Difference between revisions of "Comsol Guide"

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(Fix typo)
(Add draft GPU instructions)
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  ## Now, run COMSOL in batch mode with the input and output detailed above.
 
  ## Now, run COMSOL in batch mode with the input and output detailed above.
 
  comsol -clustersimple batch -inputfile $INPUTFILE -outputfile $OUTPUTFILE $TMPDIR
 
  comsol -clustersimple batch -inputfile $INPUTFILE -outputfile $OUTPUTFILE $TMPDIR
 +
 +
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:
 
Then submit the script by issuing:

Revision as of 11:00, 29 September 2017

comsol with MPI

$ 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 -N 2 #specify the number of nodes to change total number of cores
#DO NOT CHANGE the following two lines
#SBATCH -c12
#SBATCH --ntasks-per-node=1

# Set your email address to be notified of jobs updates
#SBATCH --mail-type=ALL
#SBATCH --mail-user=your@email.address

# Specify the run time you require, in the format HH:MM:SS
#SBATCH --time=04:00:00

# 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 intelics/2013.1.039-compiler zlib/1.2.8-ics mpi/mvapich2/2.0a-ics-slurm comsol/5.2

######## 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 -clustersimple batch -inputfile $INPUTFILE -outputfile $OUTPUTFILE $TMPDIR

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