Update comsol-multiphysics.md

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