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gmx-cmake.log

Vedran Miletic, 06/25/2014 07:00 PM

 
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$ cmake .. -DCMAKE_BUILD_TYPE=Debug -DCMAKE_INSTALL_PREFIX=/home/vedranm/software/gromacs
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-- The C compiler identification is GNU 4.8.2
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-- The CXX compiler identification is GNU 4.8.2
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-- Check for working C compiler: /usr/bin/cc
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-- Check for working C compiler: /usr/bin/cc -- works
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-- Detecting C compiler ABI info
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-- Detecting C compiler ABI info - done
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-- Check for working CXX compiler: /usr/bin/c++
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-- Check for working CXX compiler: /usr/bin/c++ -- works
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-- Detecting CXX compiler ABI info
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-- Detecting CXX compiler ABI info - done
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-- Looking for NVIDIA GPUs present in the system
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-- Could not detect NVIDIA GPUs
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-- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration
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-- Checking for GCC x86 inline asm
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-- Checking for GCC x86 inline asm - supported
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-- Detecting best SIMD instructions for this CPU
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-- Detected best SIMD instructions for this CPU - SSE2
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-- Try OpenMP C flag = [-fopenmp]
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-- Performing Test OpenMP_FLAG_DETECTED
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-- Performing Test OpenMP_FLAG_DETECTED - Success
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-- Try OpenMP CXX flag = [-fopenmp]
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-- Performing Test OpenMP_FLAG_DETECTED
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-- Performing Test OpenMP_FLAG_DETECTED - Success
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-- Found OpenMP: -fopenmp  
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-- Performing Test CFLAGS_WARN
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-- Performing Test CFLAGS_WARN - Success
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-- Performing Test CFLAGS_WARN_EXTRA
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-- Performing Test CFLAGS_WARN_EXTRA - Success
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-- Performing Test CFLAGS_WARN_REL
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-- Performing Test CFLAGS_WARN_REL - Success
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-- Performing Test CFLAGS_WARN_UNINIT
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-- Performing Test CFLAGS_WARN_UNINIT - Success
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-- Performing Test CFLAGS_EXCESS_PREC
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-- Performing Test CFLAGS_EXCESS_PREC - Success
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-- Performing Test CFLAGS_COPT
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-- Performing Test CFLAGS_COPT - Success
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-- Performing Test CFLAGS_NOINLINE
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-- Performing Test CFLAGS_NOINLINE - Success
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-- Performing Test CXXFLAGS_WARN
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-- Performing Test CXXFLAGS_WARN - Success
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-- Performing Test CXXFLAGS_WARN_EXTRA
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-- Performing Test CXXFLAGS_WARN_EXTRA - Success
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-- Performing Test CXXFLAGS_WARN_REL
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-- Performing Test CXXFLAGS_WARN_REL - Success
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-- Performing Test CXXFLAGS_EXCESS_PREC
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-- Performing Test CXXFLAGS_EXCESS_PREC - Success
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-- Performing Test CXXFLAGS_COPT
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-- Performing Test CXXFLAGS_COPT - Success
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-- Performing Test CXXFLAGS_NOINLINE
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-- Performing Test CXXFLAGS_NOINLINE - Success
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-- Looking for include file unistd.h
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-- Looking for include file unistd.h - found
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-- Looking for include file pwd.h
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-- Looking for include file pwd.h - found
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-- Looking for include file dirent.h
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-- Looking for include file dirent.h - found
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-- Looking for include file time.h
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-- Looking for include file time.h - found
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-- Looking for include file sys/time.h
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-- Looking for include file sys/time.h - found
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-- Looking for include file io.h
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-- Looking for include file io.h - not found
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-- Looking for include file sched.h
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-- Looking for include file sched.h - found
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-- Looking for include file regex.h
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-- Looking for include file regex.h - found
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-- Looking for C++ include regex
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-- Looking for C++ include regex - not found
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-- Looking for posix_memalign
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-- Looking for posix_memalign - found
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-- Looking for memalign
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-- Looking for memalign - found
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-- Looking for _aligned_malloc
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-- Looking for _aligned_malloc - not found
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-- Looking for gettimeofday
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-- Looking for gettimeofday - found
