cmake3 .. -DCMAKE_INSTALL_PREFIX=~/gromacs/gmx2019.4 -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_HWLOC=ON -- The C compiler identification is GNU 4.8.5 -- The CXX compiler identification is GNU 4.8.5 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - 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 -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Performing Test CXXFLAG_STD_CXX0X -- Performing Test CXXFLAG_STD_CXX0X - Success -- Performing Test CXX11_SUPPORTED -- Performing Test CXX11_SUPPORTED - Success -- Performing Test CXX11_STDLIB_PRESENT -- Performing Test CXX11_STDLIB_PRESENT - Success -- Looking for NVIDIA GPUs present in the system -- Number of NVIDIA GPUs detected: 5 -- Found CUDA: /usr/local/cuda (found suitable version "10.1", minimum required is "7.0") -- Found OpenMP_C: -fopenmp (found version "3.1") -- Found OpenMP_CXX: -fopenmp (found version "3.1") -- Found OpenMP: TRUE (found version "3.1") -- 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_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 -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file regex.h -- Looking for include file regex.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - 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 -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- hwloc version: 1.11.8 -- Found Hwloc: /usr/lib64/libhwloc.so (found suitable version "1.11.8", minimum required is "1.5") -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Check for working NVCC/C++ compiler combination with nvcc '/usr/local/cuda/bin/nvcc' -- Check for working NVCC/C++ compiler combination - works -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - Intel -- Detected build CPU brand - Intel(R) Xeon(R) CPU E5-2697A v4 @ 2.60GHz -- Detected build CPU family - 6 -- Detected build CPU model - 79 -- Detected build CPU stepping - 1 -- Detected build CPU features - aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -- Enabling RDTSCP support - detected on the build host -- 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 pipe support -- Looking for C++ include regex -- Looking for C++ include regex - found -- Checking for system XDR support -- Checking for system XDR support - present -- Detecting best SIMD instructions for this CPU -- Detected best SIMD instructions for this CPU - AVX2_256 -- Performing Test C_mavx2_mfma_FLAG_ACCEPTED -- Performing Test C_mavx2_mfma_FLAG_ACCEPTED - Success -- Performing Test C_mavx2_mfma_COMPILE_WORKS -- Performing Test C_mavx2_mfma_COMPILE_WORKS - Success -- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED -- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED - Success -- Performing Test CXX_mavx2_mfma_COMPILE_WORKS -- Performing Test CXX_mavx2_mfma_COMPILE_WORKS - Success -- Enabling 256-bit AVX2 SIMD instructions using CXX flags: -mavx2 -mfma -- Detecting flags to enable runtime detection of AVX-512 units on newer CPUs -- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED -- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed -- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED -- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED - Failed -- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED -- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED - Failed -- Performing Test C_mavx512f_FLAG_ACCEPTED -- Performing Test C_mavx512f_FLAG_ACCEPTED - Failed -- Performing Test C_arch_AVX_FLAG_ACCEPTED -- Performing Test C_arch_AVX_FLAG_ACCEPTED - Failed -- Performing Test C_hgnu_FLAG_ACCEPTED -- Performing Test C_hgnu_FLAG_ACCEPTED - Failed -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed -- Could not find any flag to build test source (this could be due to either the compiler or binutils) -- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED -- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed -- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED -- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED - Failed -- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED -- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED - Failed -- Performing Test CXX_mavx512f_FLAG_ACCEPTED -- Performing Test CXX_mavx512f_FLAG_ACCEPTED - Failed -- Performing Test CXX_arch_AVX_FLAG_ACCEPTED -- Performing Test CXX_arch_AVX_FLAG_ACCEPTED - Failed -- Performing Test CXX_hgnu_FLAG_ACCEPTED -- Performing Test CXX_hgnu_FLAG_ACCEPTED - Failed -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed -- Could not find any flag to build test source (this could be due to either the compiler or binutils) -- Detecting flags to enable runtime detection of AVX-512 units on newer CPUs - not supported -- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED -- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED - Success -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2;--enable-avx;--enable-avx2 -- Using external FFT library - FFTW3 build managed by GROMACS -- Could NOT find BLAS (missing: BLAS_LIBRARIES) -- Using GROMACS built-in BLAS. -- LAPACK requires BLAS -- A library with LAPACK API not found. Please specify library location. -- Using GROMACS built-in LAPACK. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Using dynamic plugins (e.g VMD-supported file formats) -- Checking for suitable VMD version -- VMD plugins not found. Path to VMD can be set with VMDDIR. -- Using default binary suffix: "" -- Using default library suffix: "" -- Could not convert sample image, ImageMagick convert can not be used -- Found PythonInterp: /usr/bin/python2.7 (found suitable version "2.7.5", minimum required is "2.7") -- Performing Test HAS_NO_UNUSED_VARIABLE -- Performing Test HAS_NO_UNUSED_VARIABLE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_MISSING_DECL -- Performing Test HAS_NO_MISSING_DECL - Success -- Performing Test HAS_NO_MISSING_PROTO -- Performing Test HAS_NO_MISSING_PROTO - Failed -- Performing Test HAS_NO_MSVC_UNUSED -- Performing Test HAS_NO_MSVC_UNUSED - Failed -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Check if the system is big endian -- Searching 16 bit integer -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/build