Introduction to running R, Matlab and Julia in HPC

Content

  • This course aims to give a brief, but comprehensive introduction to using R, Matlab, and Julia in an HPC environment.

  • You will learn how to

    • start the interpreters of Julia, R, and Matlab by the HPC module system

    • find site installed packages/libraries

    • install packages/libraries yourself

    • use virtual environments

    • use the computation nodes

      • write and submit batch scripts

      • work interactivly

      • access parallel tools and run parallel codes

      • access GPUs and run such code

  • This course will consist of lectures interspersed with hands-on sessions where you get to try out what you have just learned.

  • We aim to give this course in spring and fall every year.

Schedule Spring 2025

Day

Language

Monday 24 March

R

Tuesday 25 March

Matlab

Wednesday 26 March

Julia

Course approach to deal with multiple HPC centers

  • The course is a NAISS cooperation with teachers from UPPMAX (Rackham, Snowy, Bianca), HPC2N (Kebnekaise), and LUNARC (Cosmos) and will focus on systems at the Swedish academic HPC centres with NAISS personnel.

  • Although there are differences we will only have few seperate sessions.

  • Most participants will use NSC’s Tetralith system or PDC’s Dardel system for the course.

    • Alvis at C3SE (Chalmers) may be added in the future.

  • Users with the “local” affiliation below, can work at the following clusters:

    • Kebnekaise: UmU, IRF, MIUN, SLU, LTU.

    • Cosmos: LU.

    • Rackham/Snowy: UU.

  • The general information given in the course will be true for all/most HPC centres in Sweden.

    • The examples will often have specific information, like module names and versions, which may vary. What you learn here should help you to make any changes needed for the other centres.

    • When present, links to the Julia/R/Matlab documentation at other NAISS centres are given in the corresponding session.

Collaboration document

  • Q/A collaboration document

  • Use this page for the workshop with your questions

  • It helps us identify content that is missing in the course material

  • We answer those questions as soon as possible

Some practicals

  • Code of Conduct

    • Be nice to each other!

  • Zoom

    • You should have gotten an email with the links

    • Zoom policy:

      • Zoom chat (maintained by co-teachers):

        • technical issues of zoom

        • technical issues of your settings

        • direct communication

        • each teacher may have somewhat different approach

      • collaboration document (see below):

        • “explain again”

        • elaborating the course content

        • solutions for your own work

    • Recording policy:

      • All lectures and demos will be available on HPC2Ns Youtube channel after the course.

      • Due to different teaching styles, the teacher of a session decides if a lesson will be:

        • recorded without learners

        • recorded live with learners

      • The teachers will be clear if it is recorded or not and it will be visible in the ZOOM.

      • For the live-recordings

        • The questions asked per microphone during these sessions will be recorded

        • If you don’t want your voice to appear:

          • use the collaboration document (see below)

    • The Zoom main room is used for most lectures

    • Some sessions use breakout rooms for exercises, some of which use a silent room

Warning

  • Please be sure that you have gone through the pre-requirements

    • It mentions the familiarity with the LINUX command line.

    • The applications to connect to the clusters: terminals and ThinLinc (remote graphical desktop)

  • This course does not aim to improve your coding skills. Rather you will learn to understand the ecosystems and navigations for the the different languages on a HPC cluster.

Content of the course

Pre-requirements:

COMMON:

R Lessons:

Matlab Lessons:

Julia Lessons:

Extra reading: