Singularity containers: usage in HPC infrastructure

Overview

Singularity containers are an alternative to Docker. They are better suited for HPC environments and can be used to package entire scientific workflows, software and libraries, and even data. This means that you don’t have to ask your cluster admin to install anything for you - you can put it in a Singularity container and run, addressing issues related to reproducibility and interoperability. This course will cover an introduction of Singularity and what it can be used for, followed by a guided hands-on session on using Singularity in an HPC context. Participants can also bring their own projects.

Audience

The course is targeted at researchers who are familiar with using HPC infrastructure and want to use Singularity containers.

Learning objectives

At the end of this course, participants will have an understanding of what Singularity is and where it can be usefully applied to address issues of reproducibility and interoperability in scientific workflows. More specifically, participants will have the skills necessary to create, distribute, and execute scientific workflows encapsulated in Singularity containers.

Prerequisites

Knowledge / competencies

You should be familiar with using Linux/UNIX and basic HPC infrastructure.

Technical

Please bring your laptop with Virtualbox (https://www.virtualbox.org/) and Vagrant (https://www.vagrantup.com/) installed.

Venue and time

University of Basel, Sky Lounge Biozentrum Annex, 13th Floor, Klingelberstrasse 61.

The course will start at 10:00 and end around 16:00. Precise information will be provided to the participants on due time.

Additional information

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

For more information, please contact training@sib.swiss.