Difference between revisions of "Comsol Guide"

Latest revision as of 07:50, 20 April 2020

NOTE REGARDING COMSOL 5.5

Starting version 5.5, COMSOL is built on a newer GLIBC version (2.14) and is no longer compatible wih RHEL6.x. To use COMSOL 5.5, submit jobs to the GeneralSky or any GPU partition.

comsol with MPI

To run comsol with SLURM, please create following comsol.sh:

#!/bin/bash

# For general partition
#SBATCH --nodes 8-16
#SBATCH --cpus-per-task 12
#SBATCH --ntasks-per-node 1
#SBATCH --output comsol.log

# Clear the output log
echo -n > comsol.log

# Add debugging information.
scontrol show job $SLURM_JOBID

# Details of input and output files.
INPUTFILE=/path/to/input_model.mph
OUTPUTFILE=/path/to/output_model.mph

# Load our comsol module.
module purge
module load intelics/2013.1.039-compiler zlib/1.2.8-ics mpi/mvapich2/2.0a-ics-slurm comsol/5.3a

# Run comsol.
comsol batch \
    -clustersimple \
    -np $SLURM_CPUS_PER_TASK \
    -mpifabrics shm:ofa \
    -inputfile $INPUTFILE \
    -outputfile $OUTPUTFILE \
    -tmpdir temp

Then submit the script by issuing:

$ sbatch comsol.sh

comsol with GPU

$ ssh <NetID>@login.storrs.hpc.uconn.edu
$ module load intelics/2013.1.039-compiler zlib/1.2.8-ics mpi/mvapich2/2.0a-ics-slurm comsol/5.2

To run comsol with SLURM, please create following comsol.sh:

#!/bin/bash

# Ask for a number of compute nodes
#SBATCH -p gpu
#SBATCH --gres=gpu:1
#SBATCH -N 1
#SBATCH -n 12
# Set your email address to be notified of jobs updates
#SBATCH --mail-type=ALL
#SBATCH --mail-user=your@email.address

# Details of your input and output files
INPUTFILE=/path/to/input_model.mph
OUTPUTFILE=/path/to/output_model.mph
TMPDIR=

# Load our comsol module
source /etc/profile.d/modules.sh
module purge
module load comsol/5.2a

######## DO NOT EDIT BELOW THIS LINE ########
# check if tmpdir exists
if [ ! -z $TMPDIR ]; then 
  TMPDIR="-tmpdir $TMPDIR"
fi
## Now, run COMSOL in batch mode with the input and output detailed above.
comsol -3drend ogl -np $SLURM_NTASKS -inputfile $INPUTFILE -outputfile $OUTPUTFILE $TMPDIR

Then submit the script by issuing:

$ sbatch comsol.sh

comsol on single node

Some comsol algorithms like PARDISO do not make use of MPI like . To run these, you can specify -np instead of -clustersimple as follows

#!/bin/bash

# Ask for a number of compute nodes
#SBATCH -N 1
#SBATCH -n 24

# Details of your input and output files
INPUTFILE=input_model.mph
OUTPUTFILE=output_model.mph
TMPDIR=temp

######## DO NOT EDIT BELOW THIS LINE ########

# Load our comsol module
source /etc/profile.d/modules.sh
module purge
module load comsol/5.2

## Now, run COMSOL in batch mode with the input and output detailed above.
comsol batch -np $SLURM_NTASKS -inputfile $INPUTFILE -outputfile $OUTPUTFILE -tmpdir $TMPDIR

Then submit the script by issuing:

$ sbatch comsol.sh