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--- howto:matlab [2025/03/06 12:23]
kevin created
+++ howto:matlab [2025/05/22 16:56] (current)
kevin [Example job script]
@@ Line 4: / Line 4: @@
 Matlab is commercial software and the CSIR has a site license which allows for non-commercial use on the CHPC cluster.
+===If you are already a CHPC user:===
 Please send an email to helpdesk@chpc.ac.za to request access to run Matlab M-files on the cluster.  Please mention your use case and project.
+===If you are not a CHPC user and would like to apply to be one:===
+The CHPC is free for students and researchers and you can apply for a //normal user// account on our [[https://users.chpc.ac.za/|User Portal]] as described in our [[chpc:accounts#registration|Registrations guide]].
+Note that after you register as a user, you will only receive a cluster account and access to a cpu-hour allocation once a CHPC //principal investigator// (PI) has added you to their research programme.
+If you are a student, then the PI would normally be your thesis supervisor.  If they are not currently a CHPC PI, then they can register as a PI on our [[https://users.chpc.ac.za/|User Portal]] as described in the [[chpc:accounts#registration|Registrations guide]].
 =====Environment Module=====
@@ Line 21: / Line 31: @@
 Note that you will only have access to the text mode user interface on the cluster.  Make sure your M-files can run without needing the Matlab GUI.
-Additionally, your M-files need to be able to work non-interactively to run within a job script.
+Additionally, your M-files need to be able to work non-interactively to run within a job script, i.e., using ''matlab -batch "command"''.
+====Example job script====
+> This job script assumes you want to use all 24 cores on one compute node.  If your job needs fewer cores then change the ''-l'' parameter below, e.g., ''-l select=1:ncpus=8:mpiprocs=8'' and use ''-q serial'' instead of the ''smp'' queue.
+**Note:** set the ''walltime'' parameter to the maximum run time you expect your job to need.
+<code bash>
+#!/bin/bash
+#PBS -N YOURJOBNAME
+#PBS -l select=1:ncpus=24:mpiprocs=24
+#PBS -P YOURPROJECT
+#PBS -q smp
+#PBS -l walltime=0:30:00
+CWD=/mnt/lustre/users/$USER/yourmatlabfiles/
+cd $CWD
+echo "Working directory is" `pwd`
+echo
+module purge
+module load chpc/math/matlab/R2020a
+echo "Modules loaded:"
+module list |& cat
+echo
+echo "Matlab interpreter:"
+which matlab
+echo
+nproc=`cat $PBS_NODEFILE | wc -l`
+echo "nproc is $nproc"
+echo
+echo "Threads & nodes used by this job:"
+cat $PBS_NODEFILE | sort | uniq -c
+echo
+echo "This script is running on node" `hostname`
+echo
+echo "Starting run..."
+# Run matlab on the m-file hello.m
+matlab -batch "hello"
+echo
+echo "... done."
+</code>
+If the ''matlab -batch "hello"'' command does not work then try the command
+  matlab -nodesktop -nojvm < ./hello.m
+See the [[https://www.mathworks.com/help/matlab/ref/matlablinux.html|Matlab on Linux]] doc for more options.

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