Skip to content

Software Exercise 1.4: Build, Test, and Deploy an Apptainer Container

Objective: to practice building and using a custom apptainer container

Why learn this?: You may need to go through this process if you want to use a container for your jobs and can't find one that has what you need.

Motivating Script

  1. Create a script called

    #!/usr/bin/env python3
    import cowsay
    cowsay.cow('Hello OSG User School')
  2. Give it executable permissions:

    $ chmod +x
  3. Try running the script:

    $ ./

    It will likely fail, because the cowsay library isn't installed. This is a scenario where we will want to build our own container that includes a base Python installation and the cowsay Python library.

Preparing a Definition File

We can describe our desired Apptainer image in a special format called a definition file. This has special keywords that will direct Apptainer when it builds the container image.

  1. Create a file called py-cowsay.def with these contents:
    Bootstrap: docker
    From: opensciencegrid/osgvo-ubuntu-20.04:latest
        apt-get update -y
        apt-get install -y \
                python3-pip \
        python3 -m pip install cowsay

Note that we are starting with the same ubuntu base we used in previous exercises. The %post statement includes our installation commands, including updating the pip and numpy packages, and then using pip to install cowsay.

To learn more about definition files, see Exercise 3.1

Build the Container

Once the definition file is complete, we can build the container.

  1. Run the following command to build the container:
    $ apptainer build py-cowsay.sif py-cowsay.def

As with the Docker image in the previous exercise, the first argument is the name to give to the newly create image file and the second argument is how to build the container image - in this case, the definition file.

Testing the Image Locally

  1. Do you remember how to interactively test an image? Look back at Exercise 1.1 and guess what command would allow us to test our new container.

  2. Try running:

    $ singularity shell first-image.sif
  3. Then try running the script:

    Singularity< ./
  4. If it produces an output, our container works! We can now exit (by typing exit) and submit a job.

Submit a Job

  1. Make a copy of a submit file from a previous exercise in this section. Can you guess what options need to be used or modified?

  2. Make sure you have the following (in addition to log, error, output and CPU and memory requests):

    universe = container
    container_image = py-cowsay.sif
    executable =
  3. Submit the job and verify the output when it completes.

    | Hello OSG User School! |
                             (__)\       )\/\
                                 ||----w |
                                 ||     ||