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Normalise performance improvements - #66

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tomwhite merged 3 commits into
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normalise-parallelism
Apr 29, 2026
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tomwhite merged 3 commits into
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normalise-parallelism

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@tomwhite

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WIP attempt to process a batch of chunks at a time. A workload of 700k variants, 1 sample went from 43s to 5s, so this is worth doing.

@jeromekelleher you mentioned using a memory budget - do we have any code that does something like that already?

@jeromekelleher

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It's fiddly - let's just use the absolute chunk count for now, it's a good starting point.

@tomwhite

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OK, here's the minimal useful version. Waiting for #65 to go in.

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tomwhite marked this pull request as ready for review April 29, 2026 15:54
@jeromekelleher

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Can we standardise on explicitly saying variant-chunks for things like this I wonder (like, variants_chunks_in_batch)? I get confused about whether we're talking about sample chunks or variant chunks a lot.

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tomwhite force-pushed the normalise-parallelism branch from f2b63d9 to f776670 Compare April 29, 2026 17:16
@tomwhite tomwhite changed the title Normalise parallelism Normalise performance improvements Apr 29, 2026
@jeromekelleher

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LGTM

@tomwhite
tomwhite force-pushed the normalise-parallelism branch from fc13415 to db02298 Compare April 29, 2026 19:51
@tomwhite
tomwhite merged commit 5a18629 into main Apr 29, 2026
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@tomwhite
tomwhite deleted the normalise-parallelism branch April 29, 2026 19:55
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2 participants