Segmentation fault while importing dolphin in python
Hello,
I am trying to install fenics on a redhat-7.7 machine. I was able to successfully install dolfin c++ version from source and the poisson_demo code runs successfully.
I am trying to install the python module for dolfin, so following the instructions on the doflin python directory, I installed pybind11, defined the PYBIND11_DIR environment variable, and ran “pip install .” to install the module to the local site-packages directory. The installation went through successfully without any error messages. But when I try to import the dolfin module, I get a segmentation fault message. Here is the full error message being printed out.
Caught signal 11 (Segmentation fault: address not mapped to object at address 0x440000e9)
==== backtrace (tid: 6171) ====
0 0x0000000000050b35 ucs_debug_print_backtrace() ???:0
1 0x000000000006d113 PMPI_Comm_set_errhandler() ???:0
2 0x000000000007fd00 __pyx_f_6mpi4py_3MPI_initialize() MPI.c:0
3 0x000000000002ecb3 __pyx_pymod_exec_MPI() MPI.c:0
4 0x00000000001fb0ea PyModule_ExecDef() /tmp/build/80754af9/python_1565725737370/work/Objects/moduleobject.c:414
5 0x00000000001fb158 exec_builtin_or_dynamic() /tmp/build/80754af9/python_1565725737370/work/Python/import.c:2115
6 0x00000000001fb158 _imp_exec_builtin_impl() /tmp/build/80754af9/python_1565725737370/work/Python/import.c:2208
7 0x00000000001fb158 _imp_exec_builtin() /tmp/build/80754af9/python_1565725737370/work/Python/clinic/import.c.h:347
8 0x00000000001356da _PyMethodDef_RawFastCallDict() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:497
9 0x00000000001357c1 _PyCFunction_FastCallDict() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:586
10 0x00000000001d1007 do_call_core() /tmp/build/80754af9/python_1565725737370/work/Python/ceval.c:4641
11 0x00000000001d1007 _PyEval_EvalFrameDefault() /tmp/build/80754af9/python_1565725737370/work/Python/ceval.c:3191
12 0x0000000000114539 _PyEval_EvalCodeWithName() /tmp/build/80754af9/python_1565725737370/work/Python/ceval.c:3930
13 0x0000000000163f57 _PyFunction_FastCallKeywords() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:433
14 0x00000000001cff29 call_function() /tmp/build/80754af9/python_1565725737370/work/Python/ceval.c:4616
15 0x00000000001cff29 _PyEval_EvalFrameDefault() /tmp/build/80754af9/python_1565725737370/work/Python/ceval.c:3093
16 0x0000000000163ccb function_code_fastcall() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:283
17 0x0000000000163ccb _PyFunction_FastCallKeywords() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:408
18 0x00000000001cba93 call_function() /tmp/build/80754af9/python_1565725737370/work/Python/ceval.c:4616
19 0x00000000001cba93 _PyEval_EvalFrameDefault() /tmp/build/80754af9/python_1565725737370/work/Python/ceval.c:3110
20 0x0000000000163ccb function_code_fastcall() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:283
21 0x0000000000163ccb _PyFunction_FastCallKeywords() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:408
22 0x00000000001cb806 call_function() /tmp/build/80754af9/python_1565725737370/work/Python/ceval.c:4616
23 0x00000000001cb806 _PyEval_EvalFrameDefault() /tmp/build/80754af9/python_1565725737370/work/Python/ceval.c:3124
24 0x0000000000163ccb function_code_fastcall() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:283
25 0x0000000000163ccb _PyFunction_FastCallKeywords() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:408
26 0x00000000001cb806 call_function() /tmp/build/80754af9/python_1565725737370/work/Python/ceval.c:4616
27 0x00000000001cb806 _PyEval_EvalFrameDefault() /tmp/build/80754af9/python_1565725737370/work/Python/ceval.c:3124
28 0x000000000011556b function_code_fastcall() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:283
29 0x000000000011556b PyFunction_FastCallDict() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:322
30 0x000000000013414e object_vacall() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:1202
31 0x000000000018f68d PyObject_CallMethodIdObjArgs() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:1252
32 0x000000000011decc import_find_and_load() /tmp/build/80754af9/python_1565725737370/work/Python/import.c:1645
33 0x000000000011decc PyImport_ImportModuleLevelObject() /tmp/build/80754af9/python_1565725737370/work/Python/import.c:1757
34 0x00000000001a2fba builtin___import() /tmp/build/80754af9/python_1565725737370/work/Python/bltinmodule.c:312
35 0x000000000013563d _PyMethodDef_RawFastCallDict() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:515
36 0x00000000001357c1 _PyCFunction_FastCallDict() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:586
37 0x000000000012d3dd _PyObject_CallFunctionVa() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:961
38 0x000000000012d3dd PyObject_CallFunction() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:981
39 0x000000000011e58e PyImport_Import() /tmp/build/80754af9/python_1565725737370/work/Python/import.c:1945
