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MATLAB

Scientific computing and visualisation.

Interactive usage

After connecting to Stanage (see Establishing a SSH connection), start an interactive session with the following command:

srun --pty bash -i

A version of MATLAB is made available by running one of the following:

module load MATLAB/2023b
module load MATLAB/2022a

You can then run MATLAB by entering matlab. This provides a matlab terminal (Please note that graphical sessions are not yet available on Stanage, so the matlab GUI will not load).

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=8G                # Request  8 GB of real memory

# Load the MATLAB module
module load MATLAB/2023b

matlab -nodisplay -batch 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 -batch helloworld rather than -batch 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 64 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=16G
#SBATCH --ntasks-per-node=4
#SBATCH --time=00:05:00
#SBATCH --job-name=matlab_par_test

module load MATLAB/2022a

matlab -nodisplay -batch "parallel_example($SLURM_NTASKS)"

sleep 10

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,1);

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

    time = toc;
    fprintf('Wall clock duration: %.2f seconds\n', time);

    h5create('out.h5', '/maxeigen', [n 1]);
    h5write('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 method

MATLAB was installed using Easybuild 4.7.0, build details can be found in folder $EBROOTMATLAB/easybuild with a given module loaded.