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Singularity support #150

@alecgunny

Description

@alecgunny

When launching omicron jobs from a singularity container, the corresponding executable path will, in general, not exist in the environment in which the jobs get run. At a high level, it seems like this could be supported by:

  • introducing a --singularity-image (or similar) to the command line parser that defaults to os.getenv("SINGULARITY_CONTAINER"), which will be the full path to the running container's image if currently inside a container
  • Add a similar argument to OmicronProcessJob
  • During OmicronProcessJob.write_sub_file, check if self.singularity_image is not None, and if not add something like this to the sub file
f"""
+SingularityImage = "{self.singularity_image}"
Requirements = HasSingularity
"""
  • Longer term, the functionality from the point could even be worth upstreaming into glue.pipeline.CondorDAGJob.

If this is something the team thinks might be valuable, happy to take a stab at making a PR for this.

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