From 45099ad05eac0fbc864df377fd7cbaacdaff9588 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Mon, 24 Jun 2024 13:07:37 +0200
Subject: [PATCH] Refactor `dna.rs` code in `lightmotif-bench`
---
lightmotif-bench/dna.rs | 376 ++++++++++++++++++++++------------------
1 file changed, 205 insertions(+), 171 deletions(-)
diff --git a/lightmotif-bench/dna.rs b/lightmotif-bench/dna.rs
index 906f5b2..79c77ed 100644
--- a/lightmotif-bench/dna.rs
+++ b/lightmotif-bench/dna.rs
@@ -1,6 +1,5 @@
#![feature(test)]
-#[cfg(feature = "bio")]
extern crate bio;
extern crate lightmotif;
extern crate test;
@@ -22,186 +21,221 @@ use lightmotif::seq::EncodedSequence;
const SEQUENCE: &str = include_str!("../lightmotif/benches/ecoli.txt");
const N: usize = SEQUENCE.len() / 10;
-#[bench]
-fn bench_scanner_max_by(bencher: &mut test::Bencher) {
- let seq = &SEQUENCE[..N];
- let encoded = EncodedSequence::<Dna>::encode(seq).unwrap();
- let mut striped = Pipeline::generic().stripe(encoded);
-
- let bg = Background::<Dna>::uniform();
- let cm = CountMatrix::<Dna>::from_sequences([
- EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(),
- EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(),
- ])
- .unwrap();
- let pbm = cm.to_freq(0.1);
- let pssm = pbm.to_scoring(bg);
-
- striped.configure(&pssm);
- let mut best = 0;
- bencher.iter(|| {
- best = Scanner::new(&pssm, &striped)
- .max_by(|x, y| x.score.partial_cmp(&y.score).unwrap())
- .unwrap()
- .position;
- });
- bencher.bytes = seq.len() as u64;
-
- println!("best: {:?}", best);
+mod scanner {
+ use super::*;
+
+ /// Bench how long `Scanner::max_by` takes to find the highest hit using
+ /// the score as a comparison key.
+ #[bench]
+ fn max_by(bencher: &mut test::Bencher) {
+ let seq = &SEQUENCE[..N];
+ let encoded = EncodedSequence::<Dna>::encode(seq).unwrap();
+ let mut striped = Pipeline::generic().stripe(encoded);
+
+ let bg = Background::<Dna>::uniform();
+ let cm = CountMatrix::<Dna>::from_sequences([
+ EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(),
+ EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(),
+ ])
+ .unwrap();
+ let pbm = cm.to_freq(0.1);
+ let pssm = pbm.to_scoring(bg);
+
+ striped.configure(&pssm);
+ bencher.iter(|| {
+ Scanner::new(&pssm, &striped).max_by(|x, y| x.score.partial_cmp(&y.score).unwrap());
+ });
+ bencher.bytes = seq.len() as u64;
+ }
+
+ /// Bench how long `Scanner::max` takes to find the highest hit using
+ /// the custom implementation of `Iterator::max` sorting hits by score
+ /// and position keys.
+ #[bench]
+ fn max(bencher: &mut test::Bencher) {
+ let seq = &SEQUENCE[..N];
+ let encoded = EncodedSequence::<Dna>::encode(seq).unwrap();
+ let mut striped = Pipeline::generic().stripe(encoded);
+
+ let bg = Background::<Dna>::uniform();
+ let cm = CountMatrix::<Dna>::from_sequences([
+ EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(),
+ EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(),
+ ])
+ .unwrap();
+ let pbm = cm.to_freq(0.1);
+ let pssm = pbm.to_scoring(bg);
+
+ striped.configure(&pssm);
+ bencher.iter(|| Scanner::new(&pssm, &striped).max().unwrap());
+ bencher.bytes = seq.len() as u64;
+ }
}
-#[bench]
-fn bench_scanner_best(bencher: &mut test::Bencher) {
- let seq = &SEQUENCE[..N];
- let encoded = EncodedSequence::<Dna>::encode(seq).unwrap();
- let mut striped = Pipeline::generic().stripe(encoded);
-
- let bg = Background::<Dna>::uniform();
- let cm = CountMatrix::<Dna>::from_sequences([
- EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(),
- EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(),
- ])
- .unwrap();
- let pbm = cm.to_freq(0.1);
- let pssm = pbm.to_scoring(bg);
-
- striped.configure(&pssm);
- let mut best = 0;
- bencher.iter(|| best = Scanner::new(&pssm, &striped).max().unwrap().position);
- bencher.bytes = seq.len() as u64;
-
- println!("best: {:?}", best);
+mod f32 {
+ use super::*;
+
+ /// Bench how long `Pipeline::score` and `Pipeline::argmax` take for
+ /// an arbitrary pipeline.
