Hi, yes that is a bug with cmake (see http://bugzilla.gromacs.org/show_bug.cgi?id=549). You can either disable BUILD_SHARED_LIBS and or you can ran "make install" as a workaround until the bug is fixed.
Roland On Tue, Sep 28, 2010 at 3:02 AM, BIN ZHANG <zhn...@gmail.com> wrote: > Hi, there: > > I was trying to compile gromacs4.5.1 on a GPU cluster ( > https://secure.nersc.gov/nusers/systems/dirac/). > > The compilation seems to work fine, but in the installation folder, only > "bin/mdrun-gpu" presents. Is it supposed to be so? > > When I type "./mdrun-gpu -h", the following error occurs: > ./mdrun-gpu: error while loading shared libraries: libgmxpreprocess.so.6: > cannot open shared object file: No such file or directory > > Do you have any idea what this means? > > Thanks a lot, > Bin > > ===================================== > Here are steps I did for compiling: > export OPENMM_ROOT_DIR=/global/homes/b/bingo/Program/OpenMM2.0-Linux64 > cmake -DGMX_OPENMM=ON > -DCMAKE_INSTALL_PREFIX=/global/homes/b/bingo/Program/gromacs_gpu > make mdrun > make install-mdrun > > ====================================== > Here are the outputs from the cmake > > -- The C compiler identification is GNU > -- The CXX compiler identification is GNU > -- Check for working C compiler: /usr/bin/gcc > -- Check for working C compiler: /usr/bin/gcc -- works > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Check for working CXX compiler: /usr/bin/c++ > -- Check for working CXX compiler: /usr/bin/c++ -- works > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- CTest cannot determine repository type. Please set UPDATE_TYPE to 'cvs' > or 'svn'. CTest update will not work. > -- Performing Test CFLAGS_WARN > -- Performing Test CFLAGS_WARN - Success > -- Performing Test CFLAGS_EXCESS_PREC > -- Performing Test CFLAGS_EXCESS_PREC - Failed > -- Performing Test CFLAGS_COPT > -- Performing Test CFLAGS_COPT - Success > -- Performing Test CFLAGS_NOINLINE > -- Performing Test CFLAGS_NOINLINE - Success > -- Performing Test CXXFLAGS_WARN > -- Performing Test CXXFLAGS_WARN - Success > -- Performing Test CXXFLAGS_EXCESS_PREC > -- Performing Test CXXFLAGS_EXCESS_PREC - Failed > -- Performing Test CXXFLAGS_COPT > -- Performing Test CXXFLAGS_COPT - Success > -- Performing Test CXXFLAGS_NOINLINE > -- Performing Test CXXFLAGS_NOINLINE - Success > -- No external FFT libraries needed for the OpenMM build, using fftpack! > -- Threads not compatible with OpenMM build, disabled! > CMake Warning at CMakeLists.txt:183 (message): > CPU-based acceleration turned off, OpenMM does not support/need any! > > > -- Looking for include files HAVE_STRING_H > -- Looking for include files HAVE_STRING_H - found > -- Looking for include files HAVE_MATH_H > -- Looking for include files HAVE_MATH_H - found > -- Looking for include files HAVE_LIMITS_H > -- Looking for include files HAVE_LIMITS_H - found > -- Looking for include files HAVE_MEMORY_H > -- Looking for include files HAVE_MEMORY_H - found > -- Looking for include files HAVE_UNISTD_H > -- Looking for include files HAVE_UNISTD_H - found > -- Looking for include files HAVE_PWD_H > -- Looking for include files HAVE_PWD_H - found > -- Looking for include files HAVE_STDINT_H > -- Looking for include files HAVE_STDINT_H - found > -- Looking for include files HAVE_STDLIB_H > -- Looking for include files HAVE_STDLIB_H - found > -- Looking for include files HAVE_PTHREAD_H > -- Looking for include files HAVE_PTHREAD_H - found > -- Looking for include files HAVE_DIRENT_H > -- Looking for include files HAVE_DIRENT_H - found > -- Looking for include files HAVE_INTTYPES_H > -- Looking for include files HAVE_INTTYPES_H - found > -- Looking for include files HAVE_REGEX_H > -- Looking for include files HAVE_REGEX_H - found > -- Looking for include files HAVE_SYS_TYPES_H > -- Looking for include files HAVE_SYS_TYPES_H - found > -- Looking for include files HAVE_SYS_STAT_H > -- Looking for include files HAVE_SYS_STAT_H - found > -- Looking for include files HAVE_SYS_TIME_H > -- Looking for include files HAVE_SYS_TIME_H - found > -- Looking for include files HAVE_RPC_RPC_H > -- Looking for include