as cryptographic functions, linear algebra functions and many more.
Check out IPP before implementing own math functions for data processing, it is likely already there.
@@ -13,8 +12,7 @@ Check out IPP before implementing own math functions for data processing, it is
The module sets up environment variables, required for linking and running ipp enabled applications.
-IPP example
------------
+## IPP example
```cpp
#include "ipp.h"
@@ -75,8 +73,8 @@ You will need the ipp module loaded to run the ipp enabled executable. This may
$ icc testipp.c -o testipp.x -Wl,-rpath=$LIBRARY_PATH -lippi -lipps -lippcore
```
-Code samples and documentation
-------------------------------
+## Code samples and documentation
+
Intel provides number of [Code Samples for IPP](https://software.intel.com/en-us/articles/code-samples-for-intel-integrated-performance-primitives-library), illustrating use of IPP.
Read full documentation on IPP [on Intel website,](http://software.intel.com/sites/products/search/search.php?q=&x=15&y=6&product=ipp&version=7.1&docos=lin) in particular the [IPP Reference manual.](http://software.intel.com/sites/products/documentation/doclib/ipp_sa/71/ipp_manual/index.htm)
diff --git a/docs.it4i/salomon/software/intel-suite/intel-mkl.md b/docs.it4i/salomon/software/intel-suite/intel-mkl.md
index 43a2ff1e310d33d6bc0c9d8984a71c5eb4681454..43278dbc0b30d6569b14f51507503780984f04aa 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-mkl.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-mkl.md
@@ -1,14 +1,12 @@
-Intel MKL
-=========
+# Intel MKL
+## Intel Math Kernel Library
-Intel Math Kernel Library
--------------------------
Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, extensively threaded and optimized for maximum performance. Intel MKL provides these basic math kernels:
- BLAS (level 1, 2, and 3) and LAPACK linear algebra routines, offering vector, vector-matrix, and matrix-matrix operations.
- The PARDISO direct sparse solver, an iterative sparse solver, and supporting sparse BLAS (level 1, 2, and 3) routines for solving sparse systems of equations.
-- ScaLAPACK distributed processing linear algebra routines for Linux* and Windows* operating systems, as well as the Basic Linear Algebra Communications Subprograms (BLACS) and the Parallel Basic Linear Algebra Subprograms (PBLAS).
+- ScaLAPACK distributed processing linear algebra routines for Linux_ and Windows_ operating systems, as well as the Basic Linear Algebra Communications Subprograms (BLACS) and the Parallel Basic Linear Algebra Subprograms (PBLAS).
- Fast Fourier transform (FFT) functions in one, two, or three dimensions with support for mixed radices (not limited to sizes that are powers of 2), as well as distributed versions of these functions.
- Vector Math Library (VML) routines for optimized mathematical operations on vectors.
- Vector Statistical Library (VSL) routines, which offer high-performance vectorized random number generators (RNG) for several probability distributions, convolution and correlation routines, and summary statistics functions.
@@ -31,10 +29,10 @@ Intel MKL library may be linked using any compiler. With intel compiler use -mkl
Intel MKL library provides number of interfaces. The fundamental once are the LP64 and ILP64. The Intel MKL ILP64 libraries use the 64-bit integer type (necessary for indexing large arrays, with more than 231^-1 elements), whereas the LP64 libraries index arrays with the 32-bit integer type.
-|Interface|Integer type|
-|---|---|
-|LP64|32-bit, int, integer(kind=4), MPI_INT|
-|ILP64|64-bit, long int, integer(kind=8), MPI_INT64|
+| Interface | Integer type |
+| --------- | -------------------------------------------- |
+| LP64 | 32-bit, int, integer(kind=4), MPI_INT |
+| ILP64 | 64-bit, long int, integer(kind=8), MPI_INT64 |
### Linking
@@ -59,8 +57,8 @@ For this to work, the application must link the threaded MKL library (default).
The application will run with 24 threads with affinity optimized for fine grain parallelization.
-Examples
-------------
+## Examples
+
Number of examples, demonstrating use of the Intel MKL library and its linking is available on clusters, in the $MKL_EXAMPLES directory. In the examples below, we demonstrate linking Intel MKL to Intel and GNU compiled program for multi-threaded matrix multiplication.
### Working with examples
@@ -113,14 +111,14 @@ In this example, we compile and link the cblas_dgemm example, using LP64 interf
In this example, we compile, link and run the cblas_dgemm example, using LP64 interface to threaded MKL and gnu OMP threads implementation.
-MKL and MIC accelerators
-------------------------
+## MKL and MIC accelerators
+
The Intel MKL is capable to automatically offload the computations o the MIC accelerator. See section [Intel Xeon Phi](../intel-xeon-phi/) for details.
-LAPACKE C Interface
--------------------
+## LAPACKE C Interface
+
MKL includes LAPACKE C Interface to LAPACK. For some reason, although Intel is the author of LAPACKE, the LAPACKE header files are not present in MKL. For this reason, we have prepared LAPACKE module, which includes Intel's LAPACKE headers from official LAPACK, which you can use to compile code using LAPACKE interface against MKL.
-Further reading
----------------
+## Further reading
+
Read more on [Intel website](http://software.intel.com/en-us/intel-mkl), in particular the [MKL users guide](https://software.intel.com/en-us/intel-mkl/documentation/linux).
diff --git a/docs.it4i/salomon/software/intel-suite/intel-parallel-studio-introduction.md b/docs.it4i/salomon/software/intel-suite/intel-parallel-studio-introduction.md
index 1fc21927a1f199d775f1894c5405069a3ea50069..c3d12d970eb39b9977cc253de2f0fa94a6cfdf1e 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-parallel-studio-introduction.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-parallel-studio-introduction.md
@@ -1,10 +1,9 @@
-Intel Parallel Studio
-=====================
+# Intel Parallel Studio
The Salomon cluster provides following elements of the Intel Parallel Studio XE
|Intel Parallel Studio XE|
-| -------------------------------------------------|
+\| -------------------------------------------------\|
|Intel Compilers|
|Intel Debugger|
|Intel MKL Library|
@@ -14,8 +13,7 @@ The Salomon cluster provides following elements of the Intel Parallel Studio XE
|Intel Advisor|
|Intel Inspector|
-Intel compilers
----------------
+## Intel compilers
The Intel compilers version 131.3 are available, via module iccifort/2013.5.192-GCC-4.8.3. The compilers include the icc C and C++ compiler and the ifort fortran 77/90/95 compiler.
@@ -27,11 +25,12 @@ The Intel compilers version 131.3 are available, via module iccifort/2013.5.192-
Read more at the [Intel Compilers](intel-compilers/) page.
-Intel debugger
---------------
+## Intel debugger
+
IDB is no longer available since Parallel Studio 2015.
The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment.
+
```bash
$ module load intel
$ idb
@@ -39,8 +38,8 @@ The intel debugger version 13.0 is available, via module intel. The debugger wor
Read more at the [Intel Debugger](intel-debugger/) page.
-Intel Math Kernel Library
--------------------------
+## Intel Math Kernel Library
+
Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, extensively threaded and optimized for maximum performance. Intel MKL unites and provides these basic components: BLAS, LAPACK, ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and many more.
```bash
@@ -49,8 +48,8 @@ Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, e
Read more at the [Intel MKL](intel-mkl/) page.
-Intel Integrated Performance Primitives
----------------------------------------
+## Intel Integrated Performance Primitives
+
Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is available, via module ipp. The IPP is a library of highly optimized algorithmic building blocks for media and data applications. This includes signal, image and frame processing algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many more.