+ fn bench_lightmotif<C: StrictlyPositive, P: Score<f32, Dna, C> + Maximum<f32, C>>(
+ bencher: &mut test::Bencher,
+ pli: &P,
+ ) {
+ let seq = &SEQUENCE[..N];
+ let encoded = EncodedSequence::<Dna>::encode(seq).unwrap();
+ let mut striped = Pipeline::generic().stripe(encoded);
+
+ let bg = Background::<Dna>::uniform();
+ let cm = CountMatrix::<Dna>::from_sequences([
+ EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(),
+ EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(),
+ ])
+ .unwrap();
+ let pbm = cm.to_freq(0.1);
+ let pssm = pbm.to_scoring(bg);
+
+ striped.configure(&pssm);
+ let mut scores = StripedScores::empty();
+ scores.resize(striped.matrix().rows(), striped.len());
+ bencher.bytes = seq.len() as u64;
+ bencher.iter(|| {
+ test::black_box(pli.score_into(&pssm, &striped, &mut scores));
+ scores.offset(test::black_box(pli.argmax(&scores).unwrap()));
+ });
+ }
+
+ /// Bench how long `Pipeline::<_, Generic>` takes.
+ #[bench]
+ fn generic(bencher: &mut test::Bencher) {
+ let pli = Pipeline::generic();
+ bench_lightmotif::<U1, _>(bencher, &pli);
+ }
+
+ /// Bench how long `Pipeline::<_, Sse2>` takes.
+ #[cfg(target_feature = "sse2")]
+ #[bench]
+ fn sse2(bencher: &mut test::Bencher) {
+ let pli = Pipeline::sse2().unwrap();
+ bench_lightmotif::<U16, _>(bencher, &pli);
+ }
+
+ /// Bench how long `Pipeline::<_, Dispatch>` takes.
+ #[bench]
+ fn dispatch(bencher: &mut test::Bencher) {
+ let pli = Pipeline::dispatch();
+ bench_lightmotif(bencher, &pli);
+ }
+
+ /// Bench how long `Pipeline::<_, Avx2>` takes.
+ #[cfg(target_feature = "avx2")]
+ #[bench]
+ fn avx2(bencher: &mut test::Bencher) {
+ let pli = Pipeline::avx2().unwrap();
+ bench_lightmotif(bencher, &pli);
+ }
+
+ /// Bench how long `Pipeline::<_, Neon>` takes.
+ #[cfg(target_feature = "neon")]
+ #[bench]
+ fn neon(bencher: &mut test::Bencher) {
+ let pli = Pipeline::neon().unwrap();
+ bench_lightmotif(bencher, &pli);
+ }
}
-fn bench_lightmotif<C: StrictlyPositive, P: Score<f32, Dna, C> + Maximum<f32, C>>(
- bencher: &mut test::Bencher,
- pli: &P,
-) {
- let seq = &SEQUENCE[..N];
- let encoded = EncodedSequence::<Dna>::encode(seq).unwrap();
- let mut striped = Pipeline::generic().stripe(encoded);
-
- let bg = Background::<Dna>::uniform();
- let cm = CountMatrix::<Dna>::from_sequences([
- EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(),
- EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(),
- ])
- .unwrap();
- let pbm = cm.to_freq(0.1);
- let pssm = pbm.to_scoring(bg);
-
- striped.configure(&pssm);
- let mut scores = StripedScores::empty();
- scores.resize(striped.matrix().rows(), striped.len());
- bencher.bytes = seq.len() as u64;
- let mut best = 0;
- bencher.iter(|| {
- test::black_box(pli.score_into(&pssm, &striped, &mut scores));
- best = scores.offset(test::black_box(pli.argmax(&scores).unwrap()));
- });
-
- println!("best: {:?}", best);
+mod u8 {
+ use super::*;
+
+ /// Bench how long `Pipeline::score` and `Pipeline::argmax` take for
+ /// an arbitrary pipeline using discrete scores.
