Containers

Singularity/Apptainer is a widely used open-source container system. It is designed to run applications with bare metal performance while being somewhat secure, portable and repeatable. With Singularity/Apptainer containers, users can work in reproducible environments of their choice and design. The main advantage of using a container is that it establishes a self-contained software environment for each application, which simplifies the installation of complex applications.

Available containers

The AMD Infinity Hub contains a collection of software for AMD GPUs. The Infinity Hub images have been made available in this directory Adastra /opt/software/containers/images/infinity-hub/.

Additionally, if the user whishes to uses custom containers, he can contact svp@cines.fr. We will place the containers in /opt/software/containers/images/users/<project_identifier>/<container_name>.sif.

Using a container

The Singularity/Apptainer binary dedicated to image execution is accessible on all Adastra compute nodes but not on the login nodes.

Running as a SLURM batch job

Here is an example of a SLURM script to launch the LAMMPS application :

#!/bin/bash
#SBATCH --account=<account_to_charge>
#SBATCH --job-name="<job_name>"
#SBATCH --constraint=MI250
#SBATCH --nodes=1
#SBATCH --exclusive
#SBATCH --time=1:00:00

singularity run --writable-tmpfs -B</path/to/input> -B/sys -B/dev -B/proc -B/lus /opt/software/containers/images/<container>.sif <executable> <arguments>
Where :

  • --writable-tmpfs makes the file system accessible as read-write with non persistent data (with overlay support only);

  • -B, --bind strings binds a path. Where strings has the format src[:dest[:opts]], where src and dest are outside and inside paths. If dest is not given, it is set equal to src. Mount options (opts) may be specified as ro (read-only) or rw (read/write, which is the default). Multiple bind paths can be given by a comma separated list.

Running as a SLURM interactive session

We start by allocating a whole node (note the --exclusive):

$ salloc --account=<account_to_charge> --job-name="interactive" --constraint=GENOA --nodes=1 --time=1:00:00 --exclusive

Get the name of the node with squeue and the NODELIST column:

$ squeue --me

Connect to the node:

$ ssh <node_hostname>

Then, repeat what was specified in the script above:

$ singularity run --writable-tmpfs -B</path/to/input> -B/sys -B/dev -B/proc -B/lus /opt/software/containers/images/<container>.sif <executable> <arguments>

You can run a shell in the container using the following command:

$ singularity shell --writable-tmpfs -B</path/to/input> -B/sys -B/dev -B/proc -B/lus /opt/software/containers/images/<container>.sif