[gmx-users] cygwin_mpi_gmx installation

[Mark Abraham]

That looks really strange. CMake claims to detect CUDA but the right
variables are not set.

1) Can you reproduce this in a clean build directory?
2) If so, what CUDA is present?

Mark


On Thu, Apr 11, 2013 at 2:57 PM, 라지브간디 <rajiv at kaist.ac.kr> wrote:

> 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!
>
>
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>