From 4183147db3fd62bf4273ded6ac6f70e2ab358c41 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Thu, 20 Jun 2024 23:01:16 +0200
Subject: [PATCH] Reorganise code for benchmarks
---
lightmotif-bench/dna.rs | 80 ++++++++++++-
lightmotif/benches/score.rs | 184 ++++++++++++++++++++---------
lightmotif/benches/threshold.rs | 198 +++++++++++++++++++++++---------
3 files changed, 344 insertions(+), 118 deletions(-)
diff --git a/lightmotif-bench/dna.rs b/lightmotif-bench/dna.rs
index 7a1612d..e2c96ae 100644
--- a/lightmotif-bench/dna.rs
+++ b/lightmotif-bench/dna.rs
@@ -38,12 +38,16 @@ fn bench_scanner_max_by(bencher: &mut test::Bencher) {
let pssm = pbm.to_scoring(bg);
striped.configure(&pssm);
+ let mut best = 0;
bencher.iter(|| {
- Scanner::new(&pssm, &striped)
+ best = Scanner::new(&pssm, &striped)
.max_by(|x, y| x.score.partial_cmp(&y.score).unwrap())
- .unwrap();
+ .unwrap()
+ .position;
});
bencher.bytes = seq.len() as u64;
+
+ println!("best: {:?}", best);
}
#[bench]
@@ -62,8 +66,11 @@ fn bench_scanner_best(bencher: &mut test::Bencher) {
let pssm = pbm.to_scoring(bg);
striped.configure(&pssm);
- bencher.iter(|| Scanner::new(&pssm, &striped).best().unwrap());
+ let mut best = 0;
+ bencher.iter(|| best = Scanner::new(&pssm, &striped).best().unwrap().position);
bencher.bytes = seq.len() as u64;
+
+ println!("best: {:?}", best);
}
fn bench_lightmotif<C: StrictlyPositive, P: Score<f32, Dna, C> + Maximum<f32, C>>(
@@ -87,10 +94,44 @@ fn bench_lightmotif<C: StrictlyPositive, P: Score<f32, Dna, C> + Maximum<f32, C>
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));
- test::black_box(pli.argmax(&scores));
+ best = scores.offset(test::black_box(pli.argmax(&scores).unwrap()));
});
+
+ println!("best: {:?}", best);
+}
+
+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]
@@ -119,6 +160,32 @@ fn bench_avx2(bencher: &mut test::Bencher) {
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);
+}
+
+#[cfg(target_feature = "avx2")]
+#[bench]
+fn bench_discrete_avx2(bencher: &mut test::Bencher) {
+ let pli = Pipeline::avx2().unwrap();
+ bench_lightmotif_discrete(bencher, &pli);
+}
+
#[bench]
fn bench_bio(bencher: &mut test::Bencher) {
use bio::pattern_matching::pssm::DNAMotif;
@@ -133,5 +200,8 @@ fn bench_bio(bencher: &mut test::Bencher) {
.unwrap();
bencher.bytes = seq.len() as u64;
- bencher.iter(|| test::black_box(pssm.score(seq.as_bytes()).unwrap()));
+ let mut best = 0;
+ bencher.iter(|| best = test::black_box(pssm.score(seq.as_bytes()).unwrap()).loc);
+
+ println!("best: {:?}", best);
}
diff --git a/lightmotif/benches/score.rs b/lightmotif/benches/score.rs
index 54c16ea..44ee5df 100644
--- a/lightmotif/benches/score.rs
+++ b/lightmotif/benches/score.rs
@@ -20,65 +20,135 @@ mod dna {
const SEQUENCE: &str = include_str!("ecoli.txt");
- fn bench<C: StrictlyPositive, P: Score<f32, Dna, C>>(bencher: &mut test::Bencher, pli: &P) {
- let encoded = EncodedSequence::<Dna>::encode(SEQUENCE).unwrap();
- let mut striped = Pipeline::generic().stripe(encoded);
-
- 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(None);
-
- striped.configure(&pssm);
- let mut scores = StripedScores::empty();
