Submit Matlab jobs on Abel
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Revision as of 11:44, 5 January 2015 by Annefou@uio.no (talk | contribs) (Created page with "<div class="vrtx-introduction"> This is an example of a Matlab submit script for use on the Abel cluster. Abel usage is documented at [http://www.uio.no/english/services/it/re...")
This is an example of a Matlab submit script for use on the Abel cluster. Abel usage is documented at UiOs HPC pages
For normal off-line non-parallell Matlab running on any Linux server, you can simply do e.g.
nohup matlab -nodisplay -nojvm -nodesktop -nosplash < Matlabprog.m > outdata.txt &
For large jobs, this script should set you up OK at the Abel cluster:
#!/bin/bash # Job name: #SBATCH --job-name=Matlab # # Project: #SBATCH --account=metos # # Wall clock limit: #SBATCH --time=1000:0:0 # # Max memory usage per core (MB): #SBATCH --mem-per-cpu=2000M
#
- Number of tasks (cores):
- SBATCH --ntasks=1
- Set up job environment
source /site/bin/jobsetup
- Check if we have enough input arguments
if [ $# -lt 2 ]; then
# No, print a usage message and exit script echo echo -e "\nUsage: sbatch submitscript.sh program dataset\n" exitfi
- Load matlab module
module load matlab
- Make a result directory
RESULT=$SUBMITDIR/Result_`date +%d_%b_%H.%M.%S` mkdir -p $RESULT
- Save the name of the matlab program and the dataset
PROG=$1 DATA=$2
- Copy files to work directory:
cp $SUBMITDIR/$PROG $SCRATCH cp $SUBMITDIR/$DATA $SCRATCH
- Change directory to the work directory
cd $SCRATCH
- Start matlab
matlab -nodisplay -nojvm -nodesktop -nosplash < $PROG
- Copy the necessary files from $SCRATCH to the Result directory
cp $SCRATCH/*.txt $RESULT cp $SCRATCH/*.eps $RESULT
- End of script