https://bugzilla.redhat.com/show_bug.cgi?id=2395128
Bug ID: 2395128 Summary: Segmentation fault during open_dataset() with dask and netcdf4 Product: Fedora Version: rawhide URL: https://github.com/pydata/xarray/issues/9779 OS: Linux Status: NEW Component: python-xarray Severity: medium Assignee: quantum.analyst@gmail.com Reporter: david08741@gmail.com QA Contact: extras-qa@fedoraproject.org CC: epel-packagers-sig@lists.fedoraproject.org, jonathan@almalinux.org, python-packagers-sig@lists.fedoraproject.org, quantum.analyst@gmail.com Target Milestone: --- Classification: Fedora
dask is broken with xarray and netcdf, as netcdf is not thread safe.
Details in upsteam bugreport: https://github.com/pydata/xarray/issues/9779
Adding the MRE as a test to the xarray build reproduces the issue in e.g. copr: https://copr.fedorainfracloud.org/coprs/davidsch/testing/build/9550663/
Reproducible: Always
Steps to Reproduce: 1.Run upstream MRE in rawhide with python3.14 Actual Results:
+ PYTHONPATH=/builddir/build/BUILD/python-xarray-2025.4.0-build/BUILDROOT/usr/lib64/python3.14/site-packages:/builddir/build/BUILD/python-xarray-2025.4.0-build/BUILDROOT/usr/lib/python3.14/site-packages + python3 /builddir/build/SOURCES/9779_mre.py /var/tmp/rpm-tmp.8NttXy: line 49: 2258 Segmentation fault (core dumped) PYTHONPATH="${PYTHONPATH:-/builddir/build/BUILD/python-xarray-2025.4.0-build/BUILDROOT/usr/lib64/python3.14/site-packages:/builddir/build/BUILD/python-xarray-2025.4.0-build/BUILDROOT/usr/lib/python3.14/site-packages}" python3 /builddir/build/SOURCES/9779_mre.py
Expected Results: no error
https://bugzilla.redhat.com/show_bug.cgi?id=2395128
--- Comment #1 from david08741@gmail.com --- 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] [...] ```
https://bugzilla.redhat.com/show_bug.cgi?id=2395128
david08741@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Blocks| |2372202
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=2372202 [Bug 2372202] F43FailsToInstall: python3-xbout
https://bugzilla.redhat.com/show_bug.cgi?id=2395128
david08741@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Priority|unspecified |high
https://bugzilla.redhat.com/show_bug.cgi?id=2395128
--- Comment #2 from Elliott Sales de Andrade quantum.analyst@gmail.com --- 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.
https://bugzilla.redhat.com/show_bug.cgi?id=2395128
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |MODIFIED
--- Comment #3 from Fedora Update System updates@fedoraproject.org --- 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
https://bugzilla.redhat.com/show_bug.cgi?id=2395128
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|MODIFIED |ON_QA
--- Comment #4 from Fedora Update System updates@fedoraproject.org --- 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.
https://bugzilla.redhat.com/show_bug.cgi?id=2395128
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Resolution|--- |ERRATA Fixed In Version| |python-xarray-2025.9.0-3.fc | |43 Status|ON_QA |CLOSED Last Closed| |2025-10-07 00:20:27
--- Comment #5 from Fedora Update System updates@fedoraproject.org --- 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.
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