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refactor: Changed display and refactored bench
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@jspaezp
jspaezp committed Sep 19, 2024
1 parent 8ab35f3 commit a536342
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Showing 4 changed files with 196 additions and 131 deletions.
176 changes: 84 additions & 92 deletions benches/benchmark_indices.rs
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,7 @@
use criterion::{criterion_group, criterion_main, BatchSize, BenchmarkId, Criterion};
use criterion::{
criterion_group, criterion_main, measurement::Measurement, BatchSize, BenchmarkFilter,
BenchmarkGroup, BenchmarkId, Criterion,
};
use rand::{Rng, SeedableRng};
use rand_chacha::ChaCha8Rng;

Expand Down Expand Up @@ -82,8 +85,6 @@ fn build_elution_groups(raw_file_path: String) -> Vec<ElutionGroup> {
}

fn criterion_benchmark(c: &mut Criterion) {
env_logger::init();

let (raw_file_path, basename) = get_file_from_env();
let mut group = c.benchmark_group("Encoding Time");

Expand Down Expand Up @@ -112,128 +113,119 @@ fn criterion_benchmark(c: &mut Criterion) {
group.finish();
}

fn thoughput_benchmark_random(c: &mut Criterion) {
let (raw_file_path, basename) = get_file_from_env();
let mut group = c.benchmark_group("RandomAccessThroughput");
group.significance_level(0.05).sample_size(10);
group.throughput(criterion::Throughput::Elements(NUM_ELUTION_GROUPS as u64));
group.bench_function(
BenchmarkId::new("TransposedQuadIndex", basename.clone()),
|b| {
macro_rules! add_bench_random {
($group:expr, $raw_file_path:expr, $basename:expr, $name:literal, $index_type:ty, $tolerance_type:ty, ) => {
$group.bench_function(BenchmarkId::new($name, $basename.clone()), |b| {
b.iter_batched(
|| {
(
QuadSplittedTransposedIndex::from_path(&(raw_file_path.clone())).unwrap(),
build_elution_groups(raw_file_path.clone()),
DefaultTolerance::default(),
<$index_type>::from_path(&($raw_file_path.clone())).unwrap(),
build_elution_groups($raw_file_path.clone()),
<$tolerance_type>::default(),
)
},
|(qst_file_index, query_groups, tolerance)| {
let aggregator_factory = |id| RawPeakIntensityAggregator { intensity: 0 };
|(index, query_groups, tolerance)| {
let aggregator_factory = |_id| RawPeakIntensityAggregator { intensity: 0 };
let local_lambda = |elution_group: &ElutionGroup| {
query_indexed(
&qst_file_index,
&index,
&aggregator_factory,
&qst_file_index,
&index,
&tolerance,
&elution_group,
)
};
for elution_group in query_groups {
let foo = local_lambda(&elution_group);
black_box((|foo| false)(foo));
black_box((|_foo| false)(foo));
}
},
BatchSize::PerIteration,
)
},
);
group.bench_function(BenchmarkId::new("RawFileIndex", basename.clone()), |b| {
b.iter_batched(
|| {
(
RawFileIndex::from_path(&(raw_file_path.clone())).unwrap(),
build_elution_groups(raw_file_path.clone()),
DefaultTolerance::default(),
)
},
|(raw_file_index, query_groups, tolerance)| {
let aggregator_factory = |id| RawPeakIntensityAggregator { intensity: 0 };
let local_lambda = |elution_group: &ElutionGroup| {
query_indexed(
&raw_file_index,
&aggregator_factory,
&raw_file_index,
&tolerance,
&elution_group,
)
};
for elution_group in query_groups {
let foo = local_lambda(&elution_group);
black_box((|foo| false)(foo));
}
},
BatchSize::PerIteration,
)
});

