[MOAB-dev] build error on mcs machines

[Hong-Jun Kim]

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.

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./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
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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'