Dear Roy,
Thank you very much for your advice. I further comment the corresponding
codes and compile it. I get the following errors:
"----- Done Building Contributed Packages -----
----------------------------------------------
make[1]: warning: Clock skew detected. Your build may be incomplete.
make[1]: Leaving directory `/home/yujie/codes/codes/libmesh/contrib'
Building bin/amr-dbg
In file included from
/home/yujie/codes/codes/libmesh/include/base/reference_counted_object.h:29,
from
/home/yujie/codes/codes/libmesh/include/base/dof_map.h:35,
from src/apps/amr.cc:4:
/home/yujie/codes/codes/libmesh/include/base/reference_counter.h: In member
function `void ReferenceCounter::increment_constructor_count(const
std::string&)':
/home/yujie/codes/codes/libmesh/include/base/reference_counter.h:151:
warning: unused
variable `Threads::spin_mutex::scoped_lock lock'
/home/yujie/codes/codes/libmesh/include/base/reference_counter.h: In member
function `void ReferenceCounter::increment_destructor_count(const
std::string&)':
/home/yujie/codes/codes/libmesh/include/base/reference_counter.h:169:
warning: unused
variable `Threads::spin_mutex::scoped_lock lock'
/home/yujie/codes/codes/libmesh/contrib/tecplot/lib/i686-pc-linux-gnu/tecio.a(tecxxx.o)(.text+0x1a7):
In function `tecini':
: the use of `mktemp' is dangerous, better use `mkstemp'
/home/yujie/codes/codes/libmesh/lib/i686-pc-linux-gnu_dbg/libmesh.so:
undefined reference to `VecCreateGhost(_comm*, int, int, int, int const*,
_p_Vec**)'
/home/yujie/codes/codes/libmesh/lib/i686-pc-linux-gnu_dbg/libmesh.so:
undefined reference to `MatCreateShell(_comm*, int, int, int, int, void*,
_p_Mat**)'
/home/yujie/codes/codes/libmesh/lib/i686-pc-linux-gnu_dbg/libmesh.so:
undefined reference to `VecCreateMPI(_comm*, int, int, _p_Vec**)'
/home/yujie/codes/codes/libmesh/lib/i686-pc-linux-gnu_dbg/libmesh.so:
undefined reference to `DenseMatrix<std::complex<double>
>::_lu_back_substitute_lapack(DenseVector<std::complex<double> > const&,
DenseVector<std::complex<double> >&)'
/home/yujie/codes/codes/libmesh/lib/i686-pc-linux-gnu_dbg/libmesh.so:
undefined reference to `PETSC_VIEWER_STDOUT_(_comm*)'
/home/yujie/codes/codes/libmesh/lib/i686-pc-linux-gnu_dbg/libmesh.so:
undefined reference to `KSPCreate(_comm*, _p_KSP**)'
/home/yujie/codes/codes/libmesh/lib/i686-pc-linux-gnu_dbg/libmesh.so:
undefined reference to `MatCreateSeqAIJ(_comm*, int, int, int, int const*,
_p_Mat**)'
/home/yujie/codes/codes/libmesh/lib/i686-pc-linux-gnu_dbg/libmesh.so:
undefined reference to `ISCreateGeneral(_comm*, int, int const*, _p_IS**)'
/home/yujie/codes/codes/libmesh/lib/i686-pc-linux-gnu_dbg/libmesh.so:
undefined reference to `SNESCreate(_comm*, _p_SNES**)'
/home/yujie/codes/codes/libmesh/lib/i686-pc-linux-gnu_dbg/libmesh.so:
undefined reference to `PetscViewerCreate(_comm*, _p_PetscViewer**)'
/home/yujie/codes/codes/libmesh/lib/i686-pc-linux-gnu_dbg/libmesh.so:
undefined reference to `DenseMatrix<std::complex<double>
>::_matvec_blas(std::complex<double>, std::complex<double>,
DenseVector<std::complex<double> >&, DenseVector<std::complex<double> >
const&) const'
/home/yujie/codes/codes/libmesh/lib/i686-pc-linux-gnu_dbg/libmesh.so:
undefined reference to `DenseMatrix<std::complex<double>
>::_lu_decompose_lapack()'
/home/yujie/codes/codes/libmesh/lib/i686-pc-linux-gnu_dbg/libmesh.so:
undefined reference to `PetscViewerASCIIOpen(_comm*, char const*,
_p_PetscViewer**)'
/home/yujie/codes/codes/libmesh/lib/i686-pc-linux-gnu_dbg/libmesh.so:
undefined reference to `DenseMatrix<std::complex<double>
>::_multiply_blas(DenseMatrixBase<std::complex<double> > const&,
DenseMatrix<std::complex<double> >::_BLAS_Multiply_Flag)'
/home/yujie/codes/codes/libmesh/lib/i686-pc-linux-gnu_dbg/libmesh.so:
undefined reference to `PCCreate(_comm*, _p_PC**)'
/home/yujie/codes/codes/libmesh/lib/i686-pc-linux-gnu_dbg/libmesh.so:
undefined reference to `MatCreateMPIAIJ(_comm*, int, int, int, int, int, int
const*, int, int const*, _p_Mat**)'
/home/yujie/codes/codes/libmesh/lib/i686-pc-linux-gnu_dbg/libmesh.so:
undefined reference to `VecCreateSeq(_comm*, int, _p_Vec**)'
collect2: ld returned 1 exit status
mpiCC: No such file or directory
make: *** [bin/amr-dbg] Error 1"
I have included all the libs of PETSc. I also "make test" in PETSc. It
works. I don't know why libmesh.so can't find the reference to the above
functions. Your linker problem is the same with me?
Whether can I avoid to compile amr-dbg? I don't think I will use it. Thanks
a lot.
Regards,
Yujie
On Wed, Jan 20, 2010 at 2:39 PM, Roy Stogner <[email protected]>wrote:
>
> On Wed, 20 Jan 2010, Yujie wrote:
>
> Thank you very much for your advice. I will try to upgrade my GCC. Thanks
>> a
>> lot.
>>
>
> Yeah, although there's an actual bug that we need to fix here, I'd
> still agree that using gcc 4 would be a good idea. We can fix the
> --enable-complex problem, but I've just tried reverting to gcc 3.4,
> and on my system there seems to be a linker problem that might be the
> compiler's fault, not ours.
> ---
> Roy
>
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