40 0x000000000011e7e1 PyImport_ImportModule() /tmp/build/80754af9/python_1565725737370/work/Python/import.c:1389
41 0x0000000000212f81 std::set<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::less<std::__cxx11::basic_string<char, std::char_traits, std::allocator > >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > >::set() ???:0
42 0x000000000020af2a std::set<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::less<std::__cxx11::basic_string<char, std::char_traits, std::allocator > >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > >::set() ???:0
43 0x000000000023c950 PyInit_cpp() ???:0
44 0x0000000000135845 cfunction_call_varargs() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:757
45 0x0000000000135845 PyCFunction_Call() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:788
46 0x0000000000178ed2 property_descr_get() /tmp/build/80754af9/python_1565725737370/work/Objects/descrobject.c:1349
47 0x0000000000129249 type_getattro() /tmp/build/80754af9/python_1565725737370/work/Objects/typeobject.c:3221
48 0x00000000001cbcda _PyEval_EvalFrameDefault() /tmp/build/80754af9/python_1565725737370/work/Python/ceval.c:2573
49 0x0000000000114539 _PyEval_EvalCodeWithName() /tmp/build/80754af9/python_1565725737370/work/Python/ceval.c:3930
50 0x0000000000115424 PyEval_EvalCodeEx() /tmp/build/80754af9/python_1565725737370/work/Python/ceval.c:3959
51 0x000000000011544c PyEval_EvalCode() /tmp/build/80754af9/python_1565725737370/work/Python/ceval.c:524
52 0x00000000001dae81 builtin_exec_impl.isra.12() /tmp/build/80754af9/python_1565725737370/work/Python/bltinmodule.c:1079
53 0x00000000001dae81 builtin_exec() /tmp/build/80754af9/python_1565725737370/work/Python/clinic/bltinmodule.c.h:283
54 0x00000000001356a2 _PyMethodDef_RawFastCallDict() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:530
55 0x00000000001357c1 _PyCFunction_FastCallDict() /tmp/build/80754af9/python_1565725737370/work/Objects/call.c:586
56 0x00000000001d1007 do_call_core() /tmp/build/80754af9/python_1565725737370/work/Python/ceval.c:4641
57 0x00000000001d1007 _PyEval_EvalFrameDefault() /tmp/build/80754af9/python_1565725737370/work/Python/ceval.c:3191
[alto-v1:06171] *** Process received signal ***
[alto-v1:06171] Signal: Segmentation fault (11)
[alto-v1:06171] Signal code: (-6)
[alto-v1:06171] Failing at address: 0x4310000181b
[alto-v1:06171] [ 0] /lib64/libpthread.so.0(+0xf630)[0x2b0ac9275630]
[alto-v1:06171] [ 1] /app/openmpi/platform/x86-64/4.0.6/lib/libmpi.so.40(PMPI_Comm_set_errhandler+0x43)[0x2b0ad5010113]
[alto-v1:06171] [ 2] /app/python/platform/x86-64/3.7/lib/python3.7/site-packages/mpi4py/MPI.cpython-37m-x86_64-linux-gnu.so(+0x7fd00)[0x2b0af257dd00]
[alto-v1:06171] [ 3] /app/python/platform/x86-64/3.7/lib/python3.7/site-packages/mpi4py/MPI.cpython-37m-x86_64-linux-gnu.so(+0x2ecb3)[0x2b0af252ccb3]
[alto-v1:06171] [ 4] python(PyModule_ExecDef+0x7a)[0x556de79a50ea]
[alto-v1:06171] [ 5] python(+0x1fb158)[0x556de79a5158]
[alto-v1:06171] [ 6] python(_PyMethodDef_RawFastCallDict+0x2ea)[0x556de78df6da]
[alto-v1:06171] [ 7] python(_PyCFunction_FastCallDict+0x21)[0x556de78df7c1]
[alto-v1:06171] [ 8] python(_PyEval_EvalFrameDefault+0x5c17)[0x556de797b007]
[alto-v1:06171] [ 9] python(_PyEval_EvalCodeWithName+0x2f9)[0x556de78be539]
[alto-v1:06171] [10] python(_PyFunction_FastCallKeywords+0x387)[0x556de790df57]
[alto-v1:06171] [11] python(_PyEval_EvalFrameDefault+0x4b39)[0x556de7979f29]
[alto-v1:06171] [12] python(_PyFunction_FastCallKeywords+0xfb)[0x556de790dccb]
[alto-v1:06171] [13] python(_PyEval_EvalFrameDefault+0x6a3)[0x556de7975a93]
[alto-v1:06171] [14] python(_PyFunction_FastCallKeywords+0xfb)[0x556de790dccb]
[alto-v1:06171] [15] python(_PyEval_EvalFrameDefault+0x416)[0x556de7975806]
[alto-v1:06171] [16] python(_PyFunction_FastCallKeywords+0xfb)[0x556de790dccb]
[alto-v1:06171] [17] python(_PyEval_EvalFrameDefault+0x416)[0x556de7975806]
[alto-v1:06171] [18] python(_PyFunction_FastCallDict+0x10b)[0x556de78bf56b]
[alto-v1:06171] [19] python(+0x13414e)[0x556de78de14e]
[alto-v1:06171] [20] python(_PyObject_CallMethodIdObjArgs+0xbd)[0x556de793968d]
[alto-v1:06171] [21] python(PyImport_ImportModuleLevelObject+0x29c)[0x556de78c7ecc]
[alto-v1:06171] [22] python(+0x1a2fba)[0x556de794cfba]
[alto-v1:06171] [23] python(_PyMethodDef_RawFastCallDict+0x24d)[0x556de78df63d]
[alto-v1:06171] [24] python(_PyCFunction_FastCallDict+0x21)[0x556de78df7c1]
[alto-v1:06171] [25] python(PyObject_CallFunction+0x10d)[0x556de78d73dd]
[alto-v1:06171] [26] python(PyImport_Import+0x9e)[0x556de78c858e]
[alto-v1:06171] [27] python(PyImport_ImportModule+0x21)[0x556de78c87e1]
[alto-v1:06171] [28] /home/teja/.local/lib/python3.7/site-packages/dolfin/cpp.cpython-37m-x86_64-linux-gnu.so(+0x212f81)[0x2b0ad0bf1f81]
[alto-v1:06171] [29] /home/teja/.local/lib/python3.7/site-packages/dolfin/cpp.cpython-37m-x86_64-linux-gnu.so(+0x20af2a)[0x2b0ad0be9f2a]
Can anyone please point out what’s going wrong and how I can fix it.
Thank you for all the help!