```bash
@@ -59,8 +58,8 @@ Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is avai
Read more at the [Intel IPP](intel-integrated-performance-primitives/) page.
-Intel Threading Building Blocks
--------------------------------
+## Intel Threading Building Blocks
+
Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. It is designed to promote scalable data parallel programming. Additionally, it fully supports nested parallelism, so you can build larger parallel components from smaller parallel components. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner.
```bash
diff --git a/docs.it4i/salomon/software/intel-suite/intel-tbb.md b/docs.it4i/salomon/software/intel-suite/intel-tbb.md
index 7d05e24e1241192b0a390337d407a2feed0887cd..27abcfc226c3b34947301391d421e97ad1603a58 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-tbb.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-tbb.md
@@ -1,8 +1,7 @@
-Intel TBB
-=========
+# Intel TBB
+
+## Intel Threading Building Blocks
-Intel Threading Building Blocks
-------------------------------
Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner. The tasks are executed by a runtime scheduler and may be offloaded to [MIC accelerator](../intel-xeon-phi/).
Intel TBB version 4.3.5.187 is available on the cluster.
@@ -15,8 +14,8 @@ The module sets up environment variables, required for linking and running tbb e
Link the tbb library, using -ltbb
-Examples
---------
+## Examples
+
Number of examples, demonstrating use of TBB and its built-in scheduler is available on Anselm, in the $TBB_EXAMPLES directory.
```bash
@@ -36,6 +35,6 @@ You will need the tbb module loaded to run the tbb enabled executable. This may
$ icc -O2 -o primes.x main.cpp primes.cpp -Wl,-rpath=$LIBRARY_PATH -ltbb
```
-Further reading
----------------
+## Further reading
+
Read more on Intel website, <http://software.intel.com/sites/products/documentation/doclib/tbb_sa/help/index.htm>
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 62fe24fee7a803b7ba28660bf3eb1561423c85a4..9d9f9fd43d22c7dd952366b6ae1a41f854a23e17 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
@@ -1,16 +1,15 @@
-Intel Trace Analyzer and Collector
-==================================
+# Intel Trace Analyzer and Collector
Intel Trace Analyzer and Collector (ITAC) is a tool to collect and graphicaly analyze behaviour of MPI applications. It helps you to analyze communication patterns of your application, identify hotspots, perform correctnes checking (identify deadlocks, data corruption etc), simulate how your application would run on a different interconnect.
ITAC is a offline analysis tool - first you run your application to collect a trace file, then you can open the trace in a GUI analyzer to view it.
-Installed version
------------------
+## Installed version
+
Currently on Salomon is version 9.1.2.024 available as module itac/9.1.2.024
-Collecting traces
------------------
+## Collecting traces
+
ITAC can collect traces from applications that are using Intel MPI. To generate a trace, simply add -trace option to your mpirun command :
```bash
@@ -20,8 +19,8 @@ ITAC can collect traces from applications that are using Intel MPI. To generate
The trace will be saved in file myapp.stf in the current directory.
-Viewing traces
---------------
+## Viewing traces
+
To view and analyze the trace, open ITAC GUI in a [graphical environment](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/):
```bash
@@ -35,8 +34,7 @@ The GUI will launch and you can open the produced `*`.stf file.
Please refer to Intel documenation about usage of the GUI tool.
-References
-----------
+## References
+
1. [Getting Started with Intel® Trace Analyzer and Collector](https://software.intel.com/en-us/get-started-with-itac-for-linux)
2. [Intel® Trace Analyzer and Collector - Documentation](https://software.intel.com/en-us/intel-trace-analyzer)
-
diff --git a/docs.it4i/salomon/software/intel-xeon-phi.md b/docs.it4i/salomon/software/intel-xeon-phi.md
index 19ec77df6a20de50e769244affc8cc63391aceb1..3f351927e3053f511d8dd1a8cc0904c7838d0c2c 100644
--- a/docs.it4i/salomon/software/intel-xeon-phi.md
+++ b/docs.it4i/salomon/software/intel-xeon-phi.md
@@ -1,12 +1,11 @@
-Intel Xeon Phi
-==============
+# Intel Xeon Phi
-##A guide to Intel Xeon Phi usage
+\##A guide to Intel Xeon Phi usage
Intel Xeon Phi can be programmed in several modes. The default mode on Anselm is offload mode, but all modes described in this document are supported.
-Intel Utilities for Xeon Phi
-----------------------------
+## Intel Utilities for Xeon Phi
+
To get access to a compute node with Intel Xeon Phi accelerator, use the PBS interactive session
```bash
@@ -89,8 +88,8 @@ The output of the "micinfo" utility executed on one of the Anselm node is as fol
GDDR Voltage : 1501000 uV
```
-Offload Mode
-------------
+## Offload Mode
+
To compile a code for Intel Xeon Phi a MPSS stack has to be installed on the machine where compilation is executed. Currently the MPSS stack is only installed on compute nodes equipped with accelerators.
```bash
@@ -238,8 +237,8 @@ Some interesting compiler flags useful not only for code debugging are:
Performance ooptimization
xhost - FOR HOST ONLY - to generate AVX (Advanced Vector Extensions) instructions.
-Automatic Offload using Intel MKL Library
------------------------------------------
+## Automatic Offload using Intel MKL Library
+
Intel MKL includes an Automatic Offload (AO) feature that enables computationally intensive MKL functions called in user code to benefit from attached Intel Xeon Phi coprocessors automatically and transparently.
Behavioral of automatic offload mode is controlled by functions called within the program or by environmental variables. Complete list of controls is listed [here](http://software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mkl_userguide_lnx/GUID-3DC4FC7D-A1E4-423D-9C0C-06AB265FFA86.htm).
@@ -357,8 +356,8 @@ The output of a code should look similar to following listing, where lines start
Done
```
-Native Mode
------------
+## Native Mode
+
In the native mode a program is executed directly on Intel Xeon Phi without involvement of the host machine. Similarly to offload mode, the code is compiled on the host computer with Intel compilers.
To compile a code user has to be connected to a compute with MIC and load Intel compilers module. To get an interactive session on a compute node with an Intel Xeon Phi and load the module use following commands:
@@ -420,12 +419,11 @@ For your information the list of libraries and their location required for execu
!!! 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:
@@ -433,8 +431,8 @@ Finally, to run the compiled code use:
$ ~/path_to_binary/vect-add-mic
```
-OpenCL
--------------------
+## OpenCL
+
OpenCL (Open Computing Language) is an open standard for general-purpose parallel programming for diverse mix of multi-core CPUs, GPU coprocessors, and other parallel processors. OpenCL provides a flexible execution model and uniform programming environment for software developers to write portable code for systems running on both the CPU and graphics processors or accelerators like the Intel® Xeon Phi.
On Anselm OpenCL is installed only on compute nodes with MIC accelerator, therefore OpenCL code can be compiled only on these nodes.
@@ -542,8 +540,7 @@ To see the performance of Intel Xeon Phi performing the DGEMM run the example as
!!! Note "Note"
Please note: GNU compiler is used to compile the OpenCL codes for Intel MIC. You do not need to load Intel compiler module.
-MPI
------------------
+## MPI
### Environment setup and compilation
@@ -605,11 +602,11 @@ Intel MPI for the Xeon Phi coprocessors offers different MPI programming models:
!!! Note "Note"
**Host-only model** - all MPI ranks reside on the host. The coprocessors can be used by using offload pragmas. (Using MPI calls inside offloaded code is not supported.)
