Segfaulting on test_array_interface_with_dtype and numpy 2.0-dev
effigies opened this issue · comments
Started seeing this today:
Fatal Python error: Segmentation fault
Thread 0x00007f49ad787640 (most recent call first):
File "/opt/hostedtoolcache/Python/3.12.0/x64/lib/python3.12/selectors.py", line 415 in select
File "/opt/hostedtoolcache/Python/3.12.0/x64/lib/python3.12/socketserver.py", line 235 in serve_forever
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/werkzeug/serving.py", line 806 in serve_forever
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/pytest_httpserver/httpserver.py", line 710 in thread_target
File "/opt/hostedtoolcache/Python/3.12.0/x64/lib/python3.12/threading.py", line 989 in run
File "/opt/hostedtoolcache/Python/3.12.0/x64/lib/python3.12/threading.py", line 1052 in _bootstrap_inner
File "/opt/hostedtoolcache/Python/3.12.0/x64/lib/python3.12/threading.py", line 1009 in _bootstrap
Thread 0x00007f49cf3ff640 (most recent call first):
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/execnet/gateway_base.py", line 474 in read
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/execnet/gateway_base.py", line 507 in from_io
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/execnet/gateway_base.py", line 1049 in _thread_receiver
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/execnet/gateway_base.py", line 296 in run
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/execnet/gateway_base.py", line 361 in _perform_spawn
Current thread 0x00007f49d0b3fb80 (most recent call first):
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/numpy/_core/numeric.py", line 2357 in isclose
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/numpy/testing/_private/utils.py", line 1661 in compare
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/numpy/testing/_private/utils.py", line 797 in assert_array_compare
File "/opt/hostedtoolcache/Python/3.12.0/x64/lib/python3.12/contextlib.py", line 81 in inner
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/numpy/testing/_private/utils.py", line 1666 in assert_allclose
File "/home/runner/work/nibabel/nibabel/nibabel/tests/test_proxy_api.py", line 159 in validate_array_interface_with_dtype
File "/home/runner/work/nibabel/nibabel/nibabel/tests/test_api_validators.py", line 22 in meth
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/_pytest/python.py", line 194 in pytest_pyfunc_call
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/pluggy/_callers.py", line 77 in _multicall
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/pluggy/_manager.py", line 115 in _hookexec
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/pluggy/_hooks.py", line 493 in __call__
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/_pytest/python.py", line 1792 in runtest
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/_pytest/runner.py", line 169 in pytest_runtest_call
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/pluggy/_callers.py", line 77 in _multicall
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/pluggy/_manager.py", line 115 in _hookexec
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/pluggy/_hooks.py", line 493 in __call__
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/_pytest/runner.py", line 262 in <lambda>
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/_pytest/runner.py", line 341 in from_call
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/_pytest/runner.py", line 261 in call_runtest_hook
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/_pytest/runner.py", line 222 in call_and_report
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/_pytest/runner.py", line 133 in runtestprotocol
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/_pytest/runner.py", line 114 in pytest_runtest_protocol
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/pluggy/_callers.py", line 77 in _multicall
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/pluggy/_manager.py", line 115 in _hookexec
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/pluggy/_hooks.py", line 493 in __call__
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/xdist/remote.py", line 174 in run_one_test
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/xdist/remote.py", line 157 in pytest_runtestloop
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/pluggy/_callers.py", line 77 in _multicall
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/pluggy/_manager.py", line 115 in _hookexec
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/pluggy/_hooks.py", line 493 in __call__
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/_pytest/main.py", line 325 in _main
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/_pytest/main.py", line 271 in wrap_session
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/_pytest/main.py", line 318 in pytest_cmdline_main
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/pluggy/_callers.py", line 77 in _multicall
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/pluggy/_manager.py", line 115 in _hookexec
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/pluggy/_hooks.py", line 493 in __call__
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/xdist/remote.py", line 355 in <module>
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/execnet/gateway_base.py", line 1157 in executetask
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/execnet/gateway_base.py", line 296 in run
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/execnet/gateway_base.py", line 361 in _perform_spawn
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/execnet/gateway_base.py", line 343 in integrate_as_primary_thread
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/execnet/gateway_base.py", line 1142 in serve
File "/home/runner/work/nibabel/nibabel/.tox/py312-dev-x64/lib/python3.12/site-packages/execnet/gateway_base.py", line 1640 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._umath_linalg, markupsafe._speedups, indexed_gzip.indexed_gzip, pyzstd.c._zstd, scipy._lib._ccallback_c, PIL._imaging, 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.ndimage._nd_image, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._flinalg, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, 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.special._ellip_harm_2, _ni_label, scipy.ndimage._ni_label, h5py._errors, h5py.defs, h5py._objects, h5py.h5, scipy.io.matlab._mio_utils, scipy.io.matlab._streams, scipy.io.matlab._mio5_utils, matplotlib._path, kiwisolver._cext (total: 58)
---------------------- coverage: failed workers ----------------------
The following workers failed to return coverage data, ensure that pytest-cov is installed on these workers.
gw2
gw4
gw0
Coverage XML written to file cov.xml
=========================== short test summary info ============================
FAILED nibabel/tests/test_proxy_api.py::TestSpm99AnalyzeProxyAPI::test_array_interface_with_dtype
FAILED nibabel/tests/test_proxy_api.py::TestSpm2AnalyzeProxyAPI::test_array_interface_with_dtype
FAILED nibabel/tests/test_proxy_api.py::TestNifti1ProxyAPI::test_array_interface_with_dtype
= 3 failed, 5542 passed, 29 skipped, 40 xfailed, 8 xpassed, 3204 warnings in 258.25s (0:04:18) =
The most recent tests were 3 days ago, and they were passing. So we should look at things merged Dec 3-5.
@mscheltienne @larsoner If either of you has a chance to look into this, please do. Otherwise I'm likely to disable this check for the release and look into this the week after next.
This looks like numpy/numpy#25327 which should be fixed in the next nightly I think
Oh good, it's not something we'll have to work around. Thanks for digging.
New wheels have been pushed already and tests are fixed.