Hi, Usually this means, like it says, that the linker isn't able to do the required job. I don't know whether the stock RHEL 7.2 linker can, but I imagine that's the issue. Usually using a devtoolset e.g. https://www.softwarecollections.org/en/scls/rhscl/devtoolset-4/ is the way to get a machine with useful tools on it rather than one with "stable" = "old" tools, particularly when you want to use the latest hardware...
Mark On Thu, Aug 3, 2017 at 1:28 AM Guyen Gn <guyen...@gmail.com> wrote: > Any update on this one?? > > On Fri, Jul 14, 2017 at 1:30 PM, Guyen Gn <guyen...@gmail.com> wrote: > > > Any ideas on this one? Thanks! > > > > On Mon, Jul 3, 2017 at 9:33 PM, Guyen Gn <guyen...@gmail.com> wrote: > > > >> 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_sim > >> d_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. > >> > > > > > > > > -- > > Guyen G. > > > > > > -- > 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. > -- 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.