diff --git a/README.md b/README.md
index 92333675fd818974e826b3c6778ae77d37d0b308..82d31ceb8fc065ec8a7985310214a192a936b7e6 100644
--- a/README.md
+++ b/README.md
@@ -12,11 +12,6 @@ This is project contain IT4Innovations user documentation source.
* [http://facelessuser.github.io/pymdown-extensions/](http://facelessuser.github.io/pymdown-extensions/)
* [http://squidfunk.github.io/mkdocs-material/](http://squidfunk.github.io/mkdocs-material/)
-## Rules
-
-* [spellcheck https://github.com/lukeapage/node-markdown-spellcheck](spellcheck https://github.com/lukeapage/node-markdown-spellcheck)
-* [SI units http://physics.nist.gov/cuu/Units/checklist.html](SI units http://physics.nist.gov/cuu/Units/checklist.html)
-
```
fair-share
InfiniBand
diff --git a/docs.it4i/anselm/capacity-computing.md b/docs.it4i/anselm/capacity-computing.md
index 4b191d815f60c55da8facc68533ece9721a6c578..41bb930fb08f32146f13863cd2377df8fb4d5cde 100644
--- a/docs.it4i/anselm/capacity-computing.md
+++ b/docs.it4i/anselm/capacity-computing.md
@@ -83,7 +83,7 @@ $ qsub -N JOBNAME -J 1-900 jobscript
12345[].dm2
```
-In this example, we submit a job array of 900 subjobs. Each subjob will run on one full node and is assumed to take less than 2 hours (please note the #PBS directives in the beginning of the jobscript file, don't forget to set your valid PROJECT_ID and desired queue).
+In this example, we submit a job array of 900 subjobs. Each subjob will run on one full node and is assumed to take less than 2 hours (note the #PBS directives in the beginning of the jobscript file, don't forget to set your valid PROJECT_ID and desired queue).
Sometimes for testing purposes, you may need to submit a one-element only array. This is not allowed by PBSPro, but there's a workaround:
diff --git a/docs.it4i/anselm/compute-nodes.md b/docs.it4i/anselm/compute-nodes.md
index 9e5ed7135a2b28fd5db29219992f930399c3787b..2ffd491938caff7fec452a73cc524a997ba46c31 100644
--- a/docs.it4i/anselm/compute-nodes.md
+++ b/docs.it4i/anselm/compute-nodes.md
@@ -55,7 +55,7 @@ Anselm is cluster of x86-64 Intel based nodes built with Bull Extreme Computing
| Node type | Count | Range | Memory | Cores | [Access](resources-allocation-policy/) |
| ---------------------------- | ----- | ----------- | ------ | ----------- | -------------------------------------- |
| Nodes without an accelerator | 180 | cn[1-180] | 64GB | 16 @ 2.4GHz | qexp, qprod, qlong, qfree, qprace, qatlas |
-| Nodes with a GPU accelerator | 23 | cn[181-203] | 96GB | 16 @ 2.3GHz | qgpu, qexp |
+| Nodes with a GPU accelerator | 23 | cn[181-203] | 96GB | 16 @ 2.3GHz | qnvidia, qexp |
| Nodes with a MIC accelerator | 4 | cn[204-207] | 96GB | 16 @ 2.3GHz | qmic, qexp |
| Fat compute nodes | 2 | cn[208-209] | 512GB | 16 @ 2.4GHz | qfat, qexp |
diff --git a/docs.it4i/anselm/hardware-overview.md b/docs.it4i/anselm/hardware-overview.md
index f91c5bc70ef8ac2a0d4c79d39cc08fc8d62c45a6..5f10e65005221abb245649c8a9a3f15fca490e5c 100644
--- a/docs.it4i/anselm/hardware-overview.md
+++ b/docs.it4i/anselm/hardware-overview.md
@@ -57,4 +57,4 @@ The parameters are summarized in the following tables:
| 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 [Compute nodes](compute-nodes/), [Storage](storage/), and [Network](network/).
+For more details refer to [Compute nodes](compute-nodes/), [Storage](storage/), and [Network](network/).
diff --git a/docs.it4i/anselm/job-submission-and-execution.md b/docs.it4i/anselm/job-submission-and-execution.md
index 8b1e201f3819f56de5d2d377d8be09f4ba50d22d..0d5321f82229ac06e4a905bf4921616cb683bffe 100644
--- a/docs.it4i/anselm/job-submission-and-execution.md
+++ b/docs.it4i/anselm/job-submission-and-execution.md
@@ -2,7 +2,7 @@
## Job Submission
-When allocating computational resources for the job, please specify
+When allocating computational resources for the job, specify:
1. a suitable queue for your job (the default is qprod)
1. the number of computational nodes required
diff --git a/docs.it4i/anselm/software/debuggers/allinea-ddt.md b/docs.it4i/anselm/software/debuggers/allinea-ddt.md
index a5dd069ba07728662ce817cb713eeb7325002998..a1f26a9fbbb5e41f7b08c786a22d71c627e45ded 100644
--- a/docs.it4i/anselm/software/debuggers/allinea-ddt.md
+++ b/docs.it4i/anselm/software/debuggers/allinea-ddt.md
@@ -25,14 +25,14 @@ In case of debugging on accelerators:
Load all necessary modules to compile the code. For example:
```bash
- $ module load intel
- $ module load impi ... or ... module load openmpi/X.X.X-icc
+ $ ml intel
+ $ ml impi ... or ... ml openmpi/X.X.X-icc
```
Load the Allinea DDT module:
```bash
- $ module load Forge
+ $ ml Forge
```
Compile the code:
diff --git a/docs.it4i/anselm/software/debuggers/allinea-performance-reports.md b/docs.it4i/anselm/software/debuggers/allinea-performance-reports.md
index 7b519b85c094122ff7866ad8a48961ee89dbb4b9..92602c6b36ef3d253f6e230755e2625501cb0d2d 100644
--- a/docs.it4i/anselm/software/debuggers/allinea-performance-reports.md
+++ b/docs.it4i/anselm/software/debuggers/allinea-performance-reports.md
@@ -13,7 +13,7 @@ Our license is limited to 64 MPI processes.
Allinea Performance Reports version 6.0 is available
```bash
- $ module load PerformanceReports/6.0
+ $ ml PerformanceReports/6.0
```
The module sets up environment variables, required for using the Allinea Performance Reports. This particular command loads the default module, which is performance reports version 4.2.
@@ -46,7 +46,7 @@ First, we allocate some nodes via the express queue:
Then we load the modules and run the program the usual way:
```bash
- $ module load intel impi allinea-perf-report/4.2
+ $ ml intel impi allinea-perf-report/4.2
$ mpirun ./mympiprog.x
```
diff --git a/docs.it4i/anselm/software/intel-suite/intel-compilers.md b/docs.it4i/anselm/software/intel-suite/intel-compilers.md
index 9cc1f1e0af6abf09cc00d39f7c7dd1c37d78c9e1..71708a733681a4f59887852023ea4501751cb433 100644
--- a/docs.it4i/anselm/software/intel-suite/intel-compilers.md
+++ b/docs.it4i/anselm/software/intel-suite/intel-compilers.md
@@ -3,7 +3,7 @@
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.
```bash
- $ module load intel
+ $ ml intel
$ icc -v
$ ifort -v
```
diff --git a/docs.it4i/anselm/software/intel-suite/intel-debugger.md b/docs.it4i/anselm/software/intel-suite/intel-debugger.md
index d3acd2c51a364c9a48a7b26c0fcfb96256e0bc5f..c8919a1d0d50fa70a7dd3c813dcd3d36383a63fc 100644
--- a/docs.it4i/anselm/software/intel-suite/intel-debugger.md
+++ b/docs.it4i/anselm/software/intel-suite/intel-debugger.md
@@ -5,7 +5,7 @@
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
- $ module load intel
+ $ ml intel
$ idb
```
@@ -24,8 +24,8 @@ Example:
qsub: waiting for job 19654.srv11 to start
qsub: job 19654.srv11 ready
- $ module load intel
- $ module load java
+ $ ml intel
+ $ ml java
$ icc -O0 -g myprog.c -o myprog.x
$ idb ./myprog.x
```
@@ -45,7 +45,7 @@ For debugging small number of MPI ranks, you may execute and debug each rank in
qsub: waiting for job 19654.srv11 to start
qsub: job 19655.srv11 ready
- $ module load intel impi
+ $ ml intel impi
$ mpirun -ppn 1 -hostfile $PBS_NODEFILE --enable-x xterm -e idbc ./mympiprog.x
```
@@ -60,7 +60,7 @@ Run the idb debugger from within the MPI debug option. This will cause the debug
qsub: waiting for job 19654.srv11 to start
qsub: job 19655.srv11 ready
- $ module load intel impi
+ $ ml intel impi
$ mpirun -n 32 -idb ./mympiprog.x
```
diff --git a/docs.it4i/anselm/software/mpi/mpi.md b/docs.it4i/anselm/software/mpi/mpi.md
index 08be4bce682e507968cbbc0a03b32854193d3352..2990cf22244c878604bef0f1455a5cf7f3a4395d 100644
--- a/docs.it4i/anselm/software/mpi/mpi.md
+++ b/docs.it4i/anselm/software/mpi/mpi.md
@@ -14,10 +14,10 @@ The Anselm cluster provides several implementations of the MPI library:
MPI libraries are activated via the environment modules.
-Look up section modulefiles/mpi in module avail
+Look up section modulefiles/mpi in ml av
```bash
- $ module avail
+ $ ml av
------------------------- /opt/modules/modulefiles/mpi -------------------------
bullxmpi/bullxmpi-1.2.4.1 mvapich2/1.9-icc
impi/4.0.3.008 openmpi/1.6.5-gcc(default)
@@ -44,7 +44,7 @@ There are default compilers associated with any particular MPI implementation. T
Examples:
```bash
- $ module load openmpi
+ $ ml openmpi
```
In this example, we activate the latest openmpi with latest GNU compilers
@@ -52,8 +52,8 @@ In this example, we activate the latest openmpi with latest GNU compilers
To use openmpi with the intel compiler suite, use
```bash
- $ module load intel
- $ module load openmpi/1.6.5-icc
+ $ ml intel
+ $ ml openmpi/1.6.5-icc
```
In this example, the openmpi 1.6.5 using intel compilers is activated
diff --git a/docs.it4i/anselm/software/numerical-languages/matlab.md b/docs.it4i/anselm/software/numerical-languages/matlab.md
index cfc958b7e93cde09f34e424d92717f53915097d4..847b32d8b51f56b4a846024e9e07af49af277d04 100644
--- a/docs.it4i/anselm/software/numerical-languages/matlab.md
+++ b/docs.it4i/anselm/software/numerical-languages/matlab.md
@@ -10,31 +10,31 @@ Matlab is available in versions R2015a and R2015b. There are always two variants
To load the latest version of Matlab load the module
```bash
- $ module load MATLAB
+$ ml MATLAB
```
By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use
```bash
- $ module avail MATLAB
+$ ml av MATLAB
```
If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.
