What is Singularity?

Singularity is another container platform. In some ways it appears similar to Docker from a user perspective, but in others, particularly in the system’s architecture, it is fundamentally different. These differences mean that Singularity is particularly well-suited to running on distributed, High Performance Computing (HPC) infrastructure, as well as a Linux laptop or desktop!

System administrators will not, generally, install Docker on shared computing platforms such as lab desktops, research clusters or HPC platforms because the design of Docker presents potential security issues for shared platforms with multiple users. Singularity, on the other hand, can be run by end-users entirely within “user space”, that is, no special administrative privileges need to be assigned to a user in order for them to run and interact with containers on a platform where Singularity has been installed.

Getting started with Singularity

Initially developed within the research community, Singularity is open source and the repository is currently available in the “The Next Generation of High Performance Computing” GitHub organisations. Part I of this Singularity material is intended to be undertaken on a remote platform where Singularity has been pre-installed.

If you’re attending a taught version of this course, you will be provided with access details for a remote platform made available to you for use for Part I of the Singularity material. This platform will have the Singularity software pre-installed.

Installing Singularity on your own laptop/desktop

If you have a Linux system on which you have administrator access and you can install Singularity locally on this system.

Sign in to the Vega system that you’ve been provided with access to. Check that the singularity command is available in your terminal:

singularity --version

Output

SingularityPRO version 3.7-5.el8

Depending on the version of Singularity installed on your system, you may see a different version.

Singularity on HPC systems: Loading a module

HPC systems often use modules to provide access to software on the system. If you get a command not found error (e.g. bash: singularity: command not found or similar) you may need to load the singularity module before you can use the singularity command:

module load singularity

Nonetheless, for the Vega system singularity is readily available.

Images and containers

We’ll start with a brief note on the terminology used in this section of the course. We refer to both images and containers. What is the distinction between these two terms?

Images are bundles of files including an operating system, software and potentially data and other application-related files. They may sometimes be referred to as a disk image or container image and they may be stored in different ways, perhaps as a single file, or as a group of files. Either way, we refer to this file, or collection of files, as an image.

A container is a virtual environment that is based on an image. That is, the files, applications, tools, etc that are available within a running container are determined by the image that the container is started from. It may be possible to start multiple container instances from an image. You could, perhaps, consider an image to be a form of template from which running container instances can be started.

Getting an image and running a Singularity container

If you recall from learning about Docker, Docker images are formed of a set of layers that make up the complete image. When you pull a Docker image from Docker Hub, you see the different layers being downloaded to your system. They are stored in your local Docker repository on your system and you can see details of the available images using the docker command.

Singularity images are a little different. Singularity uses the Signularity Image Format (SIF) and images are provided as single SIF files. Singularity images can be pulled from Singularity Hub, a registry for container images. Singularity is also capable of running containers based on images pulled from Docker Hub and some other sources. We’ll look at accessing containers from Docker Hub later in the Singularity material.

Singularity Hub

Note that in addition to providing a repository that you can pull images from, Singularity Hub can also build Singularity images for you from a recipe - a configuration file defining the steps to build an image. We’ll look at recipes and building images later.

Let’s begin by creating a test directory, changing into it and pulling a test Hello World image from Singularity Hub:

mkdir test
cd test
singularity pull hello-world.sif shub://vsoch/hello-world

Note

What is the main difference between above and the Docker pull request?

Output

INFO:    Downloading shub image
59.75 MiB / 59.75 MiB [=====================================================================] 100.00% 52.03 MiB/s 1s

What just happened?! We pulled a SIF image from Singularity Hub using the singularity pull command and directed it to store the image file using the name hello-world.sif. If you run the ls command, you should see that the hello-world.sif file is now in your current directory. This is our image and we can now run a container based on this image:

singularity run hello-world.sif

Output

RaawwWWWWWRRRR!! Avocado!

The above command ran the hello-world container from the image we downloaded from Singularity Hub and the resulting output was shown.

How did the container determine what to do when we ran it?! What did running the container actually do to result in the displayed output?

When you run a container from an image without using any additional command line arguments, the container runs the default run script that is embedded within the image. This is a shell script that can be used to run commands, tools or applications stored within the image on container startup. We can inspect the image’s run script using the singularity inspect command:

singularity inspect -r hello-world.sif

Output

#!/bin/sh

exec /bin/bash /rawr.sh

This shows us the script within the hello-world.sif image configured to run by default when we use the singularity run command.

That concludes this introductory Singularity episode. The next episode looks in more detail at running containers.