On Wed, 23 Apr 2014 14:21:17 -0400 腾张 <[email protected]> wrote:
> Dear Garth, > > The manager of our university cluster helped to install Fenics. I > asked him about the detailed information about the compiling and > error. Here they are: > > " > Here is a gdb backtrace. > > Program terminated with signal 11, Segmentation fault. > #0 0x00007f8b5fdafefa in METIS_NodeND () from The usual reason for this is when, you configure DOLFIN with some build of ParMETIS and PETSc is configured to download (Par)METIS and SuperLU[-dist]/MUMPS, so the conflict happens with libmetis.so at runtime when SuperLU[-dist]/MUMPS calls some METIS routine for reordering matrix. Jan > /gpfs/runtime/opt/fenics/1.3.0/src/dolfin- > 1.3.0/build/dolfin/libdolfin.so.1.3 > ... > (gdb) bt > #0 0x00007f8b5fdafefa in METIS_NodeND () from > /gpfs/runtime/opt/fenics/1.3.0/src/dolfin- > 1.3.0/build/dolfin/libdolfin.so.1.3 > #1 0x00007f8b57c4b77b in get_metis () > from /gpfs/runtime/opt/petsc/3.3- > p5/arch-linux2-cxx-opt/lib/libpetsc.so #2 0x00007f8b57c4ba0e in > get_perm_c_dist () > from /gpfs/runtime/opt/petsc/3.3-p5/arch-linux2-cxx-opt/lib/libpetsc.so > #3 0x00007f8b57c36b64 in pdgssvx_ABglobal () > from /gpfs/runtime/opt/petsc/3.3-p5/arch-linux2-cxx-opt/lib/libpetsc.so > #4 0x00007f8b57b8c6f6 in MatLUFactorNumeric_SuperLU_DIST(_p_Mat*, > _p_Mat*, MatFactorInfo const*) () from /gpfs/runtime/opt/petsc/3.3- > p5/arch-linux2-cxx-opt/lib/libpetsc.so #5 0x00007f8b5797af69 in > MatLUFactorNumeric () > from /gpfs/runtime/opt/petsc/3.3-p5/arch-linux2-cxx-opt/lib/libpetsc.so > #6 0x00007f8b57921952 in PCSetUp_LU(_p_PC*) () > from /gpfs/runtime/opt/petsc/3.3-p5/arch-linux2-cxx-opt/lib/libpetsc.so > #7 0x00007f8b57a98fa9 in PCSetUp () > from /gpfs/runtime/opt/petsc/3.3- > p5/arch-linux2-cxx-opt/lib/libpetsc.so #8 0x00007f8b57900e81 in > KSPSetUp () from /gpfs/runtime/opt/petsc/3.3- > p5/arch-linux2-cxx-opt/lib/libpetsc.so #9 0x00007f8b57901dcb in > KSPSolve () from /gpfs/runtime/opt/petsc/3.3- > p5/arch-linux2-cxx-opt/lib/libpetsc.so #10 0x00007f8b5fb33a72 in > dolfin::PETScLUSolver::solve (this=0x2e3aef0, x=Unhandled dwarf > expression opcode 0xf3 ) > at /gpfs/runtime/opt/fenics/1.3.0/src/dolfin- > 1.3.0/dolfin/la/PETScLUSolver.cpp:253 #11 0x00007f8b5fb3268a in > dolfin::PETScLUSolver::solve (this=0x2e3aef0, A=Unhandled dwarf > expression opcode 0xf3 ) > at /gpfs/runtime/opt/fenics/1.3.0/src/dolfin- > 1.3.0/dolfin/la/PETScLUSolver.cpp:279 #12 0x00007f8b5fb4d594 in > dolfin::LUSolver::solve (this=0x7fff30939160, A=..., x=..., b=...) > at /gpfs/runtime/opt/fenics/1.3.0/src/dolfin- > 1.3.0/dolfin/la/LUSolver.cpp:78 #13 0x00007f8b5fc7b439 in > dolfin::LinearVariationalSolver::solve (this=0x2dfd760) > at /gpfs/runtime/opt/fenics/1.3.0/src/dolfin- > 1.3.0/dolfin/fem/LinearVariationalSolver.cpp:170 #14 > 0x00007f8b3c7b1287 in _wrap_LinearVariationalSolver_solve > (args=Unhandled dwarf expression opcode 0xf3 ) > at /gpfs/runtime/opt/fenics/1.3.0/src/dolfin- > 1.3.0/build/dolfin/swig/modules/fem/modulePYTHON_wrap.cxx:27863 #15 > 0x00007f8b6f60d59b in do_call (f=<value optimized out>, throwflag= > <value optimized out>) at Python/ceval.c:4236 #16 call_function > (f=<value optimized out>, throwflag=<value optimized > out>) at Python/ceval.c:4044 > #17 PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value > optimized out>) at Python/ceval.c:2666 > #18 0x00007f8b6f60e94e in PyEval_EvalCodeEx (co=0x2943a30, globals= > <value optimized out>, locals=<value optimized