Apptainer¶

What is it?¶

The Apptainer is a container platform widely used in scientific and HPC environments. It was designed to enable the execution of complex applications on clusters in a secure, portable, and reproducible way, ensuring that the execution environment is identical regardless of which node runs the job.

In multi-user environments, such as clusters, Apptainer stands out for operating without the need for administrative privileges, integrating naturally with workload managers such as Slurm.

Apptainer uses images in the SIF (Singularity Image Format) format, which consist of a single and immutable file containing the entire system required to run the application, including the operating system, libraries, dependencies, and additional software. This facilitates sharing, versioning, and reproducibility of experiments.

How to Use Apptainer - Apollo Cluster¶

In Cluster Apollo, the use of Apptainer is only permitted for running already built images.

For security and environmental standardization reasons:

Attention:

Building images (apptainer build) on cluster nodes is not permitted.

Images must be built externally (on a local machine or another appropriate environment) and uploaded to the cluster in .sif format.

Step-by-step Usage¶

Upload the .sif image

The user must:
- Access the LIneA Open OnDemand
- Upload the .sif file to their scratch directory
  path: /scratch/YOUR.USER/IMAGE_NAME.sif
Choose the execution method

The user can execute the application in two main ways:

Option A -- Submission via Slurm (Recommended):

Create a submission script, for example job_apptainer.sh:

#!/bin/bash
#SBATCH -p <PARTITION>                       
#SBATCH --nodes=<QT-NODE>
#SBATCH --account=<ACCOUNT-NAME>               
#SBATCH -J <JOB-NAME>           
#----------------------------------------------------------------------------#
echo "SLURM_NODELIST=$SLURM_NODELIST"

# Image path
IMAGE=/scratch/users/YOUR.USER/IMAGE_NAME.sif

# Execute command inside the container
srun apptainer run --containall $IMAGE

echo "Finished"

Option B -- Interactive Allocation:

For testing or interactive execution:

Allocate a compute node:

salloc -p PARTITION-NAME --nodelist=NODE
ssh NODE

After allocating the node and accessing it via SSH, execute:

apptainer exec /scratch/YOUR.USER/IMAGE_NAME.sif YOUR_CODE

Or, if you want to enter the container environment:
```
    apptainer shell /scratch/YOUR.USER/IMAGE_NAME.sif
```
This will open a terminal inside the image. Inside the container, the user can execute commands normally.

Best Practices on the Cluster - Apptainer¶

✔ Always execute via Slurm
✔ Use the scratch directory for image files and temporary data
✔ Test interactively before submitting long-running jobs
✔ Keep your images versioned

If you have any questions, please contact the Service Desk.

Last update: March 2, 2026