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Investigate further chunking improvements for better GWAS performance #461

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tomwhite opened this issue Feb 9, 2021 · 1 comment

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tomwhite commented Feb 9, 2021

#454 helped with GWAS performance, but as mentioned in https://github.com/pystatgen/sgkit/issues/390#issuecomment-768411149, there is scope for further improvement since the transfer time is still a significant proportion of the compute time.

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Identify lack of scalability in gwas_linear_regression #390

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tomwhite commented Feb 18, 2021

See https://github.com/pystatgen/sgkit/issues/448#issuecomment-780655217 for the best chunk size found so far

hammer mentioned this issue

Statistical genetics section sgkit-dev/sgkit-publication#78

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