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Fatal Python error: Segmentation fault - test_arpack.py::test_symmetric_modes

See original GitHub issue

My issue is about a segmentation fault when trying to run tests.

Reproducing code example:

python runtests.py -v -s  sparse

Error message:

scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py::test_symmetric_modes Fatal Python error: Segmentation fault

Current thread 0x00007fe14f9fa740 (most recent call first):
  File "/home/kaleab/Documents/Code/scipy/build/testenv/lib/python3.7/site-packages/scipy/_lib/_util.py", line 121 in _aligned_zeros
  File "/home/kaleab/Documents/Code/scipy/build/testenv/lib/python3.7/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py", line 518 in __init__
  File "/home/kaleab/Documents/Code/scipy/build/testenv/lib/python3.7/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py", line 1681 in eigsh
  File "/home/kaleab/Documents/Code/scipy/build/testenv/lib/python3.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 244 in eval_evec
  File "/home/kaleab/Documents/Code/scipy/build/testenv/lib/python3.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 404 in test_symmetric_modes
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/_pytest/python.py", line 184 in pytest_pyfunc_call
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/manager.py", line 87 in <lambda>
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/_pytest/python.py", line 1479 in runtest
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/_pytest/runner.py", line 135 in pytest_runtest_call
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/manager.py", line 87 in <lambda>
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/_pytest/runner.py", line 217 in <lambda>
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/_pytest/runner.py", line 244 in from_call
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/_pytest/runner.py", line 217 in call_runtest_hook
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/_pytest/runner.py", line 186 in call_and_report
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/_pytest/runner.py", line 100 in runtestprotocol
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/_pytest/runner.py", line 85 in pytest_runtest_protocol
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/manager.py", line 87 in <lambda>
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/_pytest/main.py", line 272 in pytest_runtestloop
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/manager.py", line 87 in <lambda>
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/_pytest/main.py", line 247 in _main
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/_pytest/main.py", line 191 in wrap_session
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/_pytest/main.py", line 240 in pytest_cmdline_main
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/manager.py", line 87 in <lambda>
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/home/kaleab/.conda/envs/scipy/lib/python3.7/site-packages/_pytest/config/__init__.py", line 125 in main
  File "/home/kaleab/Documents/Code/scipy/build/testenv/lib/python3.7/site-packages/scipy/_lib/_testutils.py", line 67 in __call__
  File "runtests.py", line 313 in main
  File "runtests.py", line 525 in <module>
Segmentation fault (core dumped)

Scipy/Numpy/Python version information:

Python 3.7.7/python 3.6.0, pytest-5.4.1/ pytest 4.0.0 , py-1.8.1, pluggy-0.13.1, numpy 1.18.1

Issue Analytics

State:
Created 3 years ago
Comments:6 (6 by maintainers)

Top GitHub Comments

1reaction

mdhabercommented, Dec 31, 2020

This test is also failing on master intermittently, but not a segfault.

_____________________________ test_symmetric_modes _____________________________
[gw1] linux -- Python 3.7.9 /home/travis/virtualenv/python3.7.9/bin/python
/home/travis/virtualenv/python3.7.9/lib/python3.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py:404: in test_symmetric_modes
    None, sigma, mattype, None, mode)
        D          = <std-symmetric>
        k          = 2
        mattype    = <function aslinearoperator at 0xffff8b48c9e0>
        mode       = 'buckling'
        modes      = ['normal', 'buckling', 'cayley']
        params     = <scipy.sparse.linalg.eigen.arpack.tests.test_arpack.SymmetricParams object at 0xffff41cb9e90>
        sigma      = 0.5
        symmetric  = True
        typ        = 'f'
        which      = 'LA'
/home/travis/virtualenv/python3.7.9/lib/python3.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py:261: in eval_evec
    assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
E   AssertionError: 
E   Not equal to tolerance rtol=0.00178814, atol=0.000357628
E   error for eigsh:standard, typ=f, which=LA, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=buckling
E   Mismatched elements: 4 / 12 (33.3%)
E   Max absolute difference: 0.01493526
E   Max relative difference: 0.01093912
E    x: array([[-1.072405,  0.563614],
E          [-1.455584, -0.239151],
E          [-1.004519, -0.42866 ],...
E    y: array([[-1.073047,  0.563611],
E          [-1.456878, -0.239156],
E          [-0.998997, -0.428643],...
        LHS        = array([[-1.0724047 ,  0.56361365],
       [-1.4555839 , -0.23915069],
       [-1.0045193 , -0.42866027],
       [-1.0440447 , -0.32811955],
       [-1.5183451 , -0.34796414],
       [-1.4869674 ,  0.7027782 ]], dtype=float32)
        OPpart     = None
        RHS        = array([[-1.0730466 ,  0.56361085],
       [-1.4568783 , -0.23915628],
       [-0.998997  , -0.42864323],
       [-1.0327474 , -0.32808444],
       [-1.5052823 , -0.3479238 ],
       [-1.4720322 ,  0.7028245 ]], dtype=float32)
        a          = array([[1.7170051 , 1.3009547 , 0.9104259 , 0.97003126, 1.4632134 ,
        1.8256624 ],
       [1.3009547 , 2.253338 ...  1.9766154 ],
       [1.8256624 , 2.0743165 , 1.1501507 , 1.3169256 , 1.9766154 ,
        2.8176725 ]], dtype=float32)
        ac         = <6x6 MatrixLinearOperator with dtype=float32>
        atol       = 0.00035762786865234375
        d          = <std-symmetric>
        eigenvalues = array([9.827495 , 1.2812405], dtype=float32)
        eigs_func  = <function eigsh at 0xffff8b5077a0>
        err        = 'error for eigsh:standard, typ=f, which=LA, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=buckling'
        evec       = array([[-0.10918821,  0.43989468],
       [-0.14824514, -0.18665995],
       [-0.10165327, -0.3345533 ],
       [-0.10508756, -0.2560678 ],
       [-0.1531705 , -0.2715523 ],
       [-0.14978713,  0.54855   ]], dtype=float32)
        exact_eval = array([9.884308+0.j, 1.281241+0.j], dtype=complex64)
        general    = False
        ind        = array([1, 0])
        k          = 2
        kwargs     = {'mode': 'buckling', 'sigma': 0.5, 'tol': 3.5762786865234375e-06, 'v0': None, ...}
        mattype    = <function aslinearoperator at 0xffff8b48c9e0>
        mode       = 'buckling'
        ntries     = 0
        rtol       = 0.0017881393432617188
        sigma      = 0.5
        symmetric  = True
        typ        = 'f'
        v0         = None
        which      = 'LA'

0reactions

rgommerscommented, Apr 26, 2020

The output of conda list may be useful here. Also OS and compiler versions.