Difference between revisions of "Submit Matlab jobs on Abel"
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For normal off-line non-parallell Matlab running on any Linux server, you can simply do e.g. | For normal off-line non-parallell Matlab running on any Linux server, you can simply do e.g. | ||
<pre>nohup matlab -nodisplay -nojvm -nodesktop -nosplash < Matlabprog.m > outdata.txt & | <pre>nohup matlab -nodisplay -nojvm -nodesktop -nosplash < Matlabprog.m > outdata.txt & | ||
| − | </pre> | + | </pre> |
For large jobs, this script should set you up OK at the Abel cluster: | For large jobs, this script should set you up OK at the Abel cluster: | ||
<pre>#!/bin/bash | <pre>#!/bin/bash | ||
| Line 12: | Line 12: | ||
#SBATCH --job-name=Matlab | #SBATCH --job-name=Matlab | ||
# | # | ||
| − | # Project: | + | # Project (change to your : |
| − | #SBATCH --account= | + | #SBATCH --account=geofag |
# | # | ||
# Wall clock limit: | # Wall clock limit: | ||
| Line 20: | Line 20: | ||
# Max memory usage per core (MB): | # Max memory usage per core (MB): | ||
#SBATCH --mem-per-cpu=2000M | #SBATCH --mem-per-cpu=2000M | ||
| − | + | # | |
# Number of tasks (cores): | # Number of tasks (cores): | ||
#SBATCH --ntasks=1 | #SBATCH --ntasks=1 | ||
| + | # | ||
| − | + | ## Setup job environment | |
| − | ## | + | source /cluster/bin/jobsetup |
| − | source / | ||
# Check if we have enough input arguments | # Check if we have enough input arguments | ||
if [ $# -lt 2 ]; then | if [ $# -lt 2 ]; then | ||
# No, print a usage message and exit script | # No, print a usage message and exit script | ||
| − | + | echo echo -e "\nUsage: sbatch submitscript.sh program dataset\n" | |
| − | + | exit | |
| + | |||
fi | fi | ||
| − | # Load matlab module | + | #Load matlab module |
| + | |||
module load matlab | module load matlab | ||
| − | # Make a result directory | + | #Make a result directory |
| − | |||
| − | |||
| − | + | RESULT=$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: | # Copy files to work directory: | ||
| − | |||
| − | |||
| − | # Change directory to the work directory | + | cp $SUBMITDIR/$PROG $SCRATCH cp $SUBMITDIR/$DATA $SCRATCH |
| + | |||
| + | #Change directory to the work directory | ||
| + | |||
cd $SCRATCH | cd $SCRATCH | ||
| − | # Start matlab | + | #Start matlab |
| + | |||
matlab -nodisplay -nojvm -nodesktop -nosplash < $PROG | matlab -nodisplay -nojvm -nodesktop -nosplash < $PROG | ||
| − | # Copy the necessary files from $SCRATCH to the Result directory | + | #Copy the necessary files from $SCRATCH to the Result directory |
| − | |||
| − | |||
| − | + | cp $SCRATCH/*.txt $RESULT cp $SCRATCH/*.eps $RESULT | |
| + | #End of script | ||
</pre> | </pre> | ||
| + | |||
| + | [[Category:Tools]][[Category:Software]][[Category:Matlab]][[Category:Abel]] | ||
Latest revision as of 17:13, 30 January 2015
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 (change to your : #SBATCH --account=geofag # # 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 # ## Setup job environment source /cluster/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
