Segmentation fault in CentOS 8.4

[Tobias Brandvik]

I have compiled 2019.1.0.post0 on CentOS 8.4, but I am getting segmentation faults when importing dolfin inside Python. This is with Open-MPI 4.0.5 and gcc 8.4.1. The stacktrace from GDB is below. Any ideas on how to fix this would be greatly appreciated - thanks!

gdb -ex r -ex bt -args python -c"import dolfin"

Program received signal SIGSEGV, Segmentation fault.

0x0000000000000000 in ?? ()

#0  0x0000000000000000 in ?? ()

#1  0x00001555459849d2 in std::pair<ompi_op_t* const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >::pair<ompi_op_t*, char const (&) [8], true> (

    __y=..., __x=<optimized out>, this=0x7fffffff9060) at /usr/include/c++/8/bits/move.h:74

#2  __static_initialization_and_destruction_0 (__initialize_p=1, __priority=65535) at /tmp/dolfin/dolfin/common/MPI.cpp:350

#3  _GLOBAL__sub_I_MPI.cpp(void) () at /tmp/dolfin/dolfin/common/MPI.cpp:370

#4  0x00001555553368ba in call_init.part () from /lib64/ld-linux-x86-64.so.2

#5  0x00001555553369ba in _dl_init () from /lib64/ld-linux-x86-64.so.2

#6  0x0000155553f9327c in _dl_catch_exception () from /lib64/libc.so.6

#7  0x000015555533b2e9 in dl_open_worker () from /lib64/ld-linux-x86-64.so.2

#8  0x0000155553f93224 in _dl_catch_exception () from /lib64/libc.so.6

#9  0x000015555533a6b1 in _dl_open () from /lib64/ld-linux-x86-64.so.2

#10 0x00001555547a71ea in dlopen_doit () from /lib64/libdl.so.2

#11 0x0000155553f93224 in _dl_catch_exception () from /lib64/libc.so.6

#12 0x0000155553f932e3 in _dl_catch_error () from /lib64/libc.so.6

Missing separate debuginfos, use: yum debuginfo-install blas-3.8.0-8.el8.x86_64 bzip2-libs-1.0.6-26.el8.x86_64 glibc-2.28-151.el8.x86_64 keyutils-libs-1.5.10-6.el8.x86_64 lapack-3.8.0-8.el8.x86_64 libX11-1.6.8-4.el8.x86_64 libXau-1.0.9-3.el8.x86_64 libffi-3.1-22.el8.x86_64 libgcc-8.4.1-1.el8.x86_64 libgfortran-8.4.1-1.el8.x86_64 libicu-60.3-2.el8_1.x86_64 libquadmath-8.4.1-1.el8.x86_64 libstdc++-8.4.1-1.el8.x86_64 libxcrypt-4.1.1-4.el8.x86_64 lustre-client-2.12.7_1_g170c1c7-1.el8.x86_64 openblas-0.3.12-1.el8.x86_64 zlib-1.2.11-17.el8.x86_64

--Type <RET> for more, q to quit, c to continue without paging--c

#13 0x00001555547a7969 in _dlerror_run () from /lib64/libdl.so.2

#14 0x00001555547a728a in dlopen@@GLIBC_2.2.5 () from /lib64/libdl.so.2

#15 0x0000155554fa31c0 in _PyImport_FindSharedFuncptr (prefix=prefix@entry=0x1555550317a7 "PyInit", shortname=shortname@entry=0x155546e6a9e0 "cpp", pathname=pathname@entry=0x155546e4fec0 "/usr/local/software/dolfin/dolfin_env/virtualenvs/dolfin/lib/python3.7/site-packages/dolfin/cpp.cpython-37m-x86_64-linux-gnu.so", fp=fp@entry=0x0) at ./Python/dynload_shlib.c:96

#16 0x0000155554f76ea7 in _PyImport_LoadDynamicModuleWithSpec (spec=spec@entry=0x1555467c1990, fp=fp@entry=0x0) at ./Python/importdl.c:129

#17 0x0000155554f74f63 in _imp_create_dynamic_impl (module=<optimized out>, file=<optimized out>, spec=0x1555467c1990) at Python/import.c:2170

#18 _imp_create_dynamic (module=<optimized out>, args=<optimized out>, nargs=<optimized out>) at Python/clinic/import.c.h:289

