Idle-start run on tank at c5334b1 (noisier than the last: compare ratios
within the run). Full reads of deflate data at 16 threads: 4944 MB/s vs
3135 for 16 h5py processes (1.58x; 0.69x-0.76x before). One thread with
the default pool: 6143 MB/s, 15x one h5py call. The concurrent-read
known issue is closed.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
The scale-offset fix (d110b1d) was covered only by unit vectors from
CVE chunks, and documented as three corner cases. The review found it
is much bigger: of 1480 scale-offset datasets h5py writes (every
integer type i1..u8, f4 and f8, both byte orders, with and without a
fill value, scaleoffset 0..full width), v2.7.0's decoder read 332
differently from h5py: 151 returned wrong values with no error (82
integer datasets with scaleoffset=0 and a wide range, 51 full-width
i4/u4/i8/u8, 18 f4 D-scale datasets with a large range) and 181 failed
to read. The cause in every case is a chunk libhdf5 stores at full
width, whose elements were decoded as offsets from minval.
tests/scaleoffset_interop.rs generates that matrix with h5py at test
time, stores h5py's decoded values uncompressed next to it, and
compares every dataset's bytes. It passes on this branch; with the
filters.rs before d110b1d it reports "332 of 1480 scale-offset datasets
differ from h5py".
CHANGELOG: a Correctness entry stating this was silent wrong data in
every release that decoded scale-offset (v2.2.0 to v2.7.0), replacing
the corner-case wording. docs/known-issues.md: a fixed entry with the
affected cases.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
For a metadata cache image libhdf5 cannot load, libhdf5 opens the file
and fails the first metadata read (the image loads on the first
H5C_protect after open); h5py reports the error on the root group. The
conformance probe reported it that way, but File::open refused the file,
so the gate counted cve-2025-6269-1..4 and cve-2025-6516 as agreeing
with h5py for behaviour the library did not have.
The library now behaves as the probe reports: File (mmap, buffered and
from_bytes) and MmapFile open the file and every object lookup (dataset,
dataset_at, group, group listings and attributes, VL decoding) fails with
the image's error; LazyFile reads the root group's header at open, so
its open is that first read and fails. Probe and library take the
three-way decision (refuse at open / image loads / image cannot load)
from the same clawhdf5_format::superblock_ext::cache_image_state.
One deliberate difference from libhdf5 remains, documented: after the
failed first read libhdf5 reads the file's own metadata, which the image
was meant to replace and may be stale; here every lookup keeps failing.
File::cache_image_error / MmapFile::cache_image_error expose the error
to code that parses as_bytes() itself; h5rs checks it before reading any
object header (h5rs ls on cve-2025-6269-1 said "invalid object header
version: 0" from the stale bytes).
Test: metadata_cache_image.rs an_image_libhdf5_cannot_load_fails_every_object
(the fixture with its image signature broken; h5py opens that file and
fails the first read with "Bad metadata cache image header signature").
It fails on the previous commit, where File::open refuses the file.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
Conformance on tank, conformance/run.sh --no-fetch (2026-09-26): 597 of
697 ok, 6 our-errors (4 corrupt objects HDF5 2.0 reads through a bug, the
Blosc2 and ZFP filters), 2 mismatches (the known h5py big-endian VL bug).
Closes the known-issues entries for metadata cache images,
cve-2024-32624, cve-2020-10810/10812, and unfiltered chunks of the wrong
size; the N-Bit / 64-bit scale-offset entry is recorded as not our bug.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
CHANGELOG entry for the chunked read changes, and the known-issues entry
on concurrent chunked reads updated: both causes it names (per-read page
faults, readers waiting on a small pool) are fixed; the 16-thread
comparison with h5py stays open until re-measured on an idle machine.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
Record the `blosc2` feature in the changelog, the README's feature table
and the crate table, and mark the Blosc2 half of the known "Filters"
issue fixed (dated, with the conformance run that shows h5ex_d_blosc2
reading). What stays open: ZFP, writing Blosc2, and the Blosc2 features
hdf5plugin never writes (dictionaries, lazy chunks, variable-length
blocks, user-defined codecs and registered filters), which are errors.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
h5py's track_order=True orders attributes as well as links; the writer
tracked links only. A tracking object's header now sets the attribute
creation order tracked/indexed flags and carries per-message creation
orders, an Attribute Info message holds the next order (inline too),
and dense storage gets a type-9 creation-order index. The file default
applies to datasets, with DatasetBuilder::track_order per dataset; more
than 65 535 attributes on a tracking object is an error (libhdf5's
counter is 2 bytes). The reader lists such attributes in creation
order.