-If you require the Matlab GUI, please follow the general information about [running graphical applications](../../../general/accessing-the-clusters/graphical-user-interface/x-window-system/).
+If you require the Matlab GUI, follow the general information about [running graphical applications](../../../general/accessing-the-clusters/graphical-user-interface/x-window-system/).
-Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part [here](../../../general/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-system/)) is recommended.
+Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (see the "GUI Applications on Compute Nodes over VNC" part [here](../../../general/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-system/)) is recommended.
To run Matlab with GUI, use
```bash
- $ matlab
+$ matlab
```
To run Matlab in text mode, without the Matlab Desktop GUI environment, use
```bash
- $ matlab -nodesktop -nosplash
+$ matlab -nodesktop -nosplash
```
plots, images, etc... will be still available.
@@ -72,8 +72,8 @@ With the new mode, MATLAB itself launches the workers via PBS, so you can either
Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see [this page](../../../general/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-system/).
```bash
- $ xhost +
- $ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00
+$ xhost +
+$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00
-l feature__matlab__MATLAB=1
```
@@ -84,8 +84,8 @@ The second part of the command shows how to request all necessary licenses. In t
Once the access to compute nodes is granted by PBS, user can load following modules and start Matlab:
```bash
- r1i0n17$ module load MATLAB/2015b-EDU
- r1i0n17$ matlab &
+r1i0n17$ ml MATLAB/2015b-EDU
+r1i0n17$ matlab &
```
### Parallel Matlab Batch Job in Local Mode
@@ -93,26 +93,26 @@ Once the access to compute nodes is granted by PBS, user can load following modu
To run matlab in batch mode, write an matlab script, then write a bash jobscript and execute via the qsub command. By default, matlab will execute one matlab worker instance per allocated core.
```bash
- #!/bin/bash
- #PBS -A PROJECT ID
- #PBS -q qprod
- #PBS -l select=1:ncpus=16:mpiprocs=16:ompthreads=1
+#!/bin/bash
+#PBS -A PROJECT ID
+#PBS -q qprod
+#PBS -l select=1:ncpus=16:mpiprocs=16:ompthreads=1
- # change to shared scratch directory
- SCR=/scratch/work/user/$USER/$PBS_JOBID
- mkdir -p $SCR ; cd $SCR || exit
+# change to shared scratch directory
+SCR=/scratch/work/user/$USER/$PBS_JOBID
+mkdir -p $SCR ; cd $SCR || exit
- # copy input file to scratch
- cp $PBS_O_WORKDIR/matlabcode.m .
+# copy input file to scratch
+cp $PBS_O_WORKDIR/matlabcode.m .
- # load modules
- module load MATLAB/2015a-EDU
+# load modules
+ml MATLAB/2015a-EDU
- # execute the calculation
- matlab -nodisplay -r matlabcode > output.out
+# execute the calculation
+matlab -nodisplay -r matlabcode > output.out
- # copy output file to home
- cp output.out $PBS_O_WORKDIR/.
+# copy output file to home
+cp output.out $PBS_O_WORKDIR/.
```
This script may be submitted directly to the PBS workload manager via the qsub command. The inputs and matlab script are in matlabcode.m file, outputs in output.out file. Note the missing .m extension in the matlab -r matlabcodefile call, **the .m must not be included**. Note that the **shared /scratch must be used**. Further, it is **important to include quit** statement at the end of the matlabcode.m script.
@@ -120,7 +120,7 @@ This script may be submitted directly to the PBS workload manager via the qsub c
Submit the jobscript using qsub
```bash
- $ qsub ./jobscript
+$ qsub ./jobscript
```
### Parallel Matlab Local Mode Program Example
@@ -128,7 +128,7 @@ Submit the jobscript using qsub
The last part of the configuration is done directly in the user Matlab script before Distributed Computing Toolbox is started.
```bash
- cluster = parcluster('local')
+cluster = parcluster('local')
```
This script creates scheduler object "cluster" of type "local" that starts workers locally.
@@ -151,28 +151,28 @@ The last step is to start matlabpool with "cluster" object and correct number of
The complete example showing how to use Distributed Computing Toolbox in local mode is shown here.
```bash
- cluster = parcluster('local');
- cluster
+cluster = parcluster('local');
+cluster
- parpool(cluster,24);
+parpool(cluster,24);
- n=2000;
+n=2000;
- W = rand(n,n);
- W = distributed(W);
- x = (1:n)';
- x = distributed(x);
- spmd
- [~, name] = system('hostname')
+W = rand(n,n);
+W = distributed(W);
+x = (1:n)';
+x = distributed(x);
+spmd
+[~, name] = system('hostname')
- T = W*x; % Calculation performed on labs, in parallel.
- % T and W are both codistributed arrays here.
- end
- T;
- whos % T and W are both distributed arrays here.
+ T = W*x; % Calculation performed on labs, in parallel.
+ % T and W are both codistributed arrays here.
+end
+T;
+whos % T and W are both distributed arrays here.
- parpool close
- quit
+parpool close
+quit
```
You can copy and paste the example in a .m file and execute. Note that the parpool size should correspond to **total number of cores** available on allocated nodes.
@@ -184,29 +184,29 @@ This mode uses PBS scheduler to launch the parallel pool. It uses the SalomonPBS
This is an example of m-script using PBS mode:
```bash
- cluster = parcluster('SalomonPBSPro');
- set(cluster, 'SubmitArguments', '-A OPEN-0-0');
- set(cluster, 'ResourceTemplate', '-q qprod -l select=10:ncpus=16');
- set(cluster, 'NumWorkers', 160);
+cluster = parcluster('SalomonPBSPro');
+set(cluster, 'SubmitArguments', '-A OPEN-0-0');
+set(cluster, 'ResourceTemplate', '-q qprod -l select=10:ncpus=16');
+set(cluster, 'NumWorkers', 160);
- pool = parpool(cluster, 160);
+pool = parpool(cluster, 160);
- n=2000;
+n=2000;
- W = rand(n,n);
- W = distributed(W);
- x = (1:n)';
- x = distributed(x);
- spmd
- [~, name] = system('hostname')
+W = rand(n,n);
+W = distributed(W);
+x = (1:n)';
+x = distributed(x);
+spmd
+[~, name] = system('hostname')
- T = W*x; % Calculation performed on labs, in parallel.
- % T and W are both codistributed arrays here.
- end
- whos % T and W are both distributed arrays here.
+ T = W*x; % Calculation performed on labs, in parallel.
+ % T and W are both codistributed arrays here.
+end
+whos % T and W are both distributed arrays here.
- % shut down parallel pool
- delete(pool)
+% shut down parallel pool
+delete(pool)
```
Note that we first construct a cluster object using the imported profile, then set some important options, namely: SubmitArguments, where you need to specify accounting id, and ResourceTemplate, where you need to specify number of nodes to run the job.
@@ -225,39 +225,39 @@ For this method, you need to use SalomonDirect profile, import it using [the sam
This is an example of m-script using direct mode:
```bash
- parallel.importProfile('/apps/all/MATLAB/2015a-EDU/SalomonDirect.settings')
- cluster = parcluster('SalomonDirect');
- set(cluster, 'NumWorkers', 48);
+parallel.importProfile('/apps/all/MATLAB/2015a-EDU/SalomonDirect.settings')
+cluster = parcluster('SalomonDirect');
+set(cluster, 'NumWorkers', 48);
- pool = parpool(cluster, 48);
+pool = parpool(cluster, 48);
- n=2000;
+n=2000;
- W = rand(n,n);
- W = distributed(W);
- x = (1:n)';
- x = distributed(x);
- spmd
- [~, name] = system('hostname')
+W = rand(n,n);
+W = distributed(W);
+x = (1:n)';
+x = distributed(x);
+spmd
+[~, name] = system('hostname')
- T = W*x; % Calculation performed on labs, in parallel.
- % T and W are both codistributed arrays here.
- end
- whos % T and W are both distributed arrays here.
+ T = W*x; % Calculation performed on labs, in parallel.
+ % T and W are both codistributed arrays here.
+end
+whos % T and W are both distributed arrays here.
- % shut down parallel pool
- delete(pool)
+% shut down parallel pool
+delete(pool)
```
### 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 [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.
+In case of non-interactive session read the [following information](../isv_licenses/) on how to modify the qsub command to test for available licenses prior getting the resource allocation.
### Matlab Distributed Computing Engines Start Up Time
-Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:
+Starting Matlab workers is an expensive process that requires certain amount of time. For your information see the following table:
| compute nodes | number of workers | start-up time[s] |
| ------------- | ----------------- | ---------------- |
diff --git a/docs.it4i/anselm/storage.md b/docs.it4i/anselm/storage.md
index 5587dccc701ca45997a72d6ede05f366a13d9ece..4842ee1790ce0585c884852a46d00e0af6b65096 100644
--- a/docs.it4i/anselm/storage.md
+++ b/docs.it4i/anselm/storage.md
@@ -98,7 +98,7 @@ The architecture of Lustre on Anselm is composed of two metadata servers (MDS) a
### HOME File System
-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.
+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, contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
!!! note
The HOME filesystem is intended for preparation, evaluation, processing and storage of data generated by active Projects.
@@ -127,7 +127,7 @@ Default stripe size is 1MB, stripe count is 1. There are 22 OSTs dedicated for t
### SCRATCH File System
-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.
+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, contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
!!! note
The Scratch filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs must use the SCRATCH filesystem as their working directory.
@@ -324,7 +324,7 @@ User of data storage CESNET (DU) association can become organizations or an indi
User may only use data storage CESNET for data transfer and storage which are associated with activities in science, research, development, the spread of education, culture and prosperity. In detail see “Acceptable Use Policy CESNET Large Infrastructure (Acceptable Use Policy, AUP)”.
-The service is documented [here](https://du.cesnet.cz/en/start). For special requirements please contact directly CESNET Storage Department via e-mail [du-support(at)cesnet.cz](mailto:du-support@cesnet.cz).
+The service is documented [here](https://du.cesnet.cz/en/start). For special requirements contact directly CESNET Storage Department via e-mail [du-support(at)cesnet.cz](mailto:du-support@cesnet.cz).
The procedure to obtain the CESNET access is quick and trouble-free.
@@ -378,7 +378,7 @@ $ cp -a mydir cesnet/.
$ cp cesnet/myfile .
