Reproducible computational environments using containers: Glossary

Containers enable you to package up an application and its dependencies.

By using containers, you can better enforce reproducibility, portability and share-ability of your computational workflows.

Apptainer (and Singularity) are container platforms and are often used in cluster/HPC/research environments.

Apptainer has a different security model to other container platforms, one of the key reasons that it is well suited to HPC and cluster environments.

Apptainer has its own container image format based off the original Singularity Image Format (SIF).

The apptainer command can be used to pull images from Docker Hub or other locations such as a website and run a container from an image file.

Apptainer caches downloaded images so that an unchanged image isn’t downloaded again when it is requested using the apptainer pull command.

You can free up space in the cache by removing all locally cached images or by specifying individual images to remove.

Cache location and configuration requirements on Mahuika cluster

The apptainer exec is an alternative to apptainer run that allows you to start a container running a specific command.

The apptainer shell command can be used to start a container and run an interactive shell within it.

Your current directory and home directory are usually available by default in a container.

You have the same username and permissions in a container as on the host system.

You can specify additional host system directories to be available in the container.

Definition filess specify what is within Apptainer container images.

The singularity build command is used to build a container image from a Definition file.

Apptainer definition files are used to define the build process and configuration for an image.

Existing images from remote registries such as Docker Hub and other public image repositories can be used as a base for creating new Apptainer images.

Apptainer definition files are used to define the build process and configuration for an image.

Apptainer’s Docker container provides a way to build images on a platform where Apptainer is not installed but Docker is available.

Existing images from remote registries such as Docker Hub and Singularity Hub can be used as a base for creating new Apptainer images.