Simple chunked pedigree kinship #1282
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Thanks @jeromekelleher, I assume we're not worried about the Cubed and Zarr 3 test runs failing for now? |
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I didn't see those @tomwhite, thoughts here? |
They are not related to this PR, so OK to merge this if it's ready. I'll be looking at the Zarr 3 changes today. |
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Happy to merge when you are @timothymillar |
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changelog.rstI've tested this with a real pedigree of ~55,000 individuals on a 4-core laptop in WSL2. I can calculate the pedigree matrix using chunks of 5000 samples and save the chunked matrix to a Zarr store in a total of < 25s using ~2.5GB of RAM. The full matrix would be ~22.5GB which exceeds the memory of this machine.
I've used the
@jitclassexperimental feature from Numba for a simple triangular matrix class. Using a triangular matrix halves the RAM needed for the intermediate matrices. It's not strictly necessary to use@jitclassfor this but it allows for greater code reuse via custom__setitem__/__getitem__. If this is an issue it could be reworked to avoid@jitclass.I've also removed the test runs with
NUMBA_DISABLE_JIT: 1because this introduces a dependency on@guvectorizeand@jitclassinpedigree.py.