+ fn bench_lightmotif_discrete<C: StrictlyPositive, P: Score<u8, Dna, C> + Maximum<u8, C>>(
+ bencher: &mut test::Bencher,
+ pli: &P,
+ ) {
+ let seq = &SEQUENCE[..N];
+ let encoded = EncodedSequence::<Dna>::encode(seq).unwrap();
+ let mut striped = Pipeline::generic().stripe(encoded);
+
+ let bg = Background::<Dna>::uniform();
+ let cm = CountMatrix::<Dna>::from_sequences([
+ EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(),
+ EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(),
+ ])
+ .unwrap();
+ let pbm = cm.to_freq(0.1);
+ let pssm = pbm.to_scoring(bg);
+ let dm = pssm.to_discrete();
+
+ striped.configure(&pssm);
+ let mut scores = StripedScores::empty();
+ scores.resize(striped.matrix().rows(), striped.len());
+ bencher.bytes = seq.len() as u64;
+ bencher.iter(|| {
+ test::black_box(pli.score_into(&dm, &striped, &mut scores));
+ scores.offset(test::black_box(pli.argmax(&scores).unwrap()));
+ });
+ }
+
+ /// Bench how long `Pipeline::<_, Generic>` takes using `u8` scores.
+ #[bench]
+ fn generic(bencher: &mut test::Bencher) {
+ let pli = Pipeline::generic();
+ bench_lightmotif_discrete::<U1, _>(bencher, &pli);
+ }
+
+ /// Bench how long `Pipeline::<_, Sse2>` takes using `u8` scores.
+ #[cfg(target_feature = "sse2")]
+ #[bench]
+ fn sse2(bencher: &mut test::Bencher) {
+ let pli = Pipeline::sse2().unwrap();
+ bench_lightmotif_discrete::<U16, _>(bencher, &pli);
+ }
+
+ /// Bench how long `Pipeline::<_, Generic>` takes using `u8` scores.
+ #[bench]
+ fn dispatch(bencher: &mut test::Bencher) {
+ let pli = Pipeline::dispatch();
+ bench_lightmotif_discrete(bencher, &pli);
+ }
+
+ /// Bench how long `Pipeline::<_, Generic>` takes using `u8` scores.
+ #[cfg(target_feature = "avx2")]
+ #[bench]
+ fn avx2(bencher: &mut test::Bencher) {
+ let pli = Pipeline::avx2().unwrap();
+ bench_lightmotif_discrete(bencher, &pli);
+ }
+
+ /// Bench how long `Pipeline::<_, Neon>` takes using `u8` scores.
