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, and HPC2N.

This material

Here you will find the content of the workshop “Login and 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 Tetralith 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

Evaluation survey

Preliminary schedule

Time Topic Activity Teacher
10:00 Welcome+Syllabus Lecture All
10:10 The module system: overview Lecture+exercise BB
10:20 The module system: versions, loading, unloading, listing Lecture+type along+exercise BB
10:50 Break
11:00 Compiler toolchains Lecture+type along RP
11:15 Software modules Lecture+type along RP
11:45 Modules in batch scripts Lecture BB
11:55 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 (Tetralith/Dardel, other Swedish HPC system)

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

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

  • NSC
    • SSH: ssh <user>@tetralith.nsc.liu.se
    • ThinLinc:
      • Server: tetralith.nsc.liu.se
      • Username: <your-nsc-username>
      • Password: <your-nsc-password>
    • Note that you need to setup TFA to use NSC!
  • HPC2N
    • SSH: ssh <user>@kebnekaise.hpc2n.umu.se
    • ThinLinc:
      • Server: kebnekaise-tl.hpc2n.umu.se
      • Username: <your-hpc2n-username>
      • Password: <yout-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 th e login box that opens and click Login
  • UPPMAX
    • SSH: ssh <user>@rackham.uppmax.uu.se
    • ThinLinc:
      • Server: rackham-gui.uppmax.uu.se
      • Username: <your-uppmax-username>
      • Password: <your-uppmax-password>
    • ThinLinc Webaccess:
      • Put https://rackham-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 may have to setup TFA for Uppmax when using either of the ThinLinc connections.
  • LUNARC
    • 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!
  • PDC
    • 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!
  • C3SE:
    • SSH: ssh <user>@alvis1.c3se.chalmers.se or ssh <user>@alvis2.c3se.chalmers.se
    • ThinLinc:
      • Server: alvis1.c3se.chalmers.se or alvis2.c3se.chalmers.se
      • Username: <your-c3se-username>
      • Password: <your-c3se-username>
    • ThinLinc Webaccess:
      • Put https://alvis1.c3se.chalmers.se:300 or https://alvis2.c3se.chalmers.se:300 in browser address bar
      • Put <your-c3se-username> and <your-c3se-password> in the login box that opens and click Login
    • OpenOndemand portal:
      • Put https://alvis.c3se.chalmers.se in browser address bar
      • Put <your-c3se-username> and <your-c3se-password> in the login box
    • Note that Alvis is accessible via SUNET networks (i.e. most Swedish university networks). If you are not on one of those networks you need to use a VPN - preferrably your own Swedish university VPN. If this is not possible, contact support@chalmers.se and ask to be added to the Chalmers’s eduVPN.

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://github.com/hpc2n/selecting-modules/raw/refs/heads/main/exercises.tar.gz

4. Extract the exercises

  • tar zxvf exercises.tar.gz

5. Enter the directory that was created

  • cd exercises