occasional segfaults on CI

[keewis]

The upstream-dev CI currently fails sometimes due to a segfault (the normal CI crashes, too, but since we use pytest-xdist we only get a message stating "worker x crashed").

I'm not sure why, and I can't reproduce locally, either. Given that dask's local scheduler is in the traceback and the failing test is test_open_mfdataset_manyfiles, I assume there's some issue with parallel disk access or the temporary file creation.

log of the segfaulting CI job

============================= test session starts ==============================
platform linux -- Python 3.10.11, pytest-7.3.1, pluggy-1.0.0
rootdir: /home/runner/work/xarray/xarray
configfile: setup.cfg
testpaths: xarray/tests, properties
plugins: env-0.8.1, xdist-3.3.1, timeout-2.1.0, cov-4.1.0, reportlog-0.1.2, hypothesis-6.75.6
timeout: 60.0s
timeout method: signal
timeout func_only: False
collected 16723 items / 2 skipped

xarray/tests/test_accessor_dt.py ....................................... [  0%]
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xarray/tests/test_accessor_str.py ...................................... [  1%]
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xarray/tests/test_array_api.py ...........                               [  3%]
xarray/tests/test_backends.py ........................X........x........ [  3%]
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Fatal Python error: Segmentation fault

Thread 0x00007f9c7b8ff640 (most recent call first):
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/concurrent/futures/thread.py", line 81 in _worker
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/threading.py", line 953 in run
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/threading.py", line 1016 in _bootstrap_inner
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/threading.py", line 973 in _bootstrap

Current thread 0x00007f9c81f1d640 (most recent call first):
  File "/home/runner/work/xarray/xarray/xarray/backends/file_manager.py", line 216 in _acquire_with_cache_info
  File "/home/runner/work/xarray/xarray/xarray/backends/file_manager.py", line 198 in acquire_context
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/contextlib.py", line 135 in __enter__
  File "/home/runner/work/xarray/xarray/xarray/backends/netCDF4_.py", line 392 in _acquire
  File "/home/runner/work/xarray/xarray/xarray/backends/netCDF4_.py", line 398 in ds
  File "/home/runner/work/xarray/xarray/xarray/backends/netCDF4_.py", line 336 in __init__
  File "/home/runner/work/xarray/xarray/xarray/backends/netCDF4_.py", line 389 in open
  File "/home/runner/work/xarray/xarray/xarray/backends/netCDF4_.py", line 588 in open_dataset
  File "/home/runner/work/xarray/xarray/xarray/backends/api.py", line 566 in open_dataset
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/utils.py", line 73 in apply
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/core.py", line 121 in _execute_task
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/local.py", line 224 in execute_task
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/local.py", line 238 in <listcomp>
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/local.py", line 238 in batch_execute_tasks
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/concurrent/futures/thread.py", line 58 in run
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/concurrent/futures/thread.py", line 83 in _worker
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/threading.py", line 953 in run
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/threading.py", line 1016 in _bootstrap_inner
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/threading.py", line 973 in _bootstrap

Thread 0x00007f9c82f1e640 (most recent call first):
  File "/home/runner/work/xarray/xarray/xarray/backends/file_manager.py", line 216 in _acquire_with_cache_info
  File "/home/runner/work/xarray/xarray/xarray/backends/file_manager.py", line 198 in acquire_context
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/contextlib.py", line 135 in __enter__
  File "/home/runner/work/xarray/xarray/xarray/backends/netCDF4_.py", line 392 in _acquire
  File "/home/runner/work/xarray/xarray/xarray/backends/netCDF4_.py", line 398 in ds
  File "/home/runner/work/xarray/xarray/xarray/backends/netCDF4_.py", line 336 in __init__
  File "/home/runner/work/xarray/xarray/xarray/backends/netCDF4_.py", line 389 in open
  File "/home/runner/work/xarray/xarray/xarray/backends/netCDF4_.py", line 588 in open_dataset
  File "/home/runner/work/xarray/xarray/xarray/backends/api.py", line 566 in open_dataset
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/utils.py", line 73 in apply
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/core.py", line 121 in _execute_task
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/local.py", line 224 in execute_task
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/local.py", line 238 in <listcomp>
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/local.py", line 238 in batch_execute_tasks
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/concurrent/futures/thread.py", line 58 in run
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/concurrent/futures/thread.py", line 83 in _worker
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/threading.py", line 953 in run
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/threading.py", line 1016 in _bootstrap_inner
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/threading.py", line 973 in _bootstrap