+ #[cfg(target_feature = "neon")]
+ #[bench]
+ fn neon(bencher: &mut test::Bencher) {
+ let pli = Pipeline::neon().unwrap();
+ bench_lightmotif_discrete(bencher, &pli);
+ }
}
-fn bench_lightmotif_discrete<C: StrictlyPositive, P: Score<u8, Dna, C> + Maximum<u8, C>>(
- bencher: &mut test::Bencher,
- pli: &P,
-) {
- let seq = &SEQUENCE[..N];
- let encoded = EncodedSequence::<Dna>::encode(seq).unwrap();
- let mut striped = Pipeline::generic().stripe(encoded);
-
- let bg = Background::<Dna>::uniform();
- let cm = CountMatrix::<Dna>::from_sequences([
- EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(),
- EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(),
- ])
- .unwrap();
- let pbm = cm.to_freq(0.1);
- let pssm = pbm.to_scoring(bg);
- let dm = pssm.to_discrete();
-
- striped.configure(&pssm);
- let mut scores = StripedScores::empty();
- let mut best = 0;
- scores.resize(striped.matrix().rows(), striped.len());
- bencher.bytes = seq.len() as u64;
- bencher.iter(|| {
- test::black_box(pli.score_into(&dm, &striped, &mut scores));
- best = scores.offset(test::black_box(pli.argmax(&scores).unwrap()));
- });
-
- println!("best: {:?}", best);
-}
-
-#[bench]
-fn bench_generic(bencher: &mut test::Bencher) {
- let pli = Pipeline::generic();
- bench_lightmotif::<U1, _>(bencher, &pli);
-}
-
-#[cfg(target_feature = "sse2")]
-#[bench]
-fn bench_sse2(bencher: &mut test::Bencher) {
- let pli = Pipeline::sse2().unwrap();
- bench_lightmotif::<U16, _>(bencher, &pli);
-}
-
-#[bench]
-fn bench_dispatch(bencher: &mut test::Bencher) {
- let pli = Pipeline::dispatch();
- bench_lightmotif(bencher, &pli);
-}
-
-#[cfg(target_feature = "avx2")]
-#[bench]
-fn bench_avx2(bencher: &mut test::Bencher) {
- let pli = Pipeline::avx2().unwrap();
- bench_lightmotif(bencher, &pli);
-}
-
-#[bench]
-fn bench_discrete_generic(bencher: &mut test::Bencher) {
- let pli = Pipeline::generic();
- bench_lightmotif_discrete::<U1, _>(bencher, &pli);
-}
-
-#[cfg(target_feature = "sse2")]
-#[bench]
-fn bench_discrete_sse2(bencher: &mut test::Bencher) {
- let pli = Pipeline::sse2().unwrap();
- bench_lightmotif_discrete::<U16, _>(bencher, &pli);
-}
-
-#[bench]
-fn bench_discrete_dispatch(bencher: &mut test::Bencher) {
- let pli = Pipeline::dispatch();
- bench_lightmotif_discrete(bencher, &pli);
-}
+mod external {
-#[cfg(target_feature = "avx2")]
-#[bench]
-fn bench_discrete_avx2(bencher: &mut test::Bencher) {
- let pli = Pipeline::avx2().unwrap();
- bench_lightmotif_discrete(bencher, &pli);
-}
+ use super::*;
-#[bench]
-fn bench_bio(bencher: &mut test::Bencher) {
- use bio::pattern_matching::pssm::DNAMotif;
- use bio::pattern_matching::pssm::Motif;
+ #[bench]
+ fn bio(bencher: &mut test::Bencher) {
+ use bio::pattern_matching::pssm::DNAMotif;
+ use bio::pattern_matching::pssm::Motif;
- let seq = &SEQUENCE[..N];
+ let seq = &SEQUENCE[..N];
- let pssm = DNAMotif::from_seqs(
- vec![b"GTTGACCTTATCAAC".to_vec(), b"GTTGATCCAGTCAAC".to_vec()].as_ref(),
- None,
- )
- .unwrap();
+ let pssm = DNAMotif::from_seqs(
+ vec![b"GTTGACCTTATCAAC".to_vec(), b"GTTGATCCAGTCAAC".to_vec()].as_ref(),
+ None,
+ )
+ .unwrap();
- bencher.bytes = seq.len() as u64;
- let mut best = 0;
- bencher.iter(|| best = test::black_box(pssm.score(seq.as_bytes()).unwrap()).loc);
+ bencher.bytes = seq.len() as u64;
+ let mut best = 0;
+ bencher.iter(|| best = test::black_box(pssm.score(seq.as_bytes()).unwrap()).loc);
- println!("best: {:?}", best);
+ println!("best: {:?}", best);
+ }
}
--
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