Source: io4dolfinx Version: 1.1.2-4 Severity: normal User: [email protected] Usertags: i386
debci is failing test_checkpointing.py MPI tests on i386. Both test-io4dolfinx-mpi and test-io4dolfinx-complex-mpi are affected. debci test failure is reproducible, but the failure is not. Timeout occurs intermittently, stopping at a different point in different runs. Sometimes there is a segfault backtrace, other times it just times out. https://ci.debian.net/packages/i/io4dolfinx/testing/i386/69502695/ https://ci.debian.net/packages/i/io4dolfinx/testing/i386/69418660/ https://ci.debian.net/packages/i/io4dolfinx/testing/i386/69366977/ But the timeout seems to occur each time in test_read_write_P_3D or test_read_write_P_3D_time e.g. https://ci.debian.net/data/autopkgtest/testing/i386/i/io4dolfinx/69366977/log.gz 598s tests/test_checkpointing.py::test_read_write_P_3D[mesh_3D0-h5py-read_comm1-4-Lagrange-True] 598s tests/test_checkpointing.py::test_read_write_P_3D[mesh_3D0-h5py-read_comm1-4-Lagrange-True] PASSED [ 21%]PASSED [ 21%] 598s tests/test_checkpointing.py::test_read_write_P_3D[mesh_3D0-h5py-read_comm1-4-Lagrange-False] 599s tests/test_checkpointing.py::test_read_write_P_3D[mesh_3D0-h5py-read_comm1-4-Lagrange-False] PASSED [ 21%]PASSED [ 21%] 599s tests/test_checkpointing.py::test_read_write_P_3D[mesh_3D0-h5py-read_comm1-4-DG-True] 599s tests/test_checkpointing.py::test_read_write_P_3D[mesh_3D0-h5py-read_comm1-4-DG-True] Fatal Python error: Segmentation fault 599s 599s Current thread 0xf7b03700 [python3.14] (most recent call first): 599s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_mpi/_hl/files.py", line 253 in make_fid 599s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_mpi/_hl/files.py", line 566 in __init__ 599s File "/usr/lib/python3/dist-packages/io4dolfinx/backends/h5py/backend.py", line 47 in h5pyfile 599s File "/usr/lib/python3.14/contextlib.py", line 141 in __enter__ 599s File "/usr/lib/python3/dist-packages/io4dolfinx/backends/h5py/backend.py", line 568 in write_function 599s File "/usr/lib/python3/dist-packages/io4dolfinx/writers.py", line 156 in write_function 599s File "/usr/lib/python3/dist-packages/io4dolfinx/checkpointing.py", line 567 in write_function 599s File "/tmp/autopkgtest-lxc.xcr9zi7p/downtmp/build.0EG/src/tests/conftest.py", line 90 in _write_function 599s File "/tmp/autopkgtest-lxc.xcr9zi7p/downtmp/build.0EG/src/tests/test_checkpointing.py", line 122 in test_read_write_P_3D 599s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 166 in pytest_pyfunc_call 599s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall 599s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec 599s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__ 599s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1720 in runtest 599s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 179 in pytest_runtest_call 599s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall 599s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec 599s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__ 599s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 245 in <lambda> 599s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 353 in from_call 599s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 244 in call_and_report 599s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 137 in runtestprotocol 599s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 118 in pytest_runtest_protocol 599s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall 599s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec 599s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__ 599s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 