h5py lists them in order (inline, dense, 20 000 on one dataset) and
keeps numbering in r+ mode, including its inline-to-dense move.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
Dense link and attribute indexes and the chunk index for several
unlimited dimensions were single leaves, capping them at 65 535
records. btree_v2_write builds trees of any depth, with node capacities
and pointer widths from libhdf5's H5B2__hdr_init arithmetic (now shared
with the reader as btree_v2::node_info) and libhdf5's node sizes (512
dense, 2048 chunks). Indexes that fit the old one-leaf layout are
written byte for byte as before (compared for 10..65 535 links, attrs
and chunks, tracked and filtered).
Tests: 100 000 links (short names; long names with creation order),
70 000 attributes, 200 000 chunks (and 80 000 deflated), read by h5py,
h5dump and clawhdf5 and edited by h5py r+; h5rs check on the same
shapes, asserting depths 2-3.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
Idle tank at 408f69e, h5py re-run in the same session. Contiguous reads
went from 0.25x to 1.44x h5py (full) and 0.12x to 6.3x (256x256
hyperslabs) on one thread; deflate full reads at 8 threads 887 -> 2943
MB/s (h5py processes 3042). Full chunked reads at 16 threads are still
0.69x-0.76x h5py processes; the issue stays open.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
libhdf5 fails to read a VL element whose global heap address is
undefined (all 0xff), even at length 0 ("addr undefined"); we returned
"" (or an empty sequence) in every reader. Checked with h5py first:
libhdf5 writes a null element with address 0, which still reads as
empty, and h5py writes "" as a zero-size heap object at a real address,
so no file they write relies on the old behaviour. read_vl_bytes now
treats address 0 as null whatever the length, as VlResolver does.
Tests, each failing before: vl_data unit test (8- and 4-byte offsets,
lengths 0 and 1); clawhdf5 vl_data_interop
a_vl_element_at_the_undefined_heap_address_fails_like_h5py (also checks
where h5py writes ""); h5rs dump --json and check --data on the patched
`undef` dataset; clawhdf5-wasm vl_strings.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
The READMEs said ds[...] reads only the selected elements, and the
facade's read_selection docs that only intersecting chunks are
decompressed. The bounding-box path runs only when the box covers at
most half the dataset; larger boxes (any strided slice across the
dataset), compact, virtual and unwritten datasets and chunked ones with
a non-default fill value decode the whole dataset. The READMEs, the
facade and format docs, the bindings' docstrings and known-issues now
say so, and how index lists are read.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
h5rs (dump, ls, diff, check --data) kept its own lenient VL decoder:
a heap object longer than its element was cut to the element's length
(libhdf5 and h5py refuse it), a null string printed "" where h5dump
prints NULL, the stored element size was trusted, and every heap
collection was kept as an owned copy for the whole run. It now resolves
each element with VlResolver::element / string_element (new: one element
in place, borrowing from the file), and refuses a VL type whose stored
element size is not 4 + offset size + 4, as File does. H5::heap_object
and its cache are gone. h5diff compares a null VL string equal to an
empty one; so does h5rs diff.
clawhdf5-wasm already resolved VL strings with read_vl_strings; it now
uses VlResolver and checks the stored element size before reading, as
File::read_string does.
Tests (h5py writes the files, patched for "a\0b", a null element and
mis-sized heap objects, with 8- and 4-byte offsets):
- h5rs_interop dump_prints_vl_data_like_h5dump: byte-identical to h5dump;
- dump_json_vl_values_match_h5py: h5py's values, errors where h5py fails;
- check_data_flags_mis_sized_vl_heap_objects;
- clawhdf5-wasm tests/vl_strings.rs: wasm, File and h5py agree.