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-- Looking for fsync
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-- Looking for fsync - found
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-- Looking for _fileno
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-- Looking for _fileno - not found
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-- Looking for fileno
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-- Looking for fileno - found
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-- Looking for _commit
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-- Looking for _commit - not found
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-- Looking for sigaction
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-- Looking for sigaction - found
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-- Looking for sysconf
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-- Looking for sysconf - found
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-- Looking for sched_setaffinity
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-- Looking for sched_setaffinity - found
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-- Looking for sched_getaffinity
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-- Looking for sched_getaffinity - found
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-- Looking for rsqrt
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-- Looking for rsqrt - not found
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-- Looking for rsqrtf
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-- Looking for rsqrtf - not found
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-- Looking for sqrtf
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-- Looking for sqrtf - not found
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-- Looking for sqrt in m
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-- Looking for sqrt in m - found
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-- Looking for clock_gettime in rt
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-- Looking for clock_gettime in rt - found
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-- Check if the system is big endian
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-- Searching 16 bit integer
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-- Looking for sys/types.h
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-- Looking for sys/types.h - found
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-- Looking for stdint.h
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-- Looking for stdint.h - found
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-- Looking for stddef.h
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-- Looking for stddef.h - found
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-- Check size of unsigned short
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-- Check size of unsigned short - done
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-- Using unsigned short
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-- Check if the system is big endian - little endian
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-- Found LibXml2: /usr/lib/i386-linux-gnu/libxml2.so (found version "2.9.1") 
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-- Looking for xmlTextWriterEndAttribute in /usr/lib/i386-linux-gnu/libxml2.so
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-- Looking for xmlTextWriterEndAttribute in /usr/lib/i386-linux-gnu/libxml2.so - found
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-- Looking for include file pthread.h
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-- Looking for include file pthread.h - found
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-- Looking for pthread_create
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-- Looking for pthread_create - not found
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-- Looking for pthread_create in pthreads
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-- Looking for pthread_create in pthreads - not found
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-- Looking for pthread_create in pthread
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-- Looking for pthread_create in pthread - found
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-- Found Threads: TRUE  
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-- Looking for include file pthread.h
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-- Looking for include file pthread.h - found
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-- Atomic operations found
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-- Performing Test PTHREAD_SETAFFINITY
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-- Performing Test PTHREAD_SETAFFINITY - Success
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-- Found Git: /usr/bin/git (found version "1.9.1") 
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-- Could NOT find Boost
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Boost >= 1.44 not found. Using minimal internal version. This may cause trouble if you plan on compiling/linking other software that uses Boost against Gromacs.
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-- Setting build user/date/host/cpu information
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-- Setting build user & time - OK
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-- Checking floating point format
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-- Checking floating point format - IEEE754 (LE byte, LE word)
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-- Checking for 64-bit off_t
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-- Checking for 64-bit off_t - present
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-- Checking for fseeko/ftello
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-- Checking for fseeko/ftello - present
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-- Checking for SIGUSR1
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-- Checking for SIGUSR1 - found
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-- Checking for pipe support
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-- Checking for isfinite
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-- Performing Test isfinite_compile_ok
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-- Performing Test isfinite_compile_ok - Success
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-- Checking for isfinite - yes
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-- Checking for _isfinite
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-- Performing Test _isfinite_compile_ok
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-- Performing Test _isfinite_compile_ok - Failed
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-- Checking for _isfinite - no
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-- Checking for _finite
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-- Performing Test _finite_compile_ok
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-- Performing Test _finite_compile_ok - Failed
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-- Checking for _finite - no
