read_raw_data_selection computed which chunks a selection intersects, threw
the answer away, decoded the entire dataset and picked elements out of it —
for contiguous layouts too. A 64x64 window of a 64 MB deflate dataset cost
105 ms, about half a full read; every selection cost the same whatever its
size.
New partial_read module: materialise only the selection's bounding box — the
overlapping rows of a contiguous dataset (straight from the file bytes) or the
overlapping chunks (only those are decompressed) — then run the existing
extractor over that buffer with the selection translated to the box origin, so
extraction semantics are exactly the full-read ones. It declines (falling back
to the old path) for All/None, compact/virtual/storage-less layouts, and boxes
covering more than half the dataset. That window now takes 0.39 ms, one row
2.7 ms, one column 5.2 ms.
Selections are validated against the dataset shape first. They were not: a
hyperslab past an edge came back padded with zeros and a point with an
out-of-range column wrapped into the next row, returning the wrong element
with no error. Now FormatError::SelectionOutOfBounds (also rank mismatch and
overlapping blocks); the facade's fill-aware path validates too.
Tests: equivalence against a reference extraction from a full read over 60
random hyperslabs/point lists per layout (contiguous, chunked, deflate) for
ranks 1-3. New read_harness bench binary with before/after in BENCHMARKS.md.
Co-Authored-By: Claude Fable 5.1 <[email protected]>
Bump all workspace crates, the node package and pyproject to 2.4.0, finalize
the changelog and add upgrade notes for the search behaviour changes.
Co-Authored-By: Claude Fable 5.1 <[email protected]>
New clawhdf5-bench binary `search_harness`, the measurement baseline for the
search hot-path work. On deterministic clustered 384-dim data it reports HNSW
build time and, per ef, recall@10 against an exact scan, QPS and p50/p99; and
for HDF5Memory: ingest, checkpoint, open, first-query-after-open and
steady-state hybrid_search latency at 1K/10K (and 100K with --full). Optional
JSON output for tracking.
Baseline recorded in BENCHMARKS.md. It shows two problems: HNSW recall@10 does
not respond to ef and falls from 0.87 (1K) to 0.31 (100K) on clustered data,
and end-to-end hybrid_search is ~1000x slower than its vector stage because
every query rebuilds BM25 and rewrites the .h5 file.
Co-Authored-By: Claude Fable 5.1 <[email protected]>
Bump all workspace crates, the node package and pyproject to 2.3.0, finalize
the changelog and add upgrade notes for the behaviour changes.
Co-Authored-By: Claude Fable 5.1 <[email protected]>
Bump all workspace crates, the node package and pyproject to 2.2.0 and
finalize the changelog. The repository URL in every manifest pointed at a
GitHub location that does not resolve; use the real origin.
Co-Authored-By: Claude Fable 5.1 <[email protected]>
Every LongMemEval number this project has published measured BM25 alone. The
bench passed zero-vector embeddings with vector_weight=0.0, so the HNSW/vector
stage — the thing the README credits for retrieval quality — contributed
nothing and was never tested.
An optional `embeddings` feature loads all-MiniLM-L6-v2 via candle and encodes
the corpus for real. It is off by default and nothing in the shipped crates
depends on it, so a project that advertises no heavyweight dependencies keeps
that property; without the feature the bench behaves exactly as before.
Full haystack, n=500, turn-level:
Hit@1 Hit@5 Hit@10 MRR
BM25 only 53.8% 75.0% 81.6% 0.6320
Vector only 36.0% 71.8% 81.6% 0.5027
Hybrid 0.7/0.3 44.4% 79.2% 86.0% 0.5868
Session-level, hybrid leads outright: 88.2 / 95.8 / 97.8 / 0.9158.
The hybrid claim holds for depth and not for precision@1. Hybrid is the best
configuration at Hit@5 and Hit@10 at both granularities — turn-level Hit@5 gains
4.2 points over BM25 and 7.4 over vector-only, which is the result that justifies
running two stages at all. But BM25 alone still leads turn-level Hit@1 and MRR,
so fusing buys deeper recall and pays at rank 1. Callers assembling five memories
of context want hybrid; callers taking a single top hit are better served by BM25
today. The 0.7/0.3 weights are the documented default, not a searched optimum.
omni-cortex's four-signal ablation found the same direction independently — there,
adding BM25 to a dense retriever raised nDCG@5 while lowering Hit@1 and MRR. Two
codebases, two fusion schemes, same trade.
Vector-only trailing BM25 at every turn-level cutoff except Hit@10 is stated
plainly rather than buried: LongMemEval questions share heavy vocabulary with
their evidence turns, which is close to the best case for lexical matching, and
MiniLM at 384-d is a small model.
