Summary

Load and run

  • You can use the module system to load a specific version of MATLAB
module load matlab
  • You can start the MATLAB GUI with
matlab &

  • except on LUNARC; then you should use On-Demand instead

  • You can run MATLAB on the terminal using

matlab -nodisplay [-singleCompThread -nosplash -nodesktop]

Slurm job scheduler and MATLAB in terminal

  • You can configure the cluster before starting MATLAB, like this:
configCluster.sh <project-id if on UPPMAX or LUNARC>

or at the MATLAB command line, like this:

configCluster
  • You can can add job settings needed to run jobs from MATLAB.
c.AdditionalProperties.<properties like AccountName/WallTime>

  • You can work in the MATLAB terminal interface.

  • It works almost the same as with GUI.

  • You can submit jobs from inside the MATLAB terminal interface.

job = batch('myScript');

  • You can write and submit a MATLAB batch script.

  • Create batchscript.sh:

    !/bin/bash
#SBATCH -A my_account
#SBATCH -t 00:10:00
module load <matlab version>
matlab -nojvm -nodisplay -r "monte_carlo_pi(100000)"

  • Run it:

    sbatch batchscript.sh``

  • You can use GPUs with MATLAB

c.AdditionalProperties.GpusPerNode = 1;

MATLAB GUI and Slurm

  • You can submit jobs from inside the MATLAB GUI using the following syntax:
c=parcluster('name-of-your-cluster');
%extra slurm settings
j = c.batch(@myfunction,'nr. outputs',{'list of input args'},'pool','nr. workers');
j.wait;                               % wait for the results
j.fetchOutputs{:};                % fetch the results

  • Note that batch also accepts script names in place of function names, but these must be given in single quotes, with no @ or .m.

  • You can work with MATLAB in parallel

  • parfor: for simple for-loops with independent iterations

  • spmd: for worker-to-worker communication and collaboration

  • parfeval: for tasks that may depend on other tasks or need to run in the background

  • You can check that you are in an interactive session.

  • After running interactive.. on UPPMAX or LUNARC you will see that the linux prompt shows another hostname.

Add-Ons

  • You can view add-ons and toolboxes.

  • It is all more or less graphical.

  • You can install add-ons

    • Search in add-ons explorer and install.
    • Installation folder will be in MATLAB’s search path, and so should be accessible from anywhere in the file tree.

Session-UPPMAX: MATLAB client on the desktop

  • You can use the MATLAB client on the desktop

  • download and decompress UPPMAX configure file.

  • run configCluster on local MATLAB and set user name.
  • Set parcluster settings, like you do otherwise.

Session: MATLAB in Jupyter

  • You can start run MATLAB in Jupyter

  • You need to configure and install some python packages the first time.

  • After that Jupyter will find the MATLAB kernel during startup.