Singularity is good friends with Docker. The reason is because the 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? <\/p>\n
You can shell, import, run, and exec. <\/p>\n
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 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! <\/p>\n
The Docker engine communicates with the Docker Hub via the Docker Remote API, and guess what, we can too! The easiest thing to do is create an image, and then pipe a Docker image directly into it from the Docker Registry. You dont need Docker installed on your machine, but you will need a working internet connection. Lets create an ubuntu operating system, from Docker: <\/p>\n
Note that the default size is 768MB, you can modify this by adding the --size or -s argument like: <\/p>\n
If you arent sure about the size? Try building into a folder first. <\/p>\n
Next, lets import a Docker image into it! <\/p>\n
Just like Docker has the Dockerfile, Singularity has a file called Singularity that (currently) applications like Singularity Hub know to sniff for. For reproducibility of your containers, our strong recommendation is that you build from these files. Any command that you issue to change a container with --writable is by default not recorded, and your container loses its reproducibility. So lets talk about how to make these files! First, lets look at the absolute minimum requirement: <\/p>\n
We would save this content to a file called Singularity and then issue the following commands to bootstrap the image from the file <\/p>\n
but just those two lines and doing bootstrap is silly, because we would achieve the same thing by doing: <\/p>\n
The power of bootstrap comes with the other stuff 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: <\/p>\n
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: <\/p>\n
Did you know that 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. <\/p>\n
Docker has two commands in the Dockerfile that have something to do with execution, CMD and ENTRYPOINT. The differences are subtle, but the best description Ive found is the following: <\/p>\n
A CMD is to provide defaults for an executing container. <\/p>\n
and <\/p>\n
An ENTRYPOINT helps you to configure a container that you can run as an executable. <\/p>\n
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: <\/p>\n
In the example above, you probably saw that we referened 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: <\/p>\n
When we put those things together, it looks like this: <\/p>\n
By default, the minimum requirement is that you specify a repository name (eg, ubuntu) and it will default to the following: <\/p>\n
If you provide a version instead of a tag, that will be used instead: <\/p>\n
You can have one or the other, both are considered a digest in Docker speak. <\/p>\n
If you want to change any of those fields, then just specify what you want in the URI. <\/p>\n
For both import and bootstrap 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: <\/p>\n
You can simply specify your additional authentication parameters in the header with the labels Username and Password: <\/p>\n
Again, this can be in addition to specification of a custom registry with the Registry parameter. <\/p>\n
You can export your username, and password for Singularity as follows: <\/p>\n
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: <\/p>\n
This should place the token in the environmental variable TOKEN. To test that your token is valid, you can do the following <\/p>\n
The above call should return the tags list as expected. And of course you should change the repo name to be one that actually exists that you have credentials for. <\/p>\n
Why wont my image bootstrap work? If you cant find an answer on this site, please ping us an issue. If youve found an answer and youd like to see it on the site for others to benefit from, then post to us here. <\/p>\n
This entire process will hopefully change in two ways. First, we hope to collapse the image creation and bootstrapping, so you have the option to do them both in one full swing. Second, we hope to eventually figure out some kind of solution to import Docker containers without needing sudo. <\/p>\n
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Continue reading here:<\/p>\n
Singularity and Docker | Singularity<\/a><\/p>\n","protected":false},"excerpt":{"rendered":" Singularity is good friends with Docker. The reason is because the 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. Continue reading