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Minimize memory usage during posterior generation #248

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sjfleming opened this issue Aug 17, 2023 · 1 comment
Open

Minimize memory usage during posterior generation #248

sjfleming opened this issue Aug 17, 2023 · 1 comment
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enhancement New feature or improvement

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@sjfleming
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There are examples where the CPU memory used to store the full posterior is quite large. For example, a deeply sequenced, multiplexed multi-donor sample (overloaded) and run with PIP-seq, which generates like 600+ ambient RNA counts per drop.

This posterior is very big, since there are lots of nonzero entries in the count matrix, and a lot of them are not small.

The question is, can we just incrementally write the posterior to disk? Something like this:
https://pandas.pydata.org/pandas-docs/stable/user_guide/io.html#table-format

@sjfleming
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Actually we really should not have to write it to disk. The (albeit compressed) posterior h5 is under 2GB.

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