```
-Once done, please remember to unmount the storage
+Once done, remember to unmount the storage
```console
$ fusermount -u cesnet
@@ -386,8 +386,8 @@ $ fusermount -u cesnet
### RSYNC Access
-!!! Note "Note"
- RSYNC provides delta transfer for best performance, can resume interrupted transfers
+!!! info
+ RSYNC provides delta transfer for best performance, can resume interrupted transfers
RSYNC is a fast and extraordinarily versatile file copying tool. It is famous for its delta-transfer algorithm, which reduces the amount of data sent over the network by sending only the differences between the source files and the existing files in the destination. RSYNC is widely used for backups and mirroring and as an improved copy command for everyday use.
diff --git a/docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md b/docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md
index 986502bdac3459063d0d61bf74096149d2a9d34a..538ed5c5b29426731354104ba671d1952ee1ca68 100644
--- a/docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md
+++ b/docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md
@@ -91,7 +91,7 @@ At your machine, create the tunnel:
local $ ssh -TN -f username@login2.cluster-name.it4i.cz -L 5961:localhost:5961
```
-Issue the following command to check the tunnel is established (please note the PID 2022 in the last column, you'll need it for closing the tunnel):
+Issue the following command to check the tunnel is established (note the PID 2022 in the last column, you'll need it for closing the tunnel):
```console
local $ netstat -natp | grep 5961
diff --git a/docs.it4i/general/obtaining-login-credentials/certificates-faq.md b/docs.it4i/general/obtaining-login-credentials/certificates-faq.md
index 4d2315dd2e8306e7d8cac5dafa5523c5b2dcbdb1..815344b2df74b591960ee4c509e30f3ae96aca42 100644
--- a/docs.it4i/general/obtaining-login-credentials/certificates-faq.md
+++ b/docs.it4i/general/obtaining-login-credentials/certificates-faq.md
@@ -31,7 +31,7 @@ Yes, provided that the CA which provides this service is also a member of IGTF.
## Q: Does IT4Innovations Support the TERENA Certificate Service?
- Yes, ITInnovations supports TERENA eScience personal certificates. For more information, please visit [TCS - Trusted Certificate Service](https://tcs-escience-portal.terena.org/), where you also can find if your organisation/country can use this service
+ Yes, ITInnovations supports TERENA eScience personal certificates. For more information, visit [TCS - Trusted Certificate Service](https://tcs-escience-portal.terena.org/), where you also can find if your organisation/country can use this service
## Q: What Format Should My Certificate Take?
@@ -53,7 +53,7 @@ Certification Authority (CA) certificates are used to verify the link between yo
To assist users, SURFsara (a member of PRACE) provides a complete and up-to-date bundle of all the CA certificates that any PRACE user (or IT4Innovations grid services user) will require. Bundle of certificates, in either p12, PEM or JKS formats, are [available here](https://winnetou.surfsara.nl/prace/certs/).
-It is worth noting that gsissh-term and DART automatically updates their CA certificates from this SURFsara website. In other cases, if you receive a warning that a server’s certificate can not be validated (not trusted), then please update your CA certificates via the SURFsara website. If this fails, then please contact the IT4Innovations helpdesk.
+It is worth noting that gsissh-term and DART automatically updates their CA certificates from this SURFsara website. In other cases, if you receive a warning that a server’s certificate can not be validated (not trusted), then update your CA certificates via the SURFsara website. If this fails, then contact the IT4Innovations helpdesk.
Lastly, if you need the CA certificates for a personal Globus 5 installation, then you can install the CA certificates from a MyProxy server with the following command.
@@ -104,7 +104,7 @@ To check your certificate (e.g., DN, validity, issuer, public key algorithm, etc
openssl x509 -in usercert.pem -text -noout
```
-To download openssl if not pre-installed, [please visit](https://www.openssl.org/source/). On Macintosh Mac OS X computers openssl is already pre-installed and can be used immediately.
+To download openssl if not pre-installed, see [here](https://www.openssl.org/source/). On Macintosh Mac OS X computers openssl is already pre-installed and can be used immediately.
## Q: How Do I Create and Then Manage a Keystore?
@@ -134,7 +134,7 @@ Most grid services require the use of your certificate; however, the format of y
If employing the PRACE version of GSISSH-term (also a Java Web Start Application), you may use either the PEM or p12 formats. Note that this service automatically installs up-to-date PRACE CA certificates.
-If the grid service is UNICORE, then you bind your certificate, in either the p12 format or JKS, to UNICORE during the installation of the client on your local machine. For more information, please visit [UNICORE6 in PRACE](http://www.prace-ri.eu/UNICORE6-in-PRACE)
+If the grid service is UNICORE, then you bind your certificate, in either the p12 format or JKS, to UNICORE during the installation of the client on your local machine. For more information visit [UNICORE6 in PRACE](http://www.prace-ri.eu/UNICORE6-in-PRACE)
If the grid service is part of Globus, such as GSI-SSH, GriFTP or GRAM5, then the certificates can be in either p12 or PEM format and must reside in the "$HOME/.globus" directory for Linux and Mac users or %HOMEPATH%.globus for Windows users. (Windows users will have to use the DOS command ’cmd’ to create a directory which starts with a ’.’). Further, user certificates should be named either "usercred.p12" or "usercert.pem" and "userkey.pem", and the CA certificates must be kept in a pre-specified directory as follows. For Linux and Mac users, this directory is either $HOME/.globus/certificates or /etc/grid-security/certificates. For Windows users, this directory is %HOMEPATH%.globuscertificates. (If you are using GSISSH-Term from prace-ri.eu then you do not have to create the .globus directory nor install CA certificates to use this tool alone).
@@ -156,7 +156,7 @@ A proxy certificate is a short-lived certificate which may be employed by UNICOR
## Q: Someone May Have Copied or Had Access to the Private Key of My Certificate Either in a Separate File or in the Browser. What Should I Do?
-Please ask the CA that issued your certificate to revoke this certificate and to supply you with a new one. In addition, please report this to IT4Innovations by contacting [the support team](https://support.it4i.cz/rt).
+Please ask the CA that issued your certificate to revoke this certificate and to supply you with a new one. In addition, report this to IT4Innovations by contacting [the support team](https://support.it4i.cz/rt).
## Q: My Certificate Expired. What Should I Do?
diff --git a/docs.it4i/general/obtaining-login-credentials/obtaining-login-credentials.md b/docs.it4i/general/obtaining-login-credentials/obtaining-login-credentials.md
index b8168ecff4353d6527b13892245d58b37e7fa645..4218af925ac75fa0969241e6743b36290e145d8f 100644
--- a/docs.it4i/general/obtaining-login-credentials/obtaining-login-credentials.md
+++ b/docs.it4i/general/obtaining-login-credentials/obtaining-login-credentials.md
@@ -117,13 +117,13 @@ Certificate generation process for academic purposes, utilizing the CESNET certi
!!! note
Certificate file can be installed into your email client. Web-based email interfaces cannot be used for secure communication, external application, such as Thunderbird or Outlook must be used. This way, your new credentials will be visible only in applications, that have access to your certificate.
-If you are not able to obtain certificate from any of the respected certification authorities, please follow the Alternative Way bellow.
+If you are not able to obtain certificate from any of the respected certification authorities, follow the Alternative Way bellow.
A FAQ about certificates can be found here: [Certificates FAQ](certificates-faq/).
## Alternative Way to Personal Certificate
-Follow these steps **only** if you can not obtain your certificate in a standard way. In case you choose this procedure, please attach a **scan of photo ID** (personal ID or passport or drivers license) when applying for login credentials.
+Follow these steps **only** if you can not obtain your certificate in a standard way. In case you choose this procedure, attach a **scan of photo ID** (personal ID or passport or drivers license) when applying for login credentials.
!!! warning
Please use Firefox (clone) for following steps. Other browsers, like Chrome, are not compatible.
diff --git a/docs.it4i/index.md b/docs.it4i/index.md
index 326416a600b044125cbb7b5aba2f4b4935616632..6506469638ba5496080d0463f556d122112df0a5 100644
--- a/docs.it4i/index.md
+++ b/docs.it4i/index.md
@@ -60,7 +60,7 @@ local $
## Errors
Although we have taken every care to ensure the accuracy of the content, mistakes do happen.
-If you find an inconsistency or error, please report it by visiting <http://support.it4i.cz/rt>, creating a new ticket, and entering the details.
+If you find an inconsistency or error, report it by visiting <http://support.it4i.cz/rt>, creating a new ticket, and entering the details.
By doing so, you can save other readers from frustration and help us improve.
!!! tip
diff --git a/docs.it4i/prace.md b/docs.it4i/prace.md
index 261489971847e428efff23ba03d51293e483f538..ceb5b53d841121e9ec5fe01935dd52d90f79d8ed 100644
--- a/docs.it4i/prace.md
+++ b/docs.it4i/prace.md
@@ -8,7 +8,7 @@ All general [PRACE User Documentation](http://www.prace-ri.eu/user-documentation
## Help and Support
-If you have any troubles, need information, request support or want to install additional software, please use [PRACE Helpdesk](http://www.prace-ri.eu/helpdesk-guide264/).
+If you have any troubles, need information, request support or want to install additional software, use [PRACE Helpdesk](http://www.prace-ri.eu/helpdesk-guide264/).
Information about the local services are provided in the [introduction of general user documentation Salomon](salomon/introduction/) and [introduction of general user documentation Anselm](anselm/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.
@@ -16,7 +16,7 @@ Information about the local services are provided in the [introduction of genera
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 a 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](general/obtaining-login-credentials/obtaining-login-credentials/).
+If there's a special need a PRACE user can get a standard (local) account at IT4Innovations. To get an account on a cluster, the user needs to obtain the login credentials. The procedure is the same as for general users of the cluster, so see the corresponding [section of the general documentation here](general/obtaining-login-credentials/obtaining-login-credentials/).
## Accessing the Cluster
@@ -24,7 +24,7 @@ If there's a special need a PRACE user can get a standard (local) account at IT4
For all PRACE users the method for interactive access (login) and data transfer based on grid services from Globus Toolkit (GSI SSH and GridFTP) is supported.
-The user will need a valid certificate and to be present in the PRACE LDAP (please contact your HOME SITE or the primary investigator of your project for LDAP account creation).
+The user will need a valid certificate and to be present in the PRACE LDAP (contact your HOME SITE or the primary investigator of your project for LDAP account creation).
Most of the information needed by PRACE users accessing the TIER-1 systems can be found here:
@@ -147,7 +147,7 @@ $ gsiscp -P 2222 anselm-prace.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_
### Access to X11 Applications (VNC)
-If the user needs to run X11 based graphical application and does not have a X11 server, the applications can be run using VNC service. If the user is using regular SSH based access, please see the [section in general documentation](general/accessing-the-clusters/graphical-user-interface/x-window-system/).
