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BUG: segfault in lobpcg on macOS CI job #15264

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rgommers opened this issue Dec 23, 2021 · 0 comments
Open

BUG: segfault in lobpcg on macOS CI job #15264

rgommers opened this issue Dec 23, 2021 · 0 comments
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defect A clear bug or issue that prevents SciPy from being installed or used as expected scipy.sparse.linalg

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@rgommers
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rgommers commented Dec 23, 2021

Describe your issue.

This segfault just showed up (CI log) on the CPython 3.10 macOS job):

scipy/sparse/linalg/_eigen/arpack/tests/test_arpack.py ................. [ 53%]
..                                                                       [ 53%]
Fatal Python error: Segmentation fault

Current thread 0x000000011e39ce00 (most recent call first):
  File "/Users/runner/work/scipy/scipy/build/testenv/lib/python3.10/site-packages/scipy/linalg/_decomp.py", line 563 in eigh
  File "/Users/runner/work/scipy/scipy/build/testenv/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/lobpcg/lobpcg.py", line 632 in lobpcg
  File "/Users/runner/work/scipy/scipy/build/testenv/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py", line 260 in test_hermitian
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/_pytest/python.py", line 183 in pytest_pyfunc_call
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/_pytest/python.py", line 1641 in runtest
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/_pytest/runner.py", line 162 in pytest_runtest_call
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/_pytest/runner.py", line 255 in <lambda>
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/_pytest/runner.py", line 311 in from_call
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/_pytest/runner.py", line 254 in call_runtest_hook
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/_pytest/runner.py", line 215 in call_and_report
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/_pytest/runner.py", line 126 in runtestprotocol
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/_pytest/runner.py", line 109 in pytest_runtest_protocol
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/_pytest/main.py", line 348 in pytest_runtestloop
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/_pytest/main.py", line 323 in _main
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/_pytest/main.py", line 269 in wrap_session
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/_pytest/main.py", line 316 in pytest_cmdline_main
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/Users/runner/hostedtoolcache/Python/3.10.0/x64/lib/python3.10/site-packages/_pytest/config/__init__.py", line 162 in main
  File "/Users/runner/work/scipy/scipy/build/testenv/lib/python3.10/site-packages/scipy/_lib/_testutils.py", line 69 in __call__
  File "/Users/runner/work/scipy/scipy/runtests.py", line 318 in main
  File "/Users/runner/work/scipy/scipy/runtests.py", line 584 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.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.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg._cythonized_array_utils, 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.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.cluster._vq, scipy.cluster._hierarchy, scipy.cluster._optimal_leaf_ordering, scipy._lib._uarray._uarray, scipy.fftpack.convolve, scipy.sparse.linalg._isolve._iterative, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, 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_module, 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, beta_ufunc, scipy.stats._boost.beta_ufunc, binom_ufunc, scipy.stats._boost.binom_ufunc, nbinom_ufunc, scipy.stats._boost.nbinom_ufunc, hypergeom_ufunc, scipy.stats._boost.hypergeom_ufunc, scipy.stats._biasedurn, scipy.stats._levy_stable.levyst, scipy.stats._statlib, scipy.stats._mvn, scipy.stats._sobol, scipy.stats._qmc_cy, scipy.stats._unuran.unuran_wrapper, scipy.io.matlab._mio_utils, scipy.io.matlab._streams, scipy.io.matlab._mio5_utils, scipy.io._test_fortran, 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, gmpy2.gmpy2, scipy.special._test_round, scipy._lib._test_deprecation_def, scipy._lib._test_deprecation_call (total: 129)
scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py .........
/Users/runner/work/_temp/3d8cdcfb-4c97-4531-a050-62759908d185.sh: line 2:  3979 Segmentation fault: 11  SCIPY_USE_PYTHRAN=`test 3.10 != 3.9; echo $?` python -u runtests.py
Error: Process completed with exit code 139.

It looks new to me. There's a related recent segfault from PROPACK in gh-15108, but that's not the same one it looks like.

@rgommers rgommers added defect A clear bug or issue that prevents SciPy from being installed or used as expected scipy.sparse.linalg labels Dec 23, 2021
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Labels
defect A clear bug or issue that prevents SciPy from being installed or used as expected scipy.sparse.linalg
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