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.