+If the user needs to run X11 based graphical application and does not have a X11 server, the applications can be run using VNC service. If the user is using regular SSH based access, see the [section in general documentation](general/accessing-the-clusters/graphical-user-interface/x-window-system/).
If the user uses GSI SSH based access, then the procedure is similar to the SSH based access ([look here](general/accessing-the-clusters/graphical-user-interface/x-window-system/)), only the port forwarding must be done using GSI SSH:
@@ -157,11 +157,11 @@ $ gsissh -p 2222 salomon.it4i.cz -L 5961:localhost:5961
### Access With SSH
-After successful obtainment of login credentials for the local IT4Innovations account, the PRACE users can access the cluster as regular users using SSH. For more information please see [the section in general documentation for Salomon](salomon/shell-and-data-access/) and [the section in general documentation for Anselm](anselm/shell-and-data-access/).
+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 see [the section in general documentation for Salomon](salomon/shell-and-data-access/) and [the section in general documentation for Anselm](anselm/shell-and-data-access/).
## File Transfers
-PRACE users can use the same transfer mechanisms as regular users (if they've undergone the full registration procedure). For information about this, please see [the section in the general documentation for Salomon](salomon/shell-and-data-access/) and [the section in general documentation for Anselm](anselm/shell-and-data-access/).
+PRACE users can use the same transfer mechanisms as regular users (if they've undergone the full registration procedure). For information about this, see [the section in the general documentation for Salomon](salomon/shell-and-data-access/) and [the section in general documentation for Anselm](anselm/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).
@@ -381,4 +381,4 @@ $ quota
$ lfs quota -u USER_LOGIN /scratch
```
-If the quota is insufficient, please contact the [support](prace/#help-and-support) and request an increase.
+If the quota is insufficient, contact the [support](prace/#help-and-support) and request an increase.
diff --git a/docs.it4i/salomon/capacity-computing.md b/docs.it4i/salomon/capacity-computing.md
index 8b0a331fb605b9ffebf9a5835ef383a48613ea55..e65e5ad99d5304d8a978f72fbb78755ee4b1f555 100644
--- a/docs.it4i/salomon/capacity-computing.md
+++ b/docs.it4i/salomon/capacity-computing.md
@@ -83,7 +83,7 @@ $ qsub -N JOBNAME -J 1-900 jobscript
506493[].isrv5
```
-In this example, we submit a job array of 900 subjobs. Each subjob will run on full node and is assumed to take less than 2 hours (please note the #PBS directives in the beginning of the jobscript file, dont' forget to set your valid PROJECT_ID and desired queue).
+In this example, we submit a job array of 900 subjobs. Each subjob will run on full node and is assumed to take less than 2 hours (note the #PBS directives in the beginning of the jobscript file, dont' forget to set your valid PROJECT_ID and desired queue).
Sometimes for testing purposes, you may need to submit only one-element array. This is not allowed by PBSPro, but there's a workaround:
diff --git a/docs.it4i/salomon/hardware-overview.md b/docs.it4i/salomon/hardware-overview.md
index d1bd65a810686a7425730dde75794ee82f285e83..4569358cfe04784158893ae3dd4d9617d4fa732d 100644
--- a/docs.it4i/salomon/hardware-overview.md
+++ b/docs.it4i/salomon/hardware-overview.md
@@ -36,7 +36,7 @@ The parameters are summarized in the following tables:
| 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/).
+For more details refer to the [Compute nodes](compute-nodes/).
## Remote Visualization Nodes
diff --git a/docs.it4i/salomon/job-submission-and-execution.md b/docs.it4i/salomon/job-submission-and-execution.md
index 8330fdd3e44ab1dd59dd7ad12658809a75d02152..0018ea9e3ddc054c531af3a7ddef20b0b2ca51b2 100644
--- a/docs.it4i/salomon/job-submission-and-execution.md
+++ b/docs.it4i/salomon/job-submission-and-execution.md
@@ -2,7 +2,7 @@
## Job Submission
-When allocating computational resources for the job, please specify
+When allocating computational resources for the job, specify:
1. suitable queue for your job (default is qprod)
1. number of computational nodes required
@@ -460,7 +460,7 @@ cp $PBS_O_WORKDIR/input .
cp $PBS_O_WORKDIR/mympiprog.x .
# load the MPI module
-module load OpenMPI
+ml OpenMPI
# execute the calculation
mpiexec -pernode ./mympiprog.x
@@ -498,7 +498,7 @@ SCRDIR=/scratch/work/user/$USER/myjob
cd $SCRDIR || exit
# load the MPI module
-module load OpenMPI
+ml OpenMPI
# execute the calculation
mpiexec ./mympiprog.x
diff --git a/docs.it4i/salomon/software/ansys/ansys-cfx.md b/docs.it4i/salomon/software/ansys/ansys-cfx.md
index 2cf29101dd4ab162de9c7f52e2b19a58cc715f42..ce25a028b5796e45e6a27eac008619021d3a5853 100644
--- a/docs.it4i/salomon/software/ansys/ansys-cfx.md
+++ b/docs.it4i/salomon/software/ansys/ansys-cfx.md
@@ -25,7 +25,7 @@ echo Directory is `pwd`
echo This jobs runs on the following processors:
echo `cat $PBS_NODEFILE`
-module load ansys
+ml ansys
#### Set number of processors per host listing
#### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)
diff --git a/docs.it4i/salomon/software/ansys/ansys-fluent.md b/docs.it4i/salomon/software/ansys/ansys-fluent.md
index f4867b5c75bcaa7b3e52400b601dd1d0cce43fe3..27afebf82126a92cb6cdf2f36165a97902124024 100644
--- a/docs.it4i/salomon/software/ansys/ansys-fluent.md
+++ b/docs.it4i/salomon/software/ansys/ansys-fluent.md
@@ -30,7 +30,7 @@ echo This jobs runs on the following processors:
echo `cat $PBS_NODEFILE`
#### Load ansys module so that we find the cfx5solve command
-module load ansys
+ml ansys
# Use following line to specify MPI for message-passing instead
NCORES=`wc -l $PBS_NODEFILE |awk '{print $1}'`
@@ -82,7 +82,7 @@ input is the name of the input file.
case is the name of the .cas file that the input file will utilize.
-fluent_args are extra ANSYS FLUENT arguments. As shown in the previous example, you can specify the interconnect by using the -p interconnect command. The available interconnects include ethernet (the default), myrinet, infiniband, vendor, altix, and crayx. The MPI is selected automatically, based on the specified interconnect.
+fluent_args are extra ANSYS FLUENT arguments. As shown in the previous example, you can specify the interconnect by using the -p interconnect command. The available interconnects include ethernet (the default), myrinet, Infiniband, vendor, altix, and crayx. The MPI is selected automatically, based on the specified interconnect.
outfile is the name of the file to which the standard output will be sent.
diff --git a/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md b/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md
index e9fda41a9d116554fe9862b854ef57ac7e556438..55be78c1412bfd42acf64c67fea158cc8f2fab59 100644
--- a/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md
+++ b/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md
@@ -30,7 +30,7 @@ NPROCS=`wc -l < $PBS_NODEFILE`
echo This job has allocated $NPROCS nodes
-module load ansys
+ml ansys
#### Set number of processors per host listing
#### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)
diff --git a/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md b/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md
index 0bde6f3a1c8b5d729f0de715863186b189beb74d..450c9750d8063f19388daa2a3ed12a0a05cc53ad 100644
--- a/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md
+++ b/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md
@@ -26,7 +26,7 @@ echo Directory is `pwd`
echo This jobs runs on the following processors:
echo `cat $PBS_NODEFILE`
-module load ansys
+ml ansys
#### Set number of processors per host listing
#### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)
diff --git a/docs.it4i/salomon/software/ansys/ansys.md b/docs.it4i/salomon/software/ansys/ansys.md
index a5cac322dbc77eb794401e4dd964dd79b9fbbc23..79fca741fe443dee12a6d7569b7a8de67e2c0061 100644
--- a/docs.it4i/salomon/software/ansys/ansys.md
+++ b/docs.it4i/salomon/software/ansys/ansys.md
@@ -1,13 +1,13 @@
# 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)
+**[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 [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/)
To load the latest version of any ANSYS product (Mechanical, Fluent, CFX, MAPDL,...) load the module:
```bash
- $ module load ansys
+ $ ml ansys
```
ANSYS supports interactive regime, but due to assumed solution of extremely difficult tasks it is not recommended.
diff --git a/docs.it4i/salomon/software/chemistry/nwchem.md b/docs.it4i/salomon/software/chemistry/nwchem.md
index 465adf2042cca69f801af48a2eb104f215a44187..bbabdd3eec5f34d3187f31004a30db11b7fdbb6c 100644
--- a/docs.it4i/salomon/software/chemistry/nwchem.md
+++ b/docs.it4i/salomon/software/chemistry/nwchem.md
@@ -16,7 +16,7 @@ The following versions are currently installed:
For a current list of installed versions, execute:
```bash
- module avail NWChem
+ ml av NWChem
```
The recommend to use version 6.5. Version 6.3 fails on Salomon nodes with accelerator, because it attempts to communicate over scif0 interface. In 6.5 this is avoided by setting ARMCI_OPENIB_DEVICE=mlx4_0, this setting is included in the module.
diff --git a/docs.it4i/salomon/software/debuggers/valgrind.md b/docs.it4i/salomon/software/debuggers/valgrind.md
index 5e6a2c8e8246888a60e7026bb04ab433b921f658..5a7cf7db08bd378c194cd5370ca666b3a4e8ae0f 100644
--- a/docs.it4i/salomon/software/debuggers/valgrind.md
+++ b/docs.it4i/salomon/software/debuggers/valgrind.md
@@ -13,7 +13,7 @@ The main tools available in Valgrind are :
* **Hellgrind** and **DRD** can detect race conditions in multi-threaded applications.
* **Cachegrind**, a cache profiler.
* **Callgrind**, a callgraph analyzer.
-* For a full list and detailed documentation, please refer to the [official Valgrind documentation](http://valgrind.org/docs/).
+* For a full list and detailed documentation, refer to the [official Valgrind documentation](http://valgrind.org/docs/).
## Installed Versions
@@ -21,7 +21,7 @@ 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 3.11.0 built by GCC with support for OpenMPI, module Valgrind/3.11.0-foss-2015b
## Usage
diff --git a/docs.it4i/salomon/software/numerical-languages/octave.md b/docs.it4i/salomon/software/numerical-languages/octave.md
index 7484d97a349b25178c75acb08c2f52db2595f4cc..787e6a325ef4ae5b46a22157d8dfda4d537c089f 100644
--- a/docs.it4i/salomon/software/numerical-languages/octave.md
+++ b/docs.it4i/salomon/software/numerical-languages/octave.md
@@ -9,7 +9,7 @@ Two versions of octave are available on the cluster, via module
| **Stable** | Octave 3.8.2 | Octave |
```bash
- $ module load Octave
+ $ ml Octave
```
The octave on the cluster is linked to highly optimized MKL mathematical library. This provides threaded parallelization to many octave kernels, notably the linear algebra subroutines. Octave runs these heavy calculation kernels without any penalty. By default, octave would parallelize to 24 threads. You may control the threads by setting the OMP_NUM_THREADS environment variable.
