[MOAB-dev] build error on mcs machines

[Jason Kraftcheck]

On 02/23/2011 04:10 PM, Hong-Jun Kim wrote:
> Yes, the library in "-L/usr/lib/mpich/lib/" and "mpicxx" being used
> (/usr/bin/mpicxx) are different versions.
> 

Are you certain?  Is there a different libmpich in /usr/lib?  What about the
other stuff:  Is mpicc consistant with mpicxx?  Where any of the other
dependencies (e.g. hdf5) built with a different mpicc/mpicxx?

- jason

> 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


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