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Software Exercise 1.2: Use Apptainer Containers in OSPool Jobs

Objective: Submit a job that uses an existing apptainer container; compare default job environment with a specific container job environment.

Why learn this?: By comparing a non-container and container job, you'll better understand what a container can do on the OSPool. This may also be how you end up submitting your jobs if you can find an existing apptainer container with your software.

Default Environment

First, let's run a job without a container to see what the typical job environment is.

  1. Create a bash script with the following lines: 

    #!/bin/bash

hostname
cat /etc/os-release 
gcc --version
python3 --version

    This will print out the version of Linux on the computer, the version of gcc, a common software compiler, and the version of Python 3.

  2. Make the script executable:

    $ chmod +x script.sh

  3. Run the script on the Access Point.

    $ ./script.sh

    What results did you get?

  4. Copy a submit file from a previous OSPool job and edit it so that the script you just wrote is the executable.

  5. Submit the job and read the standard output file when it completes. What version of Linux was used for the job? What is the version of gcc or Python?

Container Environment

Now, let's try running that same script inside a container.

  1. For this job, we will use the OSG-provided Ubuntu "Focal" image, as we did in the previous exercise. The container_image submit file option will tell HTCondor to use this container for the job: 

    universe = container
container_image = /cvmfs/singularity.opensciencegrid.org/htc/ubuntu:22.04

  2. If the submit file you copied has something like requirements = (OSGVO_OS_STRING == "RHEL 9"), remove that. When you use containers, you should not specify an OS in the requirements as that will unnecessarily limit the number of resources you can run on.

  3. Submit the job and read the standard output file when it completes. What version of Linux was used for the job? What is the version of gcc? or Python?

Experimenting With Other Containers

  1. Look at the list of OSG-Supported containers: OSG Supported Containers

  2. Try submitting a job that uses one of these containers. Change the executable script to explore different aspects of that container.