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Benchmarks: Add all from Dask tutorial #3013

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flying-sheep opened this issue Apr 18, 2024 · 4 comments · May be fixed by #3319
Open

Benchmarks: Add all from Dask tutorial #3013

flying-sheep opened this issue Apr 18, 2024 · 4 comments · May be fixed by #3319
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@flying-sheep
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Different data:

  1. subsets
  2. sparse / dense chunks

Also all from disk.

@flying-sheep flying-sheep added this to the 1.10.2 milestone Apr 18, 2024
@flying-sheep flying-sheep self-assigned this Apr 18, 2024
@ilan-gold ilan-gold modified the milestones: 1.10.2, 1.10.3 Jun 25, 2024
@ilan-gold
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Actually deploying this is probably blocked by correcting CPU affinities on the benchmarking machine, but writing the code for this should be manageable otherwise.

@flying-sheep
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We now have the big dataset tests, so this might be easy-ish to do

@flying-sheep flying-sheep modified the milestones: 1.10.3, 1.10.4 Sep 17, 2024
@ilan-gold
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Goal:

Add dask use-cases to the scanpy benchmarks so we can understand performance changes.

Nice links:

  1. Example benchmark: https://github.com/scverse/scanpy/blob/main/benchmarks/benchmarks/preprocessing_counts.py
  2. Project we use for benchmarking: https://asv.readthedocs.io/projects/asv-runner/en/latest/index.html
  3. Dask local cluster: https://distributed.dask.org/en/stable/api.html#cluster
  4. Using scanpy and dask: https://scanpy.readthedocs.io/en/stable/tutorials/experimental/dask.html. NOTE: this read_elem_as_dask function in the notebook is with anndata 0.11 i.e., pip install --pre anndata

@ilan-gold ilan-gold assigned mikelkou and unassigned flying-sheep Oct 17, 2024
@ilan-gold
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@mikelkou See #2578 for functions that have dask vs. not

@flying-sheep flying-sheep modified the milestones: 1.10.4, 1.10.5 Nov 12, 2024
@flying-sheep flying-sheep linked a pull request Nov 14, 2024 that will close this issue
@ilan-gold ilan-gold removed this from the 1.10.5 milestone Nov 21, 2024
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3 participants