This lesson is being piloted (Beta version)

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High Performance Computing with MATLAB

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Running MATLAB on Sunbird

Overview

Teaching: 20 min
Exercises: 20 min
Questions

  • How do I run MATLAB scripts from the command line?

  • How do I run MATLAB from Sunbird?

Objectives

  • To learn to use HPC resources for MATLAB programs.

  • To run MATLAB scripts from the command line.

Accessing Sunbird

The HPC facility that we will be using for today’s workshop is Sunbird, the HPC machine of Supercomputing Wales project located in Swansea.

We access Sunbird using the SSH client via the command line. Open a terminal and enter the following command by replacing uname with your username:

ssh -Y uname@sunbird.swansea.ac.uk

Once you press Enter you will probably be asked to type in your password. If you have forgotten your password, you can reset it here: My Supercomputing Wales.

Once you successfully log in to Sunbird, you should see some information about Sunbird’s usage, and also notice that the prompt has changed to uname@sl1 or uname@sl2.

Using MATLAB on Sunbird

All the libraries and software on HPC machines are available in the form of modules. To access a particular software, we have to load the corresponding module first.

To use MATLAB, we need to load it first.

module load matlab/R2019a

If you want to load a different version, then you have to specify with the module load command. Refer to Supercomputing Wales Portal for more details on modules.

We can check the version of MATLAB that is loaded by typing:

module list

By typing which matlab on the terminal we can check which MATLAB executable is called.

which matlab

/apps/local/languages/matlab/2019a/bin/matlab

Running a MATLAB script from the command line

Many users of MATLAB often use it interactively via a Graphical User Interface (GUI) to debug and run programs. This is not an effective approach when we use MATLAB on a supercomputer. While it is possible to open MATLAB on a supercomputing machine in GUI mode, it is not a recommended practice since its performance is heavily dependent on the internet speed and local X-Windows implementation.

Create matlabtest.m file in the present working directory with the Matlab code

fprintf('The program has started \n\n');

a = 2;
b = 3;
fprintf('Sum of %d and %d = %d \n\n', a, b, (a+b));

fprintf('The program has finished \n');

We use the following command to run the MATLAB script in matlabtest.m file from the command line. (Don’t run it yet on Sunbird as executing this command now will run matlab on the login node which we must avoid.)

matlab -nosplash -nodesktop -nodisplay -r "run('matlabtest.m'); quit;"

MATLAB Command line options

  • matlab is the MATLAB executable.
  • -nosplash prevents MATLAB from displaying the splash screen (logo, version, etc..).
  • -nodesktop starts MATLAB without the desktop environment.
  • -nodisplay suppresses the display of figures during MATLAB execution.
  • -r tells MATLAB to start running the specified command (or the script file with the list of commands).
  • "run('matlabtest.m'); quit;" MATLAB commands to run. If quit is not specified then the MATLAB session will remain open.

You can also use this functionality on your local computers. On Windows OS use the following command:

"C:\replace with path to MATLAB installation folder\matlab.exe" -nosplash -nodesktop -nodisplay -r "run('matlabtest.m'); quit;"

SLURM

To run a MATLAB program on Sunbird, we first have to prepare a job script. Using the nano editor, we can create a job script file matlabjob.sh using the command:

nano matlabjob.sh

and then enter the following text:

#!/bin/bash --login
###

# job name
#SBATCH --job-name=hostname

# job stdout file
#SBATCH --output=hostname.out.%J

# job stderr file
#SBATCH --error=hostname.err.%J

# maximum job time in D-HH:MM
#SBATCH --time=0-00:10:00

# maximum memory of 10 megabytes
#SBATCH --mem-per-cpu=10

# run a single task, using a single CPU core
#SBATCH --ntasks=1

# specify the current project
# change this for your own work
#SBATCH --account=scw1389

# specify the reservation we have for the training workshop
# replace XX with the code provided by your instructor
# remove this for your own work
#SBATCH --reservation=scw1389_XX
###

# load modules
module load matlab/R2019a

echo "Starting the MATLAB program"

matlab -nosplash -nodesktop -nodisplay -r "run('matlabtest.m'); quit;"

echo "MATLAB program has finished"

In this way, we need to create the job scripts for the MATLAB programs that we want to run on HPC machines. There is also an interactive way (still with commandline) of accomplishing this task. You can learn more about this interactive approach here. For this course, we will stick to the approach of using job scripts.

Key Points

  • Use ssh -Y uname@sunbird.swansea.ac.uk to access Sunbird HPC machine.

  • Use module load matlab/2019a to load MATLAB software on Sunbird.

  • Use matlab -nosplash -nodesktop -nodisplay -r "run(matlabtest.m); quit;" to run matlab script matlabtest.m from command line.

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