Hi, As the message says, you should update your binutils package. Using such distros based on old OS infrastructure with new hardware guarantees you have to update various things in order to benefit from your expensive hardware. In your case, https://ed.braaten.net/blog/2014-05-28-devtools-for-centos/ or maybe devtoolset-3 is appropriate. This will be absolutely necessary for GROMACS 2016 and up.
Mark On Sat, 3 Sep 2016 13:10 Atila Petrosian <atila.petros...@gmail.com> wrote: > Dear gromacs users, > > I am using Rocks cluster system with following info: > > Rocks 6.2 > CentOS 6.6 > Cuda 7.5 and 8 > gcc 4.4.7 > > I am installing gromacs-5.1.3. I used following command: > > cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=ON > -DGMX_MPI=ON -DGMX_GPU=ON > > But I encountered with error. The last lines are as follows: > > > ------------------------------------------------------------------------------------------ > -- gcc 4.4.7 detected, using -O3, will apply workaround for optimization > bug (disable with GMX_DISABLE_GCC44_BUG_WORKAROUND) > -- 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 posix_memalign > -- Looking for posix_memalign - found > -- Looking for memalign > -- Looking for memalign - not found > -- Looking for _aligned_malloc > -- Looking for _aligned_malloc - not 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 > -- Looking for rsqrt > -- Looking for rsqrt - not found > -- Looking for rsqrtf > -- Looking for rsqrtf - not found > -- Looking for sqrtf > -- Looking for sqrtf - found > -- 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 > -- 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 > -- MPI is not compatible with thread-MPI. Disabling thread-MPI. > -- Found MPI_C: > > /opt/openmpi/lib/libmpi.so;/usr/lib64/libibverbs.so;/usr/lib64/libdat.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so > -- Found MPI_CXX: > > /opt/openmpi/lib/libmpi_cxx.so;/opt/openmpi/lib/libmpi.so;/usr/lib64/libibverbs.so;/usr/lib64/libdat.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so > -- Checking for MPI_IN_PLACE > -- Performing Test MPI_IN_PLACE_COMPILE_OK > -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success > -- Checking for MPI_IN_PLACE - yes > -- Looking for zlibVersion in /usr/lib64/libz.so > -- Looking for zlibVersion in /usr/lib64/libz.so - found > -- Found LibXml2: /usr/lib64/libxml2.so (found version "2.7.6") > -- Looking for xmlTextWriterEndAttribute in /usr/lib64/libxml2.so > -- Looking for xmlTextWriterEndAttribute in /usr/lib64/libxml2.so - found > -- Looking for include file libxml/parser.h > -- Looking for include file libxml/parser.h - found > -- 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 > -- Could NOT find Boost > Boost >= 1.44 not found. Using minimal internal version. This may cause > trouble if you plan on compiling/linking other software that uses Boost > against GROMACS. > -- Setting build user/date/host/cpu information > -- Setting build user & time - OK > -- Checking floating point format > -- Checking floating point format - IEEE754 (LE byte, LE word) > -- 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 > -- Checking for isfinite > -- Performing Test isfinite_compile_ok > -- Performing Test isfinite_compile_ok - Success > -- Checking for isfinite - yes > -- Checking for _isfinite > -- Performing Test _isfinite_compile_ok > -- Performing Test _isfinite_compile_ok - Failed > -- Checking for _isfinite - no > -- Checking for _finite > -- Performing Test _finite_compile_ok > -- Performing Test _finite_compile_ok - Failed > -- Checking for _finite - no > -- Performing Test CXXFLAG_STD_CXX0X > -- Performing Test CXXFLAG_STD_CXX0X - Success > -- Performing Test GMX_CXX11_SUPPORTED > -- Performing Test GMX_CXX11_SUPPORTED - Failed > -- Looking for C++ include regex > -- Looking for C++ include regex - not found > -- Checking for system XDR support > -- Checking for system XDR support - present > -- Try C compiler AVX2 flag = [-march=core-avx2] > -- Performing Test C_FLAG_march_core_avx2 > -- Performing Test C_FLAG_march_core_avx2 - Failed > -- Try C compiler AVX2 flag = [-mavx2] > -- Performing Test C_FLAG_mavx2 > -- Performing Test C_FLAG_mavx2 - Failed > -- Try C compiler AVX2 flag = [/arch:AVX] > -- Performing Test C_FLAG_arch_AVX > -- Performing Test C_FLAG_arch_AVX - Failed > -- Try C compiler AVX2 flag = [-hgnu] > -- Performing Test C_FLAG_hgnu > -- Performing Test C_FLAG_hgnu - Failed > -- Try C compiler AVX2 flag = [] > -- Performing Test C_FLAG_ > -- Performing Test C_FLAG_ - Success > -- Performing Test C_SIMD_COMPILES_FLAG_ > -- Performing Test C_SIMD_COMPILES_FLAG_ - Failed > -- Compiler flag was valid, but executable did not build - perhaps update > the binutils package > -- Try C++ compiler AVX2 flag = [-march=core-avx2] > -- Performing Test CXX_FLAG_march_core_avx2 > -- Performing Test CXX_FLAG_march_core_avx2 - Failed > -- Try C++ compiler AVX2 flag = [-mavx2] > -- Performing Test CXX_FLAG_mavx2 > -- Performing Test CXX_FLAG_mavx2 - Failed > -- Try C++ compiler AVX2 flag = [/arch:AVX] > -- Performing Test CXX_FLAG_arch_AVX > -- Performing Test CXX_FLAG_arch_AVX - Failed > -- Try C++ compiler AVX2 flag = [-hgnu] > -- Performing Test CXX_FLAG_hgnu > -- Performing Test CXX_FLAG_hgnu - Failed > -- Try C++ compiler AVX2 flag = [] > -- Performing Test CXX_FLAG_ > -- Performing Test CXX_FLAG_ - Success > -- Performing Test CXX_SIMD_COMPILES_FLAG_ > -- Performing Test CXX_SIMD_COMPILES_FLAG_ - Failed > -- Compiler flag was valid, but