perf: eliminate double compression and improve shuffle filter throughput

Four independent write-path improvements:

1. Cache compressed chunks between Pass 1 and Pass 2 (chunked_write.rs,
   file_writer.rs): the two-pass layout writer previously called
   build_chunked_data_at_ext() twice per chunked dataset — once in Pass 1
   to get blob sizes and once in Pass 2 with real addresses. Add
   PrecompressedChunks / precompress_chunks() / build_chunked_data_from_
   precompressed() to compress once in Pass 1, cache the result, and only
   rebuild the address-dependent index structures in Pass 2. Expected
   ~2× speedup for chunked+deflate writes (512×512 deflate: 3.33ms → ~1.7ms).

2. SIMD-vectorisable shuffle filter (filters.rs): replace the naïve O(N·S)
   nested loop with an unrolled u32-load path for 4-byte elements (f32) and
   a cache-blocked tile loop for all other sizes. LLVM auto-vectorises the
   4-byte path into SSE2/AVX2/NEON byte-deinterleave sequences.

3. Zstd benchmark variant (h5bench_write.rs): add write_2d_chunked_zstd
   group measuring Zstd level 3 vs deflate level 6 side-by-side. Also fix
   the existing write_2d_chunked benchmark — the clawhdf5 path was missing
   .with_deflate(6), making the comparison apples-to-oranges. Add arXiv-
   backed doc recommendation on DatasetBuilder::with_zstd().

4. Zero-copy HNSW save (hnsw.rs, clawhdf5-io/lib.rs): add
   FileWriter::write_bytes_owned(Vec<u8>) that takes ownership to avoid the
   full-file clone in write_all_bytes(&[u8]). HNSW::save_to_hdf5 uses it.

Co-Authored-By: Claude Sonnet 4.6 <[email protected]>
This commit is contained in:
Omar Sobh
2026-06-30 22:36:40 +00:00
co-authored by Claude Sonnet 4.6
parent 3a1fcc5cb3
commit 2ddb22897c
7 changed files with 351 additions and 133 deletions
+1 -2
View File
@@ -16,7 +16,6 @@ use clawhdf5_format::object_header::ObjectHeader;
use clawhdf5_format::signature::find_signature;
use clawhdf5_format::superblock::Superblock;
use clawhdf5_io::FileWriter as IoFileWriter;
use clawhdf5_io::HDF5ReadWrite;
/// Distance metric for the HNSW index.
#[derive(Debug, Clone, Copy, PartialEq, Eq)]
@@ -516,7 +515,7 @@ impl HnswIndex {
pub fn save_to_hdf5(&self, writer: &mut IoFileWriter) -> Result<(), FormatError> {
let bytes = self.to_hdf5_bytes()?;
writer
.write_all_bytes(&bytes)
.write_bytes_owned(bytes)
.map_err(|e| FormatError::SerializationError(e.to_string()))?;
Ok(())
}