Omar Sobh
55959b4920
CI / test (push) Failing after 15s
- Add .gitea/workflows/ci.yml running scripts/ci-test.sh (fmt, clippy,
test, no_std check) on push/PR to main.
- Fix stale rustyhdf5-py/rustyhdf5-format package names in
ci-test.sh/check-nostd.sh, which had been silently no-op'ing those
checks (cargo warns but doesn't fail on an unknown --exclude/-p
target).
- With those checks actually running, fix the real issues they surface:
- clippy: useless_conversion in chunked_write.rs, byte_char_slices in
global_heap.rs/object_header.rs.
- cargo fmt: apply formatting across the workspace (whitespace only).
- no_std (thumbv7em-none-eabihf) build errors in clawhdf5-format:
core::sync::atomic::AtomicU64 doesn't exist on that target (no
native 64-bit atomics) — switch profiling.rs's counters to
portable-atomic, which falls back to a CAS-based emulation there
and is a no-op wrapper elsewhere. Add missing alloc imports for
Box (filters.rs), Vec (filters_szip.rs), and format! (dict_encoding.rs)
on no_std paths. Replace f64::powi (std/libm-only) with a small
local exponentiation-by-squaring helper in the scale-offset filter.
331 lines
12 KiB
Rust
331 lines
12 KiB
Rust
//! h5bench-equivalent write workloads for clawhdf5.
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//!
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//! Mirrors the sequential and chunked write patterns from the h5bench HPC
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//! benchmark suite but implemented in pure Rust using Criterion for statistical
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//! rigor. The `libhdf5-compare` feature adds matching benchmarks via the `hdf5`
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//! crate (requires a system libhdf5 install).
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use clawhdf5::{AttrValue, FileBuilder};
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use criterion::{BenchmarkId, Criterion, Throughput, criterion_group, criterion_main};
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use tempfile::TempDir;
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// ---------------------------------------------------------------------------
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// Workload: write_1d_contiguous
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// Write N × f32 as a single contiguous 1-D dataset.
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// Measures raw serialization + HDF5 superblock / object-header overhead.
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// ---------------------------------------------------------------------------
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fn bench_write_1d_contiguous(c: &mut Criterion) {
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let mut group = c.benchmark_group("write_1d_contiguous");
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for &n in &[1_000usize, 10_000, 100_000] {
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let data: Vec<f32> = (0..n).map(|i| i as f32 * 0.001).collect();
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group.throughput(Throughput::Bytes((n * size_of::<f32>()) as u64));
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group.bench_with_input(BenchmarkId::new("clawhdf5", n), &data, |b, d| {
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let tmp = TempDir::new().unwrap();
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let path = tmp.path().join("write_1d_contiguous.h5");
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b.iter(|| {
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let mut fb = FileBuilder::new();
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fb.create_dataset("data")
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.with_f32_data(d)
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.with_shape(&[n as u64]);
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fb.write(&path).unwrap();
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});
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});
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#[cfg(feature = "libhdf5-compare")]
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group.bench_with_input(BenchmarkId::new("libhdf5", n), &data, |b, d| {
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let tmp = TempDir::new().unwrap();
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let path = tmp.path().join("write_1d_libhdf5.h5");
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b.iter(|| {
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let file = hdf5::File::create(&path).unwrap();
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let ds = file
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.new_dataset::<f32>()
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.shape([d.len()])
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.create("data")
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.unwrap();
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ds.write(d.as_slice()).unwrap();
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});
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});
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}
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group.finish();
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}
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// ---------------------------------------------------------------------------
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// Workload: write_2d_chunked
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// Write an M × N f32 matrix as a chunked 2-D dataset with deflate (level 6).
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// Measures chunked layout creation + compression pipeline throughput.
