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Commit 4183147d authored by Martin Larralde's avatar Martin Larralde
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Reorganise code for benchmarks

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lightmotif-bench/dna.rs
+ 75
− 5
View file @ 4183147d
...@@ -38,12 +38,16 @@ fn bench_scanner_max_by(bencher: &mut test::Bencher) { ...@@ -38,12 +38,16 @@ fn bench_scanner_max_by(bencher: &mut test::Bencher) {
let pssm = pbm.to_scoring(bg); let pssm = pbm.to_scoring(bg);
striped.configure(&pssm); striped.configure(&pssm);
let mut best = 0;
bencher.iter(|| { bencher.iter(|| {
Scanner::new(&pssm, &striped) best = Scanner::new(&pssm, &striped)
.max_by(|x, y| x.score.partial_cmp(&y.score).unwrap()) .max_by(|x, y| x.score.partial_cmp(&y.score).unwrap())
.unwrap(); .unwrap()
.position;
}); });
bencher.bytes = seq.len() as u64; bencher.bytes = seq.len() as u64;
println!("best: {:?}", best);
} }
#[bench] #[bench]
...@@ -62,8 +66,11 @@ fn bench_scanner_best(bencher: &mut test::Bencher) { ...@@ -62,8 +66,11 @@ fn bench_scanner_best(bencher: &mut test::Bencher) {
let pssm = pbm.to_scoring(bg); let pssm = pbm.to_scoring(bg);
striped.configure(&pssm); 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; bencher.bytes = seq.len() as u64;
println!("best: {:?}", best);
} }
fn bench_lightmotif<C: StrictlyPositive, P: Score<f32, Dna, C> + Maximum<f32, C>>( 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> ...@@ -87,10 +94,44 @@ fn bench_lightmotif<C: StrictlyPositive, P: Score<f32, Dna, C> + Maximum<f32, C>
let mut scores = StripedScores::empty(); let mut scores = StripedScores::empty();
scores.resize(striped.matrix().rows(), striped.len()); scores.resize(striped.matrix().rows(), striped.len());
bencher.bytes = seq.len() as u64; bencher.bytes = seq.len() as u64;
let mut best = 0;
bencher.iter(|| { bencher.iter(|| {
test::black_box(pli.score_into(&pssm, &striped, &mut scores)); 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] #[bench]
...@@ -119,6 +160,32 @@ fn bench_avx2(bencher: &mut test::Bencher) { ...@@ -119,6 +160,32 @@ fn bench_avx2(bencher: &mut test::Bencher) {
bench_lightmotif(bencher, &pli); 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] #[bench]
fn bench_bio(bencher: &mut test::Bencher) { fn bench_bio(bencher: &mut test::Bencher) {
use bio::pattern_matching::pssm::DNAMotif; use bio::pattern_matching::pssm::DNAMotif;
...@@ -133,5 +200,8 @@ fn bench_bio(bencher: &mut test::Bencher) { ...@@ -133,5 +200,8 @@ fn bench_bio(bencher: &mut test::Bencher) {
.unwrap(); .unwrap();
bencher.bytes = seq.len() as u64; 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);
} }
lightmotif/benches/score.rs
+ 127
− 57
View file @ 4183147d
...@@ -20,65 +20,135 @@ mod dna { ...@@ -20,65 +20,135 @@ mod dna {
const SEQUENCE: &str = include_str!("ecoli.txt"); const SEQUENCE: &str = include_str!("ecoli.txt");
fn bench<C: StrictlyPositive, P: Score<f32, Dna, C>>(bencher: &mut test::Bencher, pli: &P) { mod f32 {
let encoded = EncodedSequence::<Dna>::encode(SEQUENCE).unwrap(); use super::*;
let mut striped = Pipeline::generic().stripe(encoded);
fn bench<C: StrictlyPositive, P: Score<f32, Dna, C>>(bencher: &mut test::Bencher, pli: &P) {
let cm = CountMatrix::<Dna>::from_sequences([ let encoded = EncodedSequence::<Dna>::encode(SEQUENCE).unwrap();
EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(), let mut striped = Pipeline::generic().stripe(encoded);
EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(),
]) let cm = CountMatrix::<Dna>::from_sequences([
.unwrap(); EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(),
let pbm = cm.to_freq(0.1); EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(),
let pssm = pbm.to_scoring(None); ])
.unwrap();
striped.configure(&pssm); let pbm = cm.to_freq(0.1);
let mut scores = StripedScores::empty(); let pssm = pbm.to_scoring(None);
scores.resize(striped.matrix().rows(), striped.len());
bencher.bytes = SEQUENCE.len() as u64; striped.configure(&pssm);
