[gmx-users] cygwin_mpi_gmx installation

Fri Apr 12 13:10:37 CEST 2013

Indeed it's strange. In fact, it seems that CUDA detection did not
even run, there should be a message whether it found the toolkit or
not just before the "Enabling native GPU acceleration" - and the
enabling should not even happen without CUDA detected.

Unrelated, but do you really need MPI with cygwin? Unless you are
planning to run on multiple Windows machines, the default thread-MPI
parallelization is enough to use multiple cores!

Cheers,
--
Szilárd

On Fri, Apr 12, 2013 at 1:04 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 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!
>>
>>
>> --
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