Thread 0x00007f9ca575e740 (most recent call first):
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/threading.py", line 320 in wait
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/queue.py", line 171 in get
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/local.py", line 137 in queue_get
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/local.py", line 500 in get_async
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/threaded.py", line 89 in get
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/base.py", line 595 in compute
  File "/home/runner/work/xarray/xarray/xarray/backends/api.py", line 1046 in open_mfdataset
  File "/home/runner/work/xarray/xarray/xarray/tests/test_backends.py", line 3295 in test_open_mfdataset_manyfiles
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/_pytest/python.py", line 194 in pytest_pyfunc_call
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/_pytest/python.py", line 1799 in runtest
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/_pytest/runner.py", line 169 in pytest_runtest_call
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/_pytest/runner.py", line 262 in <lambda>
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/_pytest/runner.py", line 341 in from_call
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/_pytest/runner.py", line 261 in call_runtest_hook
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/_pytest/runner.py", line 222 in call_and_report
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/_pytest/runner.py", line 133 in runtestprotocol
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/_pytest/runner.py", line 114 in pytest_runtest_protocol
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/_pytest/main.py", line 348 in pytest_runtestloop
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/_pytest/main.py", line 323 in _main
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/_pytest/main.py", line 269 in wrap_session
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/_pytest/main.py", line 316 in pytest_cmdline_main
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/_pytest/config/__init__.py", line 166 in main
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/_pytest/config/__init__.py", line 189 in console_main
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/pytest/__main__.py", line 5 in <module>
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/runpy.py", line 86 in _run_code
  File "/home/runner/micromamba-root/envs/xarray-tests/lib/python3.10/runpy.py", line 196 in _run_module_as_main

Extension modules: numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pandas._libs.ops, numexpr.interpreter, bottleneck.move, bottleneck.nonreduce, bottleneck.nonreduce_axis, bottleneck.reduce, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.indexing, pandas._libs.index, pandas._libs.internals, pandas._libs.join, pandas._libs.writers, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, cftime._cftime, yaml._yaml, cytoolz.utils, cytoolz.itertoolz, cytoolz.functoolz, cytoolz.dicttoolz, cytoolz.recipes, xxhash._xxhash, psutil._psutil_linux, psutil._psutil_posix, markupsafe._speedups, numpy.linalg.lapack_lite, matplotlib._c_internal_utils, PIL._imaging, matplotlib._path, kiwisolver._cext, scipy._lib._ccallback_c, _cffi_backend, unicodedata2, netCDF4._netCDF4, h5py._errors, h5py.defs, h5py._objects, h5py.h5, h5py.h5r, h5py.utils, h5py.h5s, h5py.h5ac, h5py.h5p, h5py.h5t, h5py._conv, h5py.h5z, h5py._proxy, h5py.h5a, h5py.h5d, h5py.h5ds, h5py.h5g, h5py.h5i, h5py.h5f, h5py.h5fd, h5py.h5pl, h5py.h5o, h5py.h5l, h5py._selector, pyproj._compat, pyproj._datadir, pyproj._network, pyproj._geod, pyproj.list, pyproj._crs, pyproj.database, pyproj._transformer, pyproj._sync, matplotlib._image, rasterio._version, rasterio._err, rasterio._filepath, rasterio._env, rasterio._transform, rasterio._base, rasterio.crs, rasterio._features, rasterio._warp, rasterio._io, numcodecs.compat_ext, numcodecs.blosc, numcodecs.zstd, numcodecs.lz4, numcodecs._shuffle, msgpack._cmsgpack, numcodecs.vlen, zstandard.backend_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._flinalg, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.ndimage._nd_image, _ni_label, scipy.ndimage._ni_label, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize.__nnls, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.optimize._direct, scipy.integrate._odepack, scipy.integrate._quadpack, scipy.integrate._vode, scipy.integrate._dop, scipy.integrate._lsoda, scipy.special.cython_special, scipy.stats._stats, scipy.stats.beta_ufunc, scipy.stats._boost.beta_ufunc, scipy.stats.binom_ufunc, scipy.stats._boost.binom_ufunc, scipy.stats.nbinom_ufunc, scipy.stats._boost.nbinom_ufunc, scipy.stats.hypergeom_ufunc, scipy.stats._boost.hypergeom_ufunc, scipy.stats.ncf_ufunc, scipy.stats._boost.ncf_ufunc, scipy.stats.ncx2_ufunc, scipy.stats._boost.ncx2_ufunc, scipy.stats.nct_ufunc, scipy.stats._boost.nct_ufunc, scipy.stats.skewnorm_ufunc, scipy.stats._boost.skewnorm_ufunc, scipy.stats.invgauss_ufunc, scipy.stats._boost.invgauss_ufunc, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, scipy.stats._biasedurn, scipy.stats._levy_stable.levyst, scipy.stats._stats_pythran, scipy._lib._uarray._uarray, scipy.stats._statlib, scipy.stats._sobol, scipy.stats._qmc_cy, scipy.stats._mvn, scipy.stats._rcont.rcont, scipy.cluster._vq, scipy.cluster._hierarchy, scipy.cluster._optimal_leaf_ordering, shapely.lib, shapely._geos, shapely._geometry_helpers, cartopy.trace, scipy.fftpack.convolve, tornado.speedups, cf_units._udunits2, scipy.io.matlab._mio_utils, scipy.io.matlab._streams, scipy.io.matlab._mio5_utils (total: 241)
/home/runner/work/_temp/b3f3888c-5349-4d19-80f6-41d140b86db5.sh: line 3:  6114 Segmentation fault      (core dumped) python -m pytest --timeout=60 -rf --report-log output-3.10-log.jsonl

[huard]

There are similar segfaults in an xncml PR: xarray-contrib/xncml#48

Googling around suggest it is related to netCDF not being thread-safe and recent python-netcdf4 releasing the GIL.

[keewis]

If I'm reading the different issues correctly, that means this is a duplicate of #7079

[max-sixty]

Defering to #7079