- **Coprocessor-only model** - all MPI ranks reside only on the coprocessors.
+ **Coprocessor-only model** - all MPI ranks reside only on the coprocessors.
- **Symmetric model** - the MPI ranks reside on both the host and the coprocessor. Most general MPI case.
+ **Symmetric model** - the MPI ranks reside on both the host and the coprocessor. Most general MPI case.
-###Host-only model
+\###Host-only model
In this case all environment variables are set by modules, so to execute the compiled MPI program on a single node, use:
@@ -652,8 +649,8 @@ Similarly to execution of OpenMP programs in native mode, since the environmenta
!!! Note "Note"
Please note:
- - this file sets up both environmental variable for both MPI and OpenMP libraries.
- - this file sets up the paths to a particular version of Intel MPI library and particular version of an Intel compiler. These versions have to match with loaded modules.
+ - this file sets up both environmental variable for both MPI and OpenMP libraries.
+ - this file sets up the paths to a particular version of Intel MPI library and particular version of an Intel compiler. These versions have to match with loaded modules.
To access a MIC accelerator located on a node that user is currently connected to, use:
@@ -706,8 +703,8 @@ or using mpirun
!!! Note "Note"
Please note:
- - the full path to the binary has to specified (here: "**>~/mpi-test-mic**")
- - the LD_LIBRARY_PATH has to match with Intel MPI module used to compile the MPI code
+ \- the full path to the binary has to specified (here: "**>~/mpi-test-mic**")
+ \- the LD_LIBRARY_PATH has to match with Intel MPI module used to compile the MPI code
The output should be again similar to:
@@ -754,9 +751,9 @@ This output means that the PBS allocated nodes cn204 and cn205, which means that
!!! Note "Note"
Please note: At this point user can connect to any of the allocated nodes or any of the allocated MIC accelerators using ssh:
- - to connect to the second node : ** $ ssh cn205**
- - to connect to the accelerator on the first node from the first node: **$ ssh cn204-mic0** or **$ ssh mic0**
- - to connect to the accelerator on the second node from the first node: **$ ssh cn205-mic0**
+ - to connect to the second node : ** $ ssh cn205**
+ - to connect to the accelerator on the first node from the first node: **$ ssh cn204-mic0** or **$ ssh mic0**
+ - to connect to the accelerator on the second node from the first node: **$ ssh cn205-mic0**
At this point we expect that correct modules are loaded and binary is compiled. For parallel execution the mpiexec.hydra is used. Again the first step is to tell mpiexec that the MPI can be executed on MIC accelerators by setting up the environmental variable "I_MPI_MIC"
@@ -774,6 +771,7 @@ The launch the MPI program use:
-host cn204-mic0 -n 4 ~/mpi-test-mic
: -host cn205-mic0 -n 6 ~/mpi-test-mic
```
+
or using mpirun:
```bash
@@ -811,7 +809,7 @@ The same way MPI program can be executed on multiple hosts:
: -host cn205 -n 6 ~/mpi-test
```
-###Symmetric model
+\###Symmetric model
In a symmetric mode MPI programs are executed on both host computer(s) and MIC accelerator(s). Since MIC has a different
architecture and requires different binary file produced by the Intel compiler two different files has to be compiled before MPI program is executed.
@@ -899,6 +897,6 @@ PBS also generates a set of node-files that can be used instead of manually crea
Please note each host or accelerator is listed only per files. User has to specify how many jobs should be executed per node using "-n" parameter of the mpirun command.
-Optimization
-------------
-For more details about optimization techniques please read Intel document [Optimization and Performance Tuning for Intel® Xeon Phi™ Coprocessors](http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization "http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization")
+## Optimization
+
+For more details about optimization techniques please read Intel document [Optimization and Performance Tuning for Intel® Xeon Phi™ Coprocessors](http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization "http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization")
diff --git a/docs.it4i/salomon/software/java.md b/docs.it4i/salomon/software/java.md
index 70b522d0b572bc9acda72317dba0baebe7465f85..f607960cd793a6a84315cf11651416157d6bd015 100644
--- a/docs.it4i/salomon/software/java.md
+++ b/docs.it4i/salomon/software/java.md
@@ -1,5 +1,4 @@
-Java
-====
+# Java
**Java on the cluster**
diff --git a/docs.it4i/salomon/software/mpi/Running_OpenMPI.md b/docs.it4i/salomon/software/mpi/Running_OpenMPI.md
index d6656a1223ca0bfe00a90865795adead81303614..a9b73cc602a5b211b1f7c96c83708e0a04ef8982 100644
--- a/docs.it4i/salomon/software/mpi/Running_OpenMPI.md
+++ b/docs.it4i/salomon/software/mpi/Running_OpenMPI.md
@@ -1,8 +1,7 @@
-Running OpenMPI
-===============
+# Running OpenMPI
+
+## OpenMPI program execution
-OpenMPI program execution
--------------------------
The OpenMPI programs may be executed only via the PBS Workload manager, by entering an appropriate queue. On the cluster, the **OpenMPI 1.8.6** is OpenMPI based MPI implementation.
### Basic usage
@@ -117,8 +116,8 @@ As of OpenMP 4.0 (supported by GCC 4.9 and later and Intel 14.0 and later) the f
$ export OMP_PLACES=cores
```
-OpenMPI Process Mapping and Binding
-------------------------------------------------
+## OpenMPI Process Mapping and Binding
+
The mpiexec allows for precise selection of how the MPI processes will be mapped to the computational nodes and how these processes will bind to particular processor sockets and cores.
MPI process mapping may be specified by a hostfile or rankfile input to the mpiexec program. Altough all implementations of MPI provide means for process mapping and binding, following examples are valid for the openmpi only.
@@ -199,15 +198,15 @@ In all cases, binding and threading may be verified by executing for example:
$ mpiexec -bysocket -bind-to-socket echo $OMP_NUM_THREADS
```
-Changes in OpenMPI 1.8
-----------------------
+## Changes in OpenMPI 1.8
+
Some options have changed in OpenMPI version 1.8.
- |version 1.6.5 |version 1.8.1 |
- | --- | --- |
- |--bind-to-none |--bind-to none |
- |--bind-to-core |--bind-to core |
- |--bind-to-socket |--bind-to socket |
- |-bysocket |--map-by socket |
- |-bycore |--map-by core |
- |-pernode |--map-by ppr:1:node |
+| version 1.6.5 | version 1.8.1 |
+| ---------------- | ------------------- |
+| --bind-to-none | --bind-to none |
+| --bind-to-core | --bind-to core |
+| --bind-to-socket | --bind-to socket |
+| -bysocket | --map-by socket |
+| -bycore | --map-by core |
+| -pernode | --map-by ppr:1:node |
diff --git a/docs.it4i/salomon/software/mpi/mpi.md b/docs.it4i/salomon/software/mpi/mpi.md
index e17e0a08c04bd1bc102ce0167049ce670d001aae..b4ea7dd7a106b3fff859b129d45668d5ad7183e1 100644
--- a/docs.it4i/salomon/software/mpi/mpi.md
+++ b/docs.it4i/salomon/software/mpi/mpi.md
@@ -1,17 +1,15 @@
-MPI
-===
+# MPI
-Setting up MPI Environment
---------------------------
+## Setting up MPI Environment
The Salomon cluster provides several implementations of the MPI library:
-|MPI Library|Thread support|
-|---|---|---
-|**Intel MPI 4.1**|Full thread support up to, MPI_THREAD_MULTIPLE|
-|**Intel MPI 5.0**|Full thread support up to, MPI_THREAD_MULTIPLE|
-|OpenMPI 1.8.6|Full thread support up to, MPI_THREAD_MULTIPLE, MPI-3.0, support|
-|SGI MPT 2.12 ||
+| MPI Library | Thread support |
+| ----------------- | ------------------------------------------------------------------------------------------------------ |
+| **Intel MPI 4.1** | Full thread support up to, MPI_THREAD_MULTIPLE |
+| **Intel MPI 5.0** | Full thread support up to, MPI_THREAD_MULTIPLE |
+| OpenMPI 1.8.6 | Full thread support up to, MPI_THREAD_MULTIPLE, MPI-3.0, support |
+| SGI MPT 2.12 | |
MPI libraries are activated via the environment modules.
