Docker and Singularity are container systems that allow users full control over their environment. You can create your own container image which your job will execute within, or choose from a set of pre-defined images. For more information about Docker, please see:

and Singularity, please see:

For jobs on OSG, it does not matter whether you provide a Docker or Singularity image. Either is compatible with our system and can be used with little to no modification. This is of course highly dependent on your workload. Please feel free to contact us if you have any questions.

Singularity has become the preferred containerization method in scientific computing. The following talk describes Singularity for scientific computing:

Derek Weitzel wrote a blog post about Singularity on OSG, which provides a good introduction on how to create images and run them, but does not cover all the functionality described further down:

Default Image

The default setup is to auto load an image on sites which support Singularity. Every job which lands on such a site, will have a container started just for that job, and then run within that container. Most users will not even know that their jobs are run within a container, but it will provide them with a consistent environment across OSG sites. The current default container is based on EL6 and contains a basic set of tools expected from OSG compute nodes. The image is loaded from /cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo-el6 and the definition file is available in GitHub https://github.com/opensciencegrid/osgvo-el6 . If you want to steer a job to run on a default Singularity instance, use HAS_SINGULARITY == True in the job requirements. For example:

universe = vanilla
executable = job.sh
Requirements = HAS_SINGULARITY == TRUE

should_transfer_files = IF_NEEDED
when_to_transfer_output = ON_EXIT

output = out
error = err
log = log

queue

To instruct the system to load a different image, use the +SingularityImage attribute in your job submit file. For example, to run your job under EL7:

universe = vanilla
executable = job.sh
Requirements = HAS_SINGULARITY == TRUE

+SingularityImage = "/cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo-el7"
+SingularityBindCVMFS = True

should_transfer_files = IF_NEEDED
when_to_transfer_output = ON_EXIT

output = out
error = err
log = log

queue

The user support team maintains a set of images. These contain a basic set of tools and libraries. The images are are:

Image Location Defintion Description
EL 6 /cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo-el6:latest GitHub A basic Enterprise Linux (CentOS) 6 based image. This is currently our default image
EL 7 /cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo-el7:latest GitHub A basic Enterprise Linux (CentOS) 7 based image.
Ubuntu Xenial /cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo-ubuntu-xenial:latest GitHub A good image if you prefer Ubuntu over EL flavors
TensorFlow /cvmfs/singularity.opensciencegrid.org/opensciencegrid/tensorflow:latest GitHub Base on the TensorFlow base image, with a few OSG package added
TensorFlow GPU /cvmfs/singularity.opensciencegrid.org/opensciencegrid/tensorflow-gpu:latest GitHub Used for running TensorFlow jobs on OSG GPU resources

Exploring Images on the Submit Host

Images can be explored interactively on the submit hosts by starting it in "shell" mode. The recommended command line, similar to how containers are started for jobs, is:

singularity shell \
            --home $PWD:/srv \
            --pwd /srv \
            --bind /cvmfs \
            --scratch /var/tmp \
            --scratch /tmp \
            --contain --ipc --pid \
            /cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo-ubuntu-xenial:latest

Custom Images

OSG Connect provides tooling for users to create, publish and load custom images. This is useful if your job requires some very specific software setup.

Creating a Custom Image

If you want to use an image you have created yourself, the image should be defined as a Docker image and published in the Docker Hub. The reason we use Docker as a source image repository is that it allows us to easily import the images into our own distribution system (see below). To get started, create a Docker user, sign in to the hub, and create a new repository. You will end up with an identifier of the namespace/repository_name format.

There are two main methods, we recommend to generating your own custom image:

  1. Editing the Dockerfile
  2. Editing the default image using local Docker

which are described below. Once you have created your custom image, you will need to register the image as described in the next section. If you prefer, you can base you image on images not already published by OSG, but if you do this, we recommend that you as one of the steps create the /cvmfs directory. This will enable the container to access tools and data published on /cvmfs. If you do not want /cvmfs mounted in the container, please add +SingularityBindCVMFS = False to your job submit file.

Editing the Dockerfile

To create an image locally using a Dockerfile, first download the Dockerfile for your desired flavor from OSG GitHub repository, see table above. For example, if you want to base the image on our Ubuntu Xenial image,

$ git clone https://github.com/opensciencegrid/osgvo-ubuntu-xenial.git

and change into the directory

$ cd osgvo-ubuntu-xenial

Edit the Dockerfile in the directory to fit your requirements. If you want /cvmfs mounted in your image please add

# required directories
RUN mkdir -p /cvmfs

to your Dockerfile

Then build the image with tag matching your Docker Hub repository:

$ docker build -t namespace/repository_name .

Once you have a successful build, push it to the hub:

$ docker push namespace/repository_name

Editing the default image using local Docker

To create an image locally using Docker, you will need to have Docker installed on your machine. For install instructions, see the Docker documentation.

With docker installed you can now get the desired image from Docker Hub. Again, we will look at OSG Ubuntu Xenial image.

$ docker pull opensciencegrid/osgvo-ubuntu-xenial

We will run the image in a docker interactive session

$ docker run -it --name <docker_session_name_here> opensciencegrid/osgvo-ubuntu-xenial /bin/bash

Giving the session a name is important because it will make it easier to reattach the session later and commit the changes later on. Now you will be greeted by a new command line prompt that will look something like this

[root@740b9db736a1 /]#

You can now install the software that you need through the image package manager, in this case apt-get. If you want /cvmfs mounted in your image please run

[root@740b9db736a1 /]# mkdir -p /cvmfs

Once you have installed all the software, you simply exit

[root@740b9db736a1 /]# exit

Now you can commit the changes to the image

docker commit <docker_session_name_here>

Alternatively, you can use the sessions hash (740b9db736a1 in the above example). Then you make a tag for your desired namespace/repository_name:

docker tag opensciencegrid/osgvo-ubuntu-xenial namespace/repository_name

And finally you simply need to push the changes:

docker push namespace/repository_name

Configuring GPU images

GPU images requires a few extra steps to get access to the host GPU libraries. We recommend that in this case you edit the Dockerfile rather than building a image through Docker.

GPU containers running under GPU slots will automatically get the host GPU libraries bound to /host-libs inside the container. For this to work, the /host-libs directory has to exist in the image, and LD_LIBRARY_PATH has to be set for the job. An example of how to do this is the TensorFlow GPU image.

Distributing Custom Images Via CVMFS

In order to be able to efficiently distribute the container images to a large of distributed compute hosts, OSG has chosen to host the images under CVMFS. Any image publicly available in Docker can be included for automatic syncing into the CVMFS repository. The result is an unpacked image under /cvmfs/singularity.opensciencegrid.org/

To get your images included, please either create a git pull request against docker_images.txt in the cvmfs-singularity-sync repository, or contact user-support@opensciencegrid.org and we can help you.

Once your image has been registered, new versions pushed to Docker Hub will automatically be detected and CVMFS will be updated accordingly.

 

This page was updated on Jun 22, 2018 at 08:00 from submitting-jobs/singularity-containers.md.