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.h5s, 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.vtkFiltersTexture, 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.vtkRenderingContextOpenGL2, 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.