@@ -30,11 +28,10 @@ Look up section modulefiles/mpi in module avail
There are default compilers associated with any particular MPI implementation. The defaults may be changed, the MPI libraries may be used in conjunction with any compiler. The defaults are selected via the modules in following way
-
-|Module|MPI|Compiler suite|
-|---|---|
-|impi-5.0.3.048-iccifort- Intel MPI 5.0.3| 2015.3.187||
-| OpenMP-1.8.6-GNU-5.1.0-2 OpenMPI 1.8.6| .25||
+| Module | MPI | Compiler suite |
+| ---------------------------------------- | ---------- | -------------- |
+| impi-5.0.3.048-iccifort- Intel MPI 5.0.3 | 2015.3.187 | |
+| OpenMP-1.8.6-GNU-5.1.0-2 OpenMPI 1.8.6 | .25 | |
Examples:
@@ -52,8 +49,8 @@ To use OpenMPI with the intel compiler suite, use
In this example, the openmpi 1.8.6 using intel compilers is activated. It's used "iompi" toolchain.
-Compiling MPI Programs
-----------------------
+## Compiling MPI Programs
+
After setting up your MPI environment, compile your program using one of the mpi wrappers
```bash
@@ -107,8 +104,8 @@ Compile the above example with
$ mpicc helloworld_mpi.c -o helloworld_mpi.x
```
-Running MPI Programs
---------------------
+## Running MPI Programs
+
The MPI program executable must be compatible with the loaded MPI module.
Always compile and execute using the very same MPI module.
@@ -121,9 +118,9 @@ The MPI program executable must be available within the same path on all nodes.
Optimal way to run an MPI program depends on its memory requirements, memory access pattern and communication pattern.
Consider these ways to run an MPI program:
-1. One MPI process per node, 24 threads per process
-2. Two MPI processes per node, 12 threads per process
-3. 24 MPI processes per node, 1 thread per process.
+1\. One MPI process per node, 24 threads per process
+2\. Two MPI processes per node, 12 threads per process
+3\. 24 MPI processes per node, 1 thread per process.
**One MPI** process per node, using 24 threads, is most useful for memory demanding applications, that make good use of processor cache memory and are not memory bound. This is also a preferred way for communication intensive applications as one process per node enjoys full bandwidth access to the network interface.
diff --git a/docs.it4i/salomon/software/mpi/mpi4py-mpi-for-python.md b/docs.it4i/salomon/software/mpi/mpi4py-mpi-for-python.md
index 00762481d2f8b26ee42f0181bff8803314627549..868637e82ad5da4d01ca8196a6371c72dfb7bc56 100644
--- a/docs.it4i/salomon/software/mpi/mpi4py-mpi-for-python.md
+++ b/docs.it4i/salomon/software/mpi/mpi4py-mpi-for-python.md
@@ -1,26 +1,25 @@
-MPI4Py (MPI for Python)
-=======================
+# MPI4Py (MPI for Python)
OpenMPI interface to Python
-Introduction
-------------
+## Introduction
+
MPI for Python provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.
This package is constructed on top of the MPI-1/2 specifications and provides an object oriented interface which closely follows MPI-2 C++ bindings. It supports point-to-point (sends, receives) and collective (broadcasts, scatters, gathers) communications of any picklable Python object, as well as optimized communications of Python object exposing the single-segment buffer interface (NumPy arrays, builtin bytes/string/array objects).
On Anselm MPI4Py is available in standard Python modules.
-Modules
--------
+## Modules
+
MPI4Py is build for OpenMPI. Before you start with MPI4Py you need to load Python and OpenMPI modules. You can use toolchain, that loads Python and OpenMPI at once.
```bash
$ module load Python/2.7.9-foss-2015g
```
-Execution
----------
+## Execution
+
You need to import MPI to your python program. Include the following line to the python script:
```bash
@@ -39,8 +38,7 @@ For example
$ mpiexec python hello_world.py
```
-Examples
---------
+## Examples
### Hello world!
@@ -54,7 +52,7 @@ Examples
comm.Barrier() # wait for everybody to synchronize
```
-###Collective Communication with NumPy arrays
+\###Collective Communication with NumPy arrays
```cpp
from __future__ import division
diff --git a/docs.it4i/salomon/software/numerical-languages/introduction.md b/docs.it4i/salomon/software/numerical-languages/introduction.md
index fdd9c0b404da6bc03bd3d5b607b5219957f75eab..50f083a91c52acc731fcbd0abe849904df757221 100644
--- a/docs.it4i/salomon/software/numerical-languages/introduction.md
+++ b/docs.it4i/salomon/software/numerical-languages/introduction.md
@@ -1,14 +1,13 @@
-Numerical languages
-===================
+# Numerical languages
Interpreted languages for numerical computations and analysis
-Introduction
-------------
+## Introduction
+
This section contains a collection of high-level interpreted languages, primarily intended for numerical computations.
-Matlab
-------
+## Matlab
+
MATLAB®^ is a high-level language and interactive environment for numerical computation, visualization, and programming.
```bash
@@ -18,8 +17,8 @@ MATLAB®^ is a high-level language and interactive environment for numerical com
Read more at the [Matlab page](matlab/).
-Octave
-------
+## Octave
+
GNU Octave is a high-level interpreted language, primarily intended for numerical computations. The Octave language is quite similar to Matlab so that most programs are easily portable.
```bash
@@ -29,8 +28,7 @@ GNU Octave is a high-level interpreted language, primarily intended for numerica
Read more at the [Octave page](octave/).
-R
----
+## R
The R is an interpreted language and environment for statistical computing and graphics.
diff --git a/docs.it4i/salomon/software/numerical-languages/matlab.md b/docs.it4i/salomon/software/numerical-languages/matlab.md
index 4347f5874a7d8a99d9c1c4540c9c32d45db53ed7..a5b339962ab4f953cb6a58a8a1883c64638cd04b 100644
--- a/docs.it4i/salomon/software/numerical-languages/matlab.md
+++ b/docs.it4i/salomon/software/numerical-languages/matlab.md
@@ -1,8 +1,7 @@
-Matlab
-======
+# Matlab
+
+## Introduction
-Introduction
-------------
Matlab is available in versions R2015a and R2015b. There are always two variants of the release:
- Non commercial or so called EDU variant, which can be used for common research and educational purposes.
@@ -40,8 +39,8 @@ To run Matlab in text mode, without the Matlab Desktop GUI environment, use
plots, images, etc... will be still available.
-Running parallel Matlab using Distributed Computing Toolbox / Engine
-------------------------------------------------------------------------
+## Running parallel Matlab using Distributed Computing Toolbox / Engine
+
Distributed toolbox is available only for the EDU variant
The MPIEXEC mode available in previous versions is no longer available in MATLAB 2015. Also, the programming interface has changed. Refer to [Release Notes](http://www.mathworks.com/help/distcomp/release-notes.html#buanp9e-1).
