<html><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><META name="Author" content="Novell GroupWise WebAccess"></head><body style='font-family: Helvetica, Arial, sans-serif; font-size: 13px; '>Hi Dan,<br><br>I tried the solution you suggested but I still have the same error<br><br>Regards<br>Cecil<br><br>Post-Doc<br>CSIR- South Africa<br><br>>>> Dan Gezelter <gezelter@nd.edu> 10/20/14 3:20 PM >>><br>Cecil,<br><br>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:<br><br> export CXX=/usr/lib64/openmpi/bin/mpicxx<br> cmake ../openmd-2.2<br> make<br><br><br>Let us know how it goes!<br><br>Best regards,<br><br> --Dan Gezelter<br><br><br>> On Oct 20, 2014, at 6:23 AM, Cecil Ouma <COuma@csir.co.za> wrote:<br>> <br>> Hi<br>> <br>> Please assist me with installation of openMD. <br>> <br>> This is what I did<br>> <br>> =================================<br>> [cecil@localhost build-openMD]$ cmake ../openmd-2.2<br>> -- QHULL found (include: /usr/local/include, lib: optimized;/usr/local/lib/libqhullstatic.a;debug;/usr/local/lib/libqhullstatic.a)<br>> -- <br>> -- ========== OpenMD Build Information ==========<br>> -- Current revision ........... = Release<br>> -- CMAKE_SYSTEM ............... = Linux-3.16.3-200.fc20.x86_64<br>> -- ==============================================<br>> -- CMAKE_BUILD_TYPE ........... = Release<br>> -- CMAKE_INSTALL_PREFIX ....... = /usr/local/openmd<br>> -- Build as SINGLE_PRECISION .. = OFF<br>> -- CMAKE_CXX_COMPILER ......... = /usr/bin/c++<br>> -- MPI_CXX_COMPILER ........... = /usr/lib64/openmpi/bin/mpicxx<br>> -- MPI_CXX_INCLUDE_PATH ....... = /usr/include/openmpi-x86_64<br>> -- MPI_CXX_LIBRARIES .......... = /usr/lib64/openmpi/lib/libmpi_cxx.so;/usr/lib64/openmpi/lib/libmpi.so<br>> -- OPENBABEL2_ROOT ............ = <br>> -- OPENBABEL2_INCLUDE_DIR ..... = /usr/include/openbabel-2.0<br>> -- OPENBABEL2_LIBRARIES ....... = /usr/lib64/libopenbabel.so<br>> -- QHULL_ROOT ................. = <br>> -- QHULL_INCLUDE_DIR .......... = /usr/local/include<br>> -- QHULL_LIBRARIES ............ = optimized;/usr/local/lib/libqhullstatic.a;debug;/usr/local/lib/libqhullstatic.a<br>> -- ZLIB_ROOT .................. = <br>> -- ZLIB_INCLUDE_DIR ........... = /usr/include<br>> -- ZLIB_LIBRARIES ............. = /usr/lib64/libz.so<br>> -- FFTW3_ROOT ................. = <br>> -- FFTW3_INCLUDE_DIR .......... = /usr/include<br>> -- FFTW3_LIBRARIES ............ = /usr/lib64/libfftw3.so<br>> -- PERL_EXECUTABLE ............ = /usr/bin/perl<br>> -- PYTHON_EXECUTABLE .......... = /usr/bin/python<br>> -- DOXYGEN_EXECUTABLE ......... = /usr/bin/doxygen<br>> -- <br>> -- To override these options, add -D{OPTION_NAME}=... to the cmake command<br>> -- Particularly useful defines are for:<br>> -- <br>> -- -DCMAKE_INSTALL_PREFIX=/usr/local/openmd (where OpenMD will be installed)<br>> -- -DOPENBABEL2_ROOT=/path/to/openbabel<br>> -- -DQHULL_ROOT=/path/to/qhull<br>> -- -DFFTW3_ROOT=/path/to/fftw3<br>> -- <br>> -- To build and install OpenMD, enter "make" and "make install"<br>> -- <br>> -- Configuring done<br>> -- Generating done<br>> -- Build files have been written to: /home/cecil/build-openMD<br>> =====================================================<br>> <br>> when I type make i get this among others<br>> ...<br>> ...<br>> ...<br>> lib/libopenmd_parallel.a(Problem.cpp.o): In function `QuantLib::Problem::computeGradientNormValue(OpenMD::DynamicVector<double, std::allocator<double> >&)':<br>> Problem.cpp:(.text+0xc4): undefined reference to `ompi_mpi_comm_world'<br>> Problem.cpp:(.text+0xca): undefined reference to `ompi_mpi_op_sum'<br>> Problem.cpp:(.text+0xcf): undefined reference to `ompi_mpi_double'<br>> Problem.cpp:(.text+0xe3): undefined reference to `MPI_Allreduce'<br>> collect2: error: ld returned 1 exit status<br>> make[2]: *** [bin/openmd_MPI] Error 1<br>> make[1]: *** [CMakeFiles/openmd_MPI.dir/all] Error 2<br>> make[1]: *** Waiting for unfinished jobs....<br>> <br>> <br>> <br>> -- <br>> This message is subject to the CSIR's copyright terms and conditions, e-mail legal notice, and implemented Open Document Format (ODF) standard. <br>> The full disclaimer details can be found at http://www.csir.co.za/disclaimer.html.<br>> <br>> This message has been scanned for viruses and dangerous content by MailScanner, <br>> and is believed to be clean.<br>> <br>> <br>> Please consider the environment before printing this email.<br>> <br>> _______________________________________________<br>> Openmd-users mailing list<br>> Openmd-users@openmd.org<br>> http://openmd.org/mailman/listinfo.cgi/openmd-users<br><br>***********************************************<br> J. Daniel Gezelter<br> Associate Professor of Chemistry<br> Department of Chemistry and Biochemistry<br> 251 Nieuwland Science Hall<br> University of Notre Dame<br> Notre Dame, IN 46556-5670<br><br> +1 (574) 631-7595<br> gezelter@nd.edu<br> http://www.nd.edu/~gezelter<br>************************************************<br><br><br><br><br><br>-- <br>This message is subject to the CSIR's copyright terms and conditions, e-mail legal notice, and implemented Open Document Format (ODF) standard. <br>The full disclaimer details can be found at http://www.csir.co.za/disclaimer.html.<br><br>This message has been scanned for viruses and dangerous content by MailScanner, <br>and is believed to be clean.<br><br>Please consider the environment before printing this email.<br><br><br><font face="Verdana,Arial,Helvetica,Trebuchet MS" size="1">
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