Apptainer

Apptainer, formerly known as Singularity, is a container platform used on HPC systems. It allows users to run software inside portable .sif container images without Docker or sudo access.

Warning

Apptainer is not a separate login system. Users log in to the cluster, load the Apptainer module, and then run containers.

While Docker is a widely used container runtime, HPC clusters commonly use Singularity or Apptainer. Here is a quick comparison:

S.NO

Docker

Apptainer

1

Infrastructure/application deployment

Scientific computing/HPC

2

System service

User application

3

Often needs elevated permissions

No extra user privileges

4

Docker-managed image layers

One portable .sif file

Apptainer is useful on HPC systems because it allows users to:

  • Run software with specific dependencies.

  • Package workflows into portable .sif images.

  • Reproduce environments across systems.

  • Run containers without Docker or sudo access.

  • Use HPC resources such as scratch storage, GPUs, and LSF jobs when configured.

A typical workflow is:

  1. Log in to the cluster.

  2. Load the Apptainer module.

  3. Download or build a container image.

  4. Test the container with shell, exec, or run.

  5. Submit real workloads through LSF.

Start with the first six pages for the normal beginner workflow. Use the troubleshooting and examples pages when testing your own containers. The advanced section contains older specialized examples that are still useful, but are not part of the basic workflow.

Getting Help

If you are not sure which Apptainer workflow is appropriate for your project, contact the IDSC support team before running GPU jobs, Jupyter/RStudio servers, long-running container jobs, or specialized workflows.

Some requests, such as fakeroot access, GPU/project access, or containerized interactive applications, may require additional guidance or approval.

Submit an IDSC support ticket with a brief description of your project requirement: IDSC Support Ticket

Apptainer