Hello all, I have a very similar problem, but compiling both Gromacs 4.6 and 4.6.1 with cmake and MPI support (no problems with non-MPI installation). I have cmake version 2.8.7, openmpi version 1.4.1, and I am using gcc version 4.6.3 in a linux Ubuntu 4.6.3. I use the cmake options:
cmake -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DGMX_BINARY_SUFFIX=_mpi A summary of the output given by this command is: CUDA_TOOLKIT_ROOT_DIR not found or specified -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (Required is at least version "3.2") -- The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2 -- Configuring done -- Generating done -- Build files have been written to: /home/smith/gromacs-4.6 I believe that not having CUDA installed is not a problem, as I do not plan to run in GPU, and nowhere in the installation manual says that it is obligatory. After running make, the simulation stops with the following message: Linking C shared library libgmx_mpi.so [ 53%] Built target gmx Scanning dependencies of target gromacs_include_links [ 53%] Generating gromacs [ 53%] Built target gromacs_include_links Scanning dependencies of target template [ 53%] Building C object share/template/CMakeFiles/template.dir/template.c.o Linking C executable template ../../src/gmxlib/libgmx_mpi.so.6: undefined reference to `__mth_i_dfloatuk' ../../src/gmxlib/libgmx_mpi.so.6: undefined reference to `__builtin_va_gparg1' ../../src/gmxlib/libgmx_mpi.so.6: undefined reference to `__pgdbg_stub' collect2: ld returned 1 exit status make[2]: *** [share/template/template] Error 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make: *** [all] Error 2 It looks like I lack one library somehow, but I do not know which one. I tried to install fftw before installing gromacs, and tried with both shared and dynamic libraries with the same result. Can anybody help? Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/gmx-4-6-mpi-installation-through-openmpi-tp5006975p5008730.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