@@ -58,7 +57,7 @@ To use Distributed Computing, you first need to setup a parallel profile. We hav
SalomonPBSPro
```
-Or in the GUI, go to tab HOME -> Parallel -> Manage Cluster Profiles..., click Import and navigate to :
+Or in the GUI, go to tab HOME -> Parallel -> Manage Cluster Profiles..., click Import and navigate to :
/apps/all/MATLAB/2015b-EDU/SalomonPBSPro.settings
@@ -246,7 +245,7 @@ This is an example of m-script using direct mode:
### Non-interactive Session and Licenses
-If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please [look here](../../../anselm-cluster-documentation/software/isv_licenses/).
+If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l **feature**matlab\_\_MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please [look here](../../../anselm-cluster-documentation/software/isv_licenses/).
The licensing feature of PBS is currently disabled.
@@ -256,15 +255,15 @@ In case of non-interactive session please read the [following information](../..
Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:
- |compute nodes|number of workers|start-up time[s]|
- |---|---|---|
- |16|384|831|
- |8|192|807|
- |4|96|483|
- |2|48|16|
+| compute nodes | number of workers | start-up time[s] |
+| ------------- | ----------------- | ---------------- |
+| 16 | 384 | 831 |
+| 8 | 192 | 807 |
+| 4 | 96 | 483 |
+| 2 | 48 | 16 |
+
+## MATLAB on UV2000
-MATLAB on UV2000
------------------
UV2000 machine available in queue "qfat" can be used for MATLAB computations. This is a SMP NUMA machine with large amount of RAM, which can be beneficial for certain types of MATLAB jobs. CPU cores are allocated in chunks of 8 for this machine.
You can use MATLAB on UV2000 in two parallel modes:
diff --git a/docs.it4i/salomon/software/numerical-languages/octave.md b/docs.it4i/salomon/software/numerical-languages/octave.md
index a73c43bb1b818b6c1f47760d13e18a796ae20452..a9a82dfc0e88d777754465e602ec9a18cf40b188 100644
--- a/docs.it4i/salomon/software/numerical-languages/octave.md
+++ b/docs.it4i/salomon/software/numerical-languages/octave.md
@@ -1,13 +1,12 @@
-Octave
-======
+# Octave
GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to Matlab so that most programs are easily portable. Read more on <http://www.gnu.org/software/octave/>
Two versions of octave are available on the cluster, via module
- |Status | Version | module|
-|---|---|
- |**Stable** | Octave 3.8.2 | Octave|
+| Status | Version | module |
+| ---------- | ------------ | ------ |
+| **Stable** | Octave 3.8.2 | Octave |
```bash
$ module load Octave
diff --git a/docs.it4i/salomon/software/numerical-languages/r.md b/docs.it4i/salomon/software/numerical-languages/r.md
index 2c1f610d2c35ded501c8fe862d5ebd8052b97080..001cce805ea0eaaf949287068e648a3c26094b1e 100644
--- a/docs.it4i/salomon/software/numerical-languages/r.md
+++ b/docs.it4i/salomon/software/numerical-languages/r.md
@@ -1,8 +1,7 @@
-R
-===
+# R
+
+## Introduction
-Introduction
-------------
The R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible.
One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control.
@@ -13,21 +12,20 @@ Extensive support for parallel computing is available within R.
Read more on <http://www.r-project.org/>, <http://cran.r-project.org/doc/manuals/r-release/R-lang.html>
-Modules
--------
+## Modules
+
**The R version 3.1.1 is available on the cluster, along with GUI interface Rstudio**
-|Application|Version|module|
-|---|---|
-|**R**|R 3.1.1|R/3.1.1-intel-2015b|
-|**Rstudio**|Rstudio 0.98.1103|Rstudio|
+| Application | Version | module |
+| ----------- | ----------------- | ------------------- |
+| **R** | R 3.1.1 | R/3.1.1-intel-2015b |
+| **Rstudio** | Rstudio 0.98.1103 | Rstudio |
```bash
$ module load R
```
-Execution
----------
+## Execution
The R on Anselm is linked to highly optimized MKL mathematical library. This provides threaded parallelization to many R kernels, notably the linear algebra subroutines. The R runs these heavy calculation kernels without any penalty. By default, the R would parallelize to 24 threads. You may control the threads by setting the OMP_NUM_THREADS environment variable.
@@ -70,12 +68,12 @@ Example jobscript:
This script may be submitted directly to the PBS workload manager via the qsub command. The inputs are in rscript.R file, outputs in routput.out file. See the single node jobscript example in the [Job execution section](../../resource-allocation-and-job-execution/job-submission-and-execution/).
-Parallel R
-----------
+## Parallel R
+
Parallel execution of R may be achieved in many ways. One approach is the implied parallelization due to linked libraries or specially enabled functions, as [described above](r/#interactive-execution). In the following sections, we focus on explicit parallelization, where parallel constructs are directly stated within the R script.
-Package parallel
---------------------
+## Package parallel
+
The package parallel provides support for parallel computation, including by forking (taken from package multicore), by sockets (taken from package snow) and random-number generation.
The package is activated this way:
@@ -100,7 +98,7 @@ The forking is the most simple to use. Forking family of functions provide paral
!!! warning
Forking via package parallel provides functionality similar to OpenMP construct omp parallel for
- Only cores of single node can be utilized this way!
+ Only cores of single node can be utilized this way!
Forking example:
@@ -144,8 +142,8 @@ The above example is the classic parallel example for calculating the number π.
Every evaluation of the integrad function runs in parallel on different process.
-Package Rmpi
-------------
+## Package Rmpi
+
package Rmpi provides an interface (wrapper) to MPI APIs.
It also provides interactive R slave environment. On the cluster, Rmpi provides interface to the [OpenMPI](../mpi/Running_OpenMPI/).
@@ -357,12 +355,12 @@ Execute the example as:
$ mpirun -np 1 R --slave --no-save --no-restore -f pi3parSapply.R
```
-Combining parallel and Rmpi
----------------------------
+## Combining parallel and Rmpi
+
Currently, the two packages can not be combined for hybrid calculations.
-Parallel execution
-------------------
+## Parallel execution
+
The R parallel jobs are executed via the PBS queue system exactly as any other parallel jobs. User must create an appropriate jobscript and submit via the **qsub**
Example jobscript for [static Rmpi](r/#static-rmpi) parallel R execution, running 1 process per core:
@@ -396,8 +394,8 @@ Example jobscript for [static Rmpi](r/#static-rmpi) parallel R execution, runnin
For more information about jobscripts and MPI execution refer to the [Job submission](../../resource-allocation-and-job-execution/job-submission-and-execution/) and general [MPI](../mpi/mpi/) sections.
-Xeon Phi Offload
-----------------
+## Xeon Phi Offload
+
By leveraging MKL, R can accelerate certain computations, most notably linear algebra operations on the Xeon Phi accelerator by using Automated Offload. To use MKL Automated Offload, you need to first set this environment variable before R execution:
```bash
diff --git a/docs.it4i/salomon/software/operating-system.md b/docs.it4i/salomon/software/operating-system.md
index cff49140243e91eab6d31415051aa2a808c2110c..1cf18dfda159662b5ceb8db420bbfc30476e3ff7 100644
--- a/docs.it4i/salomon/software/operating-system.md
+++ b/docs.it4i/salomon/software/operating-system.md
@@ -1,6 +1,5 @@
-Operating System
-================
+# Operating System
The operating system on Salomon is Linux - **CentOS 6.x**
-The CentOS Linux distribution is a stable, predictable, manageable and reproducible platform derived from the sources of Red Hat Enterprise Linux (RHEL).
