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Added CPUS_PER_TASK and a jupyterlab.sbatch #44

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emarti
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@emarti emarti commented Jun 2, 2023

Two changes: First, I added jupyterlab.sbatch so we can use jupyter lab notebooks instead of the modern ones. Second, I added a CPUS_PER_TASK parameter in param.sh so we can change the number of CPUs requested.

New parameter CPUS_PER_TASK specificies the number of cpus requested.
File sbatches/sherlock/jupyterlab.sbatch enables more modern jupyter lab notebooks
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vsoch commented Jun 2, 2023

This looks great! Two quick checks:

  • the default of --cpus-per-task on the cluster is set to 1 (so essentially adding it doesn't change current workflows)
  • you've tested this and are happy with how it works?

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emarti commented Jun 4, 2023

  1. When the memory specified is large (on our nodes bigger than 16 GB) then slurm automatically assigns more CPUs. This change will fix this.
  2. Yes, I have tested it and it works. For the jupyter lab sbatch, jupyterlab must be installed on sherlock. Perhaps further instructions are needed?

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vsoch commented Jun 4, 2023

When the memory specified is large (on our nodes bigger than 16 GB) then slurm automatically assigns more CPUs. This change will fix this.

Gotcha. In this case, we don't want to set a default to be 1, because it will break the default behavior. Let's keep the variable unset, and then only add it to the command if it's defined.

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