Containers in HPC (Pawsey Centre): Setup

The main requirement for this workshop is a personal computer with a web browser and a command line shell program.
These will allow you to follow the online materials and to login to a facility with the required software stack.

SC19 Workshop Attendee Instructions

You will will need username and password to access the training VMs, which will be provided by the instructors.

You will find a green and pink post-it note at your spot. On the green note is a 3 digit number (“XXX” below). Your login details today follow a pattern of:

username: userXXX
password: tutorialXXX

You don’t need to read further for today.

Regular users of this tutorial: read here

• 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.

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

• BYO Device: if you have a Linux box, you can install the required software yourself (might take a while):

  • Essential (core of the tutorial)
    • Singularity : script | docs
  • Desirable (to run all Singularity examples)
    • MPICH library : script | docs
    • Nvidia GPU driver (GPU card required)
    • Slurm scheduler
    • Nextflow engine : script | docs
  • Optional (extra applications for last two episodes)
    • Docker : docs (unofficial)
    • HPCCM : script | docs
    • Podman : script | docs
    • Sarus : script | docs

Notes

• 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.
• To install Singularity on a Mac or Windows machine, follow these instructions by Sylabs on Setting up Singularity with Vagrant.