Reproducible computational environments using containers

Almost all software depends on other software components to function, but these components have independent evolutionary paths.

Projects involving many software components can rapidly run into a combinatorial explosion in the number of software version configurations available, yet only a subset of possible configurations actually works as desired.

Virtualisation is an approach that can collect software components together and can help avoid software dependency problems.

Containers are a popular type of lightweight virtualisation that are widely used.

Docker and Singularity are two different software platforms that can create and manage containers and the resources they use.

A toolbar icon indicates that Docker is ready to use.

You will typically interact with Docker using the command line.

Containers are usually created using command line invocations.

The docker run command creates containers from images.

The docker image command can list and manage images that are (now) on your computer.

The docker container command can list and manage containers that have been created.

The -d -t options to docker run allow you to create a container running in the background.

The docker exec command allows you to execute commands in a running container, including getting interactive access.

The Docker Hub is an online repository of container images.

Many Docker Hub images are public, and may be officially endorsed.

Each Docker Hub page about an image provides structured information under several subheadings

Most Docker Hub pages about images contain sections that provide examples of how to use those images.

Dockerfiles specify what is within Docker images.

The docker build command is used to build an image from a Dockerfile

You can share your Docker images through the Docker Hub so that others can create Docker containers from your images.

You can include files from your Docker host into your Docker images by using the COPY instruction in your Dockerfile.

Docker allows containers to read and write files from the Docker host.

You can export and import images from files.

By using the container we avoid all the difficult installation issues of installing Jekyll.

Container images allow us to encapsulate the computation (and data) we have used in our research.

Using a service such as Docker Hub allows us to easily share computational work we have done.

Using container images along with a DOI service such as Zenodo allows us to capture our work and enables reproducibility.

Tools such as Docker Compose, Docker Swarm and Kubernetes allow us to describe how multiple containers work together.

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.

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

The singularity exec and singularity shell commands provide different options for starting containers.

Singularity can start a container from a Docker image which can be pulled directly from Docker Hub.

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.

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.

Understand the next steps for you in using containers.

Understand how you can access help and support to use containers.