- scores.resize(striped.matrix().rows(), striped.len());
- bencher.bytes = SEQUENCE.len() as u64;
- bencher.iter(|| {
- test::black_box(pli.score_into(&pssm, &striped, &mut scores));
- });
- }
-
- #[bench]
- fn bench_generic(bencher: &mut test::Bencher) {
- let pli = Pipeline::generic();
- bench::<U32, _>(bencher, &pli);
- }
-
- #[bench]
- fn bench_dispatch(bencher: &mut test::Bencher) {
- let pli = Pipeline::dispatch();
- bench(bencher, &pli);
+ mod f32 {
+ use super::*;
+
+ fn bench<C: StrictlyPositive, P: Score<f32, Dna, C>>(bencher: &mut test::Bencher, pli: &P) {
+ let encoded = EncodedSequence::<Dna>::encode(SEQUENCE).unwrap();
+ let mut striped = Pipeline::generic().stripe(encoded);
+
+ 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(None);
+
+ striped.configure(&pssm);
+ let mut scores = StripedScores::empty();
+ scores.resize(striped.matrix().rows(), striped.len());
+ bencher.bytes = SEQUENCE.len() as u64;
+ bencher.iter(|| {
+ test::black_box(pli.score_into(&pssm, &striped, &mut scores));
+ });
+ }
+
+ #[bench]
+ fn bench_generic(bencher: &mut test::Bencher) {
+ let pli = Pipeline::generic();
+ bench::<U32, _>(bencher, &pli);
+ }
+
+ #[bench]
+ fn bench_dispatch(bencher: &mut test::Bencher) {
+ let pli = Pipeline::dispatch();
+ bench(bencher, &pli);
+ }
+
+ #[cfg(target_feature = "sse2")]
+ #[bench]
+ fn bench_sse2(bencher: &mut test::Bencher) {
+ let pli = Pipeline::sse2().unwrap();
+ bench::<U16, _>(bencher, &pli);
+ }
+
+ #[cfg(target_feature = "sse2")]
+ #[bench]
+ fn bench_sse2_32(bencher: &mut test::Bencher) {
+ let pli = Pipeline::sse2().unwrap();
+ bench::<U32, _>(bencher, &pli);
+ }
+
+ #[cfg(target_feature = "avx2")]
+ #[bench]
+ fn bench_avx2(bencher: &mut test::Bencher) {
+ let pli = Pipeline::avx2().unwrap();
+ bench(bencher, &pli);
+ }
+
+ #[cfg(target_feature = "neon")]
+ #[bench]
+ fn bench_neon(bencher: &mut test::Bencher) {
+ let pli = Pipeline::neon().unwrap();
+ bench::<U16, _>(bencher, &pli);
+ }
}
- #[cfg(target_feature = "sse2")]
- #[bench]
- fn bench_sse2(bencher: &mut test::Bencher) {
- let pli = Pipeline::sse2().unwrap();
- bench::<U16, _>(bencher, &pli);
- }
-
- #[cfg(target_feature = "sse2")]
- #[bench]
- fn bench_sse2_32(bencher: &mut test::Bencher) {
- let pli = Pipeline::sse2().unwrap();
- bench::<U32, _>(bencher, &pli);
- }
-
- #[cfg(target_feature = "avx2")]
- #[bench]
- fn bench_avx2(bencher: &mut test::Bencher) {
- let pli = Pipeline::avx2().unwrap();
- bench(bencher, &pli);
- }
-
- #[cfg(target_feature = "neon")]
- #[bench]
- fn bench_neon(bencher: &mut test::Bencher) {
- let pli = Pipeline::neon().unwrap();
- bench::<U16, _>(bencher, &pli);
+ mod u8 {
+ use super::*;
+
+ fn bench<C: StrictlyPositive, P: Score<u8, Dna, C>>(bencher: &mut test::Bencher, pli: &P) {
+ let encoded = EncodedSequence::<Dna>::encode(SEQUENCE).unwrap();
+ let mut striped = Pipeline::generic().stripe(encoded);
+
+ 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(None);
+ let dm = pssm.to_discrete();
+
+ striped.configure(&pssm);
+ let mut scores = StripedScores::empty();
+ scores.resize(striped.matrix().rows(), striped.len());
+ bencher.bytes = SEQUENCE.len() as u64;
