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Do's and don'ts for HPC usage

Please Do
  1. Remember that you share the login nodes (and remote desktop environments where they are provided) with many other users. Be mindful of that.
  2. If you need to run something "strenuous" interactively, then use the batch system's qsub -I ... mechanism. This would apply to compile and/or testing code, pre-processing or post-processing data.
  3. If you need to transfer a lot of small files, it is smarter to lump them into a single tar or zip file and transfer them as part of a larger lump of data.
  4. If you are running jobs that are identical except for the input parameter and input file name, consider using job arrays instead of submitting many individual jobs of an almost identical form.
Please Don't
  1. Run processing for sustained periods on login nodes (or remote desktops). Your access to resources (CPU and RAM) is capped, but you should nonetheless avoid inconveniencing other users by running work on login nodes. Use the batch system instead.
  2. Just because you can write a shell or Python script to rapidly fire qsub commands at the batch system, you should avoid doing so. Rapidly firing jobs at HPC can cause issues for the batch submission sub-system. Having large numbers of small jobs queued can also impact scheduler performance. Please use Job Arrays or Nimrod instead when you need to run large numbers of similar jobs.
  3. Avoid abusing the login environment with the watch command. In many circumstances, the output of the command line that the watch is watching does not change anywhere near as frequently as the watch command will report.

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