Singularity

This article explains the purpose and use of Singularity.

Description

Singularity is a container system for isolating software and computing environments from the host system. It allows to package software in highly portable and reproducible environments encapsulating all dependencies, including the operating system.
It has similarities to Docker but it's security model is specifically engineered to be used in HPC environments and for easy integration in managed client environments.

A typical use case is to install a specific software with the latest tool versions and all its dependencies from third-party repositories in order to run the application in a batch job on our Slurm cluster. Providing such dependencies on our managed Linux systems would be time consuming in preparation and maintenance. On the other hand such installations can be quickly done with elevated (sudo or root) privileges in a container.

Docker is not secure as it provides a means to gain root access on the host it's running on, therefore we provide Singularity as a secure alternative.

Official documentation

The official documentation for users is a great starting point to get up and running with Singularity.
The analogue of a Docker file, a so-called Singularity recipe or Singularity Definition File is documented in detail section Definition Files.

Concepts

Image sources

Pre-built SIFs and Docker images are available in the Sylabs Cloud Library or on the Docker hub.

Common use cases

Using a Docker image

The simplest use case is to convert an existing Docker image, run commands inside it and customize it for personal requirements. A well made Docker image can be converted without elevated privileges.

Convert a Docker image to a SIF

Directly from Docker Hub:

singularity build lolcow.sif docker://godlovedc/lolcow

Converting a Docker image stored locally as tar file:

singularity build docker-image.sif docker-archive:///path/to/docker-image.tar

Run a command in a SIF

singularity exec lolcow.sif cowsay "Mooh!"

If the command to be executed from the SIF is not found in the SIF's PATH variable, it's path needs to be specified explicitly:

singularity exec lolcow.sif /usr/games/cowsay "Mooh!"

Build your own SIF

A more complex use case is to install software on a specific Linux distribution with all its dependencies. This is easier with elevated privileges, as available step-by-step guides may be followed. To run Singularity operations as user root we provide SingularityBuilder .

Create a writeable sandbox

From the Singularity Library, where the example sandbox directory ubuntu_16.04 is created in the current directory:

singularity build --sandbox ubuntu_16.04 library://library/default/ubuntu:16.04

Or from the Docker Hub:

singularity build --sandbox ubuntu docker://ubuntu:16.04

Sandbox directory paths may be relative or absolute paths.

Start a shell in a sandbox

To install the software according to an installation guide or as you see fit, start a shell in your sandbox. The --writable option is necessary for file system modifications:

singularity shell --writable ubuntu_16.04

Convert a sandbox to a SIF

After a sandbox is set up and tested it can be converted to a SIF:

singularity build my_image.sif my_sandbox

Convert a SIF to a sandbox

It's also possible to convert a SIF back to a sandbox.:

singularity build --sandbox my_sandbox my_image.sif

Running commands from SIFs

Using GPU resources

For software packaged into a SIF which requires access to the GPU resources of its host, the option --nv can be added:

singularity exec --nv lolcow.sif cowsay "Mooh!"

Accessing storage

A user's home directory is available per default from a SIF. To be able to access additional storage paths they need to be defined by using the option --bind, either by automatically creating the same path /scratch/$USER inside the SIF as it exists on the host:

singularity shell --bind /scratch/$USER lolcow.sif

or mapping a specific path on the host /scratch/$USER to a different path /mnt/$USER inside the SIF:

singularity shell --bind /scratch/$USER:/mnt/$USER lolcow.sif

Services/Singularity (last edited 2021-07-20 09:31:26 by mreimers)