Software Containers

Overview

This short course is an introduction to using and building software containers, structured as follows:

• Introduction to Software Containers
• Using Containers on Rivanna [Singularity]
  • pull and convert Docker containers
  • inspect a container
  • run containers interactively and non-interactively
  • navigate container modules
  • submit container jobs via Slurm
  • create custom Jupyter kernels
• Building Containers [Docker]
  • Dockerfile
  • best practices
  • DockerHub
  • case studies
• Minimal Containers [Docker]
  • multistage build
  • OS-less base images
  • dynamic vs static linking
• Appendix: Building Containers [Singularity]
  • pull
  • convert local Docker image
  • Singularity definition file
  • convert Dockerfile

The chapters are mutually independent, except for “Minimal Containers” that requires “Building Containers [Docker]” or equivalent knowledge. The appendix on building Singularity containers is derived from a workshop that we no longer offer.

You are strongly encouraged to repeat the examples and do the exercises.

Prerequisites

• Linux command line.
• Rivanna account for the “Using Containers” chapter.
• Docker installation and DockerHub account for the “Building Containers [Docker]” chapter.