setup.md

layout	title	root
page	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]({{ page.root }}/files/install-singularity.sh) | docs
• Desirable (to run all the base episodes)
  • Docker : [script]({{ page.root }}/files/install-docker.sh) | docs (unofficial)
  • MPICH library : [script]({{ page.root }}/files/install-mpich.sh) | docs
  • Nvidia GPU driver (GPU card required)
  • Slurm scheduler (can still run the MPI examples without it)
• Optional (bonus episodes)
  • Nextflow engine : [script]({{ page.root }}/files/install-nextflow.sh) | docs
  • Environment Modules : [script]({{ page.root }}/files/install-modules.sh) | docs
  • Lmod module system : [script]({{ page.root }}/files/install-lmod.sh) | docs
  • SHPC : [script]({{ page.root }}/files/install-shpc.sh) | docs
  • Docker Compose: [script]({{ page.root }}/files/install-dockercompose.sh) | docs
  • HPCCM : [script]({{ page.root }}/files/install-hpccm.sh) | docs
  • Spack : [script]({{ page.root }}/files/install-spack.sh) | docs
  • Podman : [script]({{ page.root }}/files/install-podman.sh) | docs
  • Charliecloud : [script]({{ page.root }}/files/install-charliecloud.sh) (uses Spack) | docs
  • Sarus : [script]({{ page.root }}/files/install-sarus.sh) | docs
  • Enroot : [script]({{ page.root }}/files/install-enroot.sh) | 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. {: .solution}

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. {: .challenge}