Still did not work. change xMIC to xCore and log is below (if it was other way around, then originally it must have not worked). Script file is all oneline.
-- Performing Test C_xCORE_AVX512_FLAG_WORKS -- Performing Test C_xCORE_AVX512_FLAG_WORKS - Failed -- Performing Test C_mavx512f_mfma_FLAG_WORKS -- Performing Test C_mavx512f_mfma_FLAG_WORKS - Failed -- Performing Test C_mavx512f_FLAG_WORKS -- Performing Test C_mavx512f_FLAG_WORKS - Failed -- Performing Test C_arch_AVX_FLAG_WORKS -- Performing Test C_arch_AVX_FLAG_WORKS - Failed -- Performing Test C_hgnu_FLAG_WORKS -- Performing Test C_hgnu_FLAG_WORKS - Failed -- Performing Test C_FLAG_WORKS -- Performing Test C_FLAG_WORKS - Success -- Performing Test C_COMPILE_WORKS -- Performing Test C_COMPILE_WORKS - Failed -- Compiler flag was valid, but executable did not build - perhaps update the binutils package -- Performing Test CXX_xCORE_AVX512_FLAG_WORKS -- Performing Test CXX_xCORE_AVX512_FLAG_WORKS - Failed -- Performing Test CXX_mavx512f_mfma_FLAG_WORKS -- Performing Test CXX_mavx512f_mfma_FLAG_WORKS - Failed -- Performing Test CXX_mavx512f_FLAG_WORKS -- Performing Test CXX_mavx512f_FLAG_WORKS - Failed -- Performing Test CXX_arch_AVX_FLAG_WORKS -- Performing Test CXX_arch_AVX_FLAG_WORKS - Failed -- Performing Test CXX_hgnu_FLAG_WORKS -- Performing Test CXX_hgnu_FLAG_WORKS - Failed -- Performing Test CXX_FLAG_WORKS -- Performing Test CXX_FLAG_WORKS - Success -- Performing Test CXX_COMPILE_WORKS -- Performing Test CXX_COMPILE_WORKS - Failed -- Compiler flag was valid, but executable did not build - perhaps update the binutils package CMake Error at cmake/gmxManageSimd.cmake:92 (message): Found a compiler flag for AVX 512F support, but some other problem exists. Update your assembler and/or linker, e.g. in the binutils package of your distribution. Call Stack (most recent call first): cmake/gmxManageSimd.cmake:314 (gmx_give_fatal_error_when_simd_support_not_found) CMakeLists.txt:666 (gmx_manage_simd) -- Configuring incomplete, errors occurred! On Mon, Jul 3, 2017 at 2:44 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Mon, Jul 3, 2017 at 10:50 PM Guyen Gn <guyen...@gmail.com> wrote: > > > Sorry for long wait on response, basically i followed the instruction at > > nvidia website: > > > > http://www.nvidia.com/object/gromacs-installation.html > > > > I instaled GPU driver versoin 369, as well as CUDA, gcc, cmake. After > that > > it tells to run following: > > > > CC=gcc CXX=g++ cmake <GROMACS_SRC_DIR> -DGMX_OPENMP=ON -DGMX_GPU=ON - > > DGPU_DEPLOYMENT_KIT_ROOT_DIR=<GDK_PATH> -DGMX_BUILD_OWN_FFTW=ON - > > DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_BUILD_TYPE=Release - > > DCMAKE_INSTALL_PREFIX=<GROMACS_INSTALL_DIR> > > > > I tweaked as follows to fit my environment I setup (basically just > > installation source and run directory: > > CC=gcc CXX=g++ cmake /root/gromacs/gromacs-2016 -DGMX_OPENMP=ON > > -DGMX_GPU=ON -DGPU_DEPLOYMENT_KIT_ROOT_DIR=/usr/local/cuda > > -DGMX_BUILD_OWN_FFTW=ON -DGMX_PREFER_STATIC_LIBS=ON > > -DCMAKE_BUILD_TYPE=Release > > -DCMAKE_INSTALL_PREFIX=/root/gromacs/gromacs-2016-run inside build.sh > shell > > script. > > > > This is the full log, I highlighted toward the end section of code where > it > > started to fail. It appears something related to AVX. Thanks., > > > > [root@localhost gromacs-2016]# ./build.sh > > CMake Error: The source directory "/root/gromacs/gromacs-2016/-" does not > > exist. > > Specify --help for usage, or press the help button on the CMake GUI. > > ./build.sh: line 2: -DGMX_BUILD_OWN_FFTW=ON: command not found > > ./build.sh: line 3: -DCMAKE_BUILD_TYPE=Release: command not found > > > > All the above is because your script needed editing to handle newlines from > your copy-paste. > > > > [root@localhost gromacs-2016]# nano -w build.sh > > [root@localhost gromacs-2016]# pwd > > /root/gromacs/gromacs-2016 > > [root@localhost gromacs-2016]# mkdir ~/gromacs/gromacs-run > > [root@localhost gromacs-2016]# ./build.sh > > -- 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/gcc > > -- Check for working C compiler: /usr/bin/gcc -- works > > -- Detecting C compiler ABI info > > -- Detecting C compiler ABI info - done > > -- Check for working CXX compiler: /usr/bin/g++ > > -- Check for working CXX compiler: /usr/bin/g++ -- works > > -- Detecting CXX compiler ABI info > > -- Detecting CXX compiler ABI info - done > > -- 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: 2 > > -- Found CUDA: /usr/local/cuda (found suitable version "8.0", minimum > > required is "5.0") > > -- Could NOT find NVML (missing: NVML_INCLUDE_DIR) > > -- Checking for GCC x86 inline asm > > -- Checking for GCC x86 inline asm - supported > > -- Detecting best SIMD instructions for this CPU > > -- Detected best SIMD instructions for this CPU - AVX_512 > > -- 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_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 > > -- 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 > > Searching for static libraries requested, so the GROMACS libraries will > > also be static (BUILD_SHARED_LIBS=OFF) > > -- Could NOT find Hwloc (missing: HWLOC_LIBRARIES HWLOC_INCLUDE_DIRS) > > (Required is at least version "1.5") > > -- Looking for include file pthread.h > > -- Looking for include file 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 > > -- Looking for include file pthread.h > > -- Looking for include file pthread.h - found > > -- Atomic operations found > > -- Performing Test PTHREAD_SETAFFINITY > > -- Performing Test PTHREAD_SETAFFINITY - Success > > -- 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 > > -- Enabling single compilation unit for the CUDA non-bonded module. > > Multiple compilation units are not compatible with CC 2.x devices, to > > enable the feature specify only CC >=3.0 target architectures in > > GMX_CUDA_TARGET_SM/GMX_CUDA_TARGET_COMPUTE. > > -- Setting build user/date/host/cpu information > > -- Setting build user & time - OK > > -- 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 > > -- Performing Test C_xMIC_AVX512_FLAG_WORKS > > > Aha. This is a known issue that we have fixed, but not yet made available > in a released version. When we wrote this code, we had no Skylake machines > to test on. See > https://gerrit.gromacs.org/c/6570/2/cmake/gmxManageSimd.cmake for the form > of the fix. You can simply edit that single line in > cmake/gmxManageSimd.cmake in your source directory and all will be fine - > maybe a fresh build directory will help. > > Mark > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Guyen G. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
