Reproducible computational environments using containers - Introduction to Docker and Singularity

This course aims to introduce the use of containers with the goal of using them to effect reproducible computational environments. Such environments are useful for ensuring reproducible research outputs and for simplifying the setup of complex software dependencies across different systems. The course will introduce the use of Docker and Singularity containers but the material will be of use for whatever container technology you plan to, or end up, using.

On completion of this course attendees should:

• Understand what containers are and what they are used for
• Understand how to manage and create Docker containers
• Appreciate decisions that need to be made around containerising research workflows
• Understand the differences between Docker and Singularity containers and why Singularity is more suitable for multi-user systems (e.g. HPC)
• Understand how to manage and create Singularity containers
• Appreciate how containers can be used to enable and improve reproducibility in research

Target Audience:

This course is aimed at researchers who have no (or very little) previous experience of using containers

Prerequisites:

• You should have basic familiarity with using a command shell, and the lesson text will at times request that you “open a shell window”, with an assumption that you know what this means.
• Under Linux or macOS it is assumed that you will access a bash shell (usually the default), using your Terminal application.
• Under Windows, Powershell and Git Bash should allow you to use the Unix instructions. We will also try to give command variants for Windows cmd.exe

Requirements:

Participants must use a laptop with a macOS, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on.

They are also required to abide by the ARCHER2 Training Code of Conduct.

Timetable:

Timetable can be found on the course website.

This course is part-funded by the PRACE project and is free to all.