Implementation notes:
- Texts are deduplicated before encoding. The haystack sessions are drawn from
a shared pool, so 500 questions x 493.5 turns collapses to 190,015 unique
strings — the difference between encoding the corpus once and per question.
- `embeddings-cuda` adds the GPU path, and it is not a convenience: 190k texts
take ~13 min on an RTX 5060 Ti, while the same work on 8 CPU cores was still
unfinished after 30 minutes. The device is selected at runtime with a CPU
fallback, so a machine without CUDA still works.
- Mean-pooling is masked and the output L2-normalised, which is the published
recipe for this checkpoint (not the [CLS] pooler).
One measurement wrinkle, recorded rather than smoothed over: on the oracle
variant BM25-only reads 84.2% Hit@5 with real embedding vectors present against
84.4% with zero vectors — one question of 500 changes rank, MRR identical at
0.6597. On the full haystack the two agree exactly. Weight 0.0 evidently does not
make the vector stage bit-for-bit absent from candidate selection on a small
corpus.
Verified on the Linux dev host: 49 groups / 1659 passed / 0 failed, clippy clean
under -D warnings, fmt clean, with and without the feature.
Add [workspace.dependencies] to the root Cargo.toml for the four
duplicated-across-many-crates dependencies flagged by the earlier review:
tempfile (7 crates), criterion (6), half (4 — real version skew, clawhdf5-gpu
pinned 2.7 while others used bare 2), and serde (4). Update every consuming
crate to `dep = { workspace = true }`, preserving crate-local `optional =
true` where it already existed. half now resolves uniformly to 2.7.x
workspace-wide instead of two separate semver ranges.
Also fixed clawhdf5-filters/Cargo.toml's stale "rustyhdf5" description
while touching the file (same class of leftover rename as prior fixes).
Not touching rayon/byteorder/clap (no skew found, lower priority).
Implements Pcodec (filter ID 32023) via the `pco` 1.0.x crate as a new
optional compression codec. Pcodec achieves 30–94% better compression
ratio than Zstd for f32/f64 columnar data at 1–5 GiB/s decompression
speed, making it ideal for write-once/read-many embedding archives.
Write throughput at 512×512: 591 MiB/s (parity with Zstd-3 at 610 MiB/s).
For smaller chunks Zstd-3 remains faster due to Pcodec's fixed per-chunk
distributional analysis overhead.
- Add FILTER_PCODEC = 32023 constant to filter_pipeline.rs
- Add pcodec_compress/pcodec_decompress using pco::standalone API
- Wire into compress_chunk/decompress_chunk dispatch
- Add ChunkOptions.pcodec field and DatasetBuilder.with_pcodec() method
- Enable pcodec as highest-priority codec in build_pipeline()
- Add pco dep (optional, feature = "pcodec") to clawhdf5-format/clawhdf5
- Add write_2d_chunked_pcodec benchmark comparing pcodec vs zstd-3
- Document results in BENCHMARKS.md
Co-Authored-By: Claude Sonnet 4.6 <[email protected]>
Add features = ["zstd"] to clawhdf5-bench dev-dependency so the
write_2d_chunked_zstd benchmark no longer panics with UnsupportedFilter(32015).
Update BENCHMARKS.md and README.md with measured results from the full
h5bench write suite (2026-06-30, post write-performance improvements):
- Zstd-3 hits 593 MiB/s at 512×512 vs deflate-6's 280 MiB/s (2.12×)
- Zstd-3 hits 330 MiB/s at 128×128 vs deflate-6's 132 MiB/s (2.51×)
- Sequential f64 batch write improved ~8-11% from owned-Vec IO path
Co-Authored-By: Claude Sonnet 4.6 <[email protected]>
Adds three Criterion benchmark suites mirroring the h5bench HPC I/O
benchmark workloads in pure Rust — no C libhdf5 required for the default
path, with an optional `libhdf5-compare` feature for side-by-side numbers.
- benches/h5bench_write.rs: write_1d_contiguous, write_2d_chunked,
write_f64_batch, write_multi_dataset, write_with_attrs
- benches/h5bench_read.rs: read_sequential, read_f64_sequential,
read_chunked_2d, read_from_disk, read_hyperslab
- benches/h5bench_meta.rs: metadata_attrs_write, metadata_attrs_read,
metadata_groups_create, metadata_groups_traverse, metadata_string_attrs
All benchmarks pass `cargo bench --bench <name> -- --test` and clippy
reports zero warnings. Run with `cargo bench -p clawhdf5-bench`.
Co-Authored-By: Claude Sonnet 4.6 <[email protected]>
Bumps [workspace.package] and all 17 crate package versions (and internal
path-dependency requirements) from 2.0.0 to 2.1.0 for a coordinated release.
Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
