134 lines
6.0 KiB
Markdown
134 lines
6.0 KiB
Markdown
# Known Issues
|
||
|
||
Bugs found during development or downstream use, tracked here because this
|
||
repository's issue tracker is disabled. One entry per bug; when an entry is
|
||
fixed, record the fix in `CHANGELOG.md` and update its status here rather than
|
||
deleting it.
|
||
|
||
---
|
||
|
||
## Compound datatype message version 5 is not parsed (HDF5 2.0)
|
||
|
||
**Status:** fixed on `main` in `a13ff51` (2026-06-03); **not in the v2.1.0
|
||
tag**, which was cut five commits earlier. Ships in the next release.
|
||
|
||
**Reported by:** M. Scot Breitenfeld (The HDF Group), 2026-09-08, against v2.1.0.
|
||
|
||
**Summary:** `clawhdf5-format` v2.1.0 rejects any dataset with a compound
|
||
(struct) datatype written by an HDF5 2.0 library in `libver='latest'` mode:
|
||
`InvalidDatatypeVersion { class: 6, version: 5 }`.
|
||
|
||
**Reproduction** (h5py 3.16.0 / HDF5 2.0.0):
|
||
|
||
```python
|
||
import h5py, numpy as np
|
||
dt = np.dtype([('x', 'f8'), ('y', 'f8'), ('id', 'i4')])
|
||
data = np.array([(1.0, 2.0, 10), (3.0, 4.0, 20)], dtype=dt)
|
||
f = h5py.File('compound.h5', 'w', libver='latest')
|
||
f.create_dataset('particles', data=data)
|
||
f.close()
|
||
```
|
||
|
||
Committed as `crates/clawhdf5-format/tests/writer_h5py_tests.rs::read_h5py_generated_compound`
|
||
(`#[ignore]`d; needs `python3` with h5py on `PATH`). Run with
|
||
`cargo test -p clawhdf5-format --test writer_h5py_tests -- --include-ignored`:
|
||
v2.1.0 gives 25 passed / 1 failed; `main` passes everything.
|
||
|
||
**Root cause:** the compound (class 6) branch of `Datatype::parse`
|
||
(`crates/clawhdf5-format/src/datatype.rs`) accepted only versions 1–4. Datatype
|
||
message versions 4 and 5 changed only the Reference and Complex classes, so a
|
||
v5-tagged compound uses the unchanged v3 member-list layout.
|
||
|
||
**Fix:** versions 3–5 are accepted for compound (class 6) and array (class 10)
|
||
datatypes, and data layout message version 5 is accepted too (needed for every
|
||
chunked dataset written by HDF5 2.0). Byte-level regression tests:
|
||
`test_compound_v5_from_hdf5_2_0`, `test_array_v5_from_hdf5_2_0`.
|
||
|
||
## Native complex datatype (class 11) is mis-parsed (HDF5 2.0)
|
||
|
||
**Status:** fixed 2026-09-18. Found while validating the report above.
|
||
|
||
**Summary:** HDF5 2.0 native complex types (`H5T_COMPLEX_IEEE_F64LE` etc.)
|
||
were parsed as if they carried a compound-style member list. The properties are
|
||
actually a single base floating-point datatype, so the parser produced a garbage
|
||
datatype, or `UnexpectedEof` when the complex type was a compound member. h5py's
|
||
default numpy-complex mapping is unaffected (it writes a `{r, i}` compound);
|
||
only files using the native type through the C API / h5py low-level API hit this.
|
||
|
||
**Fix:** class 11 parses its base type and is surfaced as the equivalent
|
||
`{r, i}` compound. Tests: `test_complex_v5_from_hdf5_2_0`,
|
||
`test_compound_with_complex_member_from_hdf5_2_0`,
|
||
`writer_h5py_tests.rs::read_h5py_generated_native_complex`.
