Using Docker images with Singularity

Overview

Teaching: 5 min
Exercises: 10 min

Questions

• How do I use Docker images with Singularity?

Objectives

• Learn how to run Singularity containers based on Docker images.

Using Docker images with Singularity

Singularity can also start containers directly from Docker images, opening up access to a huge number of existing container images available on Docker Hub and other registries.

While Singularity doesn’t actually run a container using the Docker image (it first converts it to a format suitable for use by Singularity), the approach used provides a seamless experience for the end user. When you direct Singularity to run a container based on pull a Docker image, Singularity pulls the slices or layers that make up the Docker image and converts them into a single-file Singularity SIF image.

For example, moving on from the simple Hello World examples that we’ve looked at so far, let’s pull one of the official Docker Python images. We’ll use the image with the tag 3.9.6-slim-buster which has Python 3.9.6 installed on Debian’s Buster (v10) Linux distribution:

$ singularity pull python-3.9.6.sif docker://python:3.9.6-slim-buster

INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Copying blob 33847f680f63 done  
Copying blob b693dfa28d38 done  
Copying blob ef8f1a8cefd1 done  
Copying blob 248d7d56b4a7 done  
Copying blob 478d2dfa1a8d done  
Copying config c7d70af7c3 done  
Writing manifest to image destination
Storing signatures
2021/07/27 17:23:38  info unpack layer: sha256:33847f680f63fb1b343a9fc782e267b5abdbdb50d65d4b9bd2a136291d67cf75
2021/07/27 17:23:40  info unpack layer: sha256:b693dfa28d38fd92288f84a9e7ffeba93eba5caff2c1b7d9fe3385b6dd972b5d
2021/07/27 17:23:40  info unpack layer: sha256:ef8f1a8cefd144b4ee4871a7d0d9e34f67c8c266f516c221e6d20bca001ce2a5
2021/07/27 17:23:40  info unpack layer: sha256:248d7d56b4a792ca7bdfe866fde773a9cf2028f973216160323684ceabb36451
2021/07/27 17:23:40  info unpack layer: sha256:478d2dfa1a8d7fc4d9957aca29ae4f4187bc2e5365400a842aaefce8b01c2658
INFO:    Creating SIF file...

Note how we see singularity saying that it’s “Converting OCI blobs to SIF format”. We then see the layers of the Docker image being downloaded and unpacked and written into a single SIF file. Once the process is complete, we should see the python-3.9.6.sif image file in the current directory.

We can now run a container from this image as we would with any other singularity image.

Running the Python 3.9.6 image that we just pulled from Docker Hub

Try running the Python 3.9.6 image. What happens?

Try running some simple Python statements…

Running the Python 3.9.6 image

$ singularity run python-3.9.6.sif

This should put you straight into a Python interactive shell within the running container:

Python 3.9.6 (default, Jul 22 2021, 15:24:21) 
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> 

Now try running some simple Python statements:

>>> import math
>>> math.pi
3.141592653589793
>>> 

In addition to running a container and having it run the default run script, you could also start a container running a shell in case you want to undertake any configuration prior to running Python. This is covered in the following exercise:

Open a shell within a Python container

Try to run a shell within a singularity container based on the python-3.9.6.sif image. That is, run a container that opens a shell rather than the default Python interactive console as we saw above. See if you can find more than one way to achieve this.

Within the shell, try starting the Python interactive console and running some Python commands.

Solution

Recall from the earlier material that we can use the singularity shell command to open a shell within a container. To open a regular shell within a container based on the python-3.9.6.sif image, we can therefore simply run:

$ singularity shell python-3.9.6.sif

Singularity> echo $SHELL
/bin/bash
Singularity> cat /etc/issue
Debian GNU/Linux 10 \n \l

Singularity> python
Python 3.9.6 (default, Jul 22 2021, 15:24:21) 
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> print('Hello World!')
Hello World!
>>> exit()

Singularity> exit
$ 

It is also possible to use the singularity exec command to run an executable within a container. We could, therefore, use the exec command to run /bin/bash:

$ singularity exec python-3.9.6.sif /bin/bash

Singularity> echo $SHELL
/bin/bash

You can run the Python console from your container shell simply by running the python command.

This concludes the fifth episode and Part I of the Singularity material. Part II contains a further three episodes where we’ll look at creating your own images and then more advanced use of containers for running MPI parallel applications.

References

[1] Gregory M. Kurzer, Containers for Science, Reproducibility and Mobility: Singularity P2. Intel HPC Developer Conference, 2017. Available at: https://www.intel.com/content/dam/www/public/us/en/documents/presentation/hpc-containers-singularity-advanced.pdf

Key Points

• Singularity can start a container from a Docker image which can be pulled directly from Docker Hub.