@@ -33,7 +33,7 @@ To run octave in batch mode, write an octave script, then write a bash jobscript
cp $PBS_O_WORKDIR/octcode.m .
# load octave module
- module load Octave
+ ml Octave
# execute the calculation
octave -q --eval octcode > output.out
@@ -53,4 +53,4 @@ The octave c compiler mkoctfile calls the GNU gcc 4.8.1 for compiling native c c
$ mkoctfile -v
```
-Octave may use MPI for inter-process communication This functionality is currently not supported on the cluster cluster. In case you require the octave interface to MPI, please contact our [cluster support](https://support.it4i.cz/rt/).
+Octave may use MPI for inter-process communication This functionality is currently not supported on the cluster cluster. In case you require the octave interface to MPI, contact our [cluster support](https://support.it4i.cz/rt/).
diff --git a/docs.it4i/salomon/storage.md b/docs.it4i/salomon/storage.md
index 61adc35e7ab317a7dcc29d92e853a9ac01b6f6a4..a592c1058487f89843f78c7ff994d2de4435fecb 100644
--- a/docs.it4i/salomon/storage.md
+++ b/docs.it4i/salomon/storage.md
@@ -228,7 +228,7 @@ Default ACL mechanism can be used to replace setuid/setgid permissions on direct
### Home
-Users home directories /home/username reside on HOME file system. Accessible capacity is 0.5 PB, shared among all users. Individual users are restricted by file system usage quotas, set to 250 GB per user. If 250 GB should prove as insufficient for particular user, please contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
+Users home directories /home/username reside on HOME file system. Accessible capacity is 0.5 PB, shared among all users. Individual users are restricted by file system usage quotas, set to 250 GB per user. If 250 GB should prove as insufficient for particular user, contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
!!! note
The HOME file system is intended for preparation, evaluation, processing and storage of data generated by active Projects.
@@ -274,7 +274,7 @@ The WORK workspace is hosted on SCRATCH file system. The SCRATCH is realized as
### Temp
-The TEMP workspace resides on SCRATCH file system. The TEMP workspace accesspoint is /scratch/temp. Users may freely create subdirectories and files on the workspace. Accessible capacity is 1.6 PB, shared among all users on TEMP and WORK. Individual users are restricted by file system usage quotas, set to 100 TB per user. The purpose of this quota is to prevent runaway programs from filling the entire file system and deny service to other users. >If 100 TB should prove as insufficient for particular user, please contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
+The TEMP workspace resides on SCRATCH file system. The TEMP workspace accesspoint is /scratch/temp. Users may freely create subdirectories and files on the workspace. Accessible capacity is 1.6 PB, shared among all users on TEMP and WORK. Individual users are restricted by file system usage quotas, set to 100 TB per user. The purpose of this quota is to prevent runaway programs from filling the entire file system and deny service to other users. >If 100 TB should prove as insufficient for particular user, contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
!!! note
The TEMP workspace is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs must use the TEMP workspace as their working directory.
@@ -403,7 +403,7 @@ User of data storage CESNET (DU) association can become organizations or an indi
User may only use data storage CESNET for data transfer and storage which are associated with activities in science, research, development, the spread of education, culture and prosperity. In detail see “Acceptable Use Policy CESNET Large Infrastructure (Acceptable Use Policy, AUP)”.
-The service is documented [here](https://du.cesnet.cz/en/start). For special requirements please contact directly CESNET Storage Department via e-mail [du-support(at)cesnet.cz](mailto:du-support@cesnet.cz).
+The service is documented [here](https://du.cesnet.cz/en/start). For special requirements contact directly CESNET Storage Department via e-mail [du-support(at)cesnet.cz](mailto:du-support@cesnet.cz).
The procedure to obtain the CESNET access is quick and trouble-free.
@@ -457,7 +457,7 @@ $ cp -a mydir cesnet/.
$ cp cesnet/myfile .
```
-Once done, please remember to unmount the storage
+Once done, remember to unmount the storage
```console
$ fusermount -u cesnet
diff --git a/docs.it4i/software/cae/comsol/comsol-multiphysics.md b/docs.it4i/software/cae/comsol/comsol-multiphysics.md
index 7a5d7d11fc39ee9b2e07ccb2326e0953b209c5b7..dfe98412481f17c3f5f3f57e2b109350f4d4d5ee 100644
--- a/docs.it4i/software/cae/comsol/comsol-multiphysics.md
+++ b/docs.it4i/software/cae/comsol/comsol-multiphysics.md
@@ -62,8 +62,8 @@ echo '**PBS_NODEFILE***END*********'
text_nodes < cat $PBS_NODEFILE
-module load COMSOL
-# module load COMSOL/51-EDU
+ml COMSOL
+# ml COMSOL/51-EDU
ntask=$(wc -l $PBS_NODEFILE)
@@ -76,7 +76,7 @@ Working directory has to be created before sending the (comsol.pbs) job script i
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 (on Anselm use 16 threads).
+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 (see the [ISV Licenses](../isv_licenses/)) are available. Following example shows how to start COMSOL model from MATLAB via LiveLink in the interactive mode (on Anselm use 16 threads).
```console
$ xhost +
@@ -107,8 +107,8 @@ echo '**PBS_NODEFILE***END*********'
text_nodes < cat $PBS_NODEFILE
-module load MATLAB
-module load COMSOL/51-EDU
+ml MATLAB
+ml COMSOL/51-EDU
ntask=$(wc -l $PBS_NODEFILE)
diff --git a/docs.it4i/software/compilers.md b/docs.it4i/software/compilers.md
index f35b01f254d2fd873ba9452f1522036e0b26efb4..293926cbe99407914fdc903c6d4cc9a51c535be7 100644
--- a/docs.it4i/software/compilers.md
+++ b/docs.it4i/software/compilers.md
@@ -24,14 +24,14 @@ Commercial licenses:
## Intel Compilers
-For information about the usage of Intel Compilers and other Intel products, please read the [Intel Parallel studio](intel-suite/intel-compilers/) page.
+For information about the usage of Intel Compilers and other Intel products, read the [Intel Parallel studio](intel-suite/intel-compilers/) page.
## PGI Compilers (Only on Salomon)
The Portland Group Cluster Development Kit (PGI CDK) is available on Salomon.
```console
-$ module load PGI
+$ ml PGI
$ pgcc -v
$ pgc++ -v
$ pgf77 -v
@@ -45,8 +45,8 @@ The PGI CDK also incudes tools for debugging and profiling.
PGDBG OpenMP/MPI debugger and PGPROF OpenMP/MPI profiler are available
```console
-$ module load PGI
-$ module load Java
+$ ml PGI
+$ ml Java
$ pgdbg &
$ pgprof &
```
@@ -60,7 +60,7 @@ For compatibility reasons there are still available the original (old 4.4.7-11)
It is strongly recommended to use the up to date version which comes with the module GCC:
```console
-$ module load GCC
+$ ml GCC
$ gcc -v
$ g++ -v
$ gfortran -v
@@ -76,7 +76,7 @@ $ echo $DEBUGFLAGS
-O0 -g
```
-For more information about the possibilities of the compilers, please see the man pages.
+For more information about the possibilities of the compilers, see the man pages.
## Unified Parallel C
@@ -187,8 +187,8 @@ For more information see the man pages.
## Java
-For information how to use Java (runtime and/or compiler), please read the [Java page](java/).
+For information how to use Java (runtime and/or compiler), read the [Java page](java/).
## NVIDIA CUDA
-For information how to work with NVIDIA CUDA, please read the [NVIDIA CUDA page](../anselm/software/nvidia-cuda/).
+For information how to work with NVIDIA CUDA, read the [NVIDIA CUDA page](../anselm/software/nvidia-cuda/).
diff --git a/docs.it4i/software/debuggers/aislinn.md b/docs.it4i/software/debuggers/aislinn.md
index 2a945a04e8c74218b312c2ad9d6bdd08f1f54a5b..0a10684f060175fc39b1de46fc48ef99e0372f81 100644
--- a/docs.it4i/software/debuggers/aislinn.md
+++ b/docs.it4i/software/debuggers/aislinn.md
@@ -6,7 +6,7 @@
* Web page of the project: <http://verif.cs.vsb.cz/aislinn/>
!!! note
- Aislinn is software developed at IT4Innovations and some parts are still considered experimental. If you have any questions or experienced any problems, please contact the author: <mailto: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, contact the author: <mailto:stanislav.bohm@vsb.cz>.
## Usage
diff --git a/docs.it4i/software/debuggers/intel-vtune-amplifier.md b/docs.it4i/software/debuggers/intel-vtune-amplifier.md
index 8842e4f47d6b948a2263cc458f7ef78f39034ce1..d3529ba98f1aae1ebac5e3034467bd44c4db2f74 100644
--- a/docs.it4i/software/debuggers/intel-vtune-amplifier.md
+++ b/docs.it4i/software/debuggers/intel-vtune-amplifier.md
@@ -72,7 +72,7 @@ This mode is useful for native Xeon Phi applications launched directly on the ca
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
- 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.
+ 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 contact our support to reboot the MIC card.
You may also use remote analysis to collect data from the MIC and then analyze it in the GUI later :
diff --git a/docs.it4i/software/debuggers/papi.md b/docs.it4i/software/debuggers/papi.md
index c8c6619479d1c5ae9b3d37ee2e78b1e1b987bebe..a873d3693dafe8db8f7e38583fcde13a9f702eef 100644
--- a/docs.it4i/software/debuggers/papi.md
+++ b/docs.it4i/software/debuggers/papi.md
@@ -16,7 +16,7 @@ To use PAPI, load [module](../../environment-and-modules/) PAPI:
$ ml papi
```
-This will load the default version. Execute module avail pap for a list of installed versions.
+This will load the default version. Execute ml av papi for a list of installed versions.
## Utilities
diff --git a/docs.it4i/software/debuggers/score-p.md b/docs.it4i/software/debuggers/score-p.md
index 186762617bc0ae39f624df391b0816044fc5f327..45de7f9cbbad2c035b769628f0bc87e63013f3be 100644
--- a/docs.it4i/software/debuggers/score-p.md
+++ b/docs.it4i/software/debuggers/score-p.md
@@ -114,4 +114,4 @@ subroutine foo(...)
end subroutine foo
```
-The directives are ignored if the program is compiled without Score-P. Again, please refer to the [documentation](https://silc.zih.tu-dresden.de/scorep-current/pdf/scorep.pdf) for a more elaborate description.
