parallelize reading from a PGEN file

[aryarm]

we should be able to parallelize by dividing the file into chunks and reading each chunk in a separate thread or process

multi-threading will be harder to implement than multi-processing b/c of the python GIL and thus (might?) require a compiled extension to python but multi-processing will be slower and probably require copying of each chunk into the larger array

@d-laub and I have had some very productive chats about this and are working on a strategy 💪

---

progress: #273

still to do:

• figure out why tests are failing
• check that max memory usage of the new code doesn't exceed that of the old code across a range of chunk sizes and num CPUs (b/c the memory that we use will be equivalent to the sum of the memory used in each chunk/process and we could theoretically have too many chunks running at once). We might need to adjust the chunk_size down, in that case
  • to execute py-spy, for example:

    py-spy record --subprocesses -o py-spy-flamegraph.svg -- python -c 'from haptools.data import GenotypesPLINK; GenotypesPLINK("temp/data/variant/77.pgen", num_cpus=4, chunk_size=1).read()'
    

  • and to execute memray:

    peak_mem() { { memray run -o test -c "$@" &>/dev/null && memray stats -fo /dev/stdout --json test 2>/dev/null; rm test; } | grep 'peak_memory' | sed 's/^.* //;s/,//'; }
    peak_mem 'from haptools.data import GenotypesPLINK; GenotypesPLINK("temp/data/variant/77.pgen", num_cpus=4, chunk_size=1).read()'
    

  • consider whether to set chunk_size automatically based on the available memory.
• use shared read-only memory instead of passing globals?
• fix failing nogil tests in plink-ng
• try multithreading instead of multiprocessing and benchmark with nogil from perf(pgenlib): release GIL for multithreaded PGEN reading chrchang/plink-ng#315