files HAVE_RPC_RPC_H - found > -- Looking for include files HAVE_RPC_XDR_H > -- Looking for include files HAVE_RPC_XDR_H - found > -- Looking for include files HAVE_XMMINTRIN_H > -- Looking for include files HAVE_XMMINTRIN_H - found > -- Looking for include files HAVE_EMMINTRIN_H > -- Looking for include files HAVE_EMMINTRIN_H - found > -- Looking for include files HAVE_PMMINTRIN_H > -- Looking for include files HAVE_PMMINTRIN_H - not found. > -- Looking for include files HAVE_SMMINTRIN_H > -- Looking for include files HAVE_SMMINTRIN_H - not found. > -- Looking for include files HAVE_IO_H > -- Looking for include files HAVE_IO_H - not found. > -- Looking for strcasecmp > -- Looking for strcasecmp - found > -- Looking for strdup > -- Looking for strdup - found > -- Looking for vprintf > -- Looking for vprintf - found > -- Looking for memcmp > -- Looking for memcmp - found > -- Looking for posix_memalign > -- Looking for posix_memalign - found > -- Looking for memalign > -- Looking for memalign - found > -- Looking for _aligned_malloc > -- Looking for _aligned_malloc - not found > -- Looking for gettimeofday > -- Looking for gettimeofday - found > -- Looking for isnan > -- Looking for isnan - found > -- Looking for _isnan > -- Looking for _isnan - not found > -- Looking for isfinite > -- Looking for isfinite - not found > -- Looking for _isfinite > -- Looking for _isfinite - not found > -- Looking for fsync > -- Looking for fsync - found > -- Looking for _fileno > -- Looking for _fileno - not found > -- Looking for fileno > -- Looking for fileno - found > -- Looking for _commit > -- Looking for _commit - not found > -- Looking for sqrt in m > -- Looking for sqrt in m - found > -- Looking for cbrt in m > -- Looking for cbrt in m - found > -- Looking for stddef.h > -- Looking for stddef.h - found > -- Check size of bool > -- Check size of bool - failed > -- Check size of int > -- Check size of int - done > -- Check size of long int > -- Check size of long int - done > -- Check size of long long int > -- Check size of long long int - done > -- Check size of off_t > -- Check size of off_t - done > -- Check size of void * > -- Check size of void * - done > -- Check size of uid_t > -- Check size of uid_t - done > -- Check size of gid_t > -- Check size of gid_t - done > -- Check size of size_t > -- Check size of size_t - done > -- Check size of off_t > -- Check size of off_t - done > -- Check if the system is big endian > -- Searching 16 bit integer > -- Check size of unsigned short > -- Check size of unsigned short - done > -- Using unsigned short > -- Check if the system is big endian - little endian > -- checking for module 'libxml-2.0' > -- package 'libxml-2.0' not found > -- Could NOT find LibXml2 (missing: LIBXML2_LIBRARIES > LIBXML2_INCLUDE_DIR) > -- Found CUDA: /global/common/carver/usg/cuda/3.1 > -- Found OpenMM: /global/homes/b/bingo/Program/OpenMM2.0-Linux64 > -- Setting build user & time > -- Setting build user & time - OK > -- Checking floating point format > -- Checking floating point format - unknown > -- Checking for 64-bit off_t > -- Checking for 64-bit off_t - present > -- Checking for fseeko/ftello > -- Checking for fseeko/ftello - present > -- Checking for return type of signals > -- Checking for return type of signals - void > -- Checking for SIGUSR1 > -- Checking for SIGUSR1 - found > -- Checking for inline keyword > -- Checking for inline keyword - inline > -- Checking for inline keyword > -- Checking for inline keyword - inline > -- Checking for pipe support > -- Checking for GCC x86 inline asm > -- Checking for GCC x86 inline asm - supported > -- Checking for MSVC x86 inline asm > -- Checking for MSVC x86 inline asm - not supported > -- Checking for system XDR support > -- Checking for system XDR support - present > -- Using internal FFT library - fftpack > -- Configuring done > -- Generating done > -- Build files have been written to: > /global/homes/b/bingo/Program/gromacs-4.5.1 > > > -- > 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 > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
-- 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