\ No newline at end of file
+The CentOS Linux distribution is a stable, predictable, manageable and reproducible platform derived from the sources of Red Hat Enterprise Linux (RHEL).
diff --git a/docs.it4i/salomon/storage.md b/docs.it4i/salomon/storage.md
index 85148948682990fcac444657e49fa7856ea89e4a..94745247b33ea4e13202ca1f8c37db69e5370c76 100644
--- a/docs.it4i/salomon/storage.md
+++ b/docs.it4i/salomon/storage.md
@@ -9,9 +9,9 @@ All login and compute nodes may access same data on shared file systems. Compute
## Policy (in a nutshell)
!!! note
- * Use [HOME](#home) for your most valuable data and programs.
- * Use [WORK](#work) for your large project files.
- * Use [TEMP](#temp) for large scratch data.
+ _ Use [HOME](#home) for your most valuable data and programs.
+ _ Use [WORK](#work) for your large project files.
+ \* Use [TEMP](#temp) for large scratch data.
!!! warning
Do not use for [archiving](#archiving)!
@@ -34,19 +34,19 @@ The architecture of Lustre on Salomon is composed of two metadata servers (MDS)
Configuration of the SCRATCH Lustre storage
-* SCRATCH Lustre object storage
- * Disk array SFA12KX
- * 540 x 4 TB SAS 7.2krpm disk
- * 54 x OST of 10 disks in RAID6 (8+2)
- * 15 x hot-spare disk
- * 4 x 400 GB SSD cache
-* SCRATCH Lustre metadata storage
- * Disk array EF3015
- * 12 x 600 GB SAS 15 krpm disk
+- SCRATCH Lustre object storage
+ - Disk array SFA12KX
+ - 540 x 4 TB SAS 7.2krpm disk
+ - 54 x OST of 10 disks in RAID6 (8+2)
+ - 15 x hot-spare disk
+ - 4 x 400 GB SSD cache
+- SCRATCH Lustre metadata storage
+ - Disk array EF3015
+ - 12 x 600 GB SAS 15 krpm disk
### Understanding the Lustre File systems
-[http://www.nas.nasa.gov](http://www.nas.nasa.gov)
+<http://www.nas.nasa.gov>
A user file on the Lustre file system can be divided into multiple chunks (stripes) and stored across a subset of the object storage targets (OSTs) (disks). The stripes are distributed among the OSTs in a round-robin fashion to ensure load balancing.
@@ -56,9 +56,9 @@ If multiple clients try to read and write the same part of a file at the same ti
There is default stripe configuration for Salomon Lustre file systems. However, users can set the following stripe parameters for their own directories or files to get optimum I/O performance:
-1. stripe_size: the size of the chunk in bytes; specify with k, m, or g to use units of KB, MB, or GB, respectively; the size must be an even multiple of 65,536 bytes; default is 1MB for all Salomon Lustre file systems
-1. stripe_count the number of OSTs to stripe across; default is 1 for Salomon Lustre file systems one can specify -1 to use all OSTs in the file system.
-1. 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.
+1. stripe_size: the size of the chunk in bytes; specify with k, m, or g to use units of KB, MB, or GB, respectively; the size must be an even multiple of 65,536 bytes; default is 1MB for all Salomon Lustre file systems
+2. stripe_count the number of OSTs to stripe across; default is 1 for Salomon Lustre file systems one can specify -1 to use all OSTs in the file system.
+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.
!!! Note "Note"
Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.
@@ -106,7 +106,7 @@ Another good practice is to make the stripe count be an integral factor of the n
Large stripe size allows each client to have exclusive access to its own part of a file. However, it can be counterproductive in some cases if it does not match your I/O pattern. The choice of stripe size has no effect on a single-stripe file.
-Read more on [http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html](http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html)
+Read more on <http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html>
## Disk usage and quota commands
@@ -228,13 +228,13 @@ The files on HOME will not be deleted until end of the [users lifecycle](../get-
The workspace is backed up, such that it can be restored in case of catasthropic failure resulting in significant data loss. This backup however is not intended to restore old versions of user data or to restore (accidentaly) deleted files.
-|HOME workspace||
-|---|---|
-|Accesspoint|/home/username|
-|Capacity|0.5 PB|
-|Throughput|6 GB/s|
-|User quota|250 GB|
-|Protocol|NFS, 2-Tier|
+| HOME workspace | |
+| -------------- | -------------- |
+| Accesspoint | /home/username |
+| Capacity | 0.5 PB |
+| Throughput | 6 GB/s |
+| User quota | 250 GB |
+| Protocol | NFS, 2-Tier |
### WORK
@@ -250,16 +250,16 @@ The WORK workspace is hosted on SCRATCH file system. The SCRATCH is realized as
!!! Note "Note"
Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.
-|WORK workspace||
-|---|---|
-|Accesspoints|/scratch/work/user/username, /scratch/work/user/projectid|
-|Capacity |1.6 PB|
-|Throughput|30 GB/s|
-|User quota|100 TB|
-|Default stripe size|1 MB|
-|Default stripe count|1|
-|Number of OSTs|54|
-|Protocol|Lustre|
+| WORK workspace | |
+| -------------------- | --------------------------------------------------------- |
+| Accesspoints | /scratch/work/user/username, /scratch/work/user/projectid |
+| Capacity | 1.6 PB |
+| Throughput | 30 GB/s |
+| User quota | 100 TB |
+| Default stripe size | 1 MB |
+| Default stripe count | 1 |
+| Number of OSTs | 54 |
+| Protocol | Lustre |
### TEMP
@@ -277,16 +277,16 @@ The TEMP workspace is hosted on SCRATCH file system. The SCRATCH is realized as
!!! Note "Note"
Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.
-|TEMP workspace||
-|---|---|
-|Accesspoint|/scratch/temp|
-|Capacity|1.6 PB|
-|Throughput|30 GB/s|
-|User quota|100 TB|
-|Default stripe size|1 MB|
-|Default stripe count|1|
-|Number of OSTs|54|
-|Protocol|Lustre|
+| TEMP workspace | |
+| -------------------- | ------------- |
+| Accesspoint | /scratch/temp |
+| Capacity | 1.6 PB |
+| Throughput | 30 GB/s |
+| User quota | 100 TB |
+| Default stripe size | 1 MB |
+| Default stripe count | 1 |
+| Number of OSTs | 54 |
+| Protocol | Lustre |
## RAM disk
@@ -302,23 +302,22 @@ The local RAM disk file system is intended for temporary scratch data generated
!!! Note
The local RAM disk directory /ramdisk/$PBS_JOBID will be deleted immediately after the calculation end. Users should take care to save the output data from within the jobscript.
