Running containerized applications

💬 In this tutorial we will get familiar with the basic usage of containerized software.

💭 Some software on CSC supercomputers have been installed as containers.

  • Usually, we try to make the containers as transparent as possible using wrapper scripts. This way, there should be little to no change in usage from the users’ perspective.

💭 Sometimes, however, this is impractical and there might be slight differences compared to the standard usage as described in the documentation.

  • Typically, this will also be the case for software you containerize yourself. You can, however, use Tykky to create wrapper scripts to facilitate use of containers.

‼️ Please see the software documentation in Docs CSC for details and other considerations.

  • To run these exercises on Puhti, use sinteractive or open a compute node shell in the Puhti web interface:

    sinteractive --account <project>  # replace <project> with your CSC project, e.g. project_2001234

Example: A “hidden” installation

  1. An example of a container-based installation that has been “hidden” behind a wrapper script is R. Load r-env module and check the contents of Rscript command:

    module load r-env
    cat /appl/soft/math/r-env/432/Rscript
  2. Observe that it is not the “real” Rscript command, but a wrapper script using apptainer_wrapper exec. Now, try running Rscript:

    Rscript --version
  3. As you can see, Rscript works as expected, and in most cases you don’t need to care about the fact that it is installed as a container.

    💭 You can find more details about using R in the Docs CSC page of the r-env module.

    💡 If you’re unable to open an interactive session due to high load during the course, you can try this example in a login shell instead:

    module load cutadapt
    cutadapt -h