The COMSOL Multiphysics Package

The HEC currently hosts versions of the COMSOL multiphysics modelling suite, with licenses supplied by the Engineering (for version 5.2a) and Physics (for version 5.1) departments. Please check with the relevant Department’s IT Liaison to ensure you have access to these externally-hosted licenses.

A sample serial job script for COMSOL

COMSOL batch serial jobs may be run by creating a batch job control script (for example, called like the following:


#SBATCH -p serial
#SBATCH --mem=2G

source /etc/profile
module add comsol/5.1

comsol batch -prefsdir $TMPDIR  -recoverydir $TMPDIR \
  -inputfile cylinder_flow.mph -outputfile cylinder_flow.out \
  -autosave off

For an introduction to serial batch jobs on the HEC, please refer to Submitting jobs on the HEC.

The above job takes the model described in cylinder_flow.mph and places the results in cylinder_flow.out.

The -prefsdir and -tmpdir values are set to point to a temporary directory created during the job run. This is recommended as by default COMSOL writes a large number of files to the user home area, which can quickly result in going over quota.

The -recoverydir option sets the recovery directory to the current working directory from which the job was submitted.

A sample parallel job script for COMSOL

For models suitable for parallel running, the following parallel job template can be used:


#SBATCH -p parallel
#SBATCH -C node_type=10GethAny
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=2
#SBATCH --exclusive

source /etc/profile
module add comsol/5.1

comsol batch -mpibootstrap slurm -np $OMP_NUM_THREADS \
  -prefsdir $TMPDIR -recoverydir `pwd`  -tmpdir $TMPDIR \
  -inputfile cylinder_flow.mph -outputfile cylinder_flow.out \
  -autosave off

For an introduction to parallel MPI jobs on the HEC, please see Using the Message Passing Interface (MPI) on the HEC.

It is recommended to run COMSOL in hybrid parallel mode, with one MPI process per CPU socket and the number of threads per process matching the number of CPU cores per socket. The above example requests two compute nodes of node_type 10GethAny - these nodes each have two sockets, and 8 cores per socket.

The job script contains an additional SLURM resource request line advising that the job requires two tasks per node - these will be the two MPI processes per compute node. The additional -np argument to comsol uses the environment variable OMP_NUM_THREADS which will be automatically set up by the job sceduler to a value based on the formula (# cpus per node / # of tasks per node). For the 10GethAny nodes with 16 CPUs, this will result in an OMP_NUM_THREAD value of 8 - so comsol will run with two MPI proceses per compute node, and 8 threads per MPI process.

Two important items to bear in mind when running COMSOL in parallel, to ensure that resources are not wasted:

  • Significant speedup is only seen on models with several million degrees of freedom; and

  • The meshing algorithm runs mostly in serial. For parallel runs, the mesh should be pre-computed in serial mode

Further Reading

The COMSOL home page