[MOAB-dev] build error on mcs machines

[Hong-Jun Kim]

Yes, the library in "-L/usr/lib/mpich/lib/" and "mpicxx" being used (/usr/bin/mpicxx) are different versions.

I attached my "config.log" file and all configuration checks look being done with the "/usr/bin/mpicxx".
So, I have no idea why "-L/usr/lib/mpich/lib/" is in the build command line.
Do you know why libtool put "-L/usr/lib/mpich/lib/"?
Thanks.

Hong-Jun


----- Original Message -----
> From: "Jason Kraftcheck" <kraftche at cae.wisc.edu>
> To: "Hong-Jun Kim" <hongjun at mcs.anl.gov>
> Cc: moab-dev at mcs.anl.gov
> Sent: Wednesday, February 23, 2011 3:19:39 PM
> Subject: Re: [MOAB-dev] build error on mcs machines
> 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