out>, args=<value > optimized out>, argcount=3, kws=0x7f8b6fac6068, kwcount=0, defs=0x0, > defcount=0, closure= > 0x0) at Python/ceval.c:3253 > #19 0x00007f8b6f58dd58 in function_call (func=0x2c79050, > arg=0x2c85cd0, kw=0x2d5ba20) at Objects/funcobject.c:526 > #20 0x00007f8b6f55ee03 in PyObject_Call (func=0x2c79050, arg=<value > optimized out>, kw=<value optimized out>) at Objects/abstract.c:2529 > #21 0x00007f8b6f60b5ea in ext_do_call (f=<value optimized out>, > throwflag=<value optimized out>) at Python/ceval.c:4334 > #22 PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value > optimized out>) at Python/ceval.c:2705 > #23 0x00007f8b6f60e94e in PyEval_EvalCodeEx (co=0x29439b0, globals= > <value optimized out>, locals=<value optimized out>, args=<value > optimized out>, argcount=3, kws=0x1ba1608, kwcount=0, defs=0x0, > defcount=0, closure=0x0) > at Python/ceval.c:3253 > #24 0x00007f8b6f60cafa in fast_function (f=<value optimized out>, > throwflag=<value optimized out>) at Python/ceval.c:4117 > #25 call_function (f=<value optimized out>, throwflag=<value optimized > out>) at Python/ceval.c:4042 > #26 PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value > optimized out>) at Python/ceval.c:2666 > #27 0x00007f8b6f60e94e in PyEval_EvalCodeEx (co=0x7f8b6e8dacb0, > globals= <value optimized out>, locals=<value optimized out>, > args=<value optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, > defcount=0, closure=0x0) > at Python/ceval.c:3253 > #28 0x00007f8b6f60ea62 in PyEval_EvalCode (co=<value optimized out>, > globals=<value optimized out>, locals=<value optimized out>) at > Python/ceval.c:667 > #29 0x00007f8b6f62e500 in run_mod (fp=0x1b90730, filename=<value > optimized out>, start=<value optimized out>, globals=0x1b06280, > locals=0x1b06280, closeit=1, flags=0x7fff30939be0) at > Python/pythonrun.c:1353 > #30 PyRun_FileExFlags (fp=0x1b90730, filename=<value optimized out>, > start=<value optimized out>, globals=0x1b06280, locals=0x1b06280, > closeit=1, flags=0x7fff30939be0) at Python/pythonrun.c:1339 > #31 0x00007f8b6f62e6cc in PyRun_SimpleFileExFlags (fp=0x1b90730, > filename=0x7fff3093be7f "demo_poisson.py", closeit=1, > flags=0x7fff30939be0) at Python/pythonrun.c:943 > #32 0x00007f8b6f64411c in Py_Main (argc=<value optimized out>, argv= > <value optimized out>) at Modules/main.c:639 > #33 0x00007f8b6e8fccdd in ?? () > #34 0x0000000000000000 in ?? () > > " > > Could you help to take a look into it? > > Thank you very much. > > Best, > Teng > > > > 2014-04-23 7:25 GMT-04:00 Garth N. Wells <[email protected]>: > > > There is not way anyone can help without detailed information on > > your OS, compilers, FEniCS versions, . . . . > > > > Garth > > > > On 3 Apr 2014, at 21:02, 腾张 <[email protected]> wrote: > > > > > Dear All, > > > > > > I have installed the Fenics and can use most of the function and > > variable expect the "solve". I first tested the demo_poission.py > > and got the segmentation fault > > > > > > "Solving linear variational problem. > > > Segmentation fault" > > > > > > There may be some mistakes in the install process, could anyone > > > help me > > on this/ > > > > > > Thanks a lot. > > > > > > Best, > > > Teng > > > _______________________________________________ > > > fenics mailing list > > > [email protected] > > > http://fenicsproject.org/mailman/listinfo/fenics > > > > _______________________________________________ fenics mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics
