[Openmd-users] Problem withn installation

Tue Oct 21 13:45:32 EDT 2014

Cecil,

If cmake isn't seeing that environment variable, you can also try passing the compiler to it directly:

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

If that fails, can you email me the complete output of the cmake and make process?

Best regards,

 --Dan

> On Oct 21, 2014, at 1:35 AM, Cecil Ouma <COuma at csir.co.za> wrote:
> 
> 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
> ************************************************
> 
> 
> 
> 
> 
> -- 
> This message is subject to the CSIR's copyright terms and conditions, e-mail legal notice, and implemented Open Document Format (ODF) standard. 
> The full disclaimer details can be found at http://www.csir.co.za/disclaimer.html.
> 
> This message has been scanned for viruses and dangerous content by MailScanner, 
> and is believed to be clean.
> 
> Please consider the environment before printing this email.
> 
> 
> 
> -- 
> This message is subject to the CSIR's copyright terms and conditions, e-mail legal notice, and implemented Open Document Format (ODF) standard. 
> The full disclaimer details can be found at http://www.csir.co.za/disclaimer.html.
> 
> This message has been scanned for viruses and dangerous content by MailScanner, 
> and is believed to be clean.
> 
> 
> Please consider the environment before printing this email.
> 

***********************************************
  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
************************************************