From 1e3719b0a2632dc9399d3969e5cb341169edd0f2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= <lukas.krupcik@vsb.cz>
Date: Mon, 20 Sep 2021 10:58:52 +0200
Subject: [PATCH] Update comsol-multiphysics.md
---
.../cae/comsol/comsol-multiphysics.md | 50 +++++++++----------
1 file changed, 23 insertions(+), 27 deletions(-)
diff --git a/docs.it4i/software/cae/comsol/comsol-multiphysics.md b/docs.it4i/software/cae/comsol/comsol-multiphysics.md
index 38b7f0464..db2daadf8 100644
--- a/docs.it4i/software/cae/comsol/comsol-multiphysics.md
+++ b/docs.it4i/software/cae/comsol/comsol-multiphysics.md
@@ -20,7 +20,7 @@ On the clusters, COMSOL is available in the latest stable version. There are two
* **Commercial** or so called **COM variant**, which can used also for commercial activities. **COM variant** has only subset of features compared to the **EDU variant** available. More about licensing [here][1].
-To load the `COMSOL` module, use:
+To load the default `COMSOL` module ([**not** recommended][4]), use:
```console
$ ml COMSOL
@@ -40,7 +40,7 @@ To prepare COMSOL jobs in the interactive mode, we recommend using COMSOL on the
Example for Barbora:
```console
-$ qsub -I -X -A PROJECT_ID -q qprod -l select=1:ncpus=36
+$ qsub -I -X -A PROJECT_ID -q qprod -l select=1:ncpus=36:mpiprocs=36
$ ml av COMSOL
------------------------------ /apps/modules/phys ------------------------------
@@ -50,32 +50,31 @@ $ ml COMSOL/5.2.0-EDU
$ comsol -3drend sw
```
-!!! info
- If you receive errors at startup, for example, of the following type:
+* If you receive errors at startup, for example, of the following type:
- ```console
+```console
FL3D: error at line 814 in file fl3dglcontext_x11common.c:
PBuffers are not supported by the system.
FL3D: error at line 235 in file fl3dglcontext_x11common.c:
assert: x11Handle
- ```
+```
- you need to run COMSOL with additional parameters:
+you need to run COMSOL with additional parameters:
- ```console
+```console
$ comsol -3drend sw
- ```
+```
To run COMSOL in batch mode without the COMSOL Desktop GUI environment, utilize the default (comsol.pbs) job script and execute it via the `qsub` command:
```bash
#!/bin/bash
-#PBS -l select=3:ppn=24
+#PBS -l select=3:ncpus=36:mpiprocs=36
#PBS -q qprod
#PBS -N JOB_NAME
#PBS -A PROJECT_ID
-cd /scratch/work/user/$USER/ || exit
+cd /scratch/project/PROJECT_ID/ || exit
echo Time is `date`
echo Directory is `pwd`
@@ -85,12 +84,11 @@ echo '**PBS_NODEFILE***END*********'
text_nodes < cat $PBS_NODEFILE
-ml COMSOL
-# ml COMSOL/51-EDU
+ml COMSOL/5.2.0-EDU
ntask=$(wc -l $PBS_NODEFILE)
-comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/.../$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log
+comsol -3drend sw -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/project/PROJECT_ID/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log
```
A working directory has to be created before sending the (comsol.pbs) job script into the queue. The input file (name_input_f.mph) has to be in the working directory or a full path to the input file has to be specified. The appropriate path to the temp directory of the job has to be set by the `-tmpdir` command option.
@@ -102,11 +100,9 @@ COMSOL is a software package for the numerical solution of partial differential
LiveLink for MATLAB is available in both **EDU** and **COM** **variant** of the COMSOL release. On the clusters there is 1 commercial (**COM**) and 5 educational (**EDU**) licenses of LiveLink for MATLAB (see the [ISV Licenses][3]). The following example shows how to start COMSOL model from MATLAB via LiveLink in the interactive mode.
```console
-$ xhost +
-$ qsub -I -X -A PROJECT_ID -q qexp -l select=1:ppn=24
-$ ml MATLAB
-$ ml COMSOL
-$ comsol server MATLAB
+$ qsub -I -X -A PROJECT_ID -q qexp -l select=1:ncpus=36:mpiprocs=36
+$ ml MATLAB/R2015b COMSOL/5.2.0-EDU
+$ comsol -3drend sw server MATLAB
```
On the first start of the LiveLink for MATLAB (client-MATLAB/server-COMSOL connection), the login and password is requested; this information is not requested again.
@@ -115,12 +111,12 @@ To run LiveLink for MATLAB in batch mode with (comsol_matlab.pbs) job script, yo
```bash
#!/bin/bash
-#PBS -l select=3:ppn=24
+#PBS -l select=3:ncpus=36:mpiprocs=36
#PBS -q qprod
#PBS -N JOB_NAME
#PBS -A PROJECT_ID
-cd /scratch/work/user/$USER || exit
+cd /scratch/project/PROJECT_ID || exit
echo Time is `date`
echo Directory is `pwd`
@@ -130,21 +126,21 @@ echo '**PBS_NODEFILE***END*********'
text_nodes < cat $PBS_NODEFILE
-ml MATLAB
-ml COMSOL/51-EDU
+ml MATLAB/R2015b COMSOL/5.2.0-EDU
ntask=$(wc -l $PBS_NODEFILE)
-comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/work/user/$USER/work &
-cd /apps/cae/COMSOL/51/mli
-matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/work/user/$USER/work; test_job"
+comsol -3drend sw -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/project/PROJECT_ID &
+cd $EBROOTCOMSOL/mli
+matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/project/PROJECT_ID; test_job"
```
-This example shows how to run LiveLink for MATLAB with the following configuration: 3 nodes and 16 cores per node. A working directory has to be created before submitting (comsol_matlab.pbs) job script into the queue. The input file (test_job.m) has to be in the working directory or a full path to the input file has to be specified. The Matlab command option (`-r ”mphstart”`) created a connection with a COMSOL server using the default port number.
+This example shows how to run LiveLink for MATLAB with the following configuration: 3 nodes and 36 cores per node. A working directory has to be created before submitting (comsol_matlab.pbs) job script into the queue. The input file (test_job.m) has to be in the working directory or a full path to the input file has to be specified. The Matlab command option (`-r ”mphstart”`) created a connection with a COMSOL server using the default port number.
[1]: licensing-and-available-versions.md
[2]: ../../../general/accessing-the-clusters/graphical-user-interface/x-window-system.md
[3]: ../../isv_licenses.md
+[4]: ../modules/lmod/
[a]: http://www.comsol.com
[b]: http://www.comsol.com/structural-mechanics-module
--
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