dolfin team mailing list archive

["Timothy Crone" <crone@xxxxxxxxxxxxxxxxx>]

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 <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
>>>>
>>>
>>>
>>
>>
>>
>
>



-- 
Timothy J. Crone
Lamont-Doherty Earth Observatory
Columbia University
61 Route 9W
Palisades, NY 10964
Tel: 845-365-8687

http://dactyl.ldeo.columbia.edu