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Update vsc_calcua - simplify all the things #730

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merged 6 commits into from
Aug 13, 2024

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pmoris
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@pmoris pmoris commented Aug 13, 2024

Based on the feedback in the previous PR (thanks @jfy133 and @nvnieuwk ) and inspired by the config for the UGent VSC, I've tried to simplify the CalcUA config.

See the commit messages for a full breakdown, but briefly:

  • Use a sane default profile that uses slurm scheduling.
  • Move single node execution mode to a sub-profile.
  • Dynamically set the queue and resource limits based on the partition to which the job was submitted.
  • Remove dynamic queue selector based on task requirements because it was a pain to debug.
  • Increase the queue size and lower the timeout setting.

pmoris added 6 commits August 13, 2024 12:38
Simplifies the structure of this config by allowing the
appropriate values for each partition/queue to be selected
automatically.

The general profile `vsc_calcua` now defaults to the Slurm
scheduler. For local execution mode on a single node, a sub-profile
`single_node` needs to be appended.

Regardless of the type of executor, the current Slurm partition name
is read out from the environment variables. Based on this,
the correct settings (mem, cpu, time limits and queue) are applied.

For single node execution mode, the resource limits are still read
out dynamically. For Slurm execution, they are based on the node type.

The slurm profile that allowed tasks to be submitted across different
partiions was removed, because it was a hassle to debug and configure.
I.e. note for future attempts: are task.mem-type values re-read for
each task or only on launch of the profile?
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@nvnieuwk nvnieuwk left a comment

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LGTM! Very nice!

@pmoris pmoris merged commit 245c877 into nf-core:master Aug 13, 2024
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2 participants