+The directives are ignored if the program is compiled without Score-P. Again, refer to the [documentation](https://silc.zih.tu-dresden.de/scorep-current/pdf/scorep.pdf) for a more elaborate description.
diff --git a/docs.it4i/software/debuggers/valgrind.md b/docs.it4i/software/debuggers/valgrind.md
index d94d205a7f26ce9bfdcbfa6c39aa24452bd1cad4..6acf83911ca0e73e220af73147141a08bfa776ed 100644
--- a/docs.it4i/software/debuggers/valgrind.md
+++ b/docs.it4i/software/debuggers/valgrind.md
@@ -15,7 +15,7 @@ The main tools available in Valgrind are :
* **Hellgrind** and **DRD** can detect race conditions in multi-threaded applications.
* **Cachegrind**, a cache profiler.
* **Callgrind**, a callgraph analyzer.
-* For a full list and detailed documentation, please refer to the [official Valgrind documentation](http://valgrind.org/docs/).
+* For a full list and detailed documentation, refer to the [official Valgrind documentation](http://valgrind.org/docs/).
## Installed Versions
@@ -28,7 +28,7 @@ There are two versions of Valgrind available on the Salomon.
* 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 3.11.0 built by GCC with support for OpenMPI, module Valgrind/3.11.0-foss-2015b
## Usage
diff --git a/docs.it4i/software/intel/intel-xeon-phi-anselm.md b/docs.it4i/software/intel/intel-xeon-phi-anselm.md
index b1e86256d093b4bd34fe799e48f64d38f48d0e83..009c57fd5554a58e09eec9c0ca33b8955feb1a23 100644
--- a/docs.it4i/software/intel/intel-xeon-phi-anselm.md
+++ b/docs.it4i/software/intel/intel-xeon-phi-anselm.md
@@ -258,7 +258,7 @@ or by setting environment variable
$ export MKL_MIC_ENABLE=1
```
-To get more information about automatic offload please refer to "[Using Intel® MKL Automatic Offload on Intel ® Xeon Phi™ Coprocessors](http://software.intel.com/sites/default/files/11MIC42_How_to_Use_MKL_Automatic_Offload_0.pdf)" white paper or [Intel MKL documentation](https://software.intel.com/en-us/articles/intel-math-kernel-library-documentation).
+To get more information about automatic offload refer to "[Using Intel® MKL Automatic Offload on Intel ® Xeon Phi™ Coprocessors](http://software.intel.com/sites/default/files/11MIC42_How_to_Use_MKL_Automatic_Offload_0.pdf)" white paper or [Intel MKL documentation](https://software.intel.com/en-us/articles/intel-math-kernel-library-documentation).
### Automatic Offload Example
@@ -266,7 +266,7 @@ At first get an interactive PBS session on a node with MIC accelerator and load
```console
$ qsub -I -q qmic -A OPEN-0-0 -l select=1:ncpus=16
-$ module load intel
+$ ml intel
```
Following example show how to automatically offload an SGEMM (single precision - general matrix multiply) function to MIC coprocessor. The code can be copied to a file and compiled without any necessary modification.
@@ -440,7 +440,7 @@ OpenCL (Open Computing Language) is an open standard for general-purpose paralle
On Anselm OpenCL is installed only on compute nodes with MIC accelerator, therefore OpenCL code can be compiled only on these nodes.
```console
-module load opencl-sdk opencl-rt
+ml opencl-sdk opencl-rt
```
Always load "opencl-sdk" (providing devel files like headers) and "opencl-rt" (providing dynamic library libOpenCL.so) modules to compile and link OpenCL code. Load "opencl-rt" for running your compiled code.
@@ -555,7 +555,7 @@ $ qsub -I -q qmic -A NONE-0-0
The only supported implementation of MPI standard for Intel Xeon Phi is Intel MPI. To setup a fully functional development environment a combination of Intel compiler and Intel MPI has to be used. On a host load following modules before compilation:
```console
-$ module load intel
+$ ml intel
```
To compile an MPI code for host use:
@@ -715,7 +715,7 @@ The output should be again similar to:
```
!!! note
- `mpiexec.hydra` requires a file the MIC filesystem. If the file is missing please contact the system administrators.
+ `mpiexec.hydra` requires a file the MIC filesystem. If the file is missing contact the system administrators.
A simple test to see if the file is present is to execute:
@@ -901,4 +901,4 @@ Each host or accelerator is listed only once per file. User has to specify how m
## 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")
+For more details about optimization techniques 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/software/intel/intel-xeon-phi-salomon.md b/docs.it4i/software/intel/intel-xeon-phi-salomon.md
index 8d6c9c61903b9aaf6d93073a6d338efd2a7c013a..982f2d59cd5395edb300efb2d8628d82f68e3e6a 100644
--- a/docs.it4i/software/intel/intel-xeon-phi-salomon.md
+++ b/docs.it4i/software/intel/intel-xeon-phi-salomon.md
@@ -304,7 +304,7 @@ or by setting environment variable
$ export MKL_MIC_ENABLE=1
```
-To get more information about automatic offload please refer to "[Using Intel® MKL Automatic Offload on Intel ® Xeon Phi™ Coprocessors](http://software.intel.com/sites/default/files/11MIC42_How_to_Use_MKL_Automatic_Offload_0.pdf)" white paper or [Intel MKL documentation](https://software.intel.com/en-us/articles/intel-math-kernel-library-documentation).
+To get more information about automatic offload refer to "[Using Intel® MKL Automatic Offload on Intel ® Xeon Phi™ Coprocessors](http://software.intel.com/sites/default/files/11MIC42_How_to_Use_MKL_Automatic_Offload_0.pdf)" white paper or [Intel MKL documentation](https://software.intel.com/en-us/articles/intel-math-kernel-library-documentation).
### Automatic Offload Example
@@ -532,7 +532,7 @@ OpenCL (Open Computing Language) is an open standard for general-purpose paralle
On Salomon OpenCL is installed only on compute nodes with MIC accelerator, therefore OpenCL code can be compiled only on these nodes.
```console
-module load opencl-sdk opencl-rt
+ml opencl-sdk opencl-rt
```
Always load "opencl-sdk" (providing devel files like headers) and "opencl-rt" (providing dynamic library libOpenCL.so) modules to compile and link OpenCL code. Load "opencl-rt" for running your compiled code.
@@ -640,7 +640,7 @@ $ qsub -I -q qprod -l select=1:ncpus=24:accelerator=True:naccelerators=2:acceler
The only supported implementation of MPI standard for Intel Xeon Phi is Intel MPI. To setup a fully functional development environment a combination of Intel compiler and Intel MPI has to be used. On a host load following modules before compilation:
```console
-$ module load intel
+$ ml intel
```
To compile an MPI code for host use:
@@ -815,7 +815,7 @@ Hello world from process 0 of 4 on host r38u31n1000-mic0
```
!!! hint
- **"mpiexec.hydra"** requires a file the MIC filesystem. If the file is missing please contact the system administrators.
+ **"mpiexec.hydra"** requires a file the MIC filesystem. If the file is missing contact the system administrators.
A simple test to see if the file is present is to execute:
@@ -830,7 +830,7 @@ To get access to multiple nodes with MIC accelerator, user has to use PBS to all
```console
$ qsub -I -q qprod -l select=2:ncpus=24:accelerator=True:naccelerators=2:accelerator_model=phi7120 -A NONE-0-0
-$ module load intel impi
+$ ml intel impi
```
This command connects user through ssh to one of the nodes immediately. To see the other nodes that have been allocated use:
@@ -987,4 +987,4 @@ Each host or accelerator is listed only once per file. User has to specify how m
## 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")
+For more details about optimization techniques 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/software/isv_licenses.md b/docs.it4i/software/isv_licenses.md
index 63cd44719f4c4bed5bdac8f04c3f57915977315c..ad804ef99ddd2855b325bd4faab8935dc393e373 100644
--- a/docs.it4i/software/isv_licenses.md
+++ b/docs.it4i/software/isv_licenses.md
@@ -93,7 +93,7 @@ Example of PBS Pro resource name, based on APP and FEATURE name:
| matlab-edu | MATLAB_Distrib_Comp_Engine | feature_matlab-edu_MATLAB_Distrib_Comp_Engine |
| matlab-edu | Image_Acquisition_Toolbox | feature_matlab-edu_Image_Acquisition_Toolbox\\ |
-!!! Warnig
+!!! warnig
Resource names in PBS Pro are case sensitive.
### Example of qsub Statement
diff --git a/docs.it4i/software/lang/java.md b/docs.it4i/software/lang/java.md
index d8e10e70a86d5e1b94606f72495a221d9edaa867..67e77ab26be796fca4774f0c9026992c5d6822cc 100644
--- a/docs.it4i/software/lang/java.md
+++ b/docs.it4i/software/lang/java.md
@@ -22,13 +22,13 @@ $ javac -version
$ which javac
```
-Java applications may use MPI for inter-process communication, in conjunction with Open MPI. Read more on <http://www.open-mpi.org/faq/?category=java>. This functionality is currently not supported on Anselm cluster. In case you require the java interface to MPI, please contact [cluster support](https://support.it4i.cz/rt/).
+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, contact [cluster support](https://support.it4i.cz/rt/).
## Java With OpenMPI
Because there is an increasing interest in using Java for HPC. Also, MPI can benefit from Java because its widespread use makes it likely to find new uses beyond traditional HPC applications.
-The Java bindings are integrated into Open MPI starting from the v1.7 series. Beginning with the v2.0 series, the Java bindings include coverage of MPI-3.1.
+The Java bindings are integrated into OpenMPI starting from the v1.7 series. Beginning with the v2.0 series, the Java bindings include coverage of MPI-3.1.
### Example (Hello.java)
@@ -83,4 +83,4 @@ Hello world from rank 20 of 28
Hello world from rank 5 of 28
Hello world from rank 21 of 28
Hello world from rank 22 of 28
-```
\ No newline at end of file
+```
diff --git a/docs.it4i/software/modules/lmod.md b/docs.it4i/software/modules/lmod.md
index 4aad91ce85aff13e59594cc1efaeee4ce6465d78..bb949145c61fd1247c75723cdf186647117ff8a6 100644
--- a/docs.it4i/software/modules/lmod.md
+++ b/docs.it4i/software/modules/lmod.md
@@ -6,7 +6,7 @@ Detailed documentation on Lmod is available [here](http://lmod.readthedocs.io).
