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 [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 *-- Performing Test C_xMIC_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_xMIC_AVX512_FLAG_WORKS-- Performing Test CXX_xMIC_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 packageCMake 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)* On Mon, Jun 19, 2017 at 4:21 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > We can't support third party build guides, but please follow ours and ask > questions about it here. Provide full details. > > Mark > > On Mon, 19 Jun 2017 23:39 Guyen Gn <guyen...@gmail.com> wrote: > > > I have used the Nvidia's gromacs page to buid and run the gromacs. > > Few months back, I have used the Xeon CPU to build and run > > successfully on RHEL7.2. This also used the M6 GPU card. > > Now the same build is failing with AVX related compiler error if I use > > latest Skylake processor and P100 GPU. I have tried several > > permutations and all are same. May I get a support here? if so, I can > > send the details (build error log, system configuration, version of > > gromacs used etc.,) > > -- > > 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. > > > -- > 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.
