dolfin team mailing list archive

["Timothy Crone" <crone@xxxxxxxxxxxxxxxxx>]

Okay, I uninstalled the mpich packages, and the default compiler
reverted to openmpi. Not sure how the mpich packages snuck in there.
Anyway, I recompiled with openmpi, and everything seems to work dandy.
I still get the warnings because of the swig issue, but using
enableDebug=no allows the wrapper to compile, and all the demos work
great. Thanks for your help!

Cheers,
Tim


On Tue, Aug 26, 2008 at 3:36 AM, Garth N. Wells <gnw20@xxxxxxxxx> wrote:
>
>
> 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
>>>>>>
>>>>>
>>>>
>>>>
>>>
>>
>>
>>
>



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

http://dactyl.ldeo.columbia.edu