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Matlab

Overview

There are three common ways to run Matlab:

  1. Using the Matlab graphical application through Open OnDemand.
  2. Using a module to start a graphical mode in an Open OnDemand virtual desktop.
  3. The command line version using modules. This is the most common as you will typically submit a job using Slurm.

Like any other application, Matlab has to be loaded as a module before you can use it. To see all the installed versions of the Matlab, use the command module avail matlab.

Logging Into Mathworks

With some of the latest versions, it's necessary to interactively log into Mathworks to access Matlab. This only needs to be done once using your university credentials. After your credentials are validated, they will be stored, allowing you to run batch jobs

To start, open an interactive session, load Matlab, and start an interactive instance:

Load and start Matlab
[netid@cpu37 ~]$ module load matlab/r2023b
[netid@cpu37 ~]$ matlab
MATLAB is selecting SOFTWARE OPENGL rendering.
Please enter your MathWorks Account email address and press Enter:

at the prompt, enter your university email address. For example:

Enter your university password and go to URL
Please enter your MathWorks Account email address and press Enter: netid@arizona.edu
You need a one-time password to sign in. To get a one-time password, follow these steps:
    1. Go to https://www.mathworks.com/mw_account/otp
    2. Enter your MathWorks Account email address.
    3. Copy the generated one-time password.
    4. Return here and enter the password.
Enter the one-time password:

Next, go to the URL they provide (highlighted above) and enter your university email address again

This will take you through the usual university WebAuth process. Once this is completed, you will be given a temporary code:

Copy this code to your clipboard and paste it into your terminal:

Enter one time password
Enter the one-time password:
12345


                                                          < M A T L A B (R) >
                                                Copyright 1984-2023 The MathWorks, Inc.
                                           R2023b Update 6 (23.2.0.2485118) 64-bit (glnxa64)
                                                           December 28, 2023

To get started, type doc.
For product information, visit www.mathworks.com.

Using 1 thread(s) on compute node.
>>

Once the process is complete, you should be able to use Matlab as usual.

Running Matlab Analyses in Batch

The typical procedure for performing calculations on UArizona HPC systems is to run your program non-interactively on compute nodes using a batch submission. The easiest way to run Matlab non-interactively is to use input/output redirection. This method uses Linux operators < and > to point Matlab to the input file and tell where to write the output (see the example script below). The other method is to execute a statement using the -r flag. For details, refer to the manual page for the matlab command.

An example batch script might look like the following:

#!/bin/bash
#SBATCH --job-name=matlab
#SBATCH --account=group_name
#SBATCH --partition=standard
#SBATCH --ntasks=20
#SBATCH --nodes
#SBATCH --mem-per-cpu=5gb
#SBATCH --time=01:00:00

module load matlab/<version>

matlab -nodisplay -nosplash < script_name.m > output.txt

The options -nodisplay and -nosplash in the example prevent Matlab from opening graphical elements. To view the full list of options for the matlab command, load the Matlab module and type matlab -h at the prompt. Alternatively, use the link above to see the manual page on the MathWorks website.

Parallel Computing Toolbox

Temporary Files

By default, Matlab PCT will dump files to ~/.matlab/<MATLAB_VERSION>. This causes problems when multiple Matlab PCT jobs are running simultaneously. Users should always define the environment variable MATLAB_PREFDIR so each job uses a unique temporary folder. Files there will be cleaned after the job finishes. For example: 

export MATLAB_PREFDIR=$(mktemp -d ${SLURM_JOBTMP}/matlab-XXXX)

Matlab and Slurm Resource Requests

If you are trying to run Matlab in parallel interactively, you may encounter the following error:

>> Starting parallel pool (parpool) using the 'local' profile ...
Error using parpool (line 149)
You requested a minimum of <n> workers, but the cluster "local" has the NumWorkers property set to allow a maximum of 1 workers. To run a communicating job on more workers than this
(up to a maximum of 512 for the Local cluster), increase the value of the NumWorkers property for the cluster. The default value of NumWorkers for a Local cluster is the number of
physical cores on the local machine.

This is caused by an interaction between Slurm and Matlab. To resolve this issue, when requesting <n> cores for your interactive job, you will need to set Slurm's --ntasks directive to 1 and --cpus-per-task to the number of cores you need. For example:

$ salloc --nodes=1 --ntasks=1 --cpus-per-task=6 --mem-per-cpu=5GB --time=01:00:00 --job-name=interactive --account=<GROUP> --partition=standard

External Resources

If you are getting started with Matlab or think there might be a better way, check out the training resources.

Resource Link
Self-Paced Online Courses https://matlabacademy.mathworks.com/
Matlab Parallel Server https://www.mathworks.com/products/matlab-parallel-server.html#resources
Natural Language Processing https://www.mathworks.com/discovery/natural-language-processing.html
Matlab Videos https://www.mathworks.com/videos.html