Summary and Setup

This lesson loads software from EESSI, a shared stack of scientific builds. You select a build with a module. You do not compile a private copy into your home directory.

The same Python is available on the cluster and in the EESSI client container. The container has no queue. A long run still belongs on the cluster.

Prerequisite

A terminal
A login on Snellius or the course cluster, or Apptainer 1.0 or newer for the client container
The setup page for the machine you will actually use

You need a terminal. You need one of the three places below. You do not need all three.

Snellius

Snellius is the Dutch national supercomputer. SURF sends the account mail. The public description is at https://www.surf.nl/en/services/compute/snellius-the-national-supercomputer.

BASH

ssh YOUR_LOGIN@snellius.surf.nl

Sign in to the SURF user portal before the first SSH login. If the network you are on is not trusted, the welcome mail names a door node. Use that host.

module load 2025 selects the 2025 stack. The first episode has the load lines for each machine.

The course cluster

Your trainer sends a setup link and a welcome note. The note has the address and the login. There is one login node.

BASH

ssh YOUR_LOGIN@MANAGER

MANAGER is the address in the welcome note. It is not snellius.surf.nl. module load 2025 loads EESSI 2025.06 on this cluster. The first episode’s tab has the exact lines.

The EESSI client, when you have no cluster

You need Apptainer 1.0 or newer, with --fusemount support. Access is documented at https://www.eessi.io/isc26-tutorial/getting-access/ and day-to-day use at https://www.eessi.io/isc26-tutorial/usage/.

The client mounts the same CVMFS repository the stack is published on. It does not start a queue.

You do not need the client container on Snellius. The stack is already mounted. Use module load 2025.

You do not need the client container when you are on the course cluster. module load 2025 loads EESSI 2025.06.

The EESSI client container mounts the same repository and has no Slurm.

BASH

mkdir -p "$HOME/eessi-work/var-lib-cvmfs" "$HOME/eessi-work/var-run-cvmfs" "$HOME/eessi-work/home"
export APPTAINER_BIND="$HOME/eessi-work/var-run-cvmfs:/var/run/cvmfs,$HOME/eessi-work/var-lib-cvmfs:/var/lib/cvmfs"
export APPTAINER_HOME="$HOME/eessi-work/home:/home/$USER"
apptainer shell --fusemount "container:cvmfs2 software.eessi.io /cvmfs/software.eessi.io" docker://ghcr.io/eessi/client:rocky8

Inside the container:

BASH

source /cvmfs/software.eessi.io/versions/2025.06/init/lmod/bash

sbatch and squeue are not there.

After the init script from that tab:

BASH

module load Python/3.13.5-GCCcore-14.3.0
python3 --version

python3 --version prints Python 3.13.5. The first launch downloads the image and can take a few minutes. Later launches are shorter.

Caution

No queue in the container

The container has no sbatch and no squeue. Use it for these software episodes. Use Snellius or the course cluster when the work has to wait in a queue.