dolfin team mailing list archive

[Jesper Carlsson <jesperc0@xxxxxxxxx>]

Hi again,

Seems like the problem was some old mpich libraries. Uninstalled mpich and
kept Open MPI, and it found the right libraries.

Compiling without pydolfin works fine (and the demos work fine on one
processor), but with pydolfin I get the following error:

mpic++ -o dolfin/swig/cpp_wrap.os -c -Wall -pipe -ansi -Werror -DDEBUG -g
-DNDEBUG -O2 -DHAS_MPI=1 -DMPICH_IGNORE_CXX_SEEK -DPACKAGE_VERSION=\"0.9.0\"
-DHAS_PETSC=1 -DHAS_SCOTCH=1 -DHAS_UMFPACK=1 -DHAS_GTS=1 -DHAS_TRILINOS=1
-DHAS_CHOLMOD=1 -DHAS_PARMETIS=1 -fno-strict-aliasing -fPIC -I.
-I/usr/include -I/usr/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/scotch
-I/usr/include/suitesparse -I/usr/include -I/usr/include/glib-2.0
-I/usr/lib/glib-2.0/include -I/usr/local/include -I/usr/include/suitesparse
-I/usr/include -I/usr/include/python2.5 -I/usr/include/python2.5
-I/usr/lib/python2.5/site-packages/numpy/core/include -I/usr/include
-I/usr/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/scotch
-I/usr/include/suitesparse -I/usr/include -I/usr/include/glib-2.0
-I/usr/lib/glib-2.0/include -I/usr/local/include -I/usr/include/suitesparse
-I/usr/include dolfin/swig/cpp_wrap.cc
cc1plus: warnings being treated as errors
dolfin/swig/cpp_wrap.cc: In function "PyObject*
_wrap_new_LUSolver(PyObject*, PyObject*)":
dolfin/swig/cpp_wrap.cc:57621: fel: "argv[0]" kan användas oinitierad i
denna funktion
dolfin/swig/cpp_wrap.cc: In function "PyObject* _wrap_summary(PyObject*,
PyObject*)":
dolfin/swig/cpp_wrap.cc:30721: fel: "argv[0]" kan användas oinitierad i
denna funktion
dolfin/swig/cpp_wrap.cc: In function "PyObject*
_wrap_new_TimeDependent(PyObject*, PyObject*)":
dolfin/swig/cpp_wrap.cc:28678: fel: "argv[0]" kan användas oinitierad i
denna funktion
dolfin/swig/cpp_wrap.cc: In function "PyObject*
_wrap_new_uBLASVector(PyObject*, PyObject*)":
dolfin/swig/cpp_wrap.cc:42865: fel: "argv[0]" kan användas oinitierad i
denna funktion
dolfin/swig/cpp_wrap.cc: In function "PyObject* _wrap_new_Vector(PyObject*,
PyObject*)":
dolfin/swig/cpp_wrap.cc:52979: fel: "argv[0]" kan användas oinitierad i
denna funktion
dolfin/swig/cpp_wrap.cc: In function "PyObject* _wrap_new_Table(PyObject*,
PyObject*)":
dolfin/swig/cpp_wrap.cc:31798: fel: "argv[0]" kan användas oinitierad i
denna funktion
dolfin/swig/cpp_wrap.cc: In function "PyObject*
_wrap_new_DiscreteFunction(PyObject*, PyObject*)":
dolfin/swig/cpp_wrap.cc:68434: fel: "argv[0]" kan användas oinitierad i
denna funktion

Also something is fishy with mpirun and petsc (ubuntu version), but I will
save that for later.

Best regards,
Jesper

On Sun, Feb 1, 2009 at 10:42 PM, Jesper Carlsson <jesperc0@xxxxxxxxx> wrote:

> mpic++ --show
> gives
>
> /usr/lib/gcc/i486-linux-gnu/4.3.2/../../../../lib/crt1.o: In function
> `_start':
> (.text+0x18): undefined reference to `main'
> collect2: ld returnerade avslutningsstatus 1
>
> while mpic++ --show -v
> gives
>
> mpicc for 1.2.7 (release) of : 2005/11/04 11:54:51
> Använder inbyggda specifikationer.
> Mål: i486-linux-gnu
> Konfigurerad med: ../src/configure -v --with-pkgversion='Ubuntu
> 4.3.2-1ubuntu12' --with-bugurl=file:///usr/share/doc/gcc-4.3/README.Bugs
> --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --enable-shared
> --with-system-zlib --libexecdir=/usr/lib --without-included-gettext
> --enable-threads=posix --enable-nls
> --with-gxx-include-dir=/usr/include/c++/4.3 --program-suffix=-4.3
> --enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc --enable-mpfr
> --enable-targets=all --enable-checking=release --build=i486-linux-gnu
> --host=i486-linux-gnu --target=i486-linux-gnu
> Trådmodell: posix
> gcc version 4.3.2 (Ubuntu 4.3.2-1ubuntu12)
>
> COMPILER_PATH=/usr/lib/gcc/i486-linux-gnu/4.3.2/:/usr/lib/gcc/i486-linux-gnu/4.3.2/:/usr/lib/gcc/i486-linux-gnu/:/usr/lib/gcc/i486-linux-gnu/4.3.2/:/usr/lib/gcc/i486-linux-gnu/:/usr/lib/gcc/i486-linux-gnu/4.3.2/:/usr/lib/gcc/i486-linux-gnu/
>
> LIBRARY_PATH=/usr/lib/gcc/i486-linux-gnu/4.3.2/:/usr/lib/gcc/i486-linux-gnu/4.3.2/:/usr/lib/gcc/i486-linux-gnu/4.3.2/../../../../lib/:/lib/../lib/:/usr/lib/../lib/:/usr/lib/gcc/i486-linux-gnu/4.3.2/../../../:/lib/:/usr/lib/
> COLLECT_GCC_OPTIONS='-DUSE_STDARG' '-DHAVE_STDLIB_H=1' '-DHAVE_STRING_H=1'
> '-DHAVE_UNISTD_H=1' '-DHAVE_STDARG_H=1' '-DUSE_STDARG=1'
> '-DMALLOC_RET_VOID=1' '-L/usr/lib/mpich/lib' '-fshow' '-v' '-mtune=generic'
>  /usr/lib/gcc/i486-linux-gnu/4.3.2/collect2 --eh-frame-hdr -m elf_i386
> --hash-style=both -dynamic-linker /lib/ld-linux.so.2 -z relro
> /usr/lib/gcc/i486-linux-gnu/4.3.2/../../../../lib/crt1.o
> /usr/lib/gcc/i486-linux-gnu/4.3.2/../../../../lib/crti.o
> /usr/lib/gcc/i486-linux-gnu/4.3.2/crtbegin.o -L/usr/lib/mpich/lib
> -L/usr/lib/gcc/i486-linux-gnu/4.3.2 -L/usr/lib/gcc/i486-linux-gnu/4.3.2
> -L/usr/lib/gcc/i486-linux-gnu/4.3.2/../../../../lib -L/lib/../lib
> -L/usr/lib/../lib -L/usr/lib/gcc/i486-linux-gnu/4.3.2/../../..
> -Bsymbolic-functions -lmpich -lpthread -lrt -lgcc --as-needed -lgcc_s
> --no-as-needed -lc -lgcc --as-needed -lgcc_s --no-as-needed
> /usr/lib/gcc/i486-linux-gnu/4.3.2/crtend.o
> /usr/lib/gcc/i486-linux-gnu/4.3.2/../../../../lib/crtn.o
> /usr/lib/gcc/i486-linux-gnu/4.3.2/../../../../lib/crt1.o: In function
> `_start':
> (.text+0x18): undefined reference to `main'
> collect2: ld returnerade avslutningsstatus 1
>
> /Jesper
>
>
> On Sun, Feb 1, 2009 at 10:22 PM, Johannes Ring <johannr@xxxxxxxxx> wrote:
>
>> On Sun, February 1, 2009 21:35, Jesper Carlsson wrote:
>> > Sorry, forgot the logfile. I'm using the version 0.9.0 here, but the
>> development version gives the same output.
>>
>> Thanks. It seems like this error is repeated:
>>
>>  undefined reference to `__gxx_personality_v0'
>>
>> Googling suggest that a C compiler might be in use instead of a C++
>> compiler. What does
>>
>>  mpic++ --show
>>
>> give you?
>>
>> Johannes
>>
>>
>>
>