Singularity and Docker¶

Singularity can be used with Docker images. This feature was included because developers use and really like using Docker, and scientists have already put much resources into creating Docker images. Thus, one of our early goals was to support Docker. What can you do?

You don’t need Docker installed
You can shell into a Singularity-ized Docker image
You can run a Docker image instantly as a Singularity image
You can pull a Docker image (without sudo)
You can build images with bases from assembled Docker layers that include environment, guts, and labels

TLDR (Too Long Didn’t Read)¶

You can shell, import, run, and exec Docker images directly from the Docker Registry.

singularity shell docker://ubuntu:latest

singularity run docker://ubuntu:latest

singularity exec docker://ubuntu:latest echo "Hello Dinosaur!"

singularity pull docker://ubuntu:latest

singularity build ubuntu.img docker://ubuntu:latest

Import a Docker image into a Singularity Image¶

The core of a Docker image is basically a compressed set of files, a set of .tar.gz that (if you look in your Docker image folder on your host machine, you will see the files). The Docker Registry, which you probably interact with via Docker Hub, serves these layers. These are the layers that you see downloading when you interact with the docker daemon. We are going to use these same layers for Singularity!

Quick Start: The Docker Registry¶

The Docker engine communicates with the Docker Hub via the Docker Remote API, and so can Singularity. The easiest thing to do is create an image, and then pipe a Docker image directly into it from the Docker Registry. You don’t need Docker installed on your machine, but you will need a working Internet connection. Let’s create an ubuntu operating system, from Docker. We will pull, then build:

singularity pull docker://ubuntu

WARNING: pull for Docker Hub is not guaranteed to produce the

WARNING: same image on repeated pull. Use Singularity Registry

WARNING: (shub://) to pull exactly equivalent images.

Docker image path: index.docker.io/library/ubuntu:latest

Cache folder set to /home/vanessa/.singularity/docker

[5/5] |===================================| 100.0%

Importing: base Singularity environment

Importing: /home/vanessa/.singularity/docker/sha256:9fb6c798fa41e509b58bccc5c29654c3ff4648b608f5daa67c1aab6a7d02c118.tar.gz

Importing: /home/vanessa/.singularity/docker/sha256:3b61febd4aefe982e0cb9c696d415137384d1a01052b50a85aae46439e15e49a.tar.gz

Importing: /home/vanessa/.singularity/docker/sha256:9d99b9777eb02b8943c0e72d7a7baec5c782f8fd976825c9d3fb48b3101aacc2.tar.gz

Importing: /home/vanessa/.singularity/docker/sha256:d010c8cf75d7eb5d2504d5ffa0d19696e8d745a457dd8d28ec6dd41d3763617e.tar.gz

Importing: /home/vanessa/.singularity/docker/sha256:7fac07fb303e0589b9c23e6f49d5dc1ff9d6f3c8c88cabe768b430bdb47f03a9.tar.gz

Importing: /home/vanessa/.singularity/metadata/sha256:77cece4ce6ef220f66747bb02205a00d9ca5ad0c0a6eea1760d34c744ef7b231.tar.gz

WARNING: Building container as an unprivileged user. If you run this container as root

WARNING: it may be missing some functionality.

Building Singularity image...

Cleaning up...

Singularity container built: ./ubuntu.img

The warnings are reminding you that you are creating the image on the fly from layers, and if one of those layers changes, you won’t produce the same image next time.

The Build Specification file, Singularity¶

Just like Docker has the Dockerfile, Singularity has a file called Singularity that (currently) applications like Singularity Hub know to find. For reproducibility of your containers, our strong recommendation is that you build from these files. Any command that you issue to change a container sandbox (building with --sandbox ) or to a build with --writable is by default not recorded, and your container loses its reproducibility. So let’s talk about how to make these files. First, let’s look at the absolute minimum requirement:

Bootstrap: docker

From: ubuntu

We save this content to a file called Singularity and then issue the following commands to bootstrap the image from the file:

sudo singularity build ubuntu.img Singularity

A particular tag or version can be added to the docker uri:

Bootstrap: docker

From: ubuntu:latest

Note

Note that the default is latest . If you want to customize the Registry or Namespace, just add those to the header:

Bootstrap: docker

From: ubuntu

Registry: pancakes.registry.index.io

Namespace: blue/berry/cream

The power of build comes with the other things that you can do. This means running specific install commands, specifying your containers runscript (what it does when you execute it), adding files, labels, and customizing the environment. Here is a full Singularity file:

Bootstrap: docker

From: tensorflow/tensorflow:latest

%runscript

    exec /usr/bin/python "$@"

%post

    echo "Post install stuffs!"

%files

/home/vanessa/Desktop/analysis.py /tmp/analysis.py

relative_path.py /tmp/analysis2.py

%environment

TOPSECRET=pancakes

HELLO=WORLD

export HELLO TOPSECRET

%labels

AUTHOR Vanessasaur

In the example above, I am overriding any Dockerfile ENTRYPOINT or CMD because I have defined a %runscript . If I want the Dockerfile ENTRYPOINT to take preference, I would remove the %runscript section. If I want to use CMD instead of ENTRYPOINT , I would again remove the runscript, and add IncludeCmd to the header:

Bootstrap: docker

From: tensorflow/tensorflow:latest

IncludeCmd: yes

%post

    echo "Post install stuffs!"