All four fail before. check --data over the 150 cve_hdf5 CVE and fuzzer
files now passes 15 (h5dump rejects 8 of them), was 16 and 9: the
stored-size check flags cve-2024-32608. h5rs-check-ok-files.sh --data:
0 of 422 flagged; h5rs-fuzz.sh: clean on 180 files.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
The changelog, known issues and README said a group holds up to 65 535
links while a group of about 17 000 was already unreadable. Record the
fixes (child indirect blocks, the next-block offset, the index leaf cap,
refusing oversized dense messages, hard-link memoisation, dataset
attribute overwrite) and the limits that remain true: 65 535 links or
dense attributes per object, and 65 515 bytes per dense message.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
VlResolver kept an owned copy of every object of every heap collection
it parsed, for the whole read. Collections nested inside each other's
object data, 32 bytes apart with each element pointing at a different
one, made retained memory O(elements x file size): 1.58 GB for a 744 KB
file (read_vl_strings did the same before VlResolver). Chaining every
collection's objects into one shared run of tiny objects made parse
time O(elements x objects) as well. libhdf5 refuses these files.
- The cache records where each object lies (GlobalHeapCollection::
parse_index, new) instead of copying it, and is dropped past a 32 MiB
budget.
- A collection overlapping one already read is an error: libhdf5 gives
every collection its own block, so only a crafted file has them.
- parse and parse_index refuse a collection that runs past the end of
the file and an object that runs past the end of its collection.
tests/vl_heap_bounds.rs measures peak heap use with a counting
allocator: 129 MB and 350 MB live before on its two crafted files (64 KB
and 176 KB), 97 KB and 0.9 MB now. Conformance unchanged at 575 of 697.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
The review measured the default pool unchanged (about 2900 MB/s at 16
threads before and after) and still short of 16 h5py processes; small
pools still make outside readers wait. Say so instead of marking the
scaling issue fixed.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
Full reads of chunked datasets handed their chunks to rayon. With a
one-thread pool (concurrent_read --decode-threads 1, RAYON_NUM_THREADS=1)
every thread reading through a File queued behind that single worker, so
16 readers decoded on one core: per-thread CPU time showed one thread
doing all the decoding and the readers almost none, and full reads
stopped at about 2x one thread. The cached full-read path and the
uncached reader behind verify_provenance now decode inline when the pool
cannot parallelise (parallel_read::pool_can_parallelise).
The File's chunk cache was the suspect but not the cause: datasets over
its budget were already read without inserting, and skipping its lookups
gained only a few percent at 16 threads.
The regression test keeps a one-thread global pool's worker busy and
requires a full read and verify_provenance to finish anyway; before the
fix both waited for the worker (timed out).
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
FileWriter wrote the root group plus one level of groups, and refused
path-like names. The writer now flattens its builders into a group tree
(writer_tree.rs) before layout:
- A name may be a path ("a/b/x", "/a/b/x" at the root); missing
intermediate groups are created as h5py does, and GroupBuilder gains
create_group/add_group so builders nest to any depth. A group added at a
path that already holds a group is merged into it (require_group);
any other repeated name, an empty or "." component, or an absolute path
below the root is an error.
- add_soft_link, add_hard_link and add_external_link on FileWriter,
FileBuilder and GroupBuilder. Hard-link targets are resolved to objects
at finish (through other hard links; a missing target, a soft link on the
way or a cycle of paths is an error). Objects with several hard links get
an Object Reference Count message so libhdf5 can delete one link without
freeing the object.
- track_order(true) per group, or as the file default, tracks and indexes
link creation order: Link Info flags and max order, the order in each
Link message, and a type-6 creation-order B-tree for dense groups.
- A group's link index is one B-tree leaf; more than 65535 links is an
error.
Groups are laid out depth-first from the root, datasets group by group,
and untracked groups keep writing datasets, then groups, then other links:
files with one level of groups are byte-identical to before.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
VL-string datasets (h5py's default str dtype) failed read_string with
"type mismatch: expected String, got VariableLength". read_string now
reads fixed- and variable-length strings, with h5py's values (a string
ends at a NUL, a null element is ""). New:
- Dataset::read_string_bytes: each VL string's exact bytes;
- Dataset::read_string_selection: hyperslabs/points of either kind;
- Dataset::read_vlen::<T>() and read_vlen_selection::<T>(): VL sequences
of numbers as Vec<Vec<T>>, T in f64/f32/i64/i32/u64, converted like the
other typed readers;
- File::decode_strings / decode_string_bytes / decode_vlen: VL values in
compound fields and AttrValue::Raw attributes;
- MmapDataset and LazyDataset: read_string for VL strings,
read_string_bytes and read_vlen.
tests/vl_data_interop.rs checks every path against h5py with 8- and
4-byte offsets: scalar, 1-D and 2-D, ASCII and UTF-8, empty strings,
contiguous, compact, chunked with gzip and shuffle, unwritten and partly
written chunks, hyperslabs, compound members, attributes, a big-endian
base type, and a patched file with an embedded NUL and mis-sized heap
objects. NetCDF-4 string variables read too (netCDF4-python test).
