Introduction to Containers with Docker and Singularity

This workshop provides an introduction to software containers with Docker and Singularity/Apptainer. Containers can be used to provide a reproducible computational environment and facilitate reproducible research, as well as to simplify the installation of complex software on different systems.

In this workshop we will use Docker to run containers on our local machines (laptops), and Singularity to run containers on HPC. We will look at how to find relevant containers for your research from publicly accessible resources. We will also cover how to build and modify simple containers using Docker, and make these available for running on the HPC using Singularity.

Target audience:

The course is aimed at graduate students, postdocs and other researchers who want to use containers to facilitate their computational research, for example to run specific software versions or increase reproducibility. The workshop will also provide an introduction to creating your own container images. You should be comfortable using the shell / command line to run commands, and should be familiar with submitting jobs on your institutional HPC cluster.

KCL students/staff should register on Skillsforge.

Learning objectives:

After attending this training, participants will be able to:

• use Docker (on local machines) and Singularity/Apptainer (on an HPC cluster) to run containers derived from publicly available images
• use Docker Hub to find container images relevant for their work
• use Docker to build and modify containers

Requirements:

Before joining this workshop, participants should:

• be able to navigate through a filesystem using the command line / shell
• know how to use a text editor to create or access text files in a particular directory
• have access to an HPC cluster with Singularity or Apptainer installed and be familiar with submitting jobs
  • If you do not have access to an HPC cluster, we can arrange for you to have guest access to the King's CREATE HPC
• ideally have admin rights (sudo) on the laptop they will be using for the workshop

Workshop format:

Learners will bring their own laptops (Windows/Unix/Mac). This will allow them to store notes and scripts, as well as enabling them to carry out hands-on work following the instructor. The course will use an interactive live-coding approach, combining demos, discussion, and hands-on activity.