-|RAM disk||
-|---|---|
-|Mountpoint| /ramdisk|
-|Accesspoint| /ramdisk/$PBS_JOBID|
-|Capacity|120 GB|
-|Throughput|over 1.5 GB/s write, over 5 GB/s read, single thread, over 10 GB/s write, over 50 GB/s read, 16 threads|
-|User quota|none|
-
+| RAM disk | |
+| ----------- | ------------------------------------------------------------------------------------------------------- |
+| Mountpoint | /ramdisk |
+| Accesspoint | /ramdisk/$PBS_JOBID |
+| Capacity | 120 GB |
+| Throughput | over 1.5 GB/s write, over 5 GB/s read, single thread, over 10 GB/s write, over 50 GB/s read, 16 threads |
+| User quota | none |
## Summary
-|Mountpoint|Usage|Protocol|Net|Capacity|Throughput|Limitations|Access|
-|---|---|
-| /home|home directory|NFS, 2-Tier|0.5 PB|6 GB/s|Quota 250GB|Compute and login nodes|backed up|
-|/scratch/work|large project files|Lustre|1.69 PB|30 GB/s|Quota|Compute and login nodes|none|
-|/scratch/temp|job temporary data|Lustre|1.69 PB|30 GB/s|Quota 100 TB|Compute and login nodes|files older 90 days removed|
-|/ramdisk|job temporary data, node local|local|120GB|90 GB/s|none|Compute nodes|purged after job ends|
+| Mountpoint | Usage | Protocol | Net | Capacity | Throughput | Limitations | Access |
+| ------------- | ------------------------------ | ----------- | ------- | -------- | ------------ | ----------------------- | --------------------------- |
+| /home | home directory | NFS, 2-Tier | 0.5 PB | 6 GB/s | Quota 250GB | Compute and login nodes | backed up |
+| /scratch/work | large project files | Lustre | 1.69 PB | 30 GB/s | Quota | Compute and login nodes | none |
+| /scratch/temp | job temporary data | Lustre | 1.69 PB | 30 GB/s | Quota 100 TB | Compute and login nodes | files older 90 days removed |
+| /ramdisk | job temporary data, node local | local | 120GB | 90 GB/s | none | Compute nodes | purged after job ends |
## CESNET Data Storage
@@ -344,7 +343,7 @@ The procedure to obtain the CESNET access is quick and trouble-free.
### Understanding CESNET storage
!!! 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)
+ 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.
diff --git a/docs.it4i/software/bioinformatics.md b/docs.it4i/software/bioinformatics.md
index ccb31b2a4461a47e154257f64d6af8b352997630..83fd2dd338087c7fae5cb0d09f0fdf4d24882bf6 100644
--- a/docs.it4i/software/bioinformatics.md
+++ b/docs.it4i/software/bioinformatics.md
@@ -1,20 +1,16 @@
-Bioinformatics Applications
-==========================
+# Bioinformatics Applications
-Introduction
-------------
+## Introduction
In addition to the many applications available through modules (deployed through EasyBuild packaging system) we provide an alternative source of applications on our clusters inferred from [Gentoo Linux](https://www.gentoo.org/). The user's environment is setup through a script which returns a bash instance to the user (you can think of it a starting a whole virtual machine but inside your current namespace) . The applications were optimized by gcc compiler for the SandyBridge and IvyBridge platforms. The binaries use paths from /apps/gentoo prefix to find the required runtime dependencies, config files, etc. The Gentoo Linux is a standalone installation not even relying on the glibc provided by host operating system (Redhat). The trick which allowed us to install Gentoo Linux on the host Redhat system is called Gentoo::RAP and uses a modified loader with a hardcoded path ([links](https://wiki.gentoo.org/wiki/Prefix/libc)).
-Starting the environment
-------------------------
+## Starting the environment
```bash
mmokrejs@login2~$ /apps/gentoo/startprefix
```
-Starting PBS jobs using the applications
-----------------------------------------
+## Starting PBS jobs using the applications
Create a template file which can be used and an argument to qsub command. Notably, the 'PBS -S' line specifies full PATH to the Bourne shell of the Gentoo Linux environment.
@@ -39,16 +35,14 @@ $ qsub myjob.pbs
$ qstat
```
-Reading manual pages for installed applications
------------------------------------------------
+## Reading manual pages for installed applications
```bash
mmokrejs@login2~$ man -M /apps/gentoo/usr/share/man bwa
mmokrejs@login2~$ man -M /apps/gentoo/usr/share/man samtools
```
-Listing of bioinformatics applications
---------------------------------------
+## Listing of bioinformatics applications
```bash
mmokrejs@login2~$ grep biology /scratch/mmokrejs/gentoo_rap/installed.txt
@@ -209,30 +203,28 @@ sci-libs/suitesparseconfig-4.2.1
sci-libs/umfpack-5.6.2
```
-Classification of applications
-------------------------------
-
-|Applications for bioinformatics at IT4I|
-|---|---|
-|error-correctors|6|
-|aligners|20|
-|clusterers|5|
-|assemblers|9|
-|scaffolders|6|
-|motif searching|6|
-|ORF/gene prediction/genome annotation|13|
-|genotype/haplotype/popullation genetics|3|
-|phylogenetics|1|
-|transcriptome analysis|2|
-|utilities|15|
-|GUI|3|
-|libraries|4|
-|**Total**|**93**|
+## Classification of applications
+
+| Applications for bioinformatics at IT4I | |
+| --------------------------------------- | ------ |
+| error-correctors | 6 |
+| aligners | 20 |
+| clusterers | 5 |
+| assemblers | 9 |
+| scaffolders | 6 |
+| motif searching | 6 |
+| ORF/gene prediction/genome annotation | 13 |
+| genotype/haplotype/popullation genetics | 3 |
+| phylogenetics | 1 |
+| transcriptome analysis | 2 |
+| utilities | 15 |
+| GUI | 3 |
+| libraries | 4 |
+| **Total** | **93** |
-Other applications available through Gentoo Linux
--------------------------------------------------
+## Other applications available through Gentoo Linux
Gentoo Linux is a allows compilation of its applications from source code while using compiler and optimize flags set to user's wish. This facilitates creation of optimized binaries for the host platform. Users maybe also use several versions of gcc, python and other tools.
diff --git a/docs.it4i/software/lmod.md b/docs.it4i/software/lmod.md
index dc3609023db9a9ef6415cd5e2931fa001a59f7cc..676ed2b2e57fbe31ae777b00012967943f7f2e33 100644
--- a/docs.it4i/software/lmod.md
+++ b/docs.it4i/software/lmod.md
@@ -1,36 +1,32 @@
-Lmod Environment
-================
+# Lmod Environment
Lmod as a modules tool, a modern alternative to the oudated & no longer actively maintained Tcl-based environment modules tool.
Detailed documentation on Lmod is available at [here](http://lmod.readthedocs.io).
-Benefits
---------
+## Benefits
- * significantly more responsive module commands, in particular module avail (ml av)
- * easier to use interface
- * module files can be written in either Tcl or Lua syntax (and both types of modules can be mixed together)
+- significantly more responsive module commands, in particular module avail (ml av)
+- easier to use interface
+- module files can be written in either Tcl or Lua syntax (and both types of modules can be mixed together)
-Introduction
-------------
+## Introduction
Below you will find more details and examples.
