Containers in HPC (NeSI): 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.

eRNZ20 Workshop Attendee Instructions

This tutorial is adapted from https://github.com/PawseySC/sc19-containers and delivered jointly by New Zealand eScience Infrastructure (NeSI) and Pawsey Supercomputing Centre staff.

The tutorial will be best experienced directly on NeSI’s platforms. Though it is possible to follow along on a laptop we are not providing a standard environment for this and so will have limited ability to troubleshoot machine/environment specific issues during the tutorial. All the required software and container images have been preloaded on the NeSI platform under the nesi99991 project.

If you do not already have a NeSI account then please apply to create a NeSI account well ahead of the tutorial.

Once you have a NeSI account you will need membership in the relevant training project. Please contact NeSI Support via either the form here or email and provide your NeSI username (subject: “container tutorial”). Updating project membership may take up to 15 minutes, so please do this ahead of the tutorial if possible.

If you have a NeSI user account and access to the training project then you don’t need to read further for today.

Regular users of this tutorial: read here

• Mahuika @NeSI: if you have access, a recent version of Singularity can be loaded with module load singularity.

• 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.