Public bug reported: Files written by older HDF5 versions, which read fine with hdf5 1.14.6, fail to read with hdf5 2.2.0 in stonking. Every affected read fails with:
``` HDF5-DIAG: Error detected in HDF5 (2.2.0) thread 1: [...] #006: ./src/H5Dchunk.c line 3142 in H5D__chunk_read(): unable to lock raw data chunk #007: ./src/H5Dchunk.c line 4856 in H5D__chunk_lock(): chunk size is incorrect after being unfiltered major: Dataset minor: Bad value ``` I first hit this through the uncalled autopkgtest. uncalled 2.3+ds-3ubuntu1 in stonking-proposed builds fine, but its run-unit-test regression fails on every architecture tested, so its migration out of proposed is blocked: https://autopkgtest.ubuntu.com/results/autopkgtest-stonking/stonking/amd64v3/u/uncalled/20260922_ 225035_d1f10@/log.gz The test data is an older fast5 file shipped in the uncalled source package. I checked it directly: the dataset is chunked with a compression filter, the single chunk is partial, and the writer stored the compressed stream of the valid data only, not of the whole chunk buffer. That is the pattern older writers produced, and 1.14.6 reads it without complaint. HDF5 2.2.0 added a check in H5D__chunk_lock (src/H5Dchunk.c line 4856 in the released source) that requires the unfiltered chunk to come back at exactly the full chunk size. For these older files it comes back smaller, so the read is rejected. The check is listed in the 2.2.0 changelog under "Added checks for data filter behavior". Reproducer: any program that opens one of these files read-only and reads the dataset triggers the error. I reproduced it with a build of the 2.2.0 release tarball; the same program linked against 1.14.6 succeeds. Scope: any stonking program that reads older HDF5 files with the same partial-chunk layout. This is a runtime regression: build and link work fine, and all architectures are affected. Migration impact: until hdf5 is fixed, every package whose tests or users read older HDF5 files will regress on autopkgtest or at runtime. uncalled is blocked in stonking-proposed right now. Upstream and Debian will likely hit the same issue. Upstream does not report dropping support for those legacy files in release notes so this might be an unintended side-effect. ** Affects: hdf5 (Ubuntu) Importance: Undecided Assignee: Valentin Haudiquet (vhaudiquet) Status: In Progress ** Affects: uncalled (Ubuntu) Importance: Undecided Status: Invalid ** Also affects: uncalled (Ubuntu) Importance: Undecided Status: New ** Changed in: uncalled (Ubuntu) Status: New => Invalid -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/2168435 Title: hdf5 2.2.0 fails to read legacy fast5 files: chunk size is incorrect after being unfiltered To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/hdf5/+bug/2168435/+subscriptions -- ubuntu-bugs mailing list [email protected] https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
