Introduction to running R, MATLAB and Julia in HPC

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Materials page

Topics planning

Autumn 2025

  • 6-8 October
  • R: Mon 6 Oktober
  • MATLAB: Tue 7 Oktober
  • Julia: Wed 8 Oktober
  • Advanced: Fri 10 Oct

Meeting 29 Aug 11.00

Goals

  • Get us on track
  • Decide on key things before we do further work
  • (Look a bit more on the last day)

Non-goals

  • Schedules of individual days
  • Discuss things that are unrelated to the practical matters of the course
  • Debate things based on incomplete information

Agenda

  • Status
  • Follow-up
  • General discussions and decisions
  • ToDos
  • Last day last (or another day)

Follow-up: Decided last time

  • we should convert the GitHub repo of this course to MkDocs, over waiting for Erik Lindahl to pick an MkDocs theme
    • [DECIDED] Yes, using a parallel file tree on main (e.g. docs for sphinx, docs-mk for markdown): RB, BB, BC, PO, RP

[Added 2025-08-29] RB: it has been named docs-mk and I think that that is just as fine

  • pick the MkDocs theme most of us like:
    • materials (e.g. NAISS File Transfer): RB
    • ReadTheDocs theme (e.g. NAISS Intermediate bash): BB, PO
      • better with search function
    • [DECIDED] material with ReadTheDocs theme (e.g. at Chalmers): BB, LS, BC
      • also better search function
      • we can confer with Chalmers for solutions!
      • Volunteer to do first step: BC

[Added 2025-08-29] RB: as the most used theme, the materials theme has the most options and plugins.

  • The materials theme supports more admonitions

  • Only the materials theme supports mermaid

  • Q: Should we keep having an optional login session?

    • [DECIDED] Yes: RB, RP, BC, BB

  • [Added 2025-08-29] Q: Do we have an on-boarding?

    • [DECIDED] No

  • Q: Should we have other courses as prequisites?

    • [DECIDED] No, but link to it from the prerequisites: RB, BC, LS
  • Q: Should we add fetching the tarball in the login (and preparation) session?
    • [DECIDED] No: BB (it would take away course time for people that do not do this, they will not read/do it, will give me more admin), LS, RP
  • Q: Should we have the Zoom link in the tarball?
    • [DECIDED] No: RB, BB, BC, RP, LS
  • Q: [DECIDED] cover HPC-specific topics (e.g. the module system, the job scheduler) enough to be confident and comfortable in doing the exercises
    • [BC] Knowing HPC clusters minimally is in the prereqs
  • Let prerequisites point more to other courses (e.g. the module system, the job scheduler)
    • [DECIDED, BC seems willing to do this]
  • theory minimized, just get started!
    • like:
      • train writing a batch script
    • focus on specific needs for the specific language
    • cluster understanding in preparations
    • [DECIDED] Up to teachers to teach how they think is best in their situation given their personality

[MOVED TO DAY 4] ‘Machine learning’ [MOVED TO DAY 4] ‘Parallel’

  • RB will do so at the Advanced day, for R, MATLAB and Julia. Will be discussed later in this meeting ..

[KEEP] ‘Isolated environments’

  • Q: How to teach the last day?
    • Some ideas:
      • General theory and tabs per language
      • Split per language
      • Split the day in half
    • Will discuss more later …

Status

  • How far come with MkDocs?
    • RB: his R material as good as done!
    • LS: started with Julia
    • Others not
  • Last day?
    • RB: just volunteered

General discussions and decision

  • How do people convert RST to MkDocs?
    • RB: use an editor and change by hand. This takes me minutes, not hours

NAISS chat room name

  • [Richel] I think it make us look needlessly stupid if we the NAISS matrix room is called R-Julia-Matlab when MATLAB is spelled in uppercase. Can we rename the room to R-Julia-MATLAB (or any other variation, see next point)?
    • [x] DONE
  • [Linus] I think we should try to keep the order of the three the same as scheduled order everywhere, to cut down on unnecessary confusion.
    • Leave as it is R-Julia-Matlab:
    • Rename to R-Julia-MATLAB: RB
    • Rename to R-MATLAB-Julia: LS, BC
      • reason: both order of schedule and popularity right now
    • Use alphabetic order: Julia-MATLAB-R: RB
      • reason: schedule and popularity changes, as proven by the current name :-)

Sphinx vs Mkdocs revisited

  • RB: I am happy to have a technical discussion once in a while. On the other hand, at the previous meeting, 5 out of the 5 people present voted for moving to MkDocs. Due to this, I think the chance to overturn that vote is very slim.

  • See issue #152

    • main thing is that copy button with combination of julia modes and other languages and virtual environments and terminal are much better handled in Sphinx

      • RB: I would love to see the problem in action and be convinced that a text box is not good enough! Could there be a demo?
      • BC: I realized that when prompt is changing
      • BC: Finally noticed that not even Sphinx can handle the julia complex repl when we have environments involved. That makes me leave Sphinx
      (my-first-env) pkg> add DFTK
Resolving package versions...
Updating `/path-to-my-project/$USER/julia/my-    first-    env/Project.toml`
[acf6eb54] + DFTK v0.6.2
 Updating `/path-to-my-project/$USER/julia/my-first-    env/Manifest.toml`

    • Workaround could be to either state that prompt (like ], ?, >>, $, (environmental names)) and output from command

      • should be left out when copy-pasting and
      • basically do not use copy button
    • OR to leave out all prompts and state above snippet what it refers to
    • RB: don’t forget what MkDocs does better:
    • Markdown is one of the most popular technologies according to the StackOverflow 2024 survey, where RST does not even show up.
      • Markdown is a very plausible choice for Sphinx as well because we have the myst plugin.
        • RB: I’d be happy to use that plugin then, over writing RST

    • Due to this, there are more tools for Markdown, especially continuous integration scripts for link checking: we have never been able to set it up correctly for RST.

    • I am quite fond of the ‘Automate everything’ idea.

    • Tool: text editor (replace) by hand
      • mys converter works for sphinx
    • Vote
    • [DECIDED] continue progression to MkDocs + MD: RB, RP+BB+BC (assuming we can finish), LS
      • RB volunteers to convert to MkDocs, e.g. PO’s Parallel material for last day (and will teach that too)
    • stay with sphinx but RST–> MD (myst):
    • stay with sphinx and RST (nothing changed): RP+BB+BC (assuming we cannot finish the conversion in time), PO

Other Questions to solve

Book meeting:

  • Advanced:

    • Monday 1st Sep 11:00
      • RB will be absent, will accept all decisions :-)

  • no MATLAB the 4th day?

  • everything included, need to remove something
  • mv jupyter (either extra or advanced day)

When to meet in language groups?

  • R
    • RB: this is me and BB. We’ll meet as often as we think we need :-)
    • BB: agree, this will work :-)
  • Julia
    • issues
  • MATLAB:
    • issues
  • Advanced:
    • Monday 1st Sep 11:00

Earlier meetings

Meeting 4 June

All meetings