Introduction to running R, Python, Julia and MATLAB in HPC Logo

Pre-requirements:

  • Pre-requirements
  • Prepare the environment

COMMON:

  • Log in session
  • Use the tarball with exercises
  • Use a text editor
  • NAISS projects overview
  • Desktop On Demand
  • HPC clusters
  • Parallel and multithreaded functions
  • Other courses

R Lessons:

  • Schedule
  • Introduction R
  • Load and run R
  • Packages
  • Isolated environments with renv
  • Running R in batch mode
  • Parallel and multithreaded functions
  • Interactive work on the compute nodes
  • Using RStudio
  • ML with R
  • Summary
  • Evaluation

Matlab Lessons:

  • Preliminary schedule
  • Introduction to MATLAB
  • Load and Run MATLAB
  • Slurm job scheduler and MATLAB in terminal
  • MATLAB GUI and SLURM
  • Parallel and multithreaded functions
  • Add-Ons
  • Session: Matlab in Jupyter
  • Summary
  • Evaluation

Julia Lessons:

  • Preliminary schedule
  • Introduction Julia
  • Load and run Julia
  • Packages and isolated environments
  • Running Julia in batch mode
  • Parallel and multithreaded functions
  • Sessions: Interactive work on compute nodes
  • Summary
  • Evaluation

Extra reading:

  • R - extra reading and links
  • Matlab - extra reading and links
    • Documentation
    • Courses
      • Material for improving your programming skills
    • Materials
      • Debugging
      • TO LEARN MORE
        • Interaction with other tools
    • Add-ons
  • Julia - extra reading and links
Introduction to running R, Python, Julia and MATLAB in HPC
  • Matlab - extra reading and links
  • Edit on GitHub

Matlab - extra reading and links

Documentation

  • Documentation at the HPC centres UPPMAX, HPC2N, LUNARC, NSC, and PDC
    • 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/

    • NSC: click here for general instructions and here for installations on Tetralith specifically

    • PDC: https://support.pdc.kth.se/doc/applications/?sub=matlab/

  • Official MATLAB documentation is found here

Courses

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, and offers introductions to MATLAB, its Parallel Computing Toolbox, and AI/ML toolboxes. These and other events are posted here. 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.

Materials

Session-UPPMAX: Matlab client on the desktop

Debugging

If a serial job produces an error, call the getDebugLog method to view the error log file. When submitting an independent job, specify the task.

>> c.getDebugLog(job.Tasks)

For Pool jobs, only specify the job object.

>> c.getDebugLog(job)

When troubleshooting a job, the cluster admin may request the scheduler ID of the job. This can be derived by calling getTaskSchedulerIDs (call schedID(job) before R2019b).

>> job.getTaskSchedulerIDs()
ans =
 25539

TO LEARN MORE

To learn more about the MATLAB Parallel Computing Toolbox, check out these resources:

  • Parallel Computing Coding Examples

  • Parallel Computing Documentation

  • Parallel Computing Overview

  • Parallel Computing Tutorials

  • Parallel Computing Videos

  • Parallel Computing Webinars

Interaction with other tools

Coming?

Add-ons

Some toolboxes

  • Matlab products
    • Parallel Computing Toolbox

    • MATLAB Parallel Server

    • Deep Learning Toolbox

    • Statistics and Machine Learning Toolbox

  • Simulink
    • Stateflow

    • SimEvents

    • Simscape

Some toolboxes provides GUI for their tools Apps

  • Matlab products
    • Deep Network Designer - Design and visualize deep learning networks Deep Network Designer

    • Curve Fitter - Fit curves and surfaces to data

    • Deep Learning Toolbox

    • Statistics and Machine Learning Toolbox

  • Simulink
    • Stateflow

    • SimEvents

    • Simscape

extra/img/apps.PNG
Previous Next

© Copyright 2025, UPPMAX & HPC2N.

Built with Sphinx using a theme provided by Read the Docs.