Containers on HPC and Cloud with Singularity: Setup

Key requirement

The main requirement for this workshop is a personal computer with a web browser and a command line shell program.
Windows users: get MobaXterm, Visual Studio Code or PuTTY.
This equipment will allow you to follow the online materials and to login to a facility with the required software stack.

Optional: if you want to run the episode on X11 applications and you have a Windows box, you will also need to install Cygwin/X.
If you have macOS, you will need XQuartz installed instead.

Self-paced: Pawsey users

• Nimbus Cloud @Pawsey: if you have access, both Singularity and Docker are preinstalled in the Ubuntu Pawsey base image.

• Zeus @Pawsey: if you have access, Singularity can be loaded with module load singularity. MPI libraries are configured properly, and GPU applications can be run on the Slurm partition gpuq.

Advanced self-paced: installation DIY (Do It Yourself)

If you have your own machine, you can install the required software yourself (might take a while).
Note that you will need admin privileges in the machine to finalise the installation.

Linux box: read here

• Essential (core of the tutorial)
  • Singularity : script | docs
• Desirable (to run all the base episodes)
  • Docker : script | docs (unofficial)
  • MPICH library : script | docs
  • Nvidia GPU driver (GPU card required)
  • Slurm scheduler (can still run the MPI examples without it)
• Optional (bonus episodes)
  • Nextflow engine : script | docs
  • Environment Modules : script | docs
  • Lmod module system : script | docs
  • SHPC : script | docs
  • Docker Compose: script | docs
  • HPCCM : script | docs
  • Spack : script | docs
  • Podman : script | docs
  • Charliecloud : script (uses Spack) | docs
  • Sarus : script | docs
  • Enroot : script | docs

Note: install scripts have been tested on a Ubuntu machine through a user that can run sudo commands without password prompts. There’s no warranty they will work in your Linux box, you should consider them as templates.

macOS or Windows machine

For Singularity, you will need to setup a Linux virtual machine, and then follow the same instructions as above.
It’s not as bad as it sounds… the main two options are:

• Vagrant: follow these instructions by Sylabs on Setting up Singularity with Vagrant (macOS users: DO NOT use the proposed Singularity Desktop, use Vagrant instead);
• Multipass: follow instructions from the Multipass Homepage.

For Docker, you can download and run installers for macOS and Windows.

All platforms

A more detailed discussion on how to setup Singularity can be found in a dedicated episode of this tutorial.