+ bencher.iter(|| {
+ test::black_box(pli.score_into(&dm, &striped, &mut scores));
+ });
+ }
+
+ #[bench]
+ fn bench_generic(bencher: &mut test::Bencher) {
+ let pli = Pipeline::generic();
+ bench::<U32, _>(bencher, &pli);
+ }
+
+ #[bench]
+ fn bench_dispatch(bencher: &mut test::Bencher) {
+ let pli = Pipeline::dispatch();
+ bench(bencher, &pli);
+ }
+
+ #[cfg(target_feature = "sse2")]
+ #[bench]
+ fn bench_sse2(bencher: &mut test::Bencher) {
+ let pli = Pipeline::sse2().unwrap();
+ bench::<U16, _>(bencher, &pli);
+ }
+
+ #[cfg(target_feature = "sse2")]
+ #[bench]
+ fn bench_sse2_32(bencher: &mut test::Bencher) {
+ let pli = Pipeline::sse2().unwrap();
+ bench::<U32, _>(bencher, &pli);
+ }
+
+ #[cfg(target_feature = "avx2")]
+ #[bench]
+ fn bench_avx2(bencher: &mut test::Bencher) {
+ let pli = Pipeline::avx2().unwrap();
+ bench(bencher, &pli);
+ }
+
+ #[cfg(target_feature = "neon")]
+ #[bench]
+ fn bench_neon(bencher: &mut test::Bencher) {
+ let pli = Pipeline::neon().unwrap();
+ bench::<U16, _>(bencher, &pli);
+ }
}
}
diff --git a/lightmotif/benches/threshold.rs b/lightmotif/benches/threshold.rs
index f377422..1e530e2 100644
--- a/lightmotif/benches/threshold.rs
+++ b/lightmotif/benches/threshold.rs
@@ -17,67 +17,153 @@ use lightmotif::seq::EncodedSequence;
const SEQUENCE: &str = include_str!("ecoli.txt");
-fn bench<C: StrictlyPositive, P: Score<f32, Dna, C> + Threshold<f32, C>>(
- bencher: &mut test::Bencher,
- pli: &P,
-) {
- let encoded = EncodedSequence::<Dna>::encode(SEQUENCE).unwrap();
- let mut striped = Pipeline::generic().stripe(encoded);
-
- 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(None);
-
- striped.configure(&pssm);
- let mut scores = StripedScores::empty();
- pli.score_into(&pssm, &striped, &mut scores);
-
- bencher.bytes = (std::mem::size_of::<f32>() * scores.matrix().rows() * C::USIZE) as u64;
- bencher.iter(|| {
- test::black_box(pli.threshold(&scores, 10.0));
- });
-}
+mod f32 {
-#[bench]
-fn bench_generic(bencher: &mut test::Bencher) {
- let pli = Pipeline::generic();
- bench::<U32, _>(bencher, &pli);
-}
+ use super::*;
-#[bench]
-fn bench_dispatch(bencher: &mut test::Bencher) {
- let pli = Pipeline::dispatch();
- bench(bencher, &pli);
-}
+ fn bench<C: StrictlyPositive, P: Score<f32, Dna, C> + Threshold<f32, C>>(
+ bencher: &mut test::Bencher,
+ pli: &P,
+ ) {
+ let encoded = EncodedSequence::<Dna>::encode(SEQUENCE).unwrap();
+ let mut striped = Pipeline::generic().stripe(encoded);
-#[cfg(target_feature = "sse2")]
-#[bench]
-fn bench_sse2(bencher: &mut test::Bencher) {
- let pli = Pipeline::sse2().unwrap();
- bench::<U16, _>(bencher, &pli);
-}
+ 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(None);
-#[cfg(target_feature = "sse2")]
-#[bench]
-fn bench_sse2_32(bencher: &mut test::Bencher) {
- let pli = Pipeline::sse2().unwrap();
- bench::<U32, _>(bencher, &pli);
-}
+ striped.configure(&pssm);
+ let mut scores = StripedScores::empty();
+ pli.score_into(&pssm, &striped, &mut scores);
+
+ bencher.bytes = (std::mem::size_of::<f32>() * scores.matrix().rows() * C::USIZE) as u64;
+ bencher.iter(|| {
+ test::black_box(pli.threshold(&scores, 10.0));
