This lesson is in the early stages of development (Alpha version)

This lesson is part of The Carpentries Incubator, a place to share and use each other's Carpentries-style lessons. This lesson has not been reviewed by and is not endorsed by The Carpentries.

Reproducible computational environments using containers: Introduction to Apptainer: Glossary

Key Points

Apptainer: Getting started	Apptainer is another container platform and it is 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 (SIF). The `apptainer` command can be used to pull images from Apptainer Hub and run a container from an image file.
The Apptainer cache	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.
Using Apptainer containers to run commands	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.
Files in Apptainer containers	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.
Using Docker images with Apptainer	Apptainer can start a container from a Docker image which can be pulled directly from Docker Hub.
Preparing to build Apptainer images	A Docker image is provided to run Apptainer - this avoids the need to have a local Apptainer installation on your system. The Docker Apptainer image can be used to build containers on Linux, macOS and Windows. You can also run Apptainer containers within the Docker Apptainer image.
Building 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 Apptainer Hub can be used as a base for creating new Apptainer images.
Running MPI parallel jobs using Apptainer containers	Apptainer images containing MPI applications can be built on one platform and then run on another (e.g. an HPC cluster) if the two platforms have compatible MPI implementations. When running an MPI application within a Apptainer container, use the MPI executable on the host system to launch a Apptainer container for each process. Think about parallel application performance requirements and how where you build/run your image may affect that.

Glossary

FIXME