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
.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
is by default not recorded, and your container loses its
reproducibility. The following are steps to 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 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
CMD because I have
%runscript . If I want the Dockerfile
ENTRYPOINT to take preference, I would remove
%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 step 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
ENTRYPOINT. The differences are subtle, but the a good description is the following:
CMDis to provide defaults for an executing container.
ENTRYPOINThelps 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
IncludeCmd: yes in the Spec file (see below). If you provide any sort of
your Spec file, this overrides anything provided in Docker. In summary,
the order of operations is as follows:
%runscriptis specified in the Singularity spec file, this takes prevalence over all
%runscriptis specified, or if the
importcommand is used as in the example above, the
ENTRYPOINTis used as runscript.
%runscriptis specified, but the user has a
IncludeCmd, then the Docker
%runscriptis specified, and there is no
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:
By default, the minimum requirement is that you specify a repository name (eg, ubuntu) and it will default to the following:
If you provide a version instead of a tag, that will be used instead:
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
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
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
Authentication in the Singularity Build File¶
You can simply specify your additional authentication parameters in the
header with the labels
Username: vanessa Password: [password]
Again, this can be in addition to specification of a custom registry
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
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=$(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.
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
/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,
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
$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
Have any more best practices? Please let us know!