Well that is very strange. I am also using all Lenny packages (openmpi, petsc, etc.) except for FEniCS libraries. On my machine /usr/bin/mpicxx is a link pointing to a script called /usr/lib/mpich-shmem/bin/mpicxx, which appears to choose which compiler to use. Do you have an environment variable set to choose a non-default compiler?
Thanks, Tim On Mon, Aug 25, 2008 at 5:51 PM, Garth N. Wells <[EMAIL PROTECTED]> wrote: > It works perfectly for me under Lenny. Which MPI are you using? I used Lenny > packages for all non-FEniCS libraries (petsc, openmpi, etc). > > Garth > > Timothy Crone wrote: >> >> Thanks for your reply Kent. I used enableDebug=no to get >> dolfin_wrap.cc to compile, because otherwise warnings are treated as >> errors. Not sure if this will affect the output from gdb. Anyway, here >> is the output from your suggestion: >> >> GNU gdb 6.8-debian >> Copyright (C) 2008 Free Software Foundation, Inc. >> License GPLv3+: GNU GPL version 3 or later >> <http://gnu.org/licenses/gpl.html> >> This is free software: you are free to change and redistribute it. >> There is NO WARRANTY, to the extent permitted by law. Type "show copying" >> and "show warranty" for details. >> This GDB was configured as "x86_64-linux-gnu"... >> (gdb) run demo.py >> Starting program: /usr/bin/python demo.py >> [Thread debugging using libthread_db enabled] >> [New Thread 0x7fe52a4266e0 (LWP 17418)] >> >> Program received signal SIGSEGV, Segmentation fault. >> [Switching to Thread 0x7fe52a4266e0 (LWP 17418)] >> 0x00007fe51fdadf94 in MPID_CH_InitMsgPass () from >> /home/tjc/computer/fenics/dolfin/dolfin/dolfin/libdolfin.so >> Current language: auto; currently asm >> (gdb) where >> #0 0x00007fe51fdadf94 in MPID_CH_InitMsgPass () from >> /home/tjc/computer/fenics/dolfin/dolfin/dolfin/libdolfin.so >> #1 0x00007fe51fdab053 in MPID_Init () from >> /home/tjc/computer/fenics/dolfin/dolfin/dolfin/libdolfin.so >> #2 0x00007fe51fd8faa0 in MPIR_Init () from >> /home/tjc/computer/fenics/dolfin/dolfin/dolfin/libdolfin.so >> #3 0x00007fe51fcf1271 in dolfin::SubSystemsManager::initMPI () at >> /usr/lib/openmpi/include/openmpi/ompi/mpi/cxx/functions_inln.h:104 >> #4 0x00007fe51fcf1069 in dolfin::MPI::numProcesses () at >> dolfin/main/MPI.cpp:29 >> #5 0x00007fe51fcf1099 in dolfin::MPI::receive () at >> dolfin/main/MPI.cpp:42 >> #6 0x00007fe51fd2afab in UnitSquare (this=0x2ba2390, nx=32, ny=32, >> type=dolfin::UnitSquare::right) at dolfin/mesh/UnitSquare.cpp:20 >> #7 0x00007fe522e031e4 in _wrap_new_UnitSquare (self=<value optimized >> out>, args=<value optimized out>) at dolfin/swig/dolfin_wrap.cc:90885 >> #8 0x00000000004187b3 in PyObject_Call (func=0x0, arg=0x0, >> kw=0x7fff324447a1) at ../Objects/abstract.c:1861 >> #9 0x0000000000490257 in PyEval_EvalFrameEx (f=0x2ceb3e0, >> throwflag=<value optimized out>) at ../Python/ceval.c:3855 >> #10 0x00000000004930fd in PyEval_EvalCodeEx (co=0x2b5f558, >> globals=<value optimized out>, locals=<value optimized out>, >> args=0x7fe52a3d3c98, >> argcount=3, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) >> at ../Python/ceval.c:2838 >> #11 0x00000000004dd692 in function_call (func=0x2c44b18, >> arg=0x7fe52a3d3c80, kw=0x0) at ../Objects/funcobject.c:517 >> #12 0x00000000004187b3 in PyObject_Call (func=0x0, arg=0x0, >> kw=0x7fff324447a1) at ../Objects/abstract.c:1861 >> #13 0x000000000041f658 in instancemethod_call (func=0x2c44b18, >> arg=0x7fe52a3d3c80, kw=0x0) at ../Objects/classobject.c:2519 >> #14 0x00000000004187b3 in PyObject_Call (func=0x0, arg=0x0, >> kw=0x7fff324447a1) at ../Objects/abstract.c:1861 >> #15 0x0000000000465ca6 in slot_tp_init (self=0x7fe52a3df6d0, >> args=0x7fe52a3e0ea8, kwds=0x0) at ../Objects/typeobject.c:4943 >> #16 0x000000000046df9b in type_call (type=0x2ceaa40, >> args=0x7fe52a3e0ea8, kwds=0x0) at ../Objects/typeobject.c:436 >> #17 0x00000000004187b3 in PyObject_Call (func=0x0, arg=0x0, >> kw=0x7fff324447a1) at ../Objects/abstract.c:1861 >> #18 0x000000000048feb2 in PyEval_EvalFrameEx (f=0x2245650, >> throwflag=<value optimized out>) at ../Python/ceval.c:3786 >> #19 0x00000000004930fd in PyEval_EvalCodeEx (co=0x7fe52a3d9288, >> globals=<value optimized out>, locals=<value optimized out>, args=0x0, >> argcount=0, >> kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at >> ../Python/ceval.c:2838 >> #20 0x00000000004932f2 in PyEval_EvalCode (co=0x0, globals=0x0, >> locals=0x7fff324447a1) at ../Python/ceval.c:494 >> #21 0x00000000004b2d08 in PyRun_FileExFlags (fp=0x222c010, >> filename=0x7fff324475a1 "demo.py", start=<value optimized out>, >> globals=0x224f580, >> locals=0x224f580, closeit=1, flags=0x7fff32445640) at >> ../Python/pythonrun.c:1273 >> #22 0x00000000004b2fab in PyRun_SimpleFileExFlags (fp=0x222c010, >> filename=0x7fff324475a1 "demo.py", closeit=1, flags=0x7fff32445640) >> at ../Python/pythonrun.c:879 >> ---Type <return> to continue, or q <return> to quit--- >> #23 0x0000000000414542 in Py_Main (argc=1, argv=<value optimized out>) >> at ../Modules/main.c:532 >> #24 0x00007fe5296511a6 in __libc_start_main () from /lib/libc.so.6 >> #25 0x0000000000413989 in _start () >> (gdb) >> >> By the way, the Lorenz Python demo seems to work okay, although it >> warns "Not solving the dual problem as requested" at the end. >> >> Thanks, >> Tim >> >> On Mon, Aug 25, 2008 at 4:02 PM, <[EMAIL PROTECTED]> wrote: >>> >>> Can you try with a debugger: >>> >>> gdb python >>> (gdb) run demo.py >>> .... >>> (gdb) where >>> >>> It is strange if these warnings have anything to do with the seg. fault. >>> >>> Kent >>> >>> >>>> Hello, >>>> >>>> Does anyone know a workaround to the problem of compiling the Pydolfin >>>> file dolfin_wrap.cc with mpicxx version 4.3.1? I get several warnings >>>> during compile, and segmentation faults at runtime. I am using Debian >>>> Lenny, which uses 4.3.1 as the default compiler. SWIG is version >>>> 1.3.33. Any help in this matter would be greatly appreciated. >>>> >>>> Here are the errors when enableDebug=no: >>>> >>>> mpicxx -o dolfin/swig/dolfin_wrap.os -c -Wall -pipe -ansi -DNDEBUG -O3 >>>> -DHAS_MPI=1 -DMPICH_IGNORE_CXX_SEEK -DPACKAGE_VERSION=\"0.8.0\" >>>> -DHAS_PETSC=1 -DHAS_UMFPACK=1 -DHAS_GTS=1 -DHAS_CHOLMOD=1 >>>> -fno-strict-aliasing -fPIC -I. -I/usr/include/libxml2 >>>> -I/usr/lib/petscdir/2.3.3/bmake/linux-gnu-c-opt >>>> -I/usr/lib/petscdir/2.3.3/include -I/usr/lib/openmpi/include >>>> -I/usr/lib/openmpi/lib -Idolfin -I/usr/include/suitesparse >>>> -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include >>>> -I/usr/include/suitesparse -I/usr/include/python2.5 >>>> -I/usr/include/python2.5 >>>> -I/usr/lib/python2.5/site-packages/numpy/core/include >>>> -I/usr/include/libxml2 -I/usr/lib/petscdir/2.3.3/bmake/linux-gnu-c-opt >>>> -I/usr/lib/petscdir/2.3.3/include -I/usr/lib/openmpi/include >>>> -I/usr/lib/openmpi/lib -Idolfin -I/usr/include/suitesparse >>>> -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include >>>> -I/usr/include/suitesparse dolfin/swig/dolfin_wrap.cc >>>> dolfin/swig/dolfin_wrap.cc: In constructor >>>> 'swig::PyObject_ptr::PyObject_ptr(PyObject*, bool)': >>>> dolfin/swig/dolfin_wrap.cc:3286: warning: suggest explicit braces to >>>> avoid ambiguous 'else' >>>> dolfin/swig/dolfin_wrap.cc: In destructor >>>> 'swig::PySequence_Cont<T>::~PySequence_Cont()': >>>> dolfin/swig/dolfin_wrap.cc:4727: warning: suggest explicit braces to >>>> avoid ambiguous 'else' >>>> dolfin/swig/dolfin_wrap.cc: In