Day: January 25, 2013

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Sample PBS Scripts for MATLAB

Here is a sample of PBS Scripts that can be used for MATLAB. This is just a suggested PBS script. Modify and comment at will. The script below is named as matlab_serial.sh

#!/bin/bash
#PBS -N MATLAB_Serial
#PBS -j oe
#PBS -V
#PBS -m bea
#PBS -M myemail@hotmail.com
#PBS -l nodes=1:ppn=1

# comment these out if you wish
echo "qsub host = " $PBS_O_HOST
echo "original queue = " $PBS_O_QUEUE
echo "qsub working directory absolute = " $PBS_O_WORKDIR
echo "pbs environment = " $PBS_ENVIRONMENT
echo "pbs batch = " $PBS_JOBID
echo "pbs job name from me = " $PBS_JOBNAME
echo "Name of file containing nodes = " $PBS_NODEFILE
echo "contents of nodefile = " $PBS_NODEFILE
echo "Name of queue to which job went = " $PBS_QUEUE

## pre-processing script
cd $PBS_O_WORKDIR
NCPUS=`cat $PBS_NODEFILE | wc -l`
echo "Number of requested processors = " $NCPUS

# Load MATLAB Module
module load intel/12.0.2
module load matlab/R2011b

cd $PBS_O_WORKDIR
/usr/local/MATLAB/R2011b/bin/matlab -nodisplay -r $file

The corresponding qsub command and its parameter should be something like

$ qsub -q dqueue -l nodes=1:ppn=8 matlab_serial.sh -v file=yourmatlabfile.m