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Bug 1939924 - scipy fails to build with Python 3.10: Fatal Python error: Segmentation fault
Summary: scipy fails to build with Python 3.10: Fatal Python error: Segmentation fault
Alias: None
Product: Fedora
Classification: Fedora
Component: scipy
Version: rawhide
Hardware: Unspecified
OS: Unspecified
Target Milestone: ---
Assignee: Nikola Forró
QA Contact: Fedora Extras Quality Assurance
Depends On: 1939885
Blocks: PYTHON3.10 1939917 1939931 1939941
TreeView+ depends on / blocked
Reported: 2021-03-17 10:19 UTC by Tomáš Hrnčiar
Modified: 2021-03-18 14:11 UTC (History)
7 users (show)

Fixed In Version:
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Last Closed: 2021-03-18 14:11:02 UTC
Type: Bug

Attachments (Terms of Use)

Description Tomáš Hrnčiar 2021-03-17 10:19:03 UTC
scipy fails to build with Python 3.10.0a6.

Fatal Python error: Segmentation fault

Thread 0x00007f40f6c23640 (most recent call first):
  File "/usr/lib/python3.10/site-packages/execnet/", line 400 in read
  File "/usr/lib/python3.10/site-packages/execnet/", line 432 in from_io
  File "/usr/lib/python3.10/site-packages/execnet/", line 967 in _thread_receiver
  File "/usr/lib/python3.10/site-packages/execnet/", line 220 in run
  File "/usr/lib/python3.10/site-packages/execnet/", line 285 in _perform_spawn

Current thread 0x00007f40f6f33740 (most recent call first):
  File "/usr/lib64/python3.10/", line 904 in __new__
  File "/usr/lib64/python3.10/", line 606 in __call__
  File "/usr/lib64/python3.10/", line 30 in _int_to_enum
  File "/usr/lib64/python3.10/", line 48 in signal
  File "/usr/lib/python3.10/site-packages/", line 204 in cancel
  File "/usr/lib/python3.10/site-packages/", line 229 in timeout_teardown
  File "/usr/lib/python3.10/site-packages/", line 107 in pytest_runtest_protocol
  File "/usr/lib/python3.10/site-packages/pluggy/", line 203 in _multicall
  File "/usr/lib/python3.10/site-packages/pluggy/", line 84 in <lambda>
  File "/usr/lib/python3.10/site-packages/pluggy/", line 93 in _hookexec
  File "/usr/lib/python3.10/site-packages/pluggy/", line 286 in __call__
  File "/usr/lib/python3.10/site-packages/xdist/", line 89 in run_one_test
  File "/usr/lib/python3.10/site-packages/xdist/", line 72 in pytest_runtestloop
  File "/usr/lib/python3.10/site-packages/pluggy/", line 187 in _multicall
  File "/usr/lib/python3.10/site-packages/pluggy/", line 84 in <lambda>
  File "/usr/lib/python3.10/site-packages/pluggy/", line 93 in _hookexec
  File "/usr/lib/python3.10/site-packages/pluggy/", line 286 in __call__
  File "/usr/lib/python3.10/site-packages/_pytest/", line 323 in _main
  File "/usr/lib/python3.10/site-packages/_pytest/", line 269 in wrap_session
  File "/usr/lib/python3.10/site-packages/_pytest/", line 316 in pytest_cmdline_main
  File "/usr/lib/python3.10/site-packages/pluggy/", line 187 in _multicall
  File "/usr/lib/python3.10/site-packages/pluggy/", line 84 in <lambda>
  File "/usr/lib/python3.10/site-packages/pluggy/", line 93 in _hookexec
  File "/usr/lib/python3.10/site-packages/pluggy/", line 286 in __call__
  File "/usr/lib/python3.10/site-packages/xdist/", line 244 in <module>
  File "/usr/lib/python3.10/site-packages/execnet/", line 1084 in executetask
  File "/usr/lib/python3.10/site-packages/execnet/", line 220 in run
  File "/usr/lib/python3.10/site-packages/execnet/", line 285 in _perform_spawn
  File "/usr/lib/python3.10/site-packages/execnet/", line 267 in integrate_as_primary_thread
  File "/usr/lib/python3.10/site-packages/execnet/", line 1060 in serve
  File "/usr/lib/python3.10/site-packages/execnet/", line 1554 in serve
  File "<string>", line 8 in <module>
  File "<string>", line 1 in <module>

Extension modules: numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg.lapack_lite, 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, scipy._lib._ccallback_c, scipy._lib._fpumode, scipy._lib._test_ccallback, scipy.optimize.minpack2, scipy.sparse._sparsetools, scipy.sparse._csparsetools, 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.sparse.linalg.isolve._iterative, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg._flinalg, scipy.linalg._solve_toeplitz, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg.cython_lapack, scipy.linalg._decomp_update, scipy.sparse.linalg.dsolve._superlu, scipy.sparse.linalg.eigen.arpack._arpack, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special.specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, 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_module, scipy.spatial.ckdtree, scipy.spatial.qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform.rotation, scipy.cluster._vq, scipy.cluster._hierarchy, scipy.cluster._optimal_leaf_ordering, scipy._lib._uarray._uarray, scipy.fftpack.convolve, scipy.integrate._odepack, scipy.integrate._quadpack, scipy.integrate.vode, scipy.integrate._dop, scipy.integrate.lsoda, scipy.integrate._test_odeint_banded, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd,,,,, scipy.ndimage._nd_image, _ni_label, scipy.ndimage._ni_label, scipy.special.cython_special, scipy.stats._stats, scipy.stats.statlib, scipy.stats.mvn, scipy.ndimage._ctest, _cytest, scipy.ndimage._cytest, scipy.odr.__odrpack, scipy.optimize.cython_optimize._zeros, scipy.signal.sigtools, scipy.signal._max_len_seq_inner, scipy.signal._upfirdn_apply, scipy.signal.spline, scipy.signal._sosfilt, scipy.signal._spectral, scipy.signal._peak_finding_utils, scipy.special._test_round, scipy._lib._test_deprecation_def, scipy._lib._test_deprecation_call (total: 109)
[gw0] node down: Not properly terminated
replacing crashed worker gw0

For the build logs, see:

For all our attempts to build scipy with Python 3.10, see:

Testing and mass rebuild of packages is happening in copr. You can follow these instructions to test locally in mock if your package builds with Python 3.10:

Let us know here if you have any questions.

Python 3.10 will be included in Fedora 35. To make that update smoother, we're building Fedora packages with early pre-releases of Python 3.10.
A build failure prevents us from testing all dependent packages (transitive [Build]Requires), so if this package is required a lot, it's important for us to get it fixed soon.
We'd appreciate help from the people who know this package best, but if you don't want to work on this now, let us know so we can try to work around it on our side.

Comment 1 Miro Hrončok 2021-03-18 14:11:02 UTC
This was a bug in Python. Tracked in bz1939885 and patched in Copr. Sorry for the noise.

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