## Benefits
-* significantly more responsive module commands, in particular module avail (ml av)
+* significantly more responsive module commands, in particular 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)
@@ -17,10 +17,10 @@ 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 | ml GCC/6.2.0-2.27 |
| ml -GCC/6.2.0-2.27 | module unload GCC/6.2.0-2.27 |
| ml purge | module unload all modules |
-| ml av | module avail |
+| ml av | ml av |
| 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 |
@@ -121,7 +121,7 @@ $ module spider GCC/6.2.0-2.27
Description:
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,...). - Homepage: http://gcc.gnu.org/
- This module can be loaded directly: module load GCC/6.2.0-2.27
+ This module can be loaded directly: ml GCC/6.2.0-2.27
Help:
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
diff --git a/docs.it4i/software/mpi/mpi.md b/docs.it4i/software/mpi/mpi.md
index ab774158938c0be8ba197f80fdd53c76ebf0e04b..c65c0d8d2ef853a4b5ca8891b12510f1f1634493 100644
--- a/docs.it4i/software/mpi/mpi.md
+++ b/docs.it4i/software/mpi/mpi.md
@@ -13,7 +13,7 @@ The Salomon cluster provides several implementations of the MPI library:
MPI libraries are activated via the environment modules.
-Look up section modulefiles/mpi in module avail
+Look up section modulefiles/mpi in ml av
```console
$ ml av
diff --git a/docs.it4i/software/mpi/mpi4py-mpi-for-python.md b/docs.it4i/software/mpi/mpi4py-mpi-for-python.md
index c2a2976b5bb1b27e46c47fc615846de9179fa29e..a3b3f69edb8d8294630b9e790bc0c07efb43597d 100644
--- a/docs.it4i/software/mpi/mpi4py-mpi-for-python.md
+++ b/docs.it4i/software/mpi/mpi4py-mpi-for-python.md
@@ -28,7 +28,7 @@ OpenMPI/1.8.6-GNU-5.1.0-2.25 OpenMPI/1.8.8-GNU-5.1.0-2.25 OpenMPI/1.10.1-GN
OpenMPI/1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25 OpenMPI/2.0.2-GCC-6.3.0-2.27
```
-!!! Warning "Flavours"
+!!! warning "Flavours"
* modules Python/x.x.x-intel... - intel MPI
* modules Python/x.x.x-foss... - OpenMPI
diff --git a/docs.it4i/software/mpi/ompi-examples.md b/docs.it4i/software/mpi/ompi-examples.md
index 912f7d3487bdac5fb729a87ed34bb022385a689d..b96406497fd6ec8ed64a96a26418c5c119e06ca6 100644
--- a/docs.it4i/software/mpi/ompi-examples.md
+++ b/docs.it4i/software/mpi/ompi-examples.md
@@ -1,6 +1,6 @@
# OpenMPI Sample Applications
-Sample MPI applications provided both as a trivial primer to MPI as well as simple tests to ensure that your Open MPI installation is working properly.
+Sample MPI applications provided both as a trivial primer to MPI as well as simple tests to ensure that your OpenMPI installation is working properly.
## Examples
@@ -38,11 +38,11 @@ Additionally, there's one further example application, but this one only uses th
Download [examples](../../src/ompi/ompi.tar.gz).
-The Makefile in this directory will build the examples for the supported languages (e.g., if you do not have the Fortran "use mpi" bindings compiled as part of Open MPI, those examples will be skipped).
+The Makefile in this directory will build the examples for the supported languages (e.g., if you do not have the Fortran "use mpi" bindings compiled as part of OpenMPI, those examples will be skipped).
The Makefile assumes that the wrapper compilers mpicc, mpic++, and mpifort are in your path.
-Although the Makefile is tailored for Open MPI (e.g., it checks the *mpi_info* command to see if you have support for C++, mpif.h, use mpi, and use mpi_f08 F90), all of the example programs are pure MPI, and therefore not specific to Open MPI. Hence, you can use a different MPI implementation to compile and run these programs if you wish.
+Although the Makefile is tailored for OpenMPI (e.g., it checks the *mpi_info* command to see if you have support for C++, mpif.h, use mpi, and use mpi_f08 F90), all of the example programs are pure MPI, and therefore not specific to OpenMPI. Hence, you can use a different MPI implementation to compile and run these programs if you wish.
```console
[login@cn204.anselm ]$ tar xvf ompi.tar.gz
diff --git a/docs.it4i/software/numerical-languages/matlab.md b/docs.it4i/software/numerical-languages/matlab.md
index e3bccc1a9ae9f976509dea53ad6cf4b1ac11302a..89446eb399ffa0b4b1d0f8ba5ab84805b5550de0 100644
--- a/docs.it4i/software/numerical-languages/matlab.md
+++ b/docs.it4i/software/numerical-languages/matlab.md
@@ -21,9 +21,9 @@ $ ml av MATLAB
If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.
-If you require the Matlab GUI, please follow the general information about [running graphical applications](../../general/accessing-the-clusters/graphical-user-interface/x-window-system/).
+If you require the Matlab GUI, follow the general information about [running graphical applications](../../general/accessing-the-clusters/graphical-user-interface/x-window-system/).
-Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part [here](../../general/accessing-the-clusters/graphical-user-interface/x-window-system/)) is recommended.
+Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (see the "GUI Applications on Compute Nodes over VNC" part [here](../../general/accessing-the-clusters/graphical-user-interface/x-window-system/)) is recommended.
To run Matlab with GUI, use
@@ -104,7 +104,7 @@ mkdir -p $SCR ; cd $SCR || exit
cp $PBS_O_WORKDIR/matlabcode.m .
# load modules
-module load MATLAB/2015a-EDU
+ml MATLAB/2015a-EDU
# execute the calculation
matlab -nodisplay -r matlabcode > output.out
@@ -249,15 +249,15 @@ delete(pool)
### 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, [look here](../isv_licenses/).
The licensing feature of PBS is currently disabled.
-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.
+In case of non-interactive session read the [following information](../isv_licenses/) on how to modify the qsub command to test for available licenses prior getting the resource allocation.
### Matlab Distributed Computing Engines Start Up Time
-Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:
+Starting Matlab workers is an expensive process that requires certain amount of time. For your information see the following table:
| compute nodes | number of workers | start-up time[s] |
| ------------- | ----------------- | ---------------- |
diff --git a/docs.it4i/software/numerical-languages/matlab_1314.md b/docs.it4i/software/numerical-languages/matlab_1314.md
index 9760bf63c6fdc3df08e74fcd68dc7182b66effa5..69e666994d21611e5202d829e81d5b070404e2f0 100644
--- a/docs.it4i/software/numerical-languages/matlab_1314.md
+++ b/docs.it4i/software/numerical-languages/matlab_1314.md
@@ -3,7 +3,7 @@
## Introduction
!!! note
- This document relates to the old versions R2013 and R2014. For MATLAB 2015, please use [this documentation instead](matlab/).
+ This document relates to the old versions R2013 and R2014. For MATLAB 2015 use [this documentation instead](matlab/).
Matlab is available in the latest stable version. There are always two variants of the release:
@@ -24,9 +24,9 @@ $ ml matlab
If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.
-If you require the Matlab GUI, please follow the general information about running graphical applications
+If you require the Matlab GUI, follow the general information about running graphical applications
-Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part) is recommended.
+Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (see the "GUI Applications on Compute Nodes over VNC" part) is recommended.
To run Matlab with GUI, use
@@ -111,8 +111,8 @@ mkdir -p $SCR ; cd $SCR || exit
cp $PBS_O_WORKDIR/matlabcode.m .
# load modules
-module load matlab/R2013a-EDU
-module load impi/4.1.1.036
+ml matlab/R2013a-EDU
+ml impi/4.1.1.036
# execute the calculation
matlab -nodisplay -r matlabcode > output.out
@@ -190,13 +190,13 @@ 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, [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.
+In case of non-interactive session read the [following information](../isv_licenses/) on how to modify the qsub command to test for available licenses prior getting the resource allocation.
### Matlab Distributed Computing Engines Start Up Time
-Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:
+Starting Matlab workers is an expensive process that requires certain amount of time. For your information see the following table:
| compute nodes | number of workers | start-up time[s] |
| ------------- | ----------------- | ---------------- |
diff --git a/docs.it4i/software/numerical-languages/octave.md b/docs.it4i/software/numerical-languages/octave.md
index 8a3eb55ce0b653414fe09cba1bf6f8b07c00cf42..b3ce195504de06effdd7e9d12ca5a5076635aaf3 100644
--- a/docs.it4i/software/numerical-languages/octave.md
+++ b/docs.it4i/software/numerical-languages/octave.md
@@ -36,7 +36,7 @@ cd /lscratch/$PBS_JOBID || exit
cp $PBS_O_WORKDIR/octcode.m .
# load octave module
-module load octave
+ml octave
# execute the calculation
octave -q --eval octcode > output.out
@@ -56,7 +56,7 @@ The octave c compiler mkoctfile calls the GNU gcc 4.8.1 for compiling native c c
$ mkoctfile -v
```
-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/).
+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, contact [Anselm support](https://support.it4i.cz/rt/).
## Xeon Phi Support
diff --git a/docs.it4i/software/numerical-languages/opencoarrays.md b/docs.it4i/software/numerical-languages/opencoarrays.md
index bfbbb7f65fb0681b57213fb1b821d933195118bb..d6788ef142b1c70ff309b1181a629ed32491efea 100644
--- a/docs.it4i/software/numerical-languages/opencoarrays.md
+++ b/docs.it4i/software/numerical-languages/opencoarrays.md
@@ -124,4 +124,4 @@ $ mpiexec -np 4 ./synchronization_test.x
**-np 4** is number of images to run. The parameters of **cafrun** and **mpiexec** are the same.
-For more information about running CAF program please follow [Running OpenMPI - Salomon](../mpi/Running_OpenMPI.md)
+For more information about running CAF program follow [Running OpenMPI - Salomon](../mpi/Running_OpenMPI.md)
diff --git a/docs.it4i/software/numerical-languages/r.md b/docs.it4i/software/numerical-languages/r.md
index c7f112c638786169a8a25a7150ed1b85abf3c893..e83388e60dde9febb3969ee9b68537877697b33b 100644
--- a/docs.it4i/software/numerical-languages/r.md
+++ b/docs.it4i/software/numerical-languages/r.md
@@ -14,12 +14,12 @@ Read more on <http://www.r-project.org/>, <http://cran.r-project.org/doc/manuals
## Modules
-The R version 3.1.1 is available on the cluster, along with GUI interface Rstudio
+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 |
+| **RStudio** | RStudio 0.98.1103 | RStudio |
```console
$ ml R
@@ -31,10 +31,10 @@ The R on cluster is linked to highly optimized MKL mathematical library. This pr
### Interactive Execution
-To run R interactively, using Rstudio GUI, log in with ssh -X parameter for X11 forwarding. Run rstudio:
+To run R interactively, using RStudio GUI, log in with ssh -X parameter for X11 forwarding. Run rstudio:
```console
-$ ml Rstudio
+$ ml RStudio
$ rstudio
```
@@ -54,7 +54,7 @@ cd /lscratch/$PBS_JOBID || exit
cp $PBS_O_WORKDIR/rscript.R .