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-- Performing Test CXXFLAG_STD_CXX0X
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-- Performing Test CXXFLAG_STD_CXX0X - Success
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-- Performing Test GMX_CXX11_SUPPORTED
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-- Performing Test GMX_CXX11_SUPPORTED - Success
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-- Checking for system XDR support
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-- Checking for system XDR support - present
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-- Try C compiler SSE2 flag = [-msse2]
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-- Performing Test C_FLAG_msse2
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-- Performing Test C_FLAG_msse2 - Success
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-- Performing Test C_SIMD_COMPILES_FLAG_msse2
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-- Performing Test C_SIMD_COMPILES_FLAG_msse2 - Success
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-- Try C++ compiler SSE2 flag = [-msse2]
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-- Performing Test CXX_FLAG_msse2
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-- Performing Test CXX_FLAG_msse2 - Success
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-- Performing Test CXX_SIMD_COMPILES_FLAG_msse2
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-- Performing Test CXX_SIMD_COMPILES_FLAG_msse2 - Success
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-- Enabling SSE2 SIMD instructions
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-- checking for module 'fftw3f'
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--   found fftw3f, version 3.3.3
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-- Looking for fftwf_plan_r2r_1d in /usr/lib/i386-linux-gnu/libfftw3f.so
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-- Looking for fftwf_plan_r2r_1d in /usr/lib/i386-linux-gnu/libfftw3f.so - found
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-- Looking for fftwf_have_simd_avx in /usr/lib/i386-linux-gnu/libfftw3f.so
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-- Looking for fftwf_have_simd_avx in /usr/lib/i386-linux-gnu/libfftw3f.so - found
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-- Looking for fftwf_have_simd_sse2 in /usr/lib/i386-linux-gnu/libfftw3f.so
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-- Looking for fftwf_have_simd_sse2 in /usr/lib/i386-linux-gnu/libfftw3f.so - found
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CMake Warning at cmake/gmxManageFFTLibraries.cmake:90 (message):
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  The FFTW library was compiled with --enable-avx to enable AVX SIMD
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  instructions.  That might sound like a good idea for your processor, but
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  for FFTW versions up to 3.3.3, these are slower than the SSE/SSE2 SIMD
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  instructions for the way GROMACS uses FFTs.  Limitations in the way FFTW
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  allows GROMACS to measure performance make it awkward for either GROMACS or
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  FFTW to make the decision for you based on runtime performance.  You should
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  compile a different FFTW library with --enable-sse or --enable-sse2.  If
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  you have a more recent FFTW, you may like to compare the performance of
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  GROMACS with FFTW libraries compiled with and without --enable-avx.
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  However, the GROMACS developers do not really expect the FFTW AVX
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  optimization to help, because the performance is limited by memory access,
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  not computation.
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Call Stack (most recent call first):
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  CMakeLists.txt:678 (include)
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-- Using external FFT library - FFTW3
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-- Looking for sgemm_
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-- Looking for sgemm_ - found
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-- A library with BLAS API found.
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-- Looking for cheev_
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-- Looking for cheev_ - found
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-- A library with LAPACK API found.
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-- Checking for dlopen
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-- Performing Test HAVE_DLOPEN
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-- Performing Test HAVE_DLOPEN - Success
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-- Checking for dlopen - found
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-- 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).
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-- Checking for suitable VMD version
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-- VMD plugins not found. Path to VMD can be set with VMDDIR.
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-- Using default binary suffix: ""
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-- Using default library suffix: ""
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-- Looking for zlibVersion in /usr/lib/i386-linux-gnu/libz.so
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-- Looking for zlibVersion in /usr/lib/i386-linux-gnu/libz.so - found
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-- Looking for inttypes.h
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-- Looking for inttypes.h - found
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-- Check if the system is big endian
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-- Searching 16 bit integer
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-- Using unsigned short
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-- Check if the system is big endian - little endian
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-- Found PythonInterp: /usr/bin/python (found version "2.7.6") 
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-- Performing Test HAS_NO_UNUSED_PARAMETER
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-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
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-- Performing Test HAS_NO_DEPRECATED_REGISTER
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-- Performing Test HAS_NO_DEPRECATED_REGISTER - Success
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-- Configuring done
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-- Generating done
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-- Build files have been written to: /home/vedranm/workspace/gromacs/build-normal