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.