Overview

Teaching: 15 min
Exercises: 20 min

Questions

• What environment do I need to build a Singularity image and how do I set it up?

Objectives

• Understand how to the Docker Singularity image provides an environment for building Singularity images.

• Understand different ways to run containers based on the Docker Singularity image.

Singularity - Part II

Brief recap

In the five episodes covering Part I of this Singularity material we’ve seen how Singularity can be used on a computing platform where you don’t have any administrative privileges. The software was pre-installed and it was possible to work with existing images such as Singularity image files already stored on the platform or images obtained from a remote image repository such as Singularity Hub or Docker Hub.

It is clear that between Singularity Hub and Docker Hub there is a huge array of images available, pre-configured with a wide range of software applications, tools and services. But what if you want to create your own images or customise existing images?

In this first of three episodes in Part II of the Singularity material, we’ll look at preparing to build Singularity images.

Preparing to use Singularity for building images

So far you’ve been able to work with Singularity from your own user account as a non-privileged user. This part of the Singularity material requires that you use Singularity in an environment where you have administrative (root) access. While it is possible to build Singularity containers without root access, it is highly recommended that you do this as the root user, as highlighted in this section of the Singularity documentation. Bear in mind that the system that you use to build containers doesn’t have to be the system where you intend to run the containers. If, for example, you are intending to build a container that you can subsequently run on a Linux-based cluster, you could build the container on your own Linux-based desktop or laptop computer. You could then transfer the built image directly to the target platform or upload it to an image repository and pull it onto the target platform from this repository.

There are three different options for accessing a suitable environment to undertake the material in this part of the course:

1. Run Singularity from within a Docker container - this will enable you to have the required privileges to build images
2. Install Singularity locally on a system where you have administrative access
3. Use Singularity on a system where it is already pre-installed and you have administrative (root) access

We’ll focus on the first option in this part of the course - running singularity from within a Docker container. If you would like to install Singularity directly on your system, see the box below for some further pointers. However, please note that the installation process is an advanced task that is beyond the scope of this course so we won’t be covering this.

Installing Singularity on your local system (optional) [Advanced task]

If you are running Linux and would like to install Singularity locally on your system, the source code is provided via the The Next Generation of High Performance Computing (HPCng) community’s Singularity repository. See the releases here. You will need to install various dependencies on your system and then build Singularity from source code.

If you are not familiar with building applications from source code, it is strongly recommended that you use the Docker Singularity image, as described below in the “Getting started with the Docker Singularity image” section rather than attempting to build and install Singularity yourself. The installation process is an advanced task that is beyond the scope of this session.

However, if you have Linux systems knowledge and would like to attempt a local install of Singularity, you can find details in the INSTALL.md file within the Singularity repository that explains how to install the prerequisites and build and install the software. Singularity is written in the Go programming language and Go is the main dependency that you’ll need to install on your system. The process of installing Go and any other requirements is detailed in the INSTALL.md file.

Note

If you do not have access to a system with Docker installed, or a Linux system where you can build and install Singularity but you have administrative privileges on another system, you could look at installing a virtualisation tool such as VirtualBox on which you could run a Linux Virtual Machine (VM) image. Within the Linux VM image, you will be able to install Singularity. Again this is beyond the scope of the course.

If you are not able to access/run Singularity yourself on a system where you have administrative privileges, you can still follow through this material as it is being taught (or read through it in your own time if you’re not participating in a taught version of the course) since it will be helpful to have an understanding of how Singularity images can be built.

You could also attempt to follow this section of the lesson without using root and instead using the singularity command’s --fakeroot option. However, you may encounter issues with permissions when trying to build images and run your containers and this is why running the commands as root is strongly recommended and is the approach described in this lesson.

Getting started with the Docker Singularity image

The Singularity Docker image is available from Quay.io.

Familiarise yourself with the Docker Singularity image

• Using your previously acquired Docker knowledge, get the Singularity image for v3.5.3 and ensure that you can run a Docker container using this image. For this exercise, we recommend using the image with the v3.5.3-slim tag since it’s a much smaller image.

• Create a directory (e.g. $HOME/singularity_data) on your host machine that you can use for storage of definition files (we’ll introduce these shortly) and generated image files.

  This directory should be bind mounted into the Docker container at the location /home/singularity every time you run it - this will give you a location in which to store built images so that they are available on the host system once the container exits. (take a look at the -v switch to the docker run command)

Hint: To be able to build an image using the Docker Singularity container, you’ll need to add the --privileged switch to your docker command line.

