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large dataset failed #524

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wangjiawen2013 opened this issue Jan 11, 2024 · 1 comment
Open

large dataset failed #524

wangjiawen2013 opened this issue Jan 11, 2024 · 1 comment
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@wangjiawen2013
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wangjiawen2013 commented Jan 11, 2024 •
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Hi,
I failed to run grnboost2 on a large dataset with shape 50000 cells X 28000 genes. Then I subsample the dataset to a small one and run grnboost2 sucessfully. It seems that it was caused by something related to dask:

image

Here is an issue on dask and hope it can help to improve pyscenic:
dask/distributed#8257

https://lightrun.com/answers/dask-distributed-array--2gb-hitting-msgpack-limit-

dask/distributed#527
@wangjiawen2013 wangjiawen2013 added the bug Something isn't working label Jan 11, 2024
@wangjiawen2013 wangjiawen2013 mentioned this issue Feb 23, 2024
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@wangjiawen2013
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Any improvement now ?

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