#19 0x0000155554e863f8 in _PyMethodDef_RawFastCallDict (method=0x1555552cf8e0 <imp_methods+320>, self=0x1555554c0cb0, args=<optimized out>, nargs=1, kwargs=<optimized out>) at Objects/call.c:530

#20 0x0000155554e865b5 in _PyCFunction_FastCallDict (func=0x1555554d97d0, args=<optimized out>, nargs=<optimized out>, kwargs=<optimized out>) at Objects/call.c:586

#21 0x0000155554e61cf8 in do_call_core (kwdict=0x1555467cb140, callargs=0x155546e74e90, func=0x1555554d97d0) at Python/ceval.c:4641

#22 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3191

#23 0x0000155554f5b24e in _PyEval_EvalCodeWithName (_co=0x1555554c8150, globals=<optimized out>, locals=locals@entry=0x0, args=<optimized out>, argcount=2, kwnames=0x0, kwargs=0x155555398cd0, kwcount=0, kwstep=1, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0, name=0x1555554c6300, qualname=0x1555554c6300) at Python/ceval.c:3930

#24 0x0000155554e858b3 in _PyFunction_FastCallKeywords (func=<optimized out>, stack=<optimized out>, nargs=<optimized out>, kwnames=<optimized out>) at Objects/call.c:433

#25 0x0000155554e63419 in call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>) at Python/ceval.c:4616

#26 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3093

#27 0x0000155554e59adb in function_code_fastcall (co=<optimized out>, args=<optimized out>, nargs=2, globals=<optimized out>) at Objects/call.c:283

#28 0x0000155554e859d7 in _PyFunction_FastCallKeywords (func=<optimized out>, stack=<optimized out>, nargs=<optimized out>, kwnames=<optimized out>) at Objects/call.c:415

#29 0x0000155554e625b5 in call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>) at Python/ceval.c:4616

#30 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3110

#31 0x0000155554e59adb in function_code_fastcall (co=<optimized out>, args=<optimized out>, nargs=1, globals=<optimized out>) at Objects/call.c:283

#32 0x0000155554e859d7 in _PyFunction_FastCallKeywords (func=<optimized out>, stack=<optimized out>, nargs=<optimized out>, kwnames=<optimized out>) at Objects/call.c:415

#33 0x0000155554e616a3 in call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>) at Python/ceval.c:4616

#34 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3124

#35 0x0000155554e59adb in function_code_fastcall (co=<optimized out>, args=<optimized out>, nargs=1, globals=<optimized out>) at Objects/call.c:283

#36 0x0000155554e859d7 in _PyFunction_FastCallKeywords (func=<optimized out>, stack=<optimized out>, nargs=<optimized out>, kwnames=<optimized out>) at Objects/call.c:415

#37 0x0000155554e616a3 in call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>) at Python/ceval.c:4616

#38 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3124

#39 0x0000155554e59adb in function_code_fastcall (co=<optimized out>, args=<optimized out>, nargs=2, globals=<optimized out>) at Objects/call.c:283

#40 0x0000155554e859d7 in _PyFunction_FastCallKeywords (func=<optimized out>, stack=<optimized out>, nargs=<optimized out>, kwnames=<optimized out>) at Objects/call.c:415

#41 0x0000155554e616a3 in call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>) at Python/ceval.c:4616

#42 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3124

#43 0x0000155554e59adb in function_code_fastcall (co=co@entry=0x1555554ce930, args=<optimized out>, args@entry=0x7fffffffa510, nargs=nargs@entry=2, globals=globals@entry=0x1555554d20f0) at Objects/call.c:283

#44 0x0000155554e85812 in _PyFunction_FastCallDict (func=0x1555554daa70, args=0x7fffffffa510, nargs=2, kwargs=0x0) at Objects/call.c:322

#45 0x0000155554e86c80 in object_vacall (callable=callable@entry=0x1555554daa70, vargs=vargs@entry=0x7fffffffa588) at Objects/call.c:1202

#46 0x0000155554e86ee5 in _PyObject_CallMethodIdObjArgs (obj=<optimized out>, name=name@entry=0x1555552cf560 <PyId__find_and_load.15952>) at Objects/call.c:1252

#47 0x0000155554f76047 in import_find_and_load (abs_name=0x155546e575f0) at Python/import.c:1648

