COMSOL

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COMSOL General Documentation

COMSOL[1] documentation is available in both html and pdf on hpc.mtech.edu/comsol[2]. Navigate the file directory structure to locate the desired document. Here is direct link to the Introduction to COMSOL [3]. There is also documentation available through the COMSOL desktop. The remaining documentation in the Wiki below describes how to run COMSOL on the cluster. Additional documentation for all modules is available at: http://hpc.mtech.edu/comsol/pdf/

Running desktop gui from Management Node

The COMSOL desktop gui can be run on the management node, but long simulations should be executed on the compute nodes (see below). There are two ways to start COMSOL from a Windows PC. If you have an x-server installed (Cygwin[4] works well), you can login with an ssh client(e.g. putty [5], make sure to enable X11 forwarding). Alternatively, you can run NX (start through your web browser at hpc.mtech.edu/nx[6]). Once logged in, type comsol.

Submitting batch jobs through Moab

To avoid overloading the management node, COMSOL should be used in batch mode and jobs should be submitted to the compute nodes through torque.

Single Node

  1. Create a job script for using 4 processors (cores) - put the following in a file called comsoljob
    #!/bin/sh
    #PBS -l nodes=1:ppn=4
    #PBS -j oe
    #PBS -N ComsolJob
    #PBS -d /home/mtech/YOURNAME/COMSOL_PROJECT_DIR
    #PBS -S /bin/bash
    #PBS -m be
    #PBS -M YOURNAME@mtech.edu
    #PBS -l walltime=00:20:00
    comsol batch -inputfile in.mph -outputfile out.mph -np 4
    -->be sure to update with you input/output file names and your usernames
  2. Submit to Moab
    msub comsoljob
  3. Check status with showq or qstat or Ganglia.

Multiple Nodes with Intel MPI

COMSOL is installed with Intel's MPI and can be used on multiple nodes. In order to run on 2 or more node, modify your job script to include -clustersimple -f $PBS_NODEFILE.

For example:

#!/bin/sh
#PBS -l nodes=2:ppn=32
#PBS -N Comsol-2-node-32-core
#PBS -d /home/mtech/username/comsol
#PBS -l walltime=00:30:00
hostname
comsol batch -clustersimple -f $PBS_NODEFILE -inputfile mycomsol_file.mph -outputfile mycomsol_out.mph

(edit username/path, mycomsol_file and mycomsol_out for your model)

COMSOL Examples for cluster computing

Example models for cluster testing are included in the COMSOL Model Library:

/opt/COMSOL50/models/COMSOL_Multiphysics/Tutorial_Models/micromixer_cluster.mph
/opt/COMSOL50/models/COMSOL_Multiphysics/Tutorial_Models/thermal_actuator_jh_distributed.mph

LiveLink for MATLAB

To use COMSOL with the LiveLink for MATLAB:

comsol server matlab

This will start up the MATLAB Desktop.


To run a COMSOL batch job through Moab using a .m file (e.g., myprog.m), put the following in a job script:

#!/bin/sh
#PBS -l nodes=1:ppn=32
#PBS -j oe
#PBS -N ComsolJob
#PBS -d /home/mtech/YOURNAME/COMSOL_PROJECT_DIR
#PBS -S /bin/bash
#PBS -m be
#PBS -M YOURNAME@mtech.edu
#PBS -l walltime=02:00:00
comsol server < /dev/null > comsolserver.log &
matlab -nodesktop -nosplash -r "addpath /opt/COMSOL43b/mli, mphstart, myprog, exit"

COMSOL will automatically use the 32 available processors in the node. This job would run for 2 hours and then be cancelled, if you expect a longer run, then make sure to update the walltime.

Performance

COMSOL's performance generally improves as more processors (i.e., cores) are used until a certain point. This varies with the type of simulation and model being used. The "sweet spot" might be just 4 or 8 processors. For example one test gave

np1248162432
time(s)51332418121915

While hyperthreading is currently enabled, don't expect performance to improve for np > 16 as there are 16 cores per node (32 threads run simultaneously with hyperthreading and COMSOL does not take advantage of hyperthreading).

Checking for license availability

Montana Tech has a floating network license, so COMSOL could be in use on another system. To check which licenses are available:

cd /opt/COMSOL52/license/glnxa64/

./lmstat -a -c ../license.dat