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
A 256 x 256 hyperslab of a contiguous f32 dataset read at an eighth of
h5py's speed: partial_read copied the bounding box out of the file, the
extractor then walked it element by element (a recursive call and two
bounds checks per element) into a second buffer, and read_f32_selection
converted that into a third.
Selections of contiguous data are now copied straight from the file, one
memcpy per run of elements contiguous in the file (gather.rs: a block
along the last dimension, touching blocks as one range, whole rows
merged), with no zero-filled intermediate and no full copy for large
selections. The typed selection readers copy into their Vec<T> directly
when the dataset stores T natively (new data_read::read_selection_native
and sealed NativeElement trait, which the read_as_* fast paths now share;
read_as_u64 gains one) and convert as before otherwise. The general
extractor used by the chunked paths runs on the same run walker, keeping
its old handling of unvalidated selections.
Checked against h5py (contiguous_read_interop.rs) for strided, blocked,
adjacent-block and whole-row hyperslabs, points and empty selections of
every 1-8-byte type in both byte orders, ranks 1-4.
Also keeps the huge-page threshold constant out of no_std builds, where
it was unused.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
In a file with sizeof_addr = 4, a VL string attribute came back as
AttrValue::Raw, a compound's VL member failed with
GlobalHeapObjectNotFound and VL datasets failed with a size mismatch.
Two bugs: Datatype::type_size() said 16 for every VL type, while the
element is 4 + offset size + 4 bytes (12 here); and the global heap was
parsed without the padding libhdf5 puts after its collection and object
headers (both round up to 8), so with 4-byte lengths every object was
looked up 4 bytes early. Datatype::VariableLength now carries the size
its datatype message stores, and writes it back.
Checked against h5py in tests/vl_offset4_interop.rs (fails with either
fix reverted). Conformance unchanged at 575 of 697; in cve-2024-32608 a
VL attribute whose datatype claims 524304-byte elements is now an error
(h5py cannot iterate those attributes at all).
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
h5py threads stay flat (global lock); clawhdf5 hyperslab reads of deflate
data scale to 1244 MB/s at 16 threads (9.7x h5py threads, 0.89x h5py
processes). Two deficits recorded as open issues: full chunked reads stop
scaling at ~4 threads (chunk cache suspected), and contiguous reads are
4x (full) to 8x (hyperslab) slower than h5py single-threaded.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
Measured on tank on the 150 cvefiles/ and fuzzerfiles/ of cve_hdf5 (the
earlier text said 180): check --data passes 16 (was 28), and h5dump
1.14.6 rejects 9 of those (was 21). It still flags none of the 418
conformance files both readers read in full.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
The short-decoding chunk (wrong data, pre-existing), the Blosc header
underflow (crash) and filter 32023 registration, each with its date and
what it changes; the conformance count is unchanged at 573 of 697.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
The compound overlap check measured each earlier member with
Datatype::type_size, which is a fixed 16 for a variable-length type. On
disk a VL member takes 4 + offset size + 4 bytes, 12 in a file with
4-byte offsets, so a member right after one was refused as "member
overlaps with previous member" (and with the type, every attribute of
the object). libhdf5 measures members by their decoded, stored size
(times a v1 member's array dimensions); so does this now.
Reading VL values in such files is a separate, older gap, now recorded
in known-issues.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
The README said check skips only "global heap collections other than
those a value read touches", but read_dataset returns the raw heap IDs,
so no collection was ever read: a file whose global heap collection
claims a 4 GiB object passed `check --data` with no problems, while
h5dump (and h5rs dump/diff) fail on it.
With --data, every variable-length element (strings and sequences, also
inside compounds, arrays and nested sequences) of every dataset and
attribute is followed into its collection. A collection that does not
parse, a missing heap object, or a sequence longer than its heap object
is a problem at the collection's address, once per object; the summary
counts the collections read.
Measured on tank, 2026-09-26: the 418 fully-read conformance ok files
still pass (scripts/h5rs-check-ok-files.sh --data, 0 flagged), and
`check --data` now flags 152 of the 180 CVE-corpus files (was 147); of
the 28 it passes, h5dump 1.14.6 rejects 21 (was 26 of 33).