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// ---------------------------------------------------------------------------
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fn bench_write_2d_chunked(c: &mut Criterion) {
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let mut group = c.benchmark_group("write_2d_chunked");
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// (rows, cols, chunk_rows, chunk_cols)
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let configs: &[(usize, usize, u64, u64)] =
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&[(32, 32, 8, 32), (128, 128, 32, 128), (512, 512, 64, 512)];
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for &(rows, cols, cr, cc) in configs {
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let n = rows * cols;
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let data: Vec<f32> = (0..n).map(|i| i as f32).collect();
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let label = format!("{rows}x{cols}");
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group.throughput(Throughput::Bytes((n * size_of::<f32>()) as u64));
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group.bench_with_input(BenchmarkId::new("clawhdf5", &label), &data, |b, d| {
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let tmp = TempDir::new().unwrap();
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let path = tmp.path().join("write_2d_chunked.h5");
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b.iter(|| {
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let mut fb = FileBuilder::new();
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fb.create_dataset("matrix")
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.with_f32_data(d)
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.with_shape(&[rows as u64, cols as u64])
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.with_chunks(&[cr, cc])
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.with_deflate(6);
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fb.write(&path).unwrap();
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});
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});
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#[cfg(feature = "libhdf5-compare")]
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group.bench_with_input(BenchmarkId::new("libhdf5", &label), &data, |b, d| {
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let tmp = TempDir::new().unwrap();
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let path = tmp.path().join("write_2d_libhdf5.h5");
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b.iter(|| {
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let file = hdf5::File::create(&path).unwrap();
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let ds = file
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.new_dataset::<f32>()
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.shape([rows, cols])
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.chunk([cr as usize, cc as usize])
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.deflate(6)
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.create("matrix")
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.unwrap();
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ds.write_raw(d.as_slice()).unwrap();
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});
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});
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}
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group.finish();
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}
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// ---------------------------------------------------------------------------
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// Workload: write_2d_chunked_zstd
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// Same matrix sizes as write_2d_chunked but uses Zstd level 3.
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// Zstd level 3 typically encodes 500+ MiB/s vs deflate's ~300 MiB/s at the
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// same or better compression ratio (arXiv 2604.06221, ROOT I/O 2019).
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// ---------------------------------------------------------------------------
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fn bench_write_2d_chunked_zstd(c: &mut Criterion) {
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let mut group = c.benchmark_group("write_2d_chunked_zstd");
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let configs: &[(usize, usize, u64, u64)] =
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&[(32, 32, 8, 32), (128, 128, 32, 128), (512, 512, 64, 512)];
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for &(rows, cols, cr, cc) in configs {
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let n = rows * cols;
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let data: Vec<f32> = (0..n).map(|i| i as f32).collect();
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let label = format!("{rows}x{cols}");
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group.throughput(Throughput::Bytes((n * size_of::<f32>()) as u64));
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group.bench_with_input(
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BenchmarkId::new("clawhdf5/zstd-3", &label),
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&data,
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|b, d| {
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let tmp = TempDir::new().unwrap();
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let path = tmp.path().join("write_2d_chunked_zstd.h5");
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b.iter(|| {
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let mut fb = FileBuilder::new();
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fb.create_dataset("matrix")
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.with_f32_data(d)
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.with_shape(&[rows as u64, cols as u64])
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.with_chunks(&[cr, cc])
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.with_zstd(3);
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fb.write(&path).unwrap();
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});
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},
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);
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group.bench_with_input(
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BenchmarkId::new("clawhdf5/deflate-6", &label),
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&data,
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|b, d| {
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let tmp = TempDir::new().unwrap();
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let path = tmp.path().join("write_2d_chunked_deflate.h5");
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b.iter(|| {
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let mut fb = FileBuilder::new();
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fb.create_dataset("matrix")
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.with_f32_data(d)
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.with_shape(&[rows as u64, cols as u64])
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.with_chunks(&[cr, cc])
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.with_deflate(6);
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fb.write(&path).unwrap();
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});
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},
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);
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}
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group.finish();
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}
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// ---------------------------------------------------------------------------
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// Workload: write_2d_chunked_pcodec
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// Same matrix sizes as write_2d_chunked but uses Pcodec (arXiv:2502.06112).
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// Pcodec achieves 30–94% better compression ratio than Zstd for f32/f64 at
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// 1–5 GiB/s decompression speed via a quantile-based numerical codec.
