Bug 2395128
| Summary: | Segmentation fault during open_dataset() with dask and netcdf4 | ||
|---|---|---|---|
| Product: | [Fedora] Fedora | Reporter: | david08741 |
| Component: | python-xarray | Assignee: | Elliott Sales de Andrade <quantum.analyst> |
| Status: | CLOSED ERRATA | QA Contact: | Fedora Extras Quality Assurance <extras-qa> |
| Severity: | medium | Docs Contact: | |
| Priority: | high | ||
| Version: | rawhide | CC: | epel-packagers-sig, jonathan, python-packagers-sig, quantum.analyst |
| Target Milestone: | --- | ||
| Target Release: | --- | ||
| Hardware: | Unspecified | ||
| OS: | Linux | ||
| URL: | https://github.com/pydata/xarray/issues/9779 | ||
| Whiteboard: | |||
| Fixed In Version: | python-xarray-2025.9.0-3.fc43 | Doc Type: | --- |
| Doc Text: | Story Points: | --- | |
| Clone Of: | Environment: | ||
| Last Closed: | 2025-10-07 00:20:27 UTC | Type: | --- |
| Regression: | --- | Mount Type: | --- |
| Documentation: | --- | CRM: | |
| Verified Versions: | Category: | --- | |
| oVirt Team: | --- | RHEL 7.3 requirements from Atomic Host: | |
| Cloudforms Team: | --- | Target Upstream Version: | |
| Embargoed: | |||
| Bug Depends On: | |||
| Bug Blocks: | 2372202 | ||
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Description
david08741
2025-09-15 07:56:27 UTC
This is blocking xbout rebuild. There an abort is triggered, and the I got these backtraces: ``` Current thread 0x00007fe240319bc0 [pytest] (most recent call first): Garbage-collecting File "/usr/lib/python3.14/site-packages/dask/array/core.py", line 1274 in blockdims_from_blockshape File "/usr/lib/python3.14/site-packages/dask/array/core.py", line 3232 in <genexpr> File "/usr/lib/python3.14/site-packages/dask/array/core.py", line 3229 in _convert_int_chunk_to_tuple File "/usr/lib/python3.14/site-packages/dask/array/core.py", line 3203 in normalize_chunks File "/usr/lib/python3.14/site-packages/xarray/namedarray/daskmanager.py", line 57 in normalize_chunks File "/usr/lib/python3.14/site-packages/xarray/structure/chunks.py", line 86 in _get_chunk File "/usr/lib/python3.14/site-packages/xarray/backends/api.py", line 366 in _chunk_ds File "/usr/lib/python3.14/site-packages/xarray/backends/api.py", line 402 in _dataset_from_backend_dataset File "/usr/lib/python3.14/site-packages/xarray/backends/api.py", line 693 in open_dataset File "/usr/lib/python3.14/site-packages/xarray/backends/api.py", line 1635 in open_mfdataset File "/builddir/build/BUILD/python-xbout-0.3.8-build/xbout-0.3.8/xbout/load.py", line 651 in _auto_open_mfboutdataset File "/builddir/build/BUILD/python-xbout-0.3.8-build/xbout-0.3.8/xbout/load.py", line 279 in open_boutdataset File "/builddir/build/BUILD/python-xbout-0.3.8-build/xbout-0.3.8/xbout/tests/test_animate.py", line 25 in create_test_file [...] Current thread's C stack trace (most recent call first): Binary file "/lib64/libpython3.14.so.1.0", at _Py_DumpStack+0x4c [0x7fe240723813] Binary file "/lib64/libpython3.14.so.1.0", at +0x121297 [0x7fe240724297] Binary file "/lib64/libc.so.6", at +0x1a2c0 [0x7fe2404292c0] Binary file "/lib64/libc.so.6", at +0x742bc [0x7fe2404832bc] Binary file "/lib64/libc.so.6", at gsignal+0x1e [0x7fe24042918e] Binary file "/lib64/libc.so.6", at abort+0x26 [0x7fe2404106d0] Binary file "/lib64/libc.so.6", at __assert_perror_fail+0x0 [0x7fe240410639] Binary file "/lib64/libnetcdf.so.22", at +0x11256 [0x7fe22997e256] Binary file "/lib64/libnetcdf.so.22", at nc4_close_hdf5_file+0x55 [0x7fe2299d42b5] Binary file "/lib64/libnetcdf.so.22", at NC4_close+0x68 [0x7fe2299d46b8] Binary file "/lib64/libnetcdf.so.22", at nc_close+0x40 [0x7fe22998c3b0] Binary file "/usr/lib64/python3.14/site-packages/netCDF4/_netCDF4.cpython-314-x86_64-linux-gnu.so", at +0x4a62d [0x7fe229b7062d] Binary file "/lib64/libpython3.14.so.1.0", at +0x1e6fa6 [0x7fe2407e9fa6] Binary file "/lib64/libpython3.14.so.1.0", at PyObject_VectorcallMethod+0x90 [0x7fe2407ed680] Binary file "/usr/lib64/python3.14/site-packages/netCDF4/_netCDF4.cpython-314-x86_64-linux-gnu.so", at +0x111560 [0x7fe229c37560] Binary file "/lib64/libpython3.14.so.1.0", at +0x1f78e6 [0x7fe2407fa8e6] Binary file "/lib64/libpython3.14.so.1.0", at +0x25e289 [0x7fe240861289] [...] ``` If upstream doesn't have a fix, I'm not sure I can do anything about it. From the upstream issue, it looks like if you can modify the test to use `engine='h5netcdf'` then you might avoid the problem. FEDORA-2025-653d7f2ca9 (python-xarray-2025.9.0-3.fc43 and python-xbout-0.3.8-3.fc43) has been submitted as an update to Fedora 43. https://bodhi.fedoraproject.org/updates/FEDORA-2025-653d7f2ca9 FEDORA-2025-653d7f2ca9 has been pushed to the Fedora 43 testing repository. Soon you'll be able to install the update with the following command: `sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2025-653d7f2ca9` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2025-653d7f2ca9 See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates. FEDORA-2025-653d7f2ca9 (python-xarray-2025.9.0-3.fc43 and python-xbout-0.3.8-3.fc43) has been pushed to the Fedora 43 stable repository. If problem still persists, please make note of it in this bug report. |