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feat: switch to signed int striped simd, small qol updates #55

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sstadick merged 1 commit into from
Jul 21, 2025
Merged

feat: switch to signed int striped simd, small qol updates #55

sstadick merged 1 commit into from
Jul 21, 2025

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@sstadick sstadick commented Jul 18, 2025 •
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Major updates:

  • Convert semi-global from using unsigned ints to signed ints

Small QOL changes for doing some debugging.

  • Allows specifying simd width at compile time.
  • Updates the bench aligner.

striped-simd outputs checked against parasail for correctness:

./apps/parasail_aligner -a sg_striped_avx2_256_16 -x -o 3 -e 1 -m blosum62 -t 1 -q ./data/P01111.fasta -f /srv/tmp/uniprot_sprot.fasta -v -g parasail.csv
/ish-aligner --scoring-matrix Blosum62 --query-fasta ~/dev/parasail/data/P01111.fasta --target-fasta /srv/tmp/uniprot_sprot.fasta --output-file /tmp/match.txt  --score-size word --algo striped-semi-global
vimdiff <(tail +2 /tmp/match.txt ) ../parasail/parasail.csv

@sstadick sstadick force-pushed the fix/compare_v_parasail_dna branch 4 times, most recently from 5d2a0a8 to 275a67b Compare July 21, 2025 17:08
sstadick
sstadick commented Jul 21, 2025
View reviewed changes
benchmarking/ish_bench_aligner.mojo
var rev = List[UInt8](capacity=len(seq_bytes))
for s in reversed(seq_bytes):
rev.append(s[])
rev.append(s)
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@sstadick sstadick Jul 21, 2025

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All updates for latest mojo version, skippable review wise.

ishlib/gpu/searcher_device.mojo
) raises -> List[Self]:
var ret = List[Self]()
for i in range(0, min(DeviceContext.number_of_devices(), max_devices)):
for i in range(
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@sstadick sstadick Jul 21, 2025

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Hardcoded to max of 1 for now. Warning will happen in SearcherSettings if you set it above 1. This is because there isn't a good way to filter out non-compatible GPUs.

ishlib/matcher/alignment/semi_global_aln/striped.mojo

# Early termination check - match C version exactly
if not (v_f > v_h).reduce_or():
return
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@sstadick sstadick Jul 21, 2025

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An inline closure allows for something more like a goto than the kind of complex set of breaks we had before.

@sstadick sstadick force-pushed the fix/compare_v_parasail_dna branch from 275a67b to b130f19 Compare July 21, 2025 17:17
@sstadick
feat: working signed semi-global
5090c3e 
Signed-off-by: Seth Stadick <sstadick@gmail.com>
@sstadick sstadick force-pushed the fix/compare_v_parasail_dna branch from b130f19 to 5090c3e Compare July 21, 2025 17:44
@sstadick sstadick merged commit 92f4fad into main Jul 21, 2025
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@sstadick sstadick deleted the fix/compare_v_parasail_dna branch July 21, 2025 18:51
@sstadick sstadick changed the title chore: small qol fixes for comparing feat: switch to signed int striped simd, small qol updates Jul 21, 2025
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