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
CHANGELOG (Correctness): the new header, datatype, chunk and truncation
checks, what is left out on purpose (checks HDF5 2.0 lacks; the two
v2.7.0 writer quirks), the conformance numbers and the new FormatError
variants. known-issues: the "Header checks" audit gap is fixed, with the
one CVE object and two CVE files libhdf5 still refuses and we read.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
Measured on the CVE corpus: check --data passes 33 of 180 files, and
h5dump 1.14.6 rejects 26 of those. Recorded under the open "Header checks"
gap and in the crate README.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
CHANGELOG (Unreleased): LZF, bitshuffle, bzip2 and Blosc read and write
in pure Rust, their features, the ChunkOptions::plugin field (breaking for
struct-literal construction), the filter registry, the named
UnsupportedFilter message, and Blosc2/ZFP still unimplemented.
README: the clawhdf5-format feature table gains lzf (default),
bitshuffle, bzip2, blosc and plugin-filters, with how to write them and
what is not implemented; no speed claims. docs/known-issues.md: the audit's
filter gap is marked fixed 2026-09-26 for LZF/bitshuffle/bzip2/Blosc,
Blosc2 and ZFP still open. CLAUDE.md: the clawhdf5-filters row no longer
says "No Blosc". clawhdf5-format's crate docs list the new features.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
Changelog entry with the sizes measured on tank on 2026-09-26 (and the
h5wasm 0.10.3 comparison), the browser build's limits as a known-issues
entry, and where its tests run.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
Unlimited VDS mappings were refused, and printf-style source names
("f-%b.h5") were not expanded, so those regions read as fill (read-matrix
case 0470: 29 of 30 values wrong). All 7 virtual datasets in the libhdf5
test set use such mappings.
Implement H5Dvirtual.c's semantics in the vds module:
- %b is the block number, %% a literal %, other specifiers are an error;
block j of the virtual selection comes from the source named with j,
probing from 0 to the first missing source (printf gap 0);
- unlimited source/virtual selections are clipped to what the source's
current extent fills (H5S_hyper_get_clip_extent_match, partial last
block included);
- the extent is recomputed as H5Dget_space does (view "last available":
the largest clip, never below what limited mappings need), exposed as
vds::virtual_dataset_extent and used by Dataset::shape();
- a source in the other byte order is byte-swapped; other conversions stay
an error.
Tests: vds_interop::vds_printf_source_names,
vds_unlimited_mappings_follow_source_extents (h5py low-level API, earliest
and latest format) and vds_libhdf5_test_files (vds-eiger, 4_vds and
vds-percival-unlim-maxmin from HDF5's tools/test/testfiles/vds, committed
as fixtures) all compare shape and values with h5py; unit tests for the
clip arithmetic, name parsing and mapping rules.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
libhdf5 walks a local heap's free list when it loads the heap's data and
refuses the heap ("bad heap free list") when a free block starts or ends
outside the data segment, or links to offset 0. We never looked at the
free list, so a damaged old-style group listed names read from the broken
heap: once the user block of cve-2021-36977.h5 was applied, its root
listed eight garbage names where libhdf5 fails.
LocalHeap::validate_free_list (new) mirrors H5HL__fl_deserialize, with a
cycle bound, and accepts H5HL_FREE_NULL (1) or an all-ones head as the
end of the list. Like libhdf5 it runs when the first name is needed, not
on parse, so an empty group with a damaged heap still lists as empty
(cve-2018-13871.h5, cve-2024-29166.h5, gh-4431-poc-03.h5 keep matching
h5py).
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]>
A version-1 shared message (HDF5 1.6) embeds the target as a symbol-table
entry: after six reserved bytes comes a length-sized local-heap offset,
then the object header address. We read the heap offset as the address,
so datasets using a committed datatype in 1.6-era files (tcompound.h5,
tcompound2.h5) failed with InvalidObjectHeaderVersion. parse_shared_ref
now takes length_size and skips the offset, as libhdf5 does.
Resolving a reference also no longer falls back to the first message of
any type in the target header: a missing target message is
SharedMessageTargetMissing instead of garbage.
Fixture: tcompound.h5 from libhdf5's tools/test/testfiles (8 KiB).
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
HDF5 1.6 encoded a compound member that is a fixed-size array through
legacy per-member fields (dimensionality, permutation, four dimension
sizes) that the v1 decoder skipped, so a [4] i32 member read as one i32
with the wrong size. Build the array type from those fields as libhdf5
does (ignoring the permutation) and refuse more than four dimensions.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
