Matlab

Installed versions

Resource	Version
Dardel/cpe23.12	r2024a, r2024b
Dardel/cpe23.03	r2024a

General information

General usage

MATLAB is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks. MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages. In order to use Matlab you need to have a Matlab license. KTH has a site-wide license for Matlab which includes all Matlab toolboxes.

External links

How to use

Getting Started with serial and parallel MATLAB

Load the matlab module by

ml add PDC
ml matlab/r2024b

In order to use MATLAB you need to have a MATLAB license. KTH has a site license that enable academic users of PDC computers around the world (student, faculty, staff) to use MATLAB. To access the installation of MATLAB on Dardel, please contact PDC support and request access.

Running interactively

MATLAB can be run interactively on an allocated node. To book a single node for one hour, type

salloc -N 1 -t 1:00:00 -A pdc.staff -p main
# wait for a node to be reserved

A typical output will look like

salloc: Granted job allocation 591571
salloc: Waiting for resource configuration
salloc: Nodes nid001015 are ready for job

Node nid001015 is now yours for the next hour, and you can log into it and start MATLAB. On Dardel you can login to the reserved node via the login node

ssh -X nid001015

and then start MATLAB with

ml add PDC
ml matlab/r2024b
matlab

In case you do not need a full node with 128 cores, you could request cores in the shared partition. These cores are shared with other users, with the amount of memory provided proportional to the number of cores awarded.

salloc -c 24 -t 1:00:00 -A pdc.staff -p shared

In the following example, a parallel pool of 24 workers is opened and a function, parallel_example (described further below), is called

>> p=parpool(24)
Starting parallel pool (parpool) using the 'local' profile ... connected to 24 workers.
p =
Pool with properties:
Connected: true
NumWorkers: 24
Cluster: local
AttachedFiles: {}
IdleTimeout: 30 minute(s) (30 minutes remaining)
SpmdEnabled: true
>> parallel_example
t =
2.4711
ans =
2.4711

This is how parallel_example.m might look

function t = parallel_example
t0 = tic;
parfor idx = 1:24
A(idx) = idx;
pause(2)
end
t = toc(t0)

Running parallel batch jobs

You can also submit parallel workflows to the SLURM queueing system. The following job script allocates 16 cores on Dardel and runs one MATLAB program.

#!/bin/bash
#SBATCH -A naissYYYY-X-XX
#SBATCH -J myjob
#SBATCH -p shared
#SBATCH -c 16
#SBATCH -t 10:00:00

# Load the MATLAB module
ml add PDC/23.12
ml matlab/r2024b

# Launch the MATLAB calculation
matlab -nosplash -nodesktop -nodisplay <  your_matlab_program.m > your_matlab_program.out

If the program contains the parpool() command and parfor loops (as demonstrated above), MATLAB will parallelize the computation over different cores of the node. Update the SLURM directives to set your project ID and the number of nodes and hours that you wish to allocate, and save the script as run_matlab.sh. You can then submit the job with

sbatch run_matlab.sh

It is advisable to run your code with different numbers of workers to determine the ideal number to use.

Running multiple serial batch jobs

If you have several serial MATLAB jobs that can be run simultaneously (for example, one MATLAB program with different input parameters), these can be run simultaneously on a booked node (in the main partition) or on booked cores (in the shared partition). A simple bash script for submitting multiple MATLAB jobs on 24 cores in the shared partition of Dardel node can look like

#!/bin/bash
#SBATCH -A naissYYYY-X-XX
#SBATCH -J myjob
#SBATCH -p shared
#SBATCH -c 24
#SBATCH -t 10:00:00

# Load the Matlab module
ml add PDC/23.12
ml matlab/r2024b

# Run matlab for 24 individual programs serial_program_1.m,
# serial_program_2.m ... and print output in files logfile_1, logfile_2, ...
# The input files must be in the directory where you submit this script.
# This is also where the output will be created.

for i in {1..24} ; do
    matlab -nosplash -nodesktop -nodisplay < serial_program_${i}.m > logfile_$i &
done
# This wait command must be present since otherwise the job will terminate immediately
wait

Update the SLURM directives to set your project ID and the number of cores and hours that you wish to allocate, and save the script as run_matlab.sh. You can then submit the job with

sbatch run_matlab.sh