-|command|equivalent/explanation|
-|---|---|
-|ml|module list|
-|ml GCC/6.2.0-2.27|module load GCC/6.2.0-2.27|
-|ml -GCC/6.2.0-2.27| module unload GCC/6.2.0-2.27|
-|ml av|module avail|
-|ml show GCC/6.2.0-2.27|module show GCC|
-|ml spider|gcc searches (case-insensitive) for gcc in all available modules|
-|ml spider GCC/6.2.0-2.27|show all information about the module GCC/6.2.0-2.27|
-|ml save mycollection|stores the currently loaded modules to a collection|
-|ml restore mycollection|restores a previously stored collection of modules|
-
-Listing loaded modules: ml (module load)
--------------------------------------------
+| command | equivalent/explanation |
+| ------------------------ | ---------------------------------------------------------------- |
+| ml | module list |
+| ml GCC/6.2.0-2.27 | module load GCC/6.2.0-2.27 |
+| ml -GCC/6.2.0-2.27 | module unload GCC/6.2.0-2.27 |
+| ml av | module avail |
+| ml show GCC/6.2.0-2.27 | module show GCC |
+| ml spider | gcc searches (case-insensitive) for gcc in all available modules |
+| ml spider GCC/6.2.0-2.27 | show all information about the module GCC/6.2.0-2.27 |
+| ml save mycollection | stores the currently loaded modules to a collection |
+| ml restore mycollection | restores a previously stored collection of modules |
+
+## Listing loaded modules: ml (module load)
To get an overview of the currently loaded modules, use module list or ml (without specifying extra arguments).
@@ -45,8 +41,7 @@ Currently Loaded Modules:
!!! tip
for more details on sticky modules, see the section on [ml purge](#resetting-by-unloading-all-modules-ml-purge-module-purge)
-Searching for available modules: ml av (module avail) and ml spider
-----------------------------------------------------------------------
+## Searching for available modules: ml av (module avail) and ml spider
To get an overview of all available modules, you can use module avail or simply ml av:
@@ -64,15 +59,13 @@ $ ml av
In the current module naming scheme, each module name consists of two parts:
- * the part before the first /, corresponding to the software name; and
- * the remainder, corresponding to the software version, the compiler toolchain that was used to install the software, and a possible version suffix
-
+- the part before the first /, corresponding to the software name; and
+- the remainder, corresponding to the software version, the compiler toolchain that was used to install the software, and a possible version suffix
!!! tip
The (D) indicates that this particular version of the module is the default, but we strongly recommend to not rely on this as the default can change at any point. Usuall, the default will point to the latest version available.
-Searching for modules: ml spider
---------------------------------
+## Searching for modules: ml spider
If you just provide a software name, for example gcc, it prints on overview of all available modules for GCC.
@@ -136,8 +129,7 @@ $ module spider GCC/6.2.0-2.27
This tells you what the module contains and a URL to the homepage of the software.
-Available modules for a particular software package: ml av <name>
-------------------------------------------------------------------------------------------
+## Available modules for a particular software package: ml av <name>
To check which modules are available for a particular software package, you can provide the software name to ml av.
For example, to check which versions of git are available:
@@ -154,6 +146,7 @@ $ ml av git
Use "module spider" to find all possible modules.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
```
+
!!! tip
the specified software name is treated case-insensitively.
@@ -170,11 +163,9 @@ GCC/4.4.7-system GCC/4.8.3 GCC/4.9.2 GCC/4.9.3 GCC/5.1.0-binutils-2.25
Use "module spider" to find all possible modules.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
-
```
-Inspecting a module using ml show
---------------------------------------------------
+## Inspecting a module using ml show
To see how a module would change the environment, use module show or ml show:
@@ -202,7 +193,6 @@ setenv("EBROOTPYTHON","/apps/all/Python/3.5.2")
setenv("EBVERSIONPYTHON","3.5.2")
setenv("EBDEVELPYTHON","/apps/all/Python/3.5.2/easybuild/Python-3.5.2-easybuild-devel")
setenv("EBEXTSLISTPYTHON","setuptools-20.1.1,pip-8.0.2,nose-1.3.7")
-
```
!!! tip
@@ -210,7 +200,7 @@ setenv("EBEXTSLISTPYTHON","setuptools-20.1.1,pip-8.0.2,nose-1.3.7")
If you're not sure what all of this means: don't worry, you don't have to know; just try loading the module as try using the software.
-## Loading modules: ml <modname(s)> (module load <modname(s)>)
+## Loading modules: ml <modname(s)> (module load <modname(s)>)
The effectively apply the changes to the environment that are specified by a module, use module load or ml and specify the name of the module.
For example, to set up your environment to use intel:
@@ -236,8 +226,7 @@ Currently Loaded Modules:
!!! tip
Note that even though we only loaded a single module, the output of ml shows that a whole bunch of modules were loaded, which are required dependencies for intel/2017.00.
-Conflicting modules
--------------------
+## Conflicting modules
!!! warning
It is important to note that **only modules that are compatible with each other can be loaded together. In particular, modules must be installed either with the same toolchain as the modules that** are already loaded, or with a compatible (sub)toolchain.
@@ -246,7 +235,7 @@ For example, once you have loaded one or more modules that were installed with t
In addition, only **one single version** of each software package can be loaded at a particular time. For example, once you have the Python/3.5.2-intel-2017.00 module loaded, you can not load a different version of Python in the same session/job script; neither directly, nor indirectly as a dependency of another module you want to load.
-Unloading modules: ml -<modname(s)> (module unload <modname(s)>)
+Unloading modules: ml -<modname(s)> (module unload <modname(s)>)
To revert the changes to the environment that were made by a particular module, you can use module unload or ml -<modname>.
For example:
@@ -271,8 +260,7 @@ $ which gcc
/usr/bin/gcc
```
-Resetting by unloading all modules: ml purge (module purge)
------------------------------------------------------------
+## Resetting by unloading all modules: ml purge (module purge)
To reset your environment back to a clean state, you can use module purge or ml purge:
@@ -294,8 +282,7 @@ No modules loaded
As such, you should not (re)load the cluster module anymore after running ml purge. See also here.
-Module collections: ml save, ml restore
----------------------------------------
+## Module collections: ml save, ml restore
If you have a set of modules that you need to load often, you can save these in a collection (only works with Lmod).
diff --git a/docs.it4i/software/orca.md b/docs.it4i/software/orca.md
index 93e6473431ea7172c6cde0a1f16d383023c82b00..a6eb0fef2c8c025f4e00a5e973937bc6567c8e1a 100644
--- a/docs.it4i/software/orca.md
+++ b/docs.it4i/software/orca.md
@@ -1,10 +1,8 @@
-ORCA
-====
+# ORCA
ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.
-Making orca available
----------------------
+## Making orca available
The following module command makes the latest version of orca available to your session
@@ -30,22 +28,19 @@ Currently Loaded Modulefiles:
11) ORCA/3_0_3-linux_x86-64
```
-Example single core job
------------------------
+## Example single core job
Create a file called orca_serial.inp that contains the following orca commands
-```
-# My first ORCA calculation :-)
-#
-# Taken from the Orca manual
-# https://orcaforum.cec.mpg.de/OrcaManual.pdf
-! HF SVP
-* xyz 0 1
- C 0 0 0
- O 0 0 1.13
-*
-```
+ # My first ORCA calculation :-)
+ #
+ # Taken from the Orca manual
+ # https://orcaforum.cec.mpg.de/OrcaManual.pdf
+ ! HF SVP
+ * xyz 0 1
+ C 0 0 0
+ O 0 0 1.13
+ *
Create a Sun Grid Engine submission file called submit_serial.sh that looks like this
@@ -92,13 +87,10 @@ TOTAL RUN TIME: 0 days 0 hours 0 minutes 2 seconds 796 msec
qsub: job 196821.isrv5 completed
```
-Register as a user
-------------------
+## Register as a user
You are encouraged to register as a user of Orca at [Here](https://orcaforum.cec.mpg.de/) in order to take advantage of updates, announcements and also of the users forum.
-Documentation
--------------
+## Documentation
A comprehensive [.pdf](https://orcaforum.cec.mpg.de/OrcaManual.pdf) manual is available online.
-