Basic Singularity: running and building Singularity containers

Place: The workshop will be online via Zoom

Link will be sent a week before the workshop.
Time: 9:15-12:00, 13:15-16:00 13 February 2024
(If you need help with the workshop setup the meeting will be open from 9:00)
Workshop material online: https://pmitev.github.io/UPPMAX-Singularity-workshop/
Questions during the workshop https://hackmd.io/@pmitev/Singularity_QA_20240213
h-ttps://hackmd.io/@pmitev/Singularity_FAQ_20220928

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Send us an e-mail with subject you want to be addressed.

• How can I run MPI parallel code with Singularity

  PavlinApr 22, 2021 Have a look at this documentation page
  https://sylabs.io/guides/latest/user-guide/mpi.html

• How to run GUI programs (openGL apps for instance)

  PavlinApr 22, 2021 I have not experienced any problems with OpenGL. I have successfully containerized and used VMD in a Singularity container. Here is the recipe I have successfully used in two MD lab occasions running on Rackham.
  In contrary, I had luck installing problematic OpenGL software (XCrySDen) in Singularity that has severe problems to install and run on Rackham - recipe.

• Can we build images in Bianca? How does working in Bianca and building Singularity images look like (in terms of the steps or workflow)?

  PavlinFeb 12, 2024 In principle - yes, but with severe restrictions, since there is no Internet access on Bianca. In practice, users mostly convert from Docker to Singularity or add missing data in the container (building from another container)

• I would like to hear about conversion from Docker to Singularity recipes. I often find that research groups provide Docker images/recipes instead of singularity/appraiser versions. I know it is possible to convert or build those with singularity, but it is not always working.

  PavlinFeb 12, 2024 Indeed, most docker images are convertable, but might not work because of some particular designs (common practices for docker) that fail when running Singularity

  • running as different user (defined in the docker container)
  • running daemons or services
  • assuming the process has root access

Contacts:

• Pavlin Mitev - UPPMAX
• Pedro Ojeda May - HPC2N
• UPPMAX, HPC2N

tags: SNIC, UPPMAX, HPC2N, Singularity, workshop