Submit Matlab jobs to Abel

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"
  exit
fi

# 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

 

By Gunnar Wollan, Arnstein Orten