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// ---------------------------------------------------------------------------
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fn bench_write_2d_chunked_pcodec(c: &mut Criterion) {
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let mut group = c.benchmark_group("write_2d_chunked_pcodec");
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let configs: &[(usize, usize, u64, u64)] =
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&[(32, 32, 8, 32), (128, 128, 32, 128), (512, 512, 64, 512)];
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for &(rows, cols, cr, cc) in configs {
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let n = rows * cols;
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let data: Vec<f32> = (0..n).map(|i| i as f32).collect();
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let label = format!("{rows}x{cols}");
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group.throughput(Throughput::Bytes((n * size_of::<f32>()) as u64));
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group.bench_with_input(
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BenchmarkId::new("clawhdf5/pcodec", &label),
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&data,
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|b, d| {
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let tmp = TempDir::new().unwrap();
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let path = tmp.path().join("write_2d_chunked_pcodec.h5");
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b.iter(|| {
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let mut fb = FileBuilder::new();
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fb.create_dataset("matrix")
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.with_f32_data(d)
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.with_shape(&[rows as u64, cols as u64])
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.with_chunks(&[cr, cc])
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.with_pcodec();
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fb.write(&path).unwrap();
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});
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},
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);
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group.bench_with_input(
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BenchmarkId::new("clawhdf5/zstd-3", &label),
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&data,
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|b, d| {
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let tmp = TempDir::new().unwrap();
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let path = tmp.path().join("write_2d_chunked_zstd.h5");
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b.iter(|| {
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let mut fb = FileBuilder::new();
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fb.create_dataset("matrix")
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.with_f32_data(d)
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.with_shape(&[rows as u64, cols as u64])
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.with_chunks(&[cr, cc])
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.with_zstd(3);
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fb.write(&path).unwrap();
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});
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},
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);
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}
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group.finish();
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}
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// ---------------------------------------------------------------------------
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// Workload: write_f64_batch
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// Write batches of f64 elements — simulates the clawhdf5-agent embedding
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// write path (one f64 vector per memory entry).
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// ---------------------------------------------------------------------------
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fn bench_write_f64_batch(c: &mut Criterion) {
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let mut group = c.benchmark_group("write_f64_batch");
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for &n in &[128usize, 512, 1_024] {
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let data: Vec<f64> = (0..n).map(|i| (i as f64).sin()).collect();
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group.throughput(Throughput::Bytes((n * size_of::<f64>()) as u64));
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group.bench_with_input(BenchmarkId::new("clawhdf5", n), &data, |b, d| {
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let tmp = TempDir::new().unwrap();
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let path = tmp.path().join("write_f64_batch.h5");
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b.iter(|| {
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let mut fb = FileBuilder::new();
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fb.create_dataset("embedding")
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.with_f64_data(d)
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.with_shape(&[n as u64]);
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fb.write(&path).unwrap();
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});
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});
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}
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group.finish();
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}
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// ---------------------------------------------------------------------------
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// Workload: write_multi_dataset
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// Write K independent f32 datasets into one file — stresses the object-header
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// + link-storage path (compact → dense transition at >8 datasets).
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// ---------------------------------------------------------------------------
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fn bench_write_multi_dataset(c: &mut Criterion) {
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let mut group = c.benchmark_group("write_multi_dataset");
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for &k in &[4usize, 16, 64] {
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let rows = 100usize;
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let data: Vec<f32> = (0..rows).map(|i| i as f32).collect();
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group.throughput(Throughput::Elements(k as u64));
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group.bench_with_input(BenchmarkId::new("clawhdf5", k), &data, |b, d| {
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let tmp = TempDir::new().unwrap();
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let path = tmp.path().join("write_multi.h5");
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b.iter(|| {
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let mut fb = FileBuilder::new();
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for i in 0..k {
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fb.create_dataset(&format!("ds_{i:04}"))
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.with_f32_data(d)
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.with_shape(&[rows as u64]);
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}
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fb.write(&path).unwrap();
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});
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});
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}
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group.finish();
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}
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// ---------------------------------------------------------------------------
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// Workload: write_with_attrs
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// Write a dataset with K attributes — exercises attribute message allocation.
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// ---------------------------------------------------------------------------
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fn bench_write_with_attrs(c: &mut Criterion) {
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let mut group = c.benchmark_group("write_with_attrs");
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for &k in &[4usize, 16, 64] {
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group.throughput(Throughput::Elements(k as u64));
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group.bench_with_input(BenchmarkId::new("clawhdf5", k), &k, |b, &k| {
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let tmp = TempDir::new().unwrap();
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let path = tmp.path().join("write_attrs.h5");
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b.iter(|| {
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let mut fb = FileBuilder::new();
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let ds = fb
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.create_dataset("data")
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.with_f64_data(&[1.0, 2.0, 3.0])
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.with_shape(&[3]);
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for i in 0..k {
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ds.set_attr(&format!("attr_{i}"), AttrValue::I64(i as i64));
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}
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fb.write(&path).unwrap();
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});
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});
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}
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group.finish();
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}
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criterion_group!(
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write_benches,
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bench_write_1d_contiguous,
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bench_write_2d_chunked,
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bench_write_2d_chunked_zstd,
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bench_write_2d_chunked_pcodec,
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bench_write_f64_batch,
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bench_write_multi_dataset,
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bench_write_with_attrs,
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);
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criterion_main!(write_benches);
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