2021

Packaging software in portable containers with Singularity

by Dr Olivier Mattelaer (UCLouvain/CISM)

Europe/Brussels
bibliotheque des sciences: salle pasteur (comodal (louvain-la-neuve or remote))

bibliotheque des sciences: salle pasteur

comodal (louvain-la-neuve or remote)

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Description

Singularity is a container solution for HPC. Containers help with reproducibility as they nicely package software and data dependencies, along with libraries that are needed. It allows users to install and run software that required root access to be installed on clusters where they only have regular user permissions. The rationale is to perform all the software installation in a container image (a kind of lightweight virtual machine, that can use a different Linux distribution than the one on the compute nodes!) on a machine where you have root access and then transfer and run that image on the machine on which you do not have root access. Images can be built from recipes shared by others, and from recipes made for Docker, the leader container solution outside the HPC world.

Contents:

  • Container concepts and benefits
  • Starting a Singularity container on the cluster
  • Accessing the cluster filesystems
  • Building a container image from a recipe
  • Building a container image from scratch
  • Singularity hub

Prerequisite:

  • Being able to use SSH with private keys 
  • Being familiar with a text editor 
  • Mastering the Linux command line and the GNU utilities (mkdir, cp, scp, etc.)
  • Basic knowledge of Linux system administration


Type: Hands-on
Target audience: Advanced user
Must: This session is a must-have for anyone dealing with software that only installs on Ubuntu...

Organized by

UCLouvain/CISM

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