bencher.iter(|| { let mut scores = StripedScores::empty();
test::black_box(pli.score_into(&pssm, &striped, &mut scores)); 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_generic(bencher: &mut test::Bencher) {
let pli = Pipeline::generic();
#[bench] bench::<U32, _>(bencher, &pli);
fn bench_dispatch(bencher: &mut test::Bencher) { }
let pli = Pipeline::dispatch();
bench(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")] mod u8 {
#[bench] use super::*;
fn bench_sse2(bencher: &mut test::Bencher) {
let pli = Pipeline::sse2().unwrap(); fn bench<C: StrictlyPositive, P: Score<u8, Dna, C>>(bencher: &mut test::Bencher, pli: &P) {
bench::<U16, _>(bencher, &pli); let encoded = EncodedSequence::<Dna>::encode(SEQUENCE).unwrap();
} let mut striped = Pipeline::generic().stripe(encoded);
#[cfg(target_feature = "sse2")] let cm = CountMatrix::<Dna>::from_sequences([
#[bench] EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(),
fn bench_sse2_32(bencher: &mut test::Bencher) { EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(),
let pli = Pipeline::sse2().unwrap(); ])
bench::<U32, _>(bencher, &pli); .unwrap();
} let pbm = cm.to_freq(0.1);
let pssm = pbm.to_scoring(None);
#[cfg(target_feature = "avx2")] let dm = pssm.to_discrete();
#[bench]
fn bench_avx2(bencher: &mut test::Bencher) { striped.configure(&pssm);
let pli = Pipeline::avx2().unwrap(); let mut scores = StripedScores::empty();
bench(bencher, &pli); scores.resize(striped.matrix().rows(), striped.len());
} bencher.bytes = SEQUENCE.len() as u64;
bencher.iter(|| {
#[cfg(target_feature = "neon")] test::black_box(pli.score_into(&dm, &striped, &mut scores));
#[bench] });
fn bench_neon(bencher: &mut test::Bencher) { }
let pli = Pipeline::neon().unwrap();
bench::<U16, _>(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);
}
} }
} }
......
lightmotif/benches/threshold.rs
+ 142
− 56
View file @ 4183147d
...@@ -17,67 +17,153 @@ use lightmotif::seq::EncodedSequence; ...@@ -17,67 +17,153 @@ use lightmotif::seq::EncodedSequence;
const SEQUENCE: &str = include_str!("ecoli.txt"); const SEQUENCE: &str = include_str!("ecoli.txt");
fn bench<C: StrictlyPositive, P: Score<f32, Dna, C> + Threshold<f32, C>>( mod f32 {
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));
});
}
#[bench] use super::*;
fn bench_generic(bencher: &mut test::Bencher) {
let pli = Pipeline::generic();
bench::<U32, _>(bencher, &pli);
}
#[bench] fn bench<C: StrictlyPositive, P: Score<f32, Dna, C> + Threshold<f32, C>>(
fn bench_dispatch(bencher: &mut test::Bencher) { bencher: &mut test::Bencher,
let pli = Pipeline::dispatch(); pli: &P,
bench(bencher, &pli); ) {
} let encoded = EncodedSequence::<Dna>::encode(SEQUENCE).unwrap();
let mut striped = Pipeline::generic().stripe(encoded);
#[cfg(target_feature = "sse2")] let cm = CountMatrix::<Dna>::from_sequences([
#[bench] EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(),
fn bench_sse2(bencher: &mut test::Bencher) { EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(),
let pli = Pipeline::sse2().unwrap(); ])
bench::<U16, _>(bencher, &pli); .unwrap();
} let pbm = cm.to_freq(0.1);
let pssm = pbm.to_scoring(None);
#[cfg(target_feature = "sse2")] striped.configure(&pssm);
#[bench] let mut scores = StripedScores::empty();
fn bench_sse2_32(bencher: &mut test::Bencher) { pli.score_into(&pssm, &striped, &mut scores);
let pli = Pipeline::sse2().unwrap();
bench::<U32, _>(bencher, &pli); 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]
#[bench] fn bench_generic(bencher: &mut test::Bencher) {
fn bench_avx2(bencher: &mut test::Bencher) { let pli = Pipeline::generic();
let pli = Pipeline::avx2().unwrap(); bench::<U32, _>(bencher, &pli);
bench(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")] mod u8 {
#[bench]
fn bench_neon(bencher: &mut test::Bencher) { use super::*;
let pli = Pipeline::neon().unwrap();
bench::<U16, _>(bencher, &pli); 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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