[MOAB-dev] build error on mcs machines

[Jason Kraftcheck]

On 02/23/2011 03:12 PM, Hong-Jun Kim wrote:
> Hi, all
> 
> In ANL, we have had troubles to build parallel MOAB with our own hdf5 and mpich libraries, then I removed options for this and used the mpich installed in system as follows.
> 

Verify that the -L/usr/lib/mpich/lib/ from the link line is correct for the
mpicxx being used to compile.

Verify that 'mpicxx' is the one you think it is (i.e. 'which mpicxx').

Verify that 'mpicc' is consistent with 'mpicxx' (i.e. 'which mpicc').

Verify that none of the external libraries being linked (-lnetcdf
/usr/lib/libhdf5.so) where built with some other version of MPI.

- jason


> ------------------------------------------
> ./configure --prefix=/homes/hongjun/lib/MOAB-new --with-mpi --with-cgm=/homes/hongjun/lib/CGM --enable-debug --disable-optimize --enable-igeom --enable-imesh --enable-dagmc
> ------------------------------------------
> 
> However, I still have undefined reference errors as follows about some mpi functions.
> Actually, I have no idea why this kind of errors are coming.
> Does anybody have any idea about this?
> Thanks.
> 
> Hong-Jun
> 
> -----------------------------------------------------------
> make[3]: Entering directory `/nfs/mcs-homes138/hongjun/source/moab-new/tools'
> /bin/sh ../libtool  --tag=CXX   --mode=link mpicxx  -Wall -pipe -pedantic -Wno-long-long -g -R/homes/hongjun/lib/CGM/lib        -L/homes/hongjun/lib/CGM/lib  -L/homes/fathom/3rdparty/occ/OpenCASCADE6.3.0/gcc/lib  -o mbconvert convert.o ../src/libMOAB.la -lm
> libtool: link: mpicxx -Wall -pipe -pedantic -Wno-long-long -g -o mbconvert convert.o  -L/homes/hongjun/lib/CGM/lib -L/homes/fathom/3rdparty/occ/OpenCASCADE6.3.0/gcc/lib ../src/.libs/libMOAB.a -lnetcdf /usr/lib/libhdf5.so -L/usr/lib/mpich/lib/ -lz /homes/hongjun/lib/CGM/lib/libcgm.a /home/fathom/3rdparty/occ/OpenCASCADE6.3.0/gcc/lib/libTKSTL.so (more occ libraries....) -ldl -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/occ/OpenCASCADE6.3.0/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/occ/OpenCASCADE6.3.0/gcc/lib -Wl,-rpath -Wl,/homes/hongjun/lib/CGM/lib
> /usr/lib/libmpichcxx.so: undefined reference to `MPI_Win_unlock'
> /usr/lib/libmpichcxx.so: undefined reference to `PMPI_Type_set_name'
> /usr/lib/libmpichcxx.so: undefined reference to `MPI_Grequest_complete'
> /usr/lib/libmpichcxx.so: undefined reference to `MPI_Put'
> /usr/lib/libmpichcxx.so: undefined reference to `MPI_Comm_get_attr'
> /usr/lib/libmpichcxx.so: undefined reference to `MPI_File_call_errhandler'
> /usr/lib/libmpichcxx.so: undefined reference to `MPI_Pack_external_size'
> /usr/lib/libmpichcxx.so: undefined reference to `MPI_Win_start'
> /usr/lib/libmpichcxx.so: undefined reference to `MPI_Win_set_errhandler'
> -----------------------------------------------------------
> 
> ----- Original Message -----
>> From: "Iulian Grindeanu" <iulian at mcs.anl.gov>
>> To: moab-dev at mcs.anl.gov
>> Sent: Monday, February 21, 2011 3:53:06 PM
>> Subject: [MOAB-dev] build error on mcs machines
>> Hello,
>> I was wondering if anybody has a good build on MCS machines now.
>> I am getting errors I did not have last week, and I do not know the
>> cause
>>
>> It seems to be related to hdf5 library and dependency on netcdf. Hong
>> Jun and I have the same problems, for parallel or serial builds. It is
>> fine on my laptop, where I have only one hdf5 version.
>>
>> Does anybody have a suggestion?
>>
>> Iulian
>>
>>
>> Making all in .
>> make[3]: Entering directory
>> `/nfs/mcs-homes129/iulian/serial/MOAB/tools'
>> CXXLD mbconvert
>> /usr/bin/ld: warning: libstdc++.so.5, needed by
>> /home/fathom/3rdparty/cubit/Cubit64/cubit-10.2-amd64/bin/libcubiti19.so,
>> may conflict with libstdc++.so.6
>> /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so:
>> undefined reference to `H5DSget_num_scales'
>> /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so:
>> undefined reference to `H5DSset_scale'
>> /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so:
>> undefined reference to `H5DSget_scale_name'
>> /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so:
>> undefined reference to `H5DSis_scale'
>> /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so:
>> undefined reference to `H5DSdetach_scale'
>> /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so:
>> undefined reference to `H5DSiterate_scales'
>> /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so:
>> undefined reference to `H5DSattach_scale'


-- 
"A foolish consistency is the hobgoblin of little minds" - Ralph Waldo Emerson