dolfin team mailing list archive

["Garth N. Wells" <gnw20@xxxxxxxxx>]

Timothy Crone wrote:
> 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. 

I'm using openmpi. Try setting the environment variable CXX to point to 
the openmpi compiler. mpich provided by one of the the Debian mpich 
packages (which are MPI version 1.0) is unlikely to work. Easiest 
approach would be to just remove the mpich packages.

Garth

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 <gnw20@xxxxxxxxx> 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,  <kent-and@xxxxxxxxx> 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
> > > > > DOLFIN-dev@xxxxxxxxxx
> > > > > http://www.fenics.org/mailman/listinfo/dolfin-dev