Work with MATLAB #

MATLAB is available on Wynton HPC via a built-in environment module and is supported by a UCSF-wide MATLAB license.

Accessing MATLAB #

To load the MATLAB module, do:

[alice@dev1 ~]$ module load matlab
[alice@dev1 ~]$ matlab -nosplash -nodesktop
MATLAB is selecting SOFTWARE OPENGL rendering.

                                                        < M A T L A B (R) >
                                              Copyright 1984-2022 The MathWorks, Inc.
                                              R2022b (9.13.0.2049777) 64-bit (glnxa64)
                                                          August 24, 2022

 
To get started, type doc.
For product information, visit www.mathworks.com.
 
>> 1+2

ans =

     3

>> quit
[alice@dev1 ~]$ 

If you forget to load the MATLAB module, then you will get an error when attempting to start MATLAB:

[alice@dev1 ~]$ matlab
-bash: matlab: command not found

Using MATLAB in job scripts #

In order to run MATLAB in jobs, the MATLAB environment module needs to be loaded just as when you run it interactive on a development node. For example, to run the my_script.m script, the job script should at a minimum contain:

#! /usr/bin/env bash
#$ -S /bin/bash
#$ -cwd          # run job in the current working directory

module load matlab
matlab -singleCompThread -batch "my_script"

The -batch option tells MATLAB to call the command my_script, and since that is not a built-in command, it will look for a MATLAB script file called my_script.m, and execute that. The -singleCompThread option tells MATLAB to run in sequential mode; this prevents your job for overusing the compute nodes by mistake.

Parallel processing in MATLAB #

If your MATLAB code supports parallel processing, make sure to specify the number of CPU cores when submitting your job submit, e.g. -pe smp 4 will request four cores on one machine, which in turn will set environment variable NSLOTS to 4. To make your MATLAB script respect this, add the following at the top of your script:

%% Make MATLAB respect the number of cores that the SGE scheduler
%% has alloted the job.  If not specified, run with a single core,
%% e.g. when running on a development node
nslots = getenv('NSLOTS');              % env var is always a 'char'
if (isempty(nslots)) nslots = '1'; end  % default value
nslots = str2num(nslots);               % coerce to 'double'
maxNumCompThreads(nslots);              % number of cores MATLAB may use

and then launch your MATLAB script without option -singleCompThread, e.g. matlab -batch "my_script".