396 in pytest_runtestloop 599s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall 599s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec 599s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__ 599s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 372 in _main 599s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 318 in wrap_session 599s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 365 in pytest_cmdline_main 599s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall 599s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec 599s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__ 599s File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 199 in main 599s File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 223 in console_main 599s File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 9 in <module> 599s File "<frozen runpy>", line 88 in _run_code 599s File "<frozen runpy>", line 198 in _run_module_as_main 599s 599s Current thread's C stack trace (most recent call first): 599s Binary file "python3.14", at _Py_DumpStack+0x36 [0x80ad752] 599s Binary file "python3.14" [0x81263b7] 599s Binary file "linux-gate.so.1", at __kernel_sigreturn+0x0 [0xf7eca5a0] 599s Binary file "/usr/lib/i386-linux-gnu/libmpich.so.12", at +0x31c20d [0xf5dca20d] 599s Binary file "/usr/lib/i386-linux-gnu/libmpich.so.12", at +0x23e66c [0xf5cec66c] 599s Binary file "/usr/lib/i386-linux-gnu/libmpich.so.12", at +0x23db43 [0xf5cebb43] 599s Binary file "/usr/lib/i386-linux-gnu/libmpich.so.12", at MPI_Error_string+0x44 [0xf5ba9ec4] 599s Binary file "/usr/lib/i386-linux-gnu/libhdf5_mpich.so.310", at +0x32a09e [0xf071e09e] 599s Binary file "/usr/lib/i386-linux-gnu/libhdf5_mpich.so.310", at H5FD_open+0x178 [0xf0505fe8] 599s Binary file "/usr/lib/i386-linux-gnu/libhdf5_mpich.so.310", at H5F_open+0x466 [0xf04f4e96] 599s Binary file "/usr/lib/i386-linux-gnu/libhdf5_mpich.so.310", at H5VL__native_file_open+0x4d [0xf06ec48d] 599s Binary file "/usr/lib/i386-linux-gnu/libhdf5_mpich.so.310", at +0x2e327b [0xf06d727b] 599s Binary file "/usr/lib/i386-linux-gnu/libhdf5_mpich.so.310", at H5VL_file_open+0x86 [0xf06dd4a6] 599s Binary file "/usr/lib/i386-linux-gnu/libhdf5_mpich.so.310", at +0xef86e [0xf04e386e] 599s Binary file "/usr/lib/i386-linux-gnu/libhdf5_mpich.so.310", at H5Fopen+0x4b [0xf04e542b] 599s Binary file "/usr/lib/python3/dist-packages/h5py/_debian_h5py_mpi/defs.cpython-314-i386-linux-gnu.so", at +0x1073b [0xe69d273b] 599s Binary file "/usr/lib/python3/dist-packages/h5py/_debian_h5py_mpi/h5f.cpython-314-i386-linux-gnu.so", at +0x16feb [0xe6657feb] 599s Binary file "/usr/lib/python3/dist-packages/mpi4py/MPI.cpython-314-i386-linux-gnu.so", at +0xb10bb [0xf61170bb] 599s Binary file "/usr/lib/python3/dist-packages/h5py/_debian_h5py_mpi/_objects.cpython-314-i386-linux-gnu.so", at +0x12287 [0xe6969287] 599s Binary file "/usr/lib/python3/dist-packages/mpi4py/MPI.cpython-314-i386-linux-gnu.so", at +0xafdb7 [0xf6115db7] 599s Binary file "python3.14", at _PyObject_MakeTpCall+0x313 [0x814f443] 599s Binary file "python3.14", at PyObject_Vectorcall+0x5b [0x8154a5b] 599s Binary file "python3.14", at _PyEval_EvalFrameDefault+0x68e2 [0x81702e2] 599s Binary file "python3.14" [0x81a29a9] 599s Binary file "python3.14" [0x8155bf2] 599s Binary file "python3.14" [0x81ab699] 599s Binary file "python3.14", at _PyObject_MakeTpCall+0x23d [0x814f36d] 599s Binary file "python3.14", at PyObject_Vectorcall+0x5b [0x8154a5b] 599s Binary file "python3.14", at _PyEval_EvalFrameDefault+0x68e2 [0x81702e2] 599s Binary file "python3.14" [0x82241cc] 599s Binary file "python3.14", at _PyEval_EvalFrameDefault+0x185f [0x816b25f] 