Introduction to MATLAB

Welcome page and syllabus

• Also link at House symbol 🏠 at top of page

Learning outcomes

• Load MATLAB modules and site-installed MATLAB packages

• Create a MATLAB environment

• Install MATLAB packages with Add-Ons manager

• Write a batch script for running MATLAB

• Use MATLAB in parallel mode

• Use GPUs with MATLAB

• Use MATLAB for ML

Your expectations?

• Find best practices for using MATLAB at UPPMAX and HPC2N

• Toolboxes and Add-Ons

• HPC performance with MATLAB

Not covered

• Improve MATLAB coding skills

• Other clusters

MATLAB Exercise files

• At HPC2N, you can copy the MATLAB exercises in a tarball from /proj/nobackup/hpc2n2024-025/MatlabExercises.tar.gz

• At UPPMAX you can copy the exercises in a tarball from /proj/naiss2024-22-107/MatlabExercises.tar

• At LUNARC, you can copy the exercises in a tarball from /lunarc/nobackup/projects/lu2024-07-68/MatlabExercises.tar

Download the exercise files

• Copy the file and un-tar it in your personal project folder, which you should have created a while ago (https://uppmax.github.io/R-python-julia-matlab-HPC/index.html#prepare-your-environment-now). Then, enter the directory and list the content with the tree command.

cd /proj/naiss2024-22-107/<your-name>   # on Kebnekaise: cd /proj/nobackup/hpc2n2024-025/<your-name>
cp ../MatlabExercises.tar .
tar xvf MatlabExercises.tar
tree Matlab

Preliminary schedule

Preliminary times

Time	Topic	Activity
9:00	Syllabus	10m
9.10	Introduction, MATLAB in general	Lecture 20 m
9.30	Loading modules and running MATLAB codes	Lecture+code along 30m
9.45	Coffee break
10.00	Packages and isolated environments	Lecture+code along 45m
10.55	break
11.05	SLURM Batch scripts for MATLAB jobs	Lecture+code along + exercise 45m
11.50	Exercises and informal chat
12.00	LUNCH
13.00	Exercises and informal chat
13.15	Parallel and multithreaded functions	Lecture+code along + exercise 30m
13.50	break
14.00	Parallel session — UPPMAX: Interactive work	Lecture+code along 25m
.	Parallel session — HPC2N: Interactive work	Lecture+code along 25m
.	Parallel session — LUNARC: Interactive work	Lecture+code along 25m
14.25	Summary
14.35	Evaluation
14.45	Q&A on-demand
15.00	END

Instructor note

• Intro 10 min

• Lecture and demo 10 min

• Exercise 0 min

What is MATLAB?

MATLAB is a numerical computing environment and fourth generation programming language. Developed by MathWorks, MATLAB allows matrix manipulation, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs in other languages. Although it is numeric only, an optional toolbox uses the MuPAD symbolic engine, allowing access to computer algebra capabilities.

Features of MATLAB

Distinguishing pros of MATLAB include:

• A “low-code” interactive development environment (IDE) in which many common data import methods, analysis techniques, plotting formats, and even AI/ML techniques can be run from menus and generate the code required to reproduce the results automatically

• A rich library of Toolboxes and Add-Ons for different STEM disciplines, especially for modeling and simulations, all written and tested by professionals

• Automatic multi-threading (note: this can also be a drawback)

• The ability to set cluster configurations and parallelization settings graphically, and save them to profiles that can be reloaded at a click.

• Full documentation available straight from the command line (requires internet)

Of course MATLAB also has some drawbacks:

• It is proprietary software, so you need to buy a license and sign up for an account. Many Add-Ons require a separate license.

• With respect to the 2-language problem (where one can optimize for either performance or ease of prototyping, but not both), MATLAB even moreso than Python is geared toward usability. It can be slow.

• The way MATLAB automates multithreading means it will hog a full node unless you explicitly tell it not to by setting -SingleCompThread as an option at startup.

• The built-in plotting functions generate only very low-resolution raster graphics with no anti-aliasing, not suitable for publication.

More on MATLAB?

• Documentation at the HPC centres UPPMAX and HPC2N

  • UPPMAX: http://docs.uppmax.uu.se/software/matlab/

  • HPC2N: https://www.hpc2n.umu.se/resources/software/matlab and https://www.hpc2n.umu.se/documentation/guides/parallel-matlab

  • LUNARC: https://lunarc-documentation.readthedocs.io/en/latest/guides/applications/MATLAB/

• Official MATLAB documentation is found here:

Material for improving your programming skills

First level

If you have a Mathworks account that is less than 2 years old, you can take advantage of Mathworks’ free MATLAB self-paced online training courses at <https://matlabacademy.mathworks.com/?page=1&fq=all-matlab&sort=featured&s_tid=ln_acad_learn_oc>_. At any academic institution with a campus-wide license, students can use their university email addresses to create a free account to access these resources.

There is also the Mondays with MATLAB lecture series every September, which along with other events gets posted here: <https://se.mathworks.com/company/events.html>_.

Second level

CodeRefinery develops and maintains training material on software best practices for researchers that already write code. Their material addresses all academic disciplines and tries to be as programming language-independent as possible.

• Not yet anything MATLAB specific

ENCCS (EuroCC National Competence Centre Sweden) is a national centre that supports industry, public administration and academia accessing and using European supercomputers. They give higher-level training of programming and specific software.

• Not yet anything MATLAB specific

Other NAISS centres

• NSC

  • MATLAB

• PDC

  • MATLAB

Keypoints

• MATLAB is a 4th generation language with an interactive environment that can generate code that handles common problems for you.

• Parallelization is easy with the graphic user interface, but be careful to set -SingleCompThread when starting it at the command line or it may hog the nodes.