osobhandClaude Opus 5.5
742ed4dfb8
libhdf5 does not walk the chunk B-tree to read a dataset: it looks each chunk up (H5B_find with H5D__btree_cmp3 and H5D__btree_found), asking for the element-size coordinate as 0. collect_chunk_info_checked now parses the tree with its keys and returns each stored chunk only when that lookup, replayed over the scaled keys, finds it. A key with a non-zero element-size coordinate is therefore found in a 1-D dataset (cmp3 compares only the first coordinate there, and found compares with <=) and missed in a dataset of rank 2 or more, which reads fill values. The previous commit refused every such key, which refused 1-D files libhdf5 reads correctly; before that, the rank-2 case read the chunk's data where h5py reads fill values (cve-2025-44905 /Shuffle_float_data_le, now identical to h5py, so it leaves the conformance report's list of libhdf5 bugs). Test: chunk_keys_with_an_element_offset_read_as_libhdf5_reads_them compares 1-D and 2-D files against h5py's values. It fails on the previous commit (the 1-D file is refused) and with the refusal removed (the 2-D file reads 0..23 where h5py reads fill values). Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
Conformance sweep
Reads every HDF5 file of eight public corpora with clawhdf5 and with
h5py/libhdf5, compares the two readings object by object, and writes
CONFORMANCE.md.
CLAWHDF5_PYTHON=/path/to/venv/bin/python conformance/run.sh # ~30 s once the corpus is cached
conformance/run.sh --update-baseline # after an intended change in results
Needs Rust, git, h5dump (Debian/Ubuntu hdf5-tools), libaec (for the
probe's szip feature; libaec-dev), and a Python with the packages in
requirements.txt. The first run downloads about 450 MB of sparse checkouts.
| file | role |
|---|---|
corpus.txt |
the corpora: git URL, pinned commit, swept root, sparse-checkout patterns |
fetch-corpus.sh |
shallow, sparse, blob-filtered checkout of each pinned commit into .cache/src/ (gitignored); no-op when already there |
list_files.py |
which files are probed (HDF5/netCDF-4 extensions minus netCDF classic, plus the CVE reproducers) |
probe/ |
the clawhdf5 side: a standalone crate (outside the workspace, so cargo test --workspace never builds it) that walks a file with clawhdf5-format and prints canonical JSON |
ref.py |
the h5py side: the same JSON from h5py |
run_one.sh |
runs both sides on one file (and h5dump on the CVE corpus) under a timeout and an address-space limit |
compare.py |
classifies each file (ok / our-error / mismatch / h5py-cannot-read / panic / hang / crash / oom) and groups root causes |
report.py |
writes CONFORMANCE.md |
check.py |
the gate: fails on any panic/hang/crash/oom, on an ok count below baseline.json, or on a baseline-ok file that is no longer ok |
baseline.json |
the ok files the gate holds the line on |
requirements.txt |
pinned h5py / numpy / hdf5plugin / netCDF4 |
Results for every file (both sides' JSON and stderr, results.csv,
results.json, summary.md) are left in .cache/results/.
The nightly job is .gitea/workflows/conformance.yml; it prints the report
into the job log.
The canonical value encoding both sides hash is documented at the top of
probe/src/main.rs. Values are compared as libhdf5 presents them: a float
with a non-IEEE bit layout (N-Bit) or an integer with a bit offset is compared
as the converted number, not as raw file bytes.