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.