[gmx-users] compiling gromacs4.5 with gpu

[Roland Schulz]

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 <zhngbn at 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
>
>
> --
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-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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