Discussion Forum

Hi, see slide 19 in the attached slideshow.

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cds.comsol.com/mg/9511ca78cae71f.zip
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Included files:
- cluster_install_linux_43a.pptx
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Niklas

Hello,

I am trying to run my models from comsol on our University's super computer, and having difficulty with the $PBS_NODEFILE command. Can the PBS_NODEFILE also be used to run generic MPI programs?

Thank you,
Kelley

Thank you for redirecting me to that power point. I have seen that before, but I had forgotten about it.
I am still having trouble running anything more complicated than

comsol batch -inputfile in.mph -outputfile out.mph

With version 4.3 I was able to use clustersimple command successfully but not any longer. I keep getting the same error " $PBS_NODEFILE: ambiguous redirect"

This is how I have it in my script

total=$(wc -l < $PBS_NODEFILE)
uniq -c $PBS_NODEFILE

comsol -nn 4 -clustersimple batch -inputfile 2.14_simplemodel.mph -outputfile 2.14_out.mph -batchlog Parallel.log

Do I need to include < -f $PBS_NODEFILE > in my final command line as well?

Thank you

Is anyone familiar with running comsol on a cluster from command line? I could use some help!
Thank you!

comsol models will not run on more than 1 node. The MPD commands do not work, and it seems like the problem is communication with the nodes.
Does MPD need to be checked in the GUI before I can run a model through command line in a cluster?
Are there new commands for COMSOL 4.3a for the MPD communication and host file?
Our computer science department is not familiar with Comsol, so any help would be appreciated.

The commands I am using below

qsub -q generic -I -l nodes=4:ppn12
module load comsol/43a
total=$(w -l < $PBS_NODEFILE)
uniq -c $PBS_NODEFILE
comsol -nn 4 mpd boot -f $PBS_NODEFILE -mpirsh ssh --verbose
comsol -nn 4 -np 12 batch -inputfile in.mph -outputfile out.mph

Thank you so much,
Kelley

I've got a response from the Comsol Support, so I thought I would post it here in case anyone else has a similar questions

The problem here is likely related to the new Hydra launching method introduced in COMSOL 4.3a. Normally Hydra should automatically detect the necessary settings from the cluster environment, and with this method it is not necessary to launch mpd:s manually (as was necessary in 4.3 and earlier versions). When using PBS, it should be possible (with the Hydra launcher) to replace the two comsol commands ("comsol mpd boot" and "comsol batch") with this single comsol batch command:

comsol -nn 4 -np 12 batch -inputfile in.mph -outputfile out.mph -mpiarg -rmk -mpiarg pbs -clustersimple

Alternatively, if the Hydra method does not work satisfactorily, it is possible to revert back to the mpd launch method used in COMSOL 4.3. To use the old method, the only thing needed is to add the "-mpd" option to the comsol batch command. The COMSOL commands in your PBS script would now be:

comsol -nn 4 mpd boot -f $PBS_NODEFILE -mpirsh ssh --verbose
comsol -mpd -nn 4 -np 12 batch -inputfile in.mph -outputfile out.mp
comsol mpd allexit

thank your for sharing