# load R module
-module load R
+ml R
# execute the calculation
R CMD BATCH rscript.R routput.out
@@ -377,8 +377,8 @@ cd $SCRDIR || exit
cp $PBS_O_WORKDIR/rscript.R .
# load R and openmpi module
-module load R
-module load OpenMPI
+ml R
+ml OpenMPI
# execute the calculation
mpiexec -bycore -bind-to-core R --slave --no-save --no-restore -f rscript.R
diff --git a/docs.it4i/software/numerical-libraries/hdf5.md b/docs.it4i/software/numerical-libraries/hdf5.md
index 7b61eeb5f1e35f118654c5908523b4e0d88360ed..6ebeebe60b0bed3b166ce5853c21571c6c460f09 100644
--- a/docs.it4i/software/numerical-libraries/hdf5.md
+++ b/docs.it4i/software/numerical-libraries/hdf5.md
@@ -24,7 +24,7 @@ $ ml hdf5-parallel
The module sets up environment variables, required for linking and running HDF5 enabled applications. Make sure that the choice of HDF5 module is consistent with your choice of MPI library. Mixing MPI of different implementations may have unpredictable results.
!!! 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>
+ 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, 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.
@@ -86,4 +86,4 @@ $ mpicc hdf5test.c -o hdf5test.x -Wl,-rpath=$LIBRARY_PATH $HDF5_INC $HDF5_SHLIB
Run the example as [Intel MPI program](../mpi/running-mpich2/).
-For further information, please see the website: <http://www.hdfgroup.org/HDF5/>
+For further information, see the website: <http://www.hdfgroup.org/HDF5/>
diff --git a/docs.it4i/software/orca.md b/docs.it4i/software/orca.md
index 8215a9ead80e0acdebf245ce93d9e74fe5bf07a5..0684e29fa091a6a22c5bca80c3c17867f376ae6f 100644
--- a/docs.it4i/software/orca.md
+++ b/docs.it4i/software/orca.md
@@ -7,7 +7,7 @@ ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum c
The following module command makes the latest version of orca available to your session
```bash
-$ module load ORCA/3_0_3-linux_x86-64
+$ ml ORCA/3_0_3-linux_x86-64
```
### Dependency
@@ -49,7 +49,7 @@ Create a Sun Grid Engine submission file called submit_serial.sh that looks like
```bash
!/bin/bash
-module load ORCA/3_0_3-linux_x86-64
+ml ORCA/3_0_3-linux_x86-64
orca orca_serial.inp
```
diff --git a/docs.it4i/software/tools/ansys/ansys-cfx.md b/docs.it4i/software/tools/ansys/ansys-cfx.md
index cb77fdf45713578ca348ba4acc0847e98fed51c2..45acd6f3e04ec84dfab2063bea3d9d5ec82352d9 100644
--- a/docs.it4i/software/tools/ansys/ansys-cfx.md
+++ b/docs.it4i/software/tools/ansys/ansys-cfx.md
@@ -25,7 +25,7 @@ echo Directory is `pwd`
echo This jobs runs on the following processors:
echo `cat $PBS_NODEFILE`
-module load ansys
+ml ansys
#### Set number of processors per host listing
#### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)
diff --git a/docs.it4i/software/tools/ansys/ansys-fluent.md b/docs.it4i/software/tools/ansys/ansys-fluent.md
index ee8ac3a5e2a07cae0b7846b2f3fda08e53cebfd9..e11b8597b51e149efe037f607ff08e7399431416 100644
--- a/docs.it4i/software/tools/ansys/ansys-fluent.md
+++ b/docs.it4i/software/tools/ansys/ansys-fluent.md
@@ -30,7 +30,7 @@ echo This jobs runs on the following processors:
echo `cat $PBS_NODEFILE`
#### Load ansys module so that we find the cfx5solve command
-module load ansys
+ml ansys
# Use following line to specify MPI for message-passing instead
NCORES=`wc -l $PBS_NODEFILE |awk '{print $1}'`
@@ -82,7 +82,7 @@ input is the name of the input file.
case is the name of the .cas file that the input file will utilize.
-fluent_args are extra ANSYS FLUENT arguments. As shown in the previous example, you can specify the interconnect by using the -p interconnect command. The available interconnects include ethernet (the default), myrinet, infiniband, vendor, altix, and crayx. The MPI is selected automatically, based on the specified interconnect.
+fluent_args are extra ANSYS FLUENT arguments. As shown in the previous example, you can specify the interconnect by using the -p interconnect command. The available interconnects include ethernet (the default), myrinet, Infiniband, vendor, altix, and crayx. The MPI is selected automatically, based on the specified interconnect.
outfile is the name of the file to which the standard output will be sent.
diff --git a/docs.it4i/software/tools/ansys/ansys-ls-dyna.md b/docs.it4i/software/tools/ansys/ansys-ls-dyna.md
index 7bf643a9c40448012724d80ce02f5b7731d0c23a..e3af0318cd6f123c1982fbf9fef509d932528596 100644
--- a/docs.it4i/software/tools/ansys/ansys-ls-dyna.md
+++ b/docs.it4i/software/tools/ansys/ansys-ls-dyna.md
@@ -30,7 +30,7 @@ NPROCS=`wc -l < $PBS_NODEFILE`
echo This job has allocated $NPROCS nodes
-module load ansys
+ml ansys
#### Set number of processors per host listing
#### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)
diff --git a/docs.it4i/software/tools/ansys/ansys-mechanical-apdl.md b/docs.it4i/software/tools/ansys/ansys-mechanical-apdl.md
index 116252df5aaa64a4e9c43f9443443db050791f4f..3db398c40b67a7df75dde4b3876fec721c35dc86 100644
--- a/docs.it4i/software/tools/ansys/ansys-mechanical-apdl.md
+++ b/docs.it4i/software/tools/ansys/ansys-mechanical-apdl.md
@@ -26,7 +26,7 @@ echo Directory is `pwd`
echo This jobs runs on the following processors:
echo `cat $PBS_NODEFILE`
-module load ansys
+ml ansys
#### Set number of processors per host listing
#### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)
diff --git a/docs.it4i/software/tools/ansys/ansys.md b/docs.it4i/software/tools/ansys/ansys.md
index d1def39cd2775933d56ce89a58a2cc3c87ea388c..dcd1952529dff99caf018693cea3dc1924ab89a2 100644
--- a/docs.it4i/software/tools/ansys/ansys.md
+++ b/docs.it4i/software/tools/ansys/ansys.md
@@ -1,6 +1,6 @@
# 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)
+**[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 [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](licensing/)
diff --git a/docs.it4i/software/tools/ansys/ls-dyna.md b/docs.it4i/software/tools/ansys/ls-dyna.md
index dac7dbe9f066445cb21964aaeb031941cbd77346..8492ddbf7becd363fe3125f428fe98cd69270790 100644
--- a/docs.it4i/software/tools/ansys/ls-dyna.md
+++ b/docs.it4i/software/tools/ansys/ls-dyna.md
@@ -25,7 +25,7 @@ echo Running on host `hostname`
echo Time is `date`
echo Directory is `pwd`
-module load lsdyna
+ml lsdyna
/apps/engineering/lsdyna/lsdyna700s i=input.k
```
diff --git a/docs.it4i/software/tools/ansys/workbench.md b/docs.it4i/software/tools/ansys/workbench.md
index fc33e5082490709e61f10b842d4975aa28407503..cdbc3c799bc56b58707c5ae56badec6237bd6a0e 100644
--- a/docs.it4i/software/tools/ansys/workbench.md
+++ b/docs.it4i/software/tools/ansys/workbench.md
@@ -36,7 +36,7 @@ Now, save the project and close Workbench. We will use this script to launch the
echo This jobs runs on the following nodes:
echo `cat $PBS_NODEFILE`
- module load ANSYS
+ ml ANSYS
#### Set number of processors per host listing
procs_per_host=24
diff --git a/docs.it4i/software/tools/easybuild-images.md b/docs.it4i/software/tools/easybuild-images.md
index 14187c717990eaf4892534bd69eba63b0ab2ab40..215e7e6bcb7b94c33b42cdbf8811855e6896a6c9 100644
--- a/docs.it4i/software/tools/easybuild-images.md
+++ b/docs.it4i/software/tools/easybuild-images.md
@@ -95,7 +95,7 @@ eval "$@"
%environment
source /etc/profile
module use /app/modules/all
-module load Python/3.6.4-foss-2018a OpenMPI/2.1.2-GCC-6.4.0-2.28
+ml Python/3.6.4-foss-2018a OpenMPI/2.1.2-GCC-6.4.0-2.28
%labels
```
diff --git a/docs.it4i/software/viz/openfoam.md b/docs.it4i/software/viz/openfoam.md
index df6585429f6dc9d4fae6a52d6dcf713b534ab314..7765c5472c7948ea5405c193769ab941cc12704d 100644
--- a/docs.it4i/software/viz/openfoam.md
+++ b/docs.it4i/software/viz/openfoam.md
@@ -45,7 +45,7 @@ In /opt/modules/modulefiles/engineering you can see installed engineering softwa
lsdyna/7.x.x openfoam/2.2.1-gcc481-openmpi1.6.5-SP
```
-For information how to use modules please [look here](../../environment-and-modules/).
+For information how to use modules [look here](../../environment-and-modules/).
## Getting Started
@@ -93,7 +93,8 @@ Create a Bash script test.sh
```bash
#!/bin/bash
-module load openfoam/2.2.1-icc-openmpi1.6.5-DP
+
+ml openfoam/2.2.1-icc-openmpi1.6.5-DP
source $FOAM_BASHRC
# source to run functions
@@ -111,7 +112,7 @@ Job submission (example for Anselm):
$ 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](../../anselm/job-submission-and-execution/).
+For information about job submission [look here](../../anselm/job-submission-and-execution/).
## Running Applications in Parallel
@@ -124,7 +125,8 @@ First we must run serial application bockMesh and decomposePar for preparation o
```bash
#!/bin/bash
-module load openfoam/2.2.1-icc-openmpi1.6.5-DP
+
+ml openfoam/2.2.1-icc-openmpi1.6.5-DP
source $FOAM_BASHRC
# source to run functions
@@ -155,7 +157,7 @@ This job create simple block mesh and domain decomposition. Check your decomposi
#PBS -q qprod
#PBS -A OPEN-0-0
-module load openfoam/2.2.1-icc-openmpi1.6.5-DP
+ml openfoam/2.2.1-icc-openmpi1.6.5-DP
source $FOAM_BASHRC
cd $FOAM_RUN/tutorials/incompressible/simpleFoam/motorBike