Apptainer (formerly Singularity)

Apptainer (formerly Singularity) is a container system designed for use on High Performance Computing (HPC) systems. It allows users to run both Docker and Singularity containers.

From the Docker website: "A container image is a lightweight, stand-alone, executable package of a piece of software that includes everything needed to run it: code, runtime, system tools, system libraries, settings."

On June 21th, 2022, Singularity is replaced with Apptainer, which is just a renamed open-source project to avoid conflicts with SingularityCE so it can be accepted into the Linux Foundation. Apptainer 1.0 has the same code as Singularity after versions 3.8.x, and still provides the command singularity (apptainer is the official command). Thus, user should continue running containers on OSC systems without any issue:

1. Containers built with Apptainer will continue to work with installations of Singularity.
2. User will see warnings about SINGULARITY_ and SINGULARITYENV_ environment variables.
A future version of Apptainer may stop supporting environment variable compatibility so we recommned
users to add respective APPTAINER_ and APPTAINERENV_ counterparts in their job environments.

For more detail, pleae visit the Singularity Compatibility page.

If you experience issues using Singularity after downtime, please contact OSC help.

Availability and Restrictions

Versions

Apptainer/Singularity is available on all OSC clusters. Only one version is available at any given time. To find out the current version:

apptainer version

Check the release page for the changelog: https://github.com/apptainer/apptainer/releases

Access

Apptainer/Singularity is available to all OSC users.

Publisher/Vendor/Repository and License Type

Apptainer project, established as Apptainer a Series of LF Projects LLC; 3-clause BSD License

Usage

Set-up

No setup is required. You can use Apptainer/Singularity directly on all clusters.

Using Apptainer/Singularity

See HOWTO: Use Docker and Singularity Containers at OSC for information about using Apptainer/Singularity on all OSC clusters, including some site-specific caveats.

Example: Run a container from the Singularity hub

[pitzer-login01]$ apptainer run shub://singularityhub/hello-world
INFO:    Downloading library image
Tacotacotaco

If unsure about the amount of memory that a apptainer process will require, then be sure to request an entire node for the job. It is common for singularity jobs to be killed by the OOM killer because of using too much RAM.

Known Issues

Workshop

2019-05-14 OSC Workshop: Containers for Research Computing. Please find the link in the workshop page for the tutorial material and slides.