group.finish();
});
};
}

fn thoughput_benchmark_optim(c: &mut Criterion) {
let (raw_file_path, basename) = get_file_from_env();
let mut group = c.benchmark_group("BatchAccessThroughput");
group.significance_level(0.05).sample_size(10);
group.throughput(criterion::Throughput::Elements(NUM_ELUTION_GROUPS as u64));
group.bench_function(
BenchmarkId::new("TransposedQuadIndex", basename.clone()),
|b| {
macro_rules! add_bench_optim {
($group:expr, $raw_file_path:expr, $basename:expr, $name:literal, $index_type:ty, $tolerance_type:ty, $query_func:expr,) => {
$group.bench_function(BenchmarkId::new($name, $basename.clone()), |b| {
b.iter_batched(
|| {
(
QuadSplittedTransposedIndex::from_path(&(raw_file_path.clone())).unwrap(),
build_elution_groups(raw_file_path.clone()),
DefaultTolerance::default(),
<$index_type>::from_path(&($raw_file_path.clone())).unwrap(),
build_elution_groups($raw_file_path.clone()),
<$tolerance_type>::default(),
)
},
|(qst_file_index, query_groups, tolerance)| {
let aggregator_factory = |id| RawPeakIntensityAggregator { intensity: 0 };
|(index, query_groups, tolerance)| {
let aggregator_factory = |_id| RawPeakIntensityAggregator { intensity: 0 };
let foo = query_multi_group(
&qst_file_index,
&qst_file_index,
&index,
&index,
&tolerance,
&query_groups,
&aggregator_factory,
);
black_box((|foo| false)(foo));
black_box((|_foo| false)(foo));
},
BatchSize::PerIteration,
)
},
});
};
}

fn thoughput_benchmark_random(c: &mut Criterion) {
let (raw_file_path, basename) = get_file_from_env();
let mut group = c.benchmark_group("RandomAccessThroughput");
group.significance_level(0.05).sample_size(10);
group.throughput(criterion::Throughput::Elements(NUM_ELUTION_GROUPS as u64));

add_bench_random!(
group,
raw_file_path,
basename,
"TransposedQuadIndex",
QuadSplittedTransposedIndex,
DefaultTolerance,
);

add_bench_random!(
group,
raw_file_path,
basename,
"RawFileIndex",
RawFileIndex,
DefaultTolerance,
);

group.finish();
}

fn thoughput_benchmark_optim(c: &mut Criterion) {
env_logger::init();
let (raw_file_path, basename) = get_file_from_env();
let mut group = c.benchmark_group("BatchAccessThroughput");
group.significance_level(0.05).sample_size(10);
group.throughput(criterion::Throughput::Elements(NUM_ELUTION_GROUPS as u64));

add_bench_optim!(
group,
raw_file_path,
basename,
"TransposedQuadIndex",
QuadSplittedTransposedIndex,
DefaultTolerance,
query_multi_group,
);

add_bench_optim!(
group,
raw_file_path,
basename,
"RawFileIndex",
RawFileIndex,
DefaultTolerance,
query_multi_group,
);
group.bench_function(BenchmarkId::new("RawFileIndex", basename.clone()), |b| {
b.iter_batched(
|| {
(
RawFileIndex::from_path(&(raw_file_path.clone())).unwrap(),
build_elution_groups(raw_file_path.clone()),
DefaultTolerance::default(),
)
},
|(raw_file_index, query_groups, tolerance)| {
let aggregator_factory = |id| RawPeakIntensityAggregator { intensity: 0 };
let foo = query_multi_group(
&raw_file_index,
&raw_file_index,
&tolerance,
&query_groups,
&aggregator_factory,
);
black_box((|foo| false)(foo));
},
BatchSize::PerIteration,
)
});

group.finish();
}
Expand Down
12 changes: 12 additions & 0 deletions src/main.rs
View file
Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
use std::default;

use timsquery::models::elution_group::ElutionGroup;
use timsquery::queriable_tims_data::queriable_tims_data::query_multi_group;
use timsquery::traits::tolerance::DefaultTolerance;
Expand Down Expand Up @@ -58,6 +60,12 @@ struct Args {
command: Option<Commands>,
}

#[derive(Debug, Default, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, clap::ValueEnum)]
enum PossibleAggregator {
#[default]
RawPeakIntensityAggregator,
}

#[derive(Parser, Debug)]
struct QueryIndexArgs {
/// The path to the raw file to query.
Expand All @@ -79,6 +87,10 @@ struct QueryIndexArgs {
// Whether the output json should be pretty printed.
#[arg(short, long)]
pretty: bool,

// The aggregator to use.
#[arg(short, long, default_value_t, value_enum)]
aggregator: PossibleAggregator,
}

#[derive(Parser, Debug)]
Expand Down
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