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Reproducible Computational Environments Using Containers: Introduction to Docker and Singularity (day 2): Glossary

Key Points

Singularity: Getting started	Singularity is another container platform and it is often used in cluster/HPC/research environments. Singularity has a different security model to other container platforms, one of the key reasons that it is well suited to HPC and cluster environments. Singularity has its own container image format (SIF). The `singularity` command can be used to pull images from Singularity Hub and run a container from an image file.
The Singularity cache	Singularity caches downloaded images so that an unchanged image isn’t downloaded again when it is requested using the `singularity pull` command. You can free up space in the cache by removing all locally cached images or by specifying individual images to remove.
Using Singularity containers to run commands	The `singularity exec` is an alternative to `singularity run` that allows you to start a container running a specific command. The `singularity shell` command can be used to start a container and run an interactive shell within it.
Files in Singularity 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 Singularity	Singularity can start a container from a Docker image which can be pulled directly from Docker Hub.
Preparing to build Singularity images	A Docker image is provided to run Singularity - this avoids the need to have a local Singularity installation on your system. The Docker Singularity image can be used to build containers on Linux, macOS and Windows. You can also run Singularity containers within the Docker Singularity image.
Building Singularity images	Singularity definition files are used to define the build process and configuration for an image. Singularity’s Docker container provides a way to build images on a platform where Singularity 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 Singularity images.
Running MPI parallel jobs using Singularity containers	Singularity 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 Singularity container, use the MPI executable on the host system to launch a Singularity container for each process. Think about parallel application performance requirements and how where you build/run your image may affect that.

Glossary

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