#48 PyImport_ImportModuleLevelObject (name=name@entry=0x155546e58db0, globals=<optimized out>, locals=<optimized out>, fromlist=fromlist@entry=0x1555553f4550, level=1) at Python/import.c:1760

#49 0x0000155554e63002 in import_name (level=0x1555553074e0 <small_ints+192>, fromlist=0x1555553f4550, name=0x155546e58db0, f=0x663e00) at Python/ceval.c:4770

#50 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2600

#51 0x0000155554f5b24e in _PyEval_EvalCodeWithName (_co=_co@entry=0x1555553b71e0, globals=globals@entry=0x15555545ecd0, locals=locals@entry=0x15555545ecd0, args=args@entry=0x0, argcount=argcount@entry=0, kwnames=kwnames@entry=0x0, kwargs=0x0, kwcount=0, kwstep=2, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0, name=0x0, qualname=0x0) at Python/ceval.c:3930

#52 0x0000155554f5b4ce in PyEval_EvalCodeEx (_co=_co@entry=0x1555553b71e0, globals=globals@entry=0x15555545ecd0, locals=locals@entry=0x15555545ecd0, args=args@entry=0x0, argcount=argcount@entry=0, kws=kws@entry=0x0, kwcount=0, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0) at Python/ceval.c:3959

#53 0x0000155554f5b4fb in PyEval_EvalCode (co=co@entry=0x1555553b71e0, globals=globals@entry=0x15555545ecd0, locals=locals@entry=0x15555545ecd0) at Python/ceval.c:524

#54 0x0000155554f58a7d in builtin_exec_impl (module=<optimized out>, locals=0x15555545ecd0, globals=0x15555545ecd0, source=0x1555553b71e0) at Python/bltinmodule.c:1079

#55 builtin_exec (module=<optimized out>, args=<optimized out>, nargs=<optimized out>) at Python/clinic/bltinmodule.c.h:283

#56 0x0000155554e863f8 in _PyMethodDef_RawFastCallDict (method=0x1555552c7ba0 <builtin_methods+480>, self=0x155555520d10, args=<optimized out>, nargs=2, kwargs=<optimized out>) at Objects/call.c:530

#57 0x0000155554e865b5 in _PyCFunction_FastCallDict (func=0x155555527e10, args=<optimized out>, nargs=<optimized out>, kwargs=<optimized out>) at Objects/call.c:586

#58 0x0000155554e61cf8 in do_call_core (kwdict=0x155546e520a0, callargs=0x155546e4d870, func=0x155555527e10) at Python/ceval.c:4641

#59 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3191

#60 0x0000155554f5b24e in _PyEval_EvalCodeWithName (_co=0x1555554c8150, globals=<optimized out>, locals=locals@entry=0x0, args=<optimized out>, argcount=3, kwnames=0x0, kwargs=0x15555542b938, kwcount=0, kwstep=1, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0, name=0x1555554c6300, qualname=0x1555554c6300) at Python/ceval.c:3930

#61 0x0000155554e858b3 in _PyFunction_FastCallKeywords (func=<optimized out>, stack=<optimized out>, nargs=<optimized out>, kwnames=<optimized out>) at Objects/call.c:433

#62 0x0000155554e63419 in call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>) at Python/ceval.c:4616

#63 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3093

#64 0x0000155554e59adb in function_code_fastcall (co=<optimized out>, args=<optimized out>, nargs=2, globals=<optimized out>) at Objects/call.c:283

#65 0x0000155554e859d7 in _PyFunction_FastCallKeywords (func=<optimized out>, stack=<optimized out>, nargs=<optimized out>, kwnames=<optimized out>) at Objects/call.c:415

#66 0x0000155554e625b5 in call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>) at Python/ceval.c:4616

#67 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3110

#68 0x0000155554e59adb in function_code_fastcall (co=<optimized out>, args=<optimized out>, nargs=1, globals=<optimized out>) at Objects/call.c:283

#69 0x0000155554e859d7 in _PyFunction_FastCallKeywords (func=<optimized out>, stack=<optimized out>, nargs=<optimized out>, kwnames=<optimized out>) at Objects/call.c:415

#70 0x0000155554e616a3 in call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>) at Python/ceval.c:4616

#71 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3124

#72 0x0000155554e59adb in function_code_fastcall (co=<optimized out>, args=<optimized out>, nargs=2, globals=<optimized out>) at Objects/call.c:283

