Dear Blechta, Thank you very much. You are right. The staff of our university's cluster just fixed the issue this week, they told me the reason is as follows
"So the problem was CHOLMOD uses metis 4 while others use metis 5, and metis 5 is not backward compatible with metis 4 so there was a huge breakage." Now Fenics works well on the cluster. Thanks again. Best, Teng 2014-04-27 9:11 GMT-04:00 Jan Blechta <[email protected]>: > 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 > > > > > > > >
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