Simple Matlab Script Wrapper

Blog post edited by Anonymous - "Migration of unmigrated content due to installation of a new plugin"

Sometimes you have four or five variations on the same MATLAB script. You could write a different submissions script for each variation, or you can constantly edit the submission script every time you need to change to a different variation. However, I find that this can be confusing so I made the following script to make my life easier:

runMatlab.qsub

1
2
3
4
5
6

#!/bin/bash -login
#PBS -l walltime=01:00:00,nodes=1:ppn=1
#PBS -l software=MATLAB
cd ${PBS_O_WORKDIR}
module load matlab
matlab -nodisplay -r "${PBS_JOBNAME}"

This is a qsub wrapper script that allows you to specify the name of the MATLAB script as the name of the job. To run the script just type:

qsub -N myScriptName runMatlab.qsub

Then when you want to run a different script you can type:

qsub -N myDifferentScript runMatlab.qsub

Make sure you do not include the ".m" in the script name. Since command line resource request override requests in the script, it is possible to also change the resources from the command line. For example, if you have a really short test you need to run you can do the following:

qsub -N myquicktest -l walltime=00:05:00 runMatlab.qsub

NOTE: This above only works for MATLAB scripts (i.e. no input arguments) and not functions.

View Online

Blogpost migrated from ICER Wiki using custom python script. Comment on errors below.