Containers

Apptainer

Apptainer (https://apptainer.org) is an open-source software developed to add containers and reproducibility to scientific high performance computing.

Just like its predecessor Singularity, Apptainer is being developed to provide container technologies on HPC systems. It gives users an easy way to access different OSs on the HPC systems while still ensuring that containers runs in an established user environment, without a pathway for privilege escalation on the host.

Apptainer was born in 2021, when the Singularity open source project split into two separate projects: Apptainer and SingularityCE. The Apptainer branch has joined the Linux Foundation, while the Sylabs’ fork of Singularity, dedicated to commercial use, was renamed SingularityCE. While, at least at the beginning, there has been continual alignment between Sylabs’ SingularityCE and Apptainer, over time the paths of the projects will likely diverge as both projects continue to mature.

As part of the transition, only open community standard interfaces will be supported in Apptainer. This includes removing the “Library” and “Remote Builder” support. In the event these become open community maintained standards (and not corporate controlled), these feature may be left intact and/or re-add at a later date.
For this reason, users of the old Singularity software are encouraged to adjust their scripts accordingly.

On top of the apptainer command, Apptainer provides backwards compatibility offering singularity as a command line link. It is also committed to maintain as much of the CLI and environment functionality available in the old Singularity software as possible. From the user’s perspective, very little, if anything, should change and the wrapper around the singularity command allows users to run commands like ‘singularity pull’, ‘singularity run’, etc. just as before.

Please, visit https://apptainer.org for additional information on the Apptainer software and access to its documentation.

Examples of Apptainer commands

The following table summarizes some Apptainer commands (based on version 1.0.3). For more information see the Apptainer User Guide at https://www.apptainer.org/docs/.

General commands
help	Help about any command
Usage commands
build	Build an Apptainer image
cache	Manage the local cache
capability	Manage Linux capabilities for users and groups
exec	Run a command within a container
inspect	Show metadata for an image
instance	Manage containers running as services
key	Manage OpenPGP keys
oci	Manage OCI containers
plugin	Manage apptainer plugins
pull	Pull an image from a URI
push	Upload image to the provided URI
remote	Manage apptainer remote endpoints
run	Run the user-defined default command within a container
run-help	Show the user-defined help for an image
search	Search a Container Library for images
shell	Run a shell within a container
sif	siftool is a program for Singularity Image Format (SIF) file manipulation
sign	Attach a cryptographic signature to an image
test	Run the user-defined tests within a container
verify	Verify cryptographic signatures attached to an image
version	Show the version for Apptainer
Global options
-d --debug	print debugging information (highest verbosity)
-h --help	help for apptainer
-q --quiet	suppress normal output
-s --silent	only print errors
-v --verbose	print additional information

The help command gives an overview of Apptainer options and subcommands.
For example:

$ apptainer help <command> [<subcommand>]
$ apptainer help build
$ apptainer help instance start

Apptainer on the MPCDF HPC systems

On the HPC clusters at MPCDF, an environment module is provided in order to load the Apptainer software. For backwards compatibility, a Singularity module (singularity/link2apptainer) is also provided which will print a warning message and load the default Apptainer module. The old Singularity as well as the new SingularityCE software will not be supported on the HPC clusters.