function 'PyObject* >>>> _wrap_summary(PyObject*, PyObject*)': >>>> dolfin/swig/dolfin_wrap.cc:29893: warning: 'argv[0]' may be used >>>> uninitialized in this function >>>> dolfin/swig/dolfin_wrap.cc: In function 'PyObject* >>>> _wrap_ios_base_sync_with_stdio(PyObject*, PyObject*)': >>>> dolfin/swig/dolfin_wrap.cc:17337: warning: 'argv[0]' may be used >>>> uninitialized in this function >>>> dolfin/swig/dolfin_wrap.cc: In function 'PyObject* >>>> _wrap_new_TimeDependent(PyObject*, PyObject*)': >>>> dolfin/swig/dolfin_wrap.cc:28067: warning: 'argv[0]' may be used >>>> uninitialized in this function >>>> dolfin/swig/dolfin_wrap.cc: In function 'PyObject* >>>> _wrap_new_BoundaryMesh(PyObject*, PyObject*)': >>>> dolfin/swig/dolfin_wrap.cc:90450: warning: 'argv[0]' may be used >>>> uninitialized in this function >>>> dolfin/swig/dolfin_wrap.cc: In function 'PyObject* >>>> _wrap_new_MeshTopology(PyObject*, PyObject*)': >>>> dolfin/swig/dolfin_wrap.cc:74482: warning: 'argv[0]' may be used >>>> uninitialized in this function >>>> dolfin/swig/dolfin_wrap.cc: In function 'PyObject* >>>> _wrap_new_MeshConnectivity(PyObject*, PyObject*)': >>>> dolfin/swig/dolfin_wrap.cc:76492: warning: 'argv[0]' may be used >>>> uninitialized in this function >>>> dolfin/swig/dolfin_wrap.cc: In function 'PyObject* >>>> _wrap_new_MeshGeometry(PyObject*, PyObject*)': >>>> dolfin/swig/dolfin_wrap.cc:75192: warning: 'argv[0]' may be used >>>> uninitialized in this function >>>> dolfin/swig/dolfin_wrap.cc: In function 'PyObject* >>>> _wrap_new_Vector(PyObject*, PyObject*)': >>>> dolfin/swig/dolfin_wrap.cc:50862: warning: 'argv[0]' may be used >>>> uninitialized in this function >>>> dolfin/swig/dolfin_wrap.cc: In function 'PyObject* >>>> _wrap_new_uBLASVector(PyObject*, PyObject*)': >>>> dolfin/swig/dolfin_wrap.cc:41746: warning: 'argv[0]' may be used >>>> uninitialized in this function >>>> dolfin/swig/dolfin_wrap.cc: In function 'PyObject* >>>> _wrap_new_uBLASILUPreconditioner(PyObject*, PyObject*)': >>>> dolfin/swig/dolfin_wrap.cc:50585: warning: 'argv[0]' may be used >>>> uninitialized in this function >>>> dolfin/swig/dolfin_wrap.cc: In function 'PyObject* >>>> _wrap_new_PETScVector(PyObject*, PyObject*)': >>>> dolfin/swig/dolfin_wrap.cc:44047: warning: 'argv[0]' may be used >>>> uninitialized in this function >>>> dolfin/swig/dolfin_wrap.cc: In function 'PyObject* >>>> _wrap_new_Table(PyObject*, PyObject*)': >>>> dolfin/swig/dolfin_wrap.cc:30960: warning: 'argv[0]' may be used >>>> uninitialized in this function >>>> dolfin/swig/dolfin_wrap.cc: In function 'PyObject* >>>> _wrap_new_Mesh(PyObject*, PyObject*)': >>>> dolfin/swig/dolfin_wrap.cc:78823: warning: 'argv[0]' may be used >>>> uninitialized in this function >>>> mpicxx -o dolfin/swig/_dolfin.so -pthread -Wl,--export-dynamic -shared >>>> dolfin/swig/dolfin_wrap.os -Ldolfin >>>> -L/usr/lib/petscdir/2.3.3/lib/linux-gnu-c-opt -L/usr/lib/atlas >>>> -L/usr/lib/atlas -lxml2 -lpetscts -lpetscsnes -lpetscksp -lpetscdm >>>> -lpetscmat -lpetscvec -lpetsc -lblas -lumfpack -lamd -lgts -lm >>>> -lgthread-2.0 -lrt -lgmodule-2.0 -ldl -lglib-2.0 -llapack -lblas >>>> -lcholmod -lamd -lcolamd -ldolfin >>>> scons: done building targets. >>>> >>>> Thanks, >>>> Tim >>>> _______________________________________________ >>>> DOLFIN-dev mailing list >>>> [email protected] >>>> http://www.fenics.org/mailman/listinfo/dolfin-dev >>>> >>> >>> >> >> >> > > -- Timothy J. Crone Lamont-Doherty Earth Observatory Columbia University 61 Route 9W Palisades, NY 10964 Tel: 845-365-8687 http://dactyl.ldeo.columbia.edu _______________________________________________ DOLFIN-dev mailing list [email protected] http://www.fenics.org/mailman/listinfo/dolfin-dev