#73 0x0000155554e859d7 in _PyFunction_FastCallKeywords (func=<optimized out>, stack=<optimized out>, nargs=<optimized out>, kwnames=<optimized out>) at Objects/call.c:415

#74 0x0000155554e616a3 in call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>) at Python/ceval.c:4616

#75 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3124

#76 0x0000155554e59adb in function_code_fastcall (co=co@entry=0x1555554ce930, args=<optimized out>, args@entry=0x7fffffffb330, nargs=nargs@entry=2, globals=globals@entry=0x1555554d20f0) at Objects/call.c:283

#77 0x0000155554e85812 in _PyFunction_FastCallDict (func=0x1555554daa70, args=0x7fffffffb330, nargs=2, kwargs=0x0) at Objects/call.c:322

#78 0x0000155554e86c80 in object_vacall (callable=callable@entry=0x1555554daa70, vargs=vargs@entry=0x7fffffffb3a8) at Objects/call.c:1202

#79 0x0000155554e86ee5 in _PyObject_CallMethodIdObjArgs (obj=<optimized out>, name=name@entry=0x1555552cf560 <PyId__find_and_load.15952>) at Objects/call.c:1252

#80 0x0000155554f76047 in import_find_and_load (abs_name=0x15555545d530) at Python/import.c:1648

#81 PyImport_ImportModuleLevelObject (name=name@entry=0x15555545d530, globals=<optimized out>, locals=<optimized out>, fromlist=fromlist@entry=0x1555552b7790 <_Py_NoneStruct>, level=0) at Python/import.c:1760

#82 0x0000155554e63002 in import_name (level=0x1555553074c0 <small_ints+160>, fromlist=0x1555552b7790 <_Py_NoneStruct>, name=0x15555545d530, f=0x155555438450) at Python/ceval.c:4770

#83 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2600

#84 0x0000155554f5b24e in _PyEval_EvalCodeWithName (_co=_co@entry=0x15555547a6f0, globals=globals@entry=0x1555554a0dc0, locals=locals@entry=0x1555554a0dc0, args=args@entry=0x0, argcount=argcount@entry=0, kwnames=kwnames@entry=0x0, kwargs=0x0, kwcount=0, kwstep=2, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0, name=0x0, qualname=0x0) at Python/ceval.c:3930

#85 0x0000155554f5b4ce in PyEval_EvalCodeEx (_co=_co@entry=0x15555547a6f0, globals=globals@entry=0x1555554a0dc0, locals=locals@entry=0x1555554a0dc0, args=args@entry=0x0, argcount=argcount@entry=0, kws=kws@entry=0x0, kwcount=0, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0) at Python/ceval.c:3959

#86 0x0000155554f5b4fb in PyEval_EvalCode (co=co@entry=0x15555547a6f0, globals=globals@entry=0x1555554a0dc0, locals=locals@entry=0x1555554a0dc0) at Python/ceval.c:524

#87 0x0000155554f8ad2b in run_mod (arena=0x15555549bb10, flags=0x7fffffffb81c, locals=0x1555554a0dc0, globals=0x1555554a0dc0, filename=<optimized out>, mod=<optimized out>) at Python/pythonrun.c:1035

#88 PyRun_StringFlags (str=str@entry=0x155555498a10 "import dolfin\n", start=start@entry=257, globals=0x1555554a0dc0, locals=0x1555554a0dc0, flags=flags@entry=0x7fffffffb81c) at Python/pythonrun.c:959

#89 0x0000155554f8adab in PyRun_SimpleStringFlags (command=0x155555498a10 "import dolfin\n", flags=flags@entry=0x7fffffffb81c) at Python/pythonrun.c:455

#90 0x0000155554faa78c in pymain_run_command (cf=0x7fffffffb81c, command=<optimized out>) at Modules/main.c:385

#91 pymain_run_python (pymain=0x7fffffffb8f0) at Modules/main.c:2861

#92 pymain_main (pymain=pymain@entry=0x7fffffffb8f0) at Modules/main.c:3028

#93 0x0000155554faaf99 in _Py_UnixMain (argc=<optimized out>, argv=<optimized out>) at Modules/main.c:3063

#94 0x0000155553e7e493 in __libc_start_main () from /lib64/libc.so.6

#95 0x00000000004006ce in _start ()