|
||
|
||
## Revised reference datatype (class 7, version 4) is not parsed
|
||
|
||
**Status:** open, unconfirmed against a real file.
|
||
|
||
**Summary:** HDF5 1.12+ `H5T_STD_REF` references use datatype version 4 with
|
||
reference types 2–4 (object2 / region2 / attribute), which `Datatype::parse`
|
||
rejects with `InvalidReferenceType`. h5py still writes the legacy v1
|
||
object/region references, which read correctly, so no reproducing file has been
|
||
generated yet; one written with the C API (`H5T_STD_REF`) is needed.
|
||
|
||
## `clawhdf5-gpu` `gpu_tests` can hang under the default parallel test runner
|
||
|
||
**Status:** fixed 2026-09-19.
|
||
|
||
**Summary:** during `cargo test --workspace` the `gpu_tests` binary sat idle for
|
||
25+ minutes. Every test created its own `wgpu::Instance` + device (requesting
|
||
adapter-maximum limits) concurrently, and readback used an unbounded
|
||
`device.poll(Wait)`.
|
||
|
||
**Fix:** tests hold a process-wide lock while they own a device, and
|
||
`GpuAccelerator` readback waits time out after 30 s with `GpuError::BufferMap`.
|
||
|
||
## Compound datatype versions 1 and 2 are mis-parsed (default libver files)
|
||
|
||
**Status:** fixed 2026-09-19. Found by adding a default-libver axis to the h5py
|
||
interop tests.
|
||
|
||
**Summary:** any compound dataset written with default libver bounds (plain
|
||
`h5py.File(path, 'w')`, datatype message version 1) failed to read, typically
|
||
with `Overflow("compound member 'x': byte_offset(0) + field_size(4136977) ...")`.
|
||
Only `libver='latest'` files (version 3+) and files written by clawhdf5 itself
|
||
worked, which is why the existing tests never caught it.
|
||
|
||
**Root cause:** `Datatype::parse` skipped 24 bytes of legacy per-member array
|
||
fields for v1 where the format has 28 (dimensionality 1 + reserved 3 +
|
||
permutation 4 + reserved 4 + 4 dimension sizes 16), and treated v2 like v1 minus
|
||
name padding, whereas v2 keeps the 8-byte name padding and has no array fields.
|
||
|
||
## Attributes with unsupported datatypes are silently dropped
|
||
|
||
**Status:** open.
|
||
|
||
**Summary:** `Dataset::attrs()` / `Group::attrs()` in the `clawhdf5` facade return
|
||
only attributes convertible to `AttrValue`. An attribute with, e.g., a compound
|
||
datatype is omitted from the map with no error or indication that it exists.
|
||
Planned: surface these as an explicit `AttrValue` variant (raw bytes + datatype)
|
||
or an error, as part of the "no silent skips" robustness work.
|
||
|
||
## B-tree v2 chunk index (layout v4, index type 5) is not supported
|
||
|
||
**Status:** open.
|
||
|
||
**Summary:** a chunked dataset with **two or more unlimited dimensions** written
|
||
with `libver='latest'` indexes its chunks with a version-2 B-tree. Reading it
|
||
fails with `ChunkedReadError("unsupported chunked layout version=4,
|
||
index_type=Some(5)")`. Single-chunk, implicit, fixed-array and
|
||
extensible-array indexes (and the v3 B-tree v1) are supported.
|
||
|
||
**Repro:** `f.create_dataset("d", shape=(5, 7), chunks=(2, 3), maxshape=(None, None))`
|
||
with `h5py.File(..., libver='latest')`.
|
||
|
||
## External links and external raw data are not followed
|
||
|
||
**Status:** open (by design for now); both are explicit errors.
|
||
|
||
**Summary:** a path through an external link returns
|
||
`FormatError::ExternalLinkUnsupported { filename, object_path }`, and a dataset
|
||
created with `external=[...]` storage returns
|
||
`FormatError::ExternalDataFilesUnsupported`. Neither is resolved. If support is
|
||
added, file names must be confined to the opened file's directory, as the
|
||
virtual-dataset resolver now does.
|