[Openmd-users] Problem withn installation

[Cecil Ouma]

Hi Dan,

I tried the solution you suggested but I still have the same error

Regards
Cecil

Post-Doc
CSIR- South Africa

>>> Dan Gezelter <gezelter at nd.edu> 10/20/14 3:20 PM >>>
Cecil,

It looks like cmake set the CMAKE_CXX_COMPILER and MPI_CXX_COMPILER variables to different values, so it is trying to link with a different compiler than it used to build the object files.  The regular c++ compiler probably doesn't know where the openmpi libraries are located.  As a quick suggestion, try rebuilding as follows:

    export CXX=/usr/lib64/openmpi/bin/mpicxx
    cmake ../openmd-2.2
    make


Let us know how it goes!

Best regards,

 --Dan Gezelter


> On Oct 20, 2014, at 6:23 AM, Cecil Ouma <COuma at csir.co.za> wrote:
> 
> Hi
> 
> Please assist me with installation of openMD. 
> 
> This is what I did
> 
> =================================
> [cecil at localhost build-openMD]$ cmake ../openmd-2.2
> -- QHULL found (include: /usr/local/include, lib: optimized;/usr/local/lib/libqhullstatic.a;debug;/usr/local/lib/libqhullstatic.a)
> -- 
> -- ========== OpenMD Build Information ==========
> -- Current revision ........... = Release
> -- CMAKE_SYSTEM ............... = Linux-3.16.3-200.fc20.x86_64
> -- ==============================================
> -- CMAKE_BUILD_TYPE ........... = Release
> -- CMAKE_INSTALL_PREFIX ....... = /usr/local/openmd
> -- Build as SINGLE_PRECISION .. = OFF
> -- CMAKE_CXX_COMPILER ......... = /usr/bin/c++
> -- MPI_CXX_COMPILER ........... = /usr/lib64/openmpi/bin/mpicxx
> -- MPI_CXX_INCLUDE_PATH ....... = /usr/include/openmpi-x86_64
> -- MPI_CXX_LIBRARIES .......... = /usr/lib64/openmpi/lib/libmpi_cxx.so;/usr/lib64/openmpi/lib/libmpi.so
> -- OPENBABEL2_ROOT ............ = 
> -- OPENBABEL2_INCLUDE_DIR ..... = /usr/include/openbabel-2.0
> -- OPENBABEL2_LIBRARIES ....... = /usr/lib64/libopenbabel.so
> -- QHULL_ROOT ................. = 
> -- QHULL_INCLUDE_DIR .......... = /usr/local/include
> -- QHULL_LIBRARIES ............ = optimized;/usr/local/lib/libqhullstatic.a;debug;/usr/local/lib/libqhullstatic.a
> -- ZLIB_ROOT .................. = 
> -- ZLIB_INCLUDE_DIR ........... = /usr/include
> -- ZLIB_LIBRARIES ............. = /usr/lib64/libz.so
> -- FFTW3_ROOT ................. = 
> -- FFTW3_INCLUDE_DIR .......... = /usr/include
> -- FFTW3_LIBRARIES ............ = /usr/lib64/libfftw3.so
> -- PERL_EXECUTABLE ............ = /usr/bin/perl
> -- PYTHON_EXECUTABLE .......... = /usr/bin/python
> -- DOXYGEN_EXECUTABLE ......... = /usr/bin/doxygen
> -- 
> -- To override these options, add -D{OPTION_NAME}=... to the cmake command
> -- Particularly useful defines are for:
> -- 
> --   -DCMAKE_INSTALL_PREFIX=/usr/local/openmd (where OpenMD will be installed)
> --        -DOPENBABEL2_ROOT=/path/to/openbabel
> --             -DQHULL_ROOT=/path/to/qhull
> --             -DFFTW3_ROOT=/path/to/fftw3
> -- 
> -- To build and install OpenMD, enter "make" and "make install"
> -- 
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home/cecil/build-openMD
> =====================================================
> 
> when I type make i get this among others
> ...
> ...
> ...
> lib/libopenmd_parallel.a(Problem.cpp.o): In function `QuantLib::Problem::computeGradientNormValue(OpenMD::DynamicVector<double, std::allocator<double> >&)':
> Problem.cpp:(.text+0xc4): undefined reference to `ompi_mpi_comm_world'
> Problem.cpp:(.text+0xca): undefined reference to `ompi_mpi_op_sum'
> Problem.cpp:(.text+0xcf): undefined reference to `ompi_mpi_double'
> Problem.cpp:(.text+0xe3): undefined reference to `MPI_Allreduce'
> collect2: error: ld returned 1 exit status
> make[2]: *** [bin/openmd_MPI] Error 1
> make[1]: *** [CMakeFiles/openmd_MPI.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs....
> 
> 
> 
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***********************************************
  J. Daniel Gezelter
  Associate Professor of Chemistry
  Department of Chemistry and Biochemistry
  251 Nieuwland Science Hall
  University of Notre Dame
  Notre Dame, IN 46556-5670

  +1 (574) 631-7595
  gezelter at nd.edu
  http://www.nd.edu/~gezelter
************************************************





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