[gmx-users] compiling gromacs4.5 with gpu

[BIN ZHANG]

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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