You can commit this Singularity file to a GitHub repo and it will automatically build for you when you push to Singularity Hub?. This will ensure maximum reproducibility of your work.

How does the runscript work?¶

Docker has two commands in the Dockerfile that have something to do with execution, CMD and ENTRYPOINT. The differences are subtle, but a good description I’ve found is the following:

A CMD is to provide defaults for an executing container.

and

An ENTRYPOINT helps you to configure a container that you can run as an executable.

Given the definition, the ENTRYPOINT is most appropriate for the Singularity %runscript , and so using the default bootstrap (whether from a docker:// endpoint or a Singularity spec file) will set the ENTRYPOINT variable as the runscript. You can change this behavior by specifying IncludeCmd: yes in the Spec file (see below). If you provide any sort of %runscript in your Spec file, this overrides anything provided in Docker. In summary, the order of operations is as follows:

If a %runscript is specified in the Singularity spec file, this takes prevalence over all
If no %runscript is specified, or if the import command is used as in the example above, the ENTRYPOINT is used as runscript.
If no %runscript is specified, but the user has a Singularity spec with IncludeCmd , then the Docker CMD is used.
If no %runscript is specified, and there is no CMD or ENTRYPOINT , the image’s default execution action is to run the bash shell.

How do I specify my Docker image?¶

In the example above, you probably saw that we referenced the docker image first with the uri docker:// and that is important to tell Singularity that it will be pulling Docker layers. To ask for ubuntu, we asked for docker://ubuntu . This uri that we give to Singularity is going to be very important to choose the following Docker metadata items:

registry (e.g., “index.docker.io”)
namespace (e.g., “library”)
repository (e.g., “ubuntu”)
tag (e.g., “latest”) OR version (e.g., “@sha256:1234…)

When we put those things together, it looks like this:

docker://<registry>/<namespace>/<repo_name>:<repo_tag>

By default, the minimum requirement is that you specify a repository name (eg, ubuntu) and it will default to the following:

docker://index.docker.io/library/ubuntu:latest

If you provide a version instead of a tag, that will be used instead:

docker://index.docker.io/library/ubuntu@sha256:1235...

You can have one or the other, both are considered a “digest” in Docker speak.

If you want to change any of those fields and are having trouble with the uri, you can also just state them explicitly:

Bootstrap: docker

From: ubuntu

Registry: index.docker.io

Namespace: library

Custom Authentication¶

For both import and build using a build spec file, by default we use the Docker Registry index.docker.io . Singularity first tries the call without a token, and then asks for one with pull permissions if the request is defined. However, it may be the case that you want to provide a custom token for a private registry. You have two options. You can either provide a Username and Password in the build specification file (if stored locally and there is no need to share), or (in the case of doing an import or needing to secure the credentials) you can export these variables to environmental variables. We provide instructions for each of these cases:

Authentication in the Singularity Build File¶

You can simply specify your additional authentication parameters in the header with the labels Username and Password :

Username: vanessa

Password: [password]

Again, this can be in addition to specification of a custom registry with the Registry parameter.

Authentication in the Environment¶

You can export your username, and password for Singularity as follows:

export SINGULARITY_DOCKER_USERNAME=vanessasaur

export SINGULARITY_DOCKER_PASSWORD=rawwwwwr

Testing Authentication¶

If you are having trouble, you can test your token by obtaining it on the command line and putting it into an environmental variable, CREDENTIAL :

CREDENTIAL=$(echo -n vanessa:[password] | base64)

TOKEN=$(http 'https://auth.docker.io/token?service=registry.docker.io&scope=repository:vanessa/code-samples:pull' Authorization:"Basic $CREDENTIAL" | jq -r '.token')

This should place the token in the environmental variable TOKEN . To test that your token is valid, you can do the following

http https://index.docker.io/v2/vanessa/code-samples/tags/list Authorization:"Bearer $TOKEN"

The above call should return the tags list as expected. And of course you should change the repository(repo) name to be one that actually exists that you have credentials for.

Best Practices¶

While most docker images can import and run without a hitch, there are some special cases for which things can go wrong. Here is a general list of suggested practices, and if you discover a new one in your building ventures please let us know.

1. Installation to Root¶

When using Docker, you typically run as root, meaning that root’s home at /root is where things will install given a specification of home. This situation is fine when you stay in Docker, or if the content at /root doesn’t need any kind of write access, but generally it can lead to a lot of bugs because it is, after all, root’s home. This leads us to best practice #1.

Don’t install anything to root’s home, /root.

2. Library Configurations¶

The command ldconfig is used to update the shared library cache. If you have software that requires symbolic linking of libraries and you do the installation without updating the cache, then the Singularity image (in read only) will likely give you an error that the library is not found. If you look in the image, the library will exist but the symbolic link will not. This leads us to best practice #2:

Update the library cache at the end of your Dockerfile with a call to ldconfig.

3. Don’t install to $HOME or $TMP¶

We can assume that the most common Singularity use case has the $USER home being automatically mounted to $HOME, and $TMP also mounted. Thus, given the potential for some kind of conflict or missing files, for best practice #3 we suggest the following:

Don’t put container valuables in $TMP or $HOME

Have any more best practices? Please let us know!

Troubleshooting¶

Why won’t my image build work? If you can’t find an answer on this site, please send us an issue. If you’ve found an answer and you’d like to see it on the site for others to benefit from, then post to us here.