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======Matlab======

====Application to Access====

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=====

Matlab 2020a is available by loading the shell environment module

<code bash>
module load chpc/math/matlab/R2020a
</code>

Note that you must include this command in your job scripts too in order to load Matlab into your job script environment.

=====User Interface=====

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, 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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