The truncated-file check and the end-of-file clamp reached File,
LazyFile and MmapFile but not clawhdf5-io's readers, which still opened
truncated files and read past the recorded end of file. NativeVol
(open, and read_dataset for from_bytes), AsyncHDF5File::from_bytes and
MpiVol's collective read now view the file through the new
vol::hdf5_view: from the superblock to Superblock::data_end, refusing a
file shorter than that.
MpiVol's read is compiled only with the mpi-io feature, which needs an
MPI installation; it was not built here. The edit there only swaps its
two-line superblock setup for hdf5_view.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
libhdf5 1.14.4+ treats an integer, float or bit field wider than a byte
whose precision and offset leave more than half its bits unused as
corruption when the type sits in a header without a checksum (version 1),
unless the file is opened with H5Pset_relax_file_integrity_checks
(H5T_is_numeric_with_unusual_unused_bits). clawhdf5 read such types,
e.g. a 3-bit integer in 4 bytes (cve-2024-29162) or a 32-bit float in
65525 bytes (cve-2024-32614, tmisc38a.h5).
New Datatype::check_unused_bits (recursive) and Datatype::parse_in_header,
which applies it for version-1 headers. Dataset datatypes (facade File,
LazyFile, MmapFile; clawhdf5-io VOL, MPI VOL, async reader; the
conformance probe) and compact attributes in version-1 headers use it.
Conformance (cached corpus, tank): 570 ok, unchanged; cve-2024-29162,
cve-2024-32614 and tmisc38a.h5 now refuse the object h5py refuses, and
tmisc38b.h5 / unknown-1.h5 now fail with libhdf5's reason.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
A file may start with a user block (h5py userblock_size, h5jam), putting
the superblock at 512, 1024, ...; every address in the file is then
relative to the superblock. The signature search found it, but every
reader passed the whole file to the parsers, so addresses landed
userblock bytes early and the root group failed with
InvalidObjectHeaderVersion (twithub.h5, twithub513.h5,
h5clear_fsm_persist_user_*.h5).
Readers now view the file from the superblock on, taking the signature's
position as the base address as libhdf5 does: File (mmap, buffered,
from_bytes), MmapFile, LazyFile, AsyncHDF5File, the VOL and MPI VOL
readers, the HNSW loader and external VDS source files. File, MmapFile
and LazyFile gain user_block_size(). The new signature::split_user_block
returns the two parts, and Superblock::parse refuses a non-zero offset
(UserBlockNotStripped) so a format-level caller cannot silently apply
superblock-relative addresses to the whole file.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
Mission: 01a00c41-bac0-7eb3-a8c8-8b7044f3086d
Phase: 01a00c41-bac2-71e3-a58b-c473421200ee
Committed by the ClawMates delivery pipeline from the agents' working tree. Authored by agents, not by the named committer.
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]>
