Description
as requested, I am opening an issue.
somalier calculates relatedness between pairs of samples using bitwise operations and popcounts here
where genotypes is effectively:
type genotypes* = tuple[hom_ref:seq[uint64], het:seq[uint64], hom_alt:seq[uint64]]
and currently, those seqs have a len of about 300.
so for 10K samples, doing relatedness for all-vs-all, it will do ~50 million calls to the IBS function linked above.
the "simple" avx512 version is here which is identical in speed to the version currently in somalier
the unrolled version is here. this gives ~10-15% speedup.
this problem is embarrassingly parallel and it's currently single-threaded, so I could also improve speed that way, but I was interested to explore the simd stuff.
I'd be interested to hear your thoughts, maybe the "parallelization" scheme should be changed to load 8 samples at once instead of current 8 (*64) sites at once.