Hint: If you want to run a shell within the Docker Singularity container, you’ll need to override the entrypoint to tell the container to run /bin/bash - take a look at Docker’s --entrypoint switch.

Questions / Exercises:

1. Can you run a container from the Docker Singularity image? What is happening when you run the container?
2. Can you run an interactive /bin/sh shell in the Docker Singularity container?
3. Can you run an interactive Singularity shell in a Singularity container, within the Docker Singularity container?!

Running a container from the image

Answers:

1. Can you run a container from the Docker Singularity image? What is happening when you run the container?

   The name/tag of the Docker Singularity image we’ll be using is: quay.io/singularity/singularity:v3.5.3-slim

   Having a bound directory from the host system accessible within your running Docker Singularity container will give you somewhere to place created Singularity images so that they are accessible on the host system after the container exits. Begin by changing into the directory that you created above for storing your definiton files and built images (e.g. $HOME/singularity_data).

   Running a Docker container from the image and binding the current directory to /home/singularity within the container can be achieved as follows:

    docker run --privileged --rm -v ${PWD}:/home/singularity quay.io/singularity/singularity:v3.5.3-slim
   

   Note that the image is configured to run the singularity command by default. So, when you run a container from it with no arguments, you see the singularity help output as if you had Singularity installed locally and had typed singularity on the command line.

   To run a Singularity command, such as singularity cache list, within the docker container directly from the host system’s terminal you’d enter:

    docker run --privileged --rm -v ${PWD}:/home/singularity quay.io/singularity/singularity:v3.5.3-slim cache list
   

   The following diagram shows how the Docker Singularity image is being used to run a container on your host system and how a Singularity container can, in turn, be started within the Docker container:

   

2. Can you run an interactive shell in the Docker Singularity container?

   To start a shell within the Singularity Docker container where you can then run the singularity command directly:

   docker run -it --entrypoint=/bin/sh --privileged --rm -v ${PWD}:/home/singularity quay.io/singularity/singularity:v3.5.3-slim
   

   Here we use the --entrypoint switch to the docker command to override the default behaviour when starting the container and instead of running the singularity command directly, we run a ‘sh’ shell. We also add the -it switch to provide an interactive terminal connection.

3. Can you run an interactive Singularity shell in a Singularity container, within the Docker Singularity container?!

   As shown in the diagram above, you can do this. It is necessary to run singularity shell <image file name> within the Docker Singularity container. You would use a command similar to the following (assuming that my_test_image.sif is in the current directory where you run this command):

   docker run --rm -it --privileged -v ${PWD}:/home/singularity quay.io/singularity/singularity:v3.5.3-slim shell --contain /home/singularity/my_test_image.sif
   

   You may notice there’s a flag being passed to singularity shell (--contain - -c is the short form and also works). What is this doing? When running a singularity container, you may remember that we highlighted that some key files/directories from the host system are mapped into containers by default when you start them. The configuration in the Docker Singularity container attempts to mount the file /etc/localtime into the Singularity container but there is not a timezone configuration present in the Docker Singularity container and this file doesn’t exist resulting in an error. --contain prevents the default mounting of some key files/directories into the container and prevents this error from occurring. Later in this material, there’s an example of how to rectify the issue by creating a timezone configuration in the Docker Singularity container so that the --contain switch is no longer needed.

Summary / Comments:

You may choose to:

• open a shell within the Docker image so you can work at a command prompt and run the singularity command directly
• use the docker run command to run a new container instance every time you want to run the singularity command (the Docker Singularity image is configured with the singularity command as its entrypoint).

Either option is fine for this section of the material.

To make things easier to read in the remainder of the material, command examples will use the singularity command directly, e.g. singularity cache list. If you’re running a shell in the Docker Singularity container, you can enter the commands as they appear. If you’re using the container’s default run behaviour and running a container instance for each run of the command, you’ll need to replace singularity with docker run --privileged -v ${PWD}:/home/singularity quay.io/singularity/singularity:v3.5.3-slim or similar.

This can be a little cumbersome to work with. However, if you’re using Linux or macOS on your host system, you can add a command alias to alias the command singularity on your host system to run the Docker Singularity container, e.g. (for bash shells - syntax for other shells varies):

alias singularity='docker run --privileged -v ${PWD}:/home/singularity quay.io/singularity/singularity:v3.5.3-slim'

This means you’ll only have to type singularity at the command line as shown in the examples throughout this section of the material

Key Points

• A Docker image is provided to run Singularity - this avoids the need to have a local Singularity installation on your system.

• The Docker Singularity image can be used to build containers on Linux, macOS and Windows.

• You can also run Singularity containers within the Docker Singularity image.