[gmx-users] cygwin_mpi_gmx installation

[라지브간디]

Dear gmx,


I have installed mpich for MPI use in cygwin (Win 7 -64 bit) and encountered the following error : I dont understand what I am missing here?


$ cmake .. -DGMX_MPI=ON -DGMX_BUILD_OWN_FFTW=ON


-- The C compiler identification is GNU 4.8.0
-- Check for working C compiler: /usr/bin/gcc.exe
-- Check for working C compiler: /usr/bin/gcc.exe -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- Enabling native GPU acceleration
-- The CXX compiler identification is GNU 4.8.0
-- Check for working CXX compiler: /usr/bin/c++.exe
-- Check for working CXX compiler: /usr/bin/c++.exe -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - supported
-- Detecting best acceleration for this CPU
-- Detecting best acceleration for this CPU - AVX_256
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Performing Test CFLAGS_WARN
-- Performing Test CFLAGS_WARN - Success
-- Performing Test CFLAGS_WARN_EXTRA
-- Performing Test CFLAGS_WARN_EXTRA - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- 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_WARN_EXTRA
-- Performing Test CXXFLAGS_WARN_EXTRA - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Using default binary suffix: "_mpi"
-- Using default library suffix: "_mpi"
-- Looking for include file string.h
-- Looking for include file string.h - found
-- Looking for include file math.h
-- Looking for include file math.h - found
-- Looking for include file limits.h
-- Looking for include file limits.h - found
-- Looking for include file memory.h
-- Looking for include file memory.h - found
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file direct.h
-- Looking for include file direct.h - not found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file stdint.h
-- Looking for include file stdint.h - found
-- Looking for include file stdlib.h
-- Looking for include file stdlib.h - found
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file inttypes.h
-- Looking for include file inttypes.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for include file sys/types.h
-- Looking for include file sys/types.h - found
-- Looking for include file sys/stat.h
-- Looking for include file sys/stat.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file rpc/rpc.h
-- Looking for include file rpc/rpc.h - not found
-- Looking for include files rpc/rpc.h, rpc/xdr.h
-- Looking for include files rpc/rpc.h, rpc/xdr.h - not found
-- Looking for include file io.h
-- Looking for include file io.h - found
-- Looking for include file sched.h
-- Looking for include file sched.h - 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 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 sigaction
-- Looking for sigaction - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for sched_setaffinity
-- Looking for sched_setaffinity - not found
-- Looking for sched_getaffinity
-- Looking for sched_getaffinity - not found
-- Looking for rsqrt
-- Looking for rsqrt - not found
-- Looking for rsqrtf
-- Looking for rsqrtf - not found
-- Looking for sqrtf
-- Looking for sqrtf - 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
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Found MPI_C: /usr/local/lib/libpmpich.a;/usr/local/lib/libmpich.a;/usr/local/lib/libopa.a;/usr/local/lib/libmpl.a;/usr/lib/libpthread.a
-- Found MPI_CXX: /usr/local/lib/libmpichcxx.a;/usr/local/lib/libpmpich.a;/usr/local/lib/libmpich.a;/usr/local/lib/libopa.a;/usr/local/lib/libmpl.a;/usr/lib/libpthread.a
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Checking for CRAY XT Catamount compile
-- Checking for CRAY XT Catamount target - no
-- Atomics found
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Failed
-- Performing Test CXXFLAG_FPIC
-- Performing Test CXXFLAG_FPIC - Failed
-- Setting build user/date/host/cpu information
-- Setting build user & time - OK
-- Checking floating point format
-- Checking floating point format - IEEE754 (LE byte, LE word)
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for inline keyword
-- Checking for inline keyword - __inline__
-- Checking for restrict keyword
-- Checking for restrict keyword - __restrict__
-- Checking for pipe support
-- Checking for isfinite
-- Performing Test isfinite_compile_ok
-- Performing Test isfinite_compile_ok - Success
-- Checking for isfinite - yes
-- Checking for _isfinite
-- Performing Test _isfinite_compile_ok
-- Performing Test _isfinite_compile_ok - Failed
-- Checking for _isfinite - no
-- Checking for _finite
-- Performing Test _finite_compile_ok
-- Performing Test _finite_compile_ok - Failed
-- Checking for _finite - no
-- Checking for system XDR support
-- Checking for system XDR support - not present
-- Performing Test GNU_AVX_CFLAG
-- Performing Test GNU_AVX_CFLAG - Success
-- Performing Test GNU_AVX_CXXFLAG
-- Performing Test GNU_AVX_CXXFLAG - Success
-- Looking for immintrin.h
-- Looking for immintrin.h - found
-- Looking for x86intrin.h
-- Looking for x86intrin.h - found
-- Looking for intrin.h
-- Looking for intrin.h - found
-- Enabling 256-bit AVX Gromacs acceleration, and it will help compiler optimiza             tion.
-- Checking for gcc AVX maskload bug
-- Checking for gcc AVX maskload bug - not present
-- The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2
-- Using internal BLAS library
-- LAPACK requires BLAS
-- Using internal LAPACK library
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Found the ability to use plug-ins when building shared libaries, so will compile to use plug-ins (e.g. to read VMD-supported file formats).
-- Checking for suitable VMD version
-- VMD plugins not found. Path to VMD can be set with VMDDIR.
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
CUDA_CUDART_LIBRARY (ADVANCED)
    linked by target "cuda_tools" in directory /usr/local/bin/gmx/src/gmxlib/cuda_tools
    linked by target "gpu_utils" in directory /usr/local/bin/gmx/src/gmxlib/gpu_utils
    linked by target "nbnxn_cuda" in directory /usr/local/bin/gmx/src/mdlib/nbnxn_cuda


-- Configuring incomplete, errors occurred!