+ });
+ }
-#[cfg(target_feature = "avx2")]
-#[bench]
-fn bench_avx2(bencher: &mut test::Bencher) {
- let pli = Pipeline::avx2().unwrap();
- bench(bencher, &pli);
+ #[bench]
+ fn bench_generic(bencher: &mut test::Bencher) {
+ let pli = Pipeline::generic();
+ bench::<U32, _>(bencher, &pli);
+ }
+
+ #[bench]
+ fn bench_dispatch(bencher: &mut test::Bencher) {
+ let pli = Pipeline::dispatch();
+ bench(bencher, &pli);
+ }
+
+ #[cfg(target_feature = "sse2")]
+ #[bench]
+ fn bench_sse2(bencher: &mut test::Bencher) {
+ let pli = Pipeline::sse2().unwrap();
+ bench::<U16, _>(bencher, &pli);
+ }
+
+ #[cfg(target_feature = "sse2")]
+ #[bench]
+ fn bench_sse2_32(bencher: &mut test::Bencher) {
+ let pli = Pipeline::sse2().unwrap();
+ bench::<U32, _>(bencher, &pli);
+ }
+
+ #[cfg(target_feature = "avx2")]
+ #[bench]
+ fn bench_avx2(bencher: &mut test::Bencher) {
+ let pli = Pipeline::avx2().unwrap();
+ bench(bencher, &pli);
+ }
+
+ #[cfg(target_feature = "neon")]
+ #[bench]
+ fn bench_neon(bencher: &mut test::Bencher) {
+ let pli = Pipeline::neon().unwrap();
+ bench::<U16, _>(bencher, &pli);
+ }
}
-#[cfg(target_feature = "neon")]
-#[bench]
-fn bench_neon(bencher: &mut test::Bencher) {
- let pli = Pipeline::neon().unwrap();
- bench::<U16, _>(bencher, &pli);
+mod u8 {
+
+ use super::*;
+
+ fn bench<C: StrictlyPositive, P: Score<u8, Dna, C> + Threshold<u8, C>>(
+ bencher: &mut test::Bencher,
+ pli: &P,
+ ) {
+ let encoded = EncodedSequence::<Dna>::encode(SEQUENCE).unwrap();
+ let mut striped = Pipeline::generic().stripe(encoded);
+
+ 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(None);
+ let dm = pssm.to_discrete();
+ let threshold = dm.scale(10.0);
+
+ striped.configure(&pssm);
+ let mut scores = StripedScores::empty();
+ pli.score_into(&dm, &striped, &mut scores);
+
+ let mut hits = Vec::new();
+ bencher.bytes = (std::mem::size_of::<f32>() * scores.matrix().rows() * C::USIZE) as u64;
+ bencher.iter(|| {
+ hits.clear();
+ for mc in pli.threshold(&scores, threshold) {
+ let i = scores.offset(mc);
+ if pssm.score_position(&striped, i) >= 10.0 {
+ hits.push(i);
+ }
+ }
+ });
+
+ println!("{:?}", hits.len());
+ }
+
+ #[bench]
+ fn bench_generic(bencher: &mut test::Bencher) {
+ let pli = Pipeline::generic();
+ bench::<U32, _>(bencher, &pli);
+ }
+
+ #[bench]
+ fn bench_dispatch(bencher: &mut test::Bencher) {
+ let pli = Pipeline::dispatch();
+ bench(bencher, &pli);
+ }
+
+ #[cfg(target_feature = "sse2")]
+ #[bench]
+ fn bench_sse2(bencher: &mut test::Bencher) {
+ let pli = Pipeline::sse2().unwrap();
+ bench::<U16, _>(bencher, &pli);
+ }
+
+ #[cfg(target_feature = "sse2")]
+ #[bench]
+ fn bench_sse2_32(bencher: &mut test::Bencher) {
+ let pli = Pipeline::sse2().unwrap();
+ bench::<U32, _>(bencher, &pli);
+ }
+
+ #[cfg(target_feature = "avx2")]
+ #[bench]
+ fn bench_avx2(bencher: &mut test::Bencher) {
+ let pli = Pipeline::avx2().unwrap();
+ bench(bencher, &pli);
+ }
+
+ #[cfg(target_feature = "neon")]
+ #[bench]
+ fn bench_neon(bencher: &mut test::Bencher) {
+ let pli = Pipeline::neon().unwrap();
+ bench::<U16, _>(bencher, &pli);
+ }
}
--
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