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Update guide on using SLEAP on HPC#75

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niksirbi merged 2 commits intomainfrom
add-new-sleap-module
Oct 7, 2025
Merged

Update guide on using SLEAP on HPC#75
niksirbi merged 2 commits intomainfrom
add-new-sleap-module

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@niksirbi niksirbi commented Oct 6, 2025

Description

What is this PR

  • Bug fix
  • Addition of a new feature
  • Other

Why is this PR needed?

The guide was out of date because:

  • I installed a new SLEAP module on HPC (corresponding to v1.3.4, and built against the new Ubuntu 24.04 cluster)
  • SLEAP release v1.5 and updated links to docs

What does this PR do?

  • Mentions the new module
  • Warns about the fact that all currently installed SLEAP modules correspond to legacy (tensorflow) versions
  • Updates all SLEAP links in the guide to point to legacy docs
  • Adds nvidia-smi to example SLURM scripts (useful to have for debugging)
  • Adds instructions on how to handle RGB-to-Grayscale conversion errors during inference (I keep encountering them on some videos)

References

neuroinformatics-unit/course-animals-in-motion#21
neuroinformatics-unit/movement#681

How has this PR been tested?

Local docs build.
I have tested the new SLEAP module by succesfully running training and inference on the CalMS21 data, on two types of GPU nodes: A4500 and RTX5000.

Considerations for review

I'd like to have this merged ahead of Thursday, Oct 9th, because I will point students to this guide as a useful resource.
I've also opened #76 to remind myself to install a new SLEAP>v1.5 module and update the guide accordingly at a future time.

Checklist:

  • The code has been tested locally
  • Tests have been added to cover all new functionality
  • The documentation has been updated to reflect any changes
  • The code has been formatted with pre-commit

@niksirbi niksirbi marked this pull request as ready for review October 6, 2025 18:21
@niksirbi niksirbi requested a review from lochhh October 6, 2025 18:21
Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk>
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niksirbi commented Oct 7, 2025

Thanks @lochhh!

@niksirbi niksirbi merged commit fd370c6 into main Oct 7, 2025
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@niksirbi niksirbi deleted the add-new-sleap-module branch October 7, 2025 21:13
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2 participants