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Welcome to the course: Selecting software modules

This NAISS course is given under under NAISS, by staff working at the branches located at UPPMAX, LUNARC, HPC2N, and Chalmers, and will cover clusters at those facilities as well as at NSC (Tetralith) and PDC (Dardel).

This material

Here you will find the content of the workshop "Selecting software modules"

Prerequisites

  • Basic Linux

If you lack Linux experience, please follow a tutorial before the course.

This is from a recent NAISS course about basic Linux:

Learning outcome

  • What is the module system?
  • Why do I want to use the module system?
  • What happens when I load/unload modules?
    • paths
    • environment variables
    • more?
  • some talk about EasyBuild?
  • Useful commands
  • Load examples
  • Compiler toolchains

Cluster-specific approaches

The course will show you how to find and load modules. While the modules may be somewhat differently named and have somewhat different versions depending on the system, the procedure and commands are the same.

We will use the NAISS system Arrhenius for those who do not have other access to a Swedish HPC system, and some examples will be shown for other centres. You should be able to code-along - with minor adjustments - regardless of which center you are at.

Important info

  • There is an "important info" page for this course, containing info on the course project, login info, etc.
  • There is a Q/A page for use during the lectures. Since the lectures are recorded, you may get recorded if you ask questions in the Zoom, but you can always write questions on the Q/A and get answers there. It also has the advantage that you can go back and look at the answers later.

Evaluation survey

Preliminary schedule

Time Topic Activity Teacher
09:00 Welcome+Syllabus Lecture BB
09:10 Module system: overview Lecture+exercise BB
09:30 Module system: versions, loading, unloading, listing Lecture+type along+exercise BB
10:00 Break
10:15 Compiler toolchains Lecture+type along JH
10:45 Software modules Lecture+type along+exercise BC
11:05 Break
11:15 Software modules - exercises exercises BC
11:35 Modules in batch scripts Lecture BB
11:50 Summary All
12:00 END

Preparations

In order to type along and do the exercises, please prepare your course environment now:

1. Login

Login to the system you are using

  • You will not need a graphical user interface for this course.
  • Even so, if you do not have a favourite SSH client, we recommend using ThinLinc

Connection info for some Swedish HPC systems - use the one you have access to:

  • SSH: ssh <user>@login.hpc.arrhenius.naiss.se
  • ThinLinc:
    • Server: tl.hpc.arrhenius.naiss.se
    • Username: <your-nsc-username>
    • Password: <your-nsc-password>
  • SSH: ssh <user>@kebnekaise.hpc2n.umu.se
  • ThinLinc:
    • Server: kebnekaise-tl.hpc2n.umu.se
    • Username: <your-hpc2n-username>
    • Password: <your-hpc2n-password>
  • ThinLinc Webaccess:
    • Put https://kebnekaise-tl.hpc2n.umu.se:300/ in browser address bar
    • Put <your-hpc2n-username> and <your-hpc2n-password> in the login box that opens and click Login
  • SSH: ssh <user>@pelle.uppmax.uu.se
  • ThinLinc:
    • Server: pelle-gui.uppmax.uu.se
    • Username: <your-uppmax-username>
    • Password: <your-uppmax-password>
  • ThinLinc Webaccess:
    • Put https://pelle-gui.uppmax.uu.se in browser address bar
    • Put <your-uppmax-username> and <your-uppmax-password> in the login box that opens and click Login
  • Note that you need to setup TFA for Uppmax when using either of the ThinLinc connections.
  • SSH: ssh <user>@bianca.uppmax.uu.se
  • ThinLinc Webaccess:
    • Put https://bianca.uppmax.uu.se in browser address bar
    • Follow the instructions!
  • Note that you need to setup TFA for Uppmax when using either of the ThinLinc connections.
  • SSH: ssh <user>@cosmos.lunarc.lu.se
  • ThinLinc:
    • Server: cosmos-dt.lunarc.lu.se
    • Username: <your-lunarc-username>
    • Password: <your-lunarc-password>
  • Note that you need to setup TFA (PocketPass) to use LUNARC!
  • SSH: ssh <user>@dardel.pdc.kth.se
  • ThinLinc:
    • Server: dardel-vnc.pdc.kth.se
    • Username: <your-pdc-username>
    • Password: <your-pdc-password>
  • Note that you need to setup SSH keys or kerberos in order to login to PDC!

2. Setup a working directory

You will not need a lot of space for the exercises, so you can create the directory under your home directory.

  • Create a directory to work in (mkdir $HOME/selecting-modules)
  • and then switch to it (cd $HOME/selecting-modules)

3. Download the exercises

  • wget https://gitlab.naiss.se/hpc/training/selecting-modules/-/raw/main/exercises.tar.gz
Bianca user
  • Stay in the created folder (cd $HOME/selecting-modules)

  • Copy the tar ball from the project's folder to your created folder:

    • cp /proj/sens2025560/selecting_modules/exercises.tar.gz .

  • Let the teacher know if it is missing.

4. Extract the exercises

  • tar zxvf exercises.tar.gz

5. Enter the directory that was created

  • cd exercises