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, HPC2N, and LUNARC

• Toolboxes and Add-Ons

• HPC performance with MATLAB

Not covered

• Improve MATLAB coding skills

• Other clusters

MATLAB Exercise files

• Link to exercises tarball: https://github.com/UPPMAX/R-python-julia-matlab-HPC/raw/refs/heads/main/exercises/exercises.tar.gz

• Or you can copy them from the computer system you are on (only until 2024-11-01) and unpack them with tar -xzvf exercises.tar.gz

  • Rackham: cp /proj/r-py-jl-m-rackham/exercises.tar.gz .

  • Kebnekaise: cp /proj/nobackup/r-py-jl-m/exercises.tar.gz .

Download the exercise files

• Use wget to download the tarball from the web, if you didn’t copy it from your local computer system.

• Un-tar it with tar -xzvf <filename.tar.gz> 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).

• Enter the directory and list the content with the tree command.

Preliminary schedule

Preliminary times

Time	Topic	Teacher(s)
9:00	Log in	Several
9.45	Coffee break
10:00	Syllabus	RP
10.15	Introduction, MATLAB in general	RP
10.25	Loading modules and running MATLAB codes	RP
10.50	Break
11.05	Slurm job scheduler and Matlab	BB
12.00	LUNCH
13.00	Matlab GUI and Slurm	PO, RP
13.30	Parallel and multithreaded functions	PO
13.50	break
14.00	Cont’d Parallel and multithreaded functions	PO
14.30	Add-Ons	BC
14.50	Coffee break
15.05	Simultaneous session — UPPMAX: Client on the local desktop	BC
.	Simultaneous session — MATLAB in Jupyter	PO
.	Simultaneous session — LUNARC: MATLAB with Desktop On Demand	RP
15.35	Summary
15.40	Evaluation
15.50	Q&A on-demand
16.00	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, HPC2N, and LUNARC

  • 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

If you have a Mathworks account that is less than 2 years old, Mathworks offers free MATLAB self-paced online training courses. Students at any academic institution with a campus-wide license can use their university email addresses to create a free account to access these resources.

The Mondays with MATLAB lecture series is offered every September. These and other events are posted here. Mondays with MATLAB consist of 3 introductory lectures: - Introduction to MATLAB

If you have an account, you will be automatically signed up for the Mathworks mailing list, which will notify you of upcoming webinars as well as some featured packages. The webinars cover a broad range of topics and disciplines at varying skill levels, although these seminars tend to be more advanced.

Other NAISS centres

• MATLAB at NSC

• MATLAB at PDC

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.