Attention

WARNING: From 9am on 19th August until 5pm on 2nd September there will be no access to the Stanage HPC cluster.

We will send an email to notify you when Stanage is back online and available for job submission.

MATLAB

Scientific computing and visualisation.

Interactive usage

After connecting to Bessemer, start an interactive session with the srun --pty bash –i command.

The latest version of MATLAB (currently 2022a) is made available by running:

module load MATLAB/2022a

Alternatively, you can load earlier MATLAB versions by running:

module load MATLAB/2018b
module load MATLAB/2019a
module load MATLAB/2020a
module load MATLAB/2020b
module load MATLAB/2021a
module load MATLAB/2021b
module load MATLAB/2022a

You can then run MATLAB by entering matlab &.

Serial (one CPU) batch usage

Here, we assume that you wish to run the program helloworld.m on the system:

function helloworld
    disp('Hello World!')
end

First, you need to write a batch submission file. We assume you’ll call this my_job.slurm:

#!/bin/bash
#SBATCH --mem=16000                # Request  16 GB of real memory

module load MATLAB/2022a

matlab -nodesktop -nosplash -r helloworld

Ensure that helloworld.m and my_job.slurm are both in your current working directory, then submit your job to the batch system:

sbatch my_job.slurm

Note that we are running the script helloworld.m but we drop the .m in the call to MATLAB. That is, we do -r helloworld rather than -r helloworld.m. The output will be written to the job text file when the job finishes.

Parallel MATLAB

Parallel MATLAB using multiple nodes is restricted to a maximum of 40 cores.

Here is an example using 4 cores on a single node. Create a Slurm submission script called parallel_example.slurm containing:

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --mem=16000
#SBATCH --ntasks-per-node=4
#SBATCH --time=00:05:00
#SBATCH --job-name=matlab_par_test

module load MATLAB/2022a

matlab -nodisplay -nosplash -r "parallel_example($SLURM_NTASKS)"

And create a MATLAB script called parallel_example.m containing:

function exit_code = parallel_example(n_cores)
    tic
    pool = parpool(n_cores)

    n = 200;
    A = 500;
    max_eigenvals = zeros(n);
    parfor i = 1:n
        max_eigenvals(i) = max(abs(eig(rand(A))));
    end

    time=toc;
    fprintf('Wall clock duration: %d\n', time);

    hdf5write('out.h5', '/maxeigen', max_eigenvals);

    exit_code = 0;
end

Then submit this as a batch job using:

sbatch parallel_example.slurm

The MATLAB script, parallel_example.m, creates 200 square (500 x 500) matrices comprised of random values, calculates the eigenvalues of each and records the maximum eigenvalue for each matrix in the array max_eigenvals.

Installation note for Administrators:

MATLAB 2018b was installed using Easybuild in the following directory:

/usr/local/packages/live/eb/MATLAB/2018b

The 2018b modulefile is /usr/local/modulefiles/live/eb/all/MATLAB/2018b.

MATLAB 2019a was installed using Easybuild in the following directory:

/usr/local/packages/live/eb/MATLAB/2019a

The 2019a modulefile is /usr/local/modulefiles/live/eb/all/MATLAB/2019a.

MATLAB 2020a was installed using the MATLAB installer GUI in the following directory:

/usr/local/packages/live/noeb/MATLAB/2020a/binary/

The 2020a modulefile is /usr/local/modulefiles/live/noeb/MATLAB/2020a/binary.

MATLAB 2020b was installed using the MATLAB installer GUI in the following directory:

/usr/local/packages/live/noeb/MATLAB/2020b/binary/

The 2020b modulefile is /usr/local/modulefiles/live/noeb/MATLAB/2020b/binary.

MATLAB 2021a was installed using the MATLAB installer GUI in the following directory:

/usr/local/packages/live/noeb/MATLAB/2021a/binary/

The 2021a modulefile is /usr/local/modulefiles/live/noeb/MATLAB/2021a/binary.

MATLAB 2021b was installed using the MATLAB installer GUI in the following directory:

/usr/local/packages/live/noeb/MATLAB/2021b/binary/

The 2021b modulefile is /usr/local/modulefiles/live/noeb/MATLAB/2021b/binary.

MATLAB 2022a was installed using the MATLAB installer GUI in the following directory:

/usr/local/packages/live/noeb/MATLAB/2022a/binary/

The 2022a modulefile is /usr/local/modulefiles/live/noeb/MATLAB/2022a/binary.