599s Binary file "python3.14" [0x81a29a9] 599s <truncated rest of calls> 599s 599s Extension modules: mpi4py.MPI, numpy._core._multiarray_umath, numpy.linalg._umath_linalg, petsc4py.PETSc, zmq.backend.cython._zmq, tornado.speedups, psutil._psutil_linux, psutil._psutil_posix, h5py._debian_h5py_mpi._errors, h5py._debian_h5py_mpi.defs, h5py._debian_h5py_mpi._objects, h5py._debian_h5py_mpi.h5, h5py._debian_h5py_mpi.utils, h5py._debian_h5py_mpi.h5t, h5py._debian_h5py_mpi.h5s, h5py._debian_h5py_mpi.h5ac, h5py._debian_h5py_mpi.h5p, h5py._debian_h5py_mpi.h5r, h5py._debian_h5py_mpi._npystrings, h5py._debian_h5py_mpi._proxy, h5py._debian_h5py_mpi._conv, h5py._debian_h5py_mpi.h5z, h5py._debian_h5py_mpi.h5a, h5py._debian_h5py_mpi.h5d, h5py._debian_h5py_mpi.h5ds, h5py._debian_h5py_mpi.h5g, h5py._debian_h5py_mpi.h5i, h5py._debian_h5py_mpi.h5o, h5py._debian_h5py_mpi.h5f, h5py._debian_h5py_mpi.h5fd, h5py._debian_h5py_mpi.h5pl, h5py._debian_h5py_mpi.h5l, h5py._debian_h5py_mpi._selector, h5py.atexit, h5py._errors, h5py.defs, h5py._objects, h5py.h5, h5py.utils, h5py.h5t, h5py.h5 s, h5py.h5ac, h5py.h5p, h5py.h5r, h5py._npystrings, h5py._proxy, h5py._conv, h5py.h5z, h5py.h5a, h5py.h5d, h5py.h5ds, h5py.h5g, h5py.h5i, h5py.h5o, h5py.h5f, h5py.h5fd, h5py.h5pl, h5py.h5l, h5py._selector, vtkmodules.vtkCommonCore, vtkmodules.vtkCommonMath, vtkmodules.vtkCommonTransforms, vtkmodules.vtkCommonDataModel, vtkmodules.vtkCommonExecutionModel, vtkmodules.vtkParallelCore, vtkmodules.vtkImagingSources, vtkmodules.vtkCommonMisc, vtkmodules.vtkFiltersCore, vtkmodules.vtkFiltersPython, vtkmodules.vtkCommonComputationalGeometry, vtkmodules.vtkIOCore, vtkmodules.vtkFiltersCellGrid, vtkmodules.vtkIOCellGrid, vtkmodules.vtkIOLegacy, vtkmodules.vtkIOXMLParser, vtkmodules.vtkRenderingCore, vtkmodules.vtkDomainsChemistry, vtkmodules.vtkFiltersGeneral, vtkmodules.vtkFiltersExtraction, vtkmodules.vtkFiltersFlowPaths, vtkmodules.vtkFiltersGeometry, vtkmodules.vtkFiltersHybrid, vtkmodules.vtkFiltersModeling, vtkmodules.vtkFiltersHyperTree, vtkmodules.vtkFiltersSources, vtkmodules.vtkFilt ersTexture, vtkmodules.vtkFiltersParallel, vtkmodules.vtkFiltersParallelDIY2, vtkmodules.vtkFiltersPoints, vtkmodules.vtkFiltersStatistics, vtkmodules.vtkFiltersVerdict, vtkmodules.vtkImagingCore, vtkmodules.vtkImagingGeneral, vtkmodules.vtkImagingHybrid, vtkmodules.vtkImagingMorphological, vtkmodules.vtkImagingStencil, vtkmodules.vtkIOGeometry, vtkmodules.vtkIOHDF, vtkmodules.vtkIOXML, vtkmodules.vtkIOInfovis, vtkmodules.vtkIOPLY, vtkmodules.vtkRenderingContext2D, vtkmodules.vtkPythonContext2D, vtkmodules.vtkImagingFourier, vtkmodules.vtkIOParallelXML, vtkmodules.vtkRenderingFreeType, vtkmodules.vtkChartsCore, vtkmodules.vtkCommonColor, vtkmodules.vtkInteractionStyle, vtkmodules.vtkInteractionWidgets, vtkmodules.vtkRenderingAnnotation, vtkmodules.vtkRenderingLabel, vtkmodules.vtkRenderingUI, vtkmodules.vtkRenderingVolume, vtkmodules.vtkViewsCore, vtkmodules.vtkViewsContext2D, vtkmodules.vtkIOImage, vtkmodules.vtkRenderingHyperTreeGrid, vtkmodules.vtkRenderingOpenGL2, vtkmodules.vtk RenderingContextOpenGL2, vtkmodules.vtkImagingMath, vtkmodules.vtkRenderingVolumeOpenGL2, PIL._imaging, kiwisolver._cext (total: 124) 599s autopkgtest [17:11:15]: test test-io4dolfinx-mpi: -----------------------] 599s autopkgtest [17:11:15]: test test-io4dolfinx-mpi: - - - - - - - - - - results - - - - - - - - - - 599s test-io4dolfinx-mpi FAIL non-zero exit status 59 599s autopkgtest [17:11:15]: test test-io4dolfinx-mpi: - - - - - - - - - - stderr - - - - - - - - - - As a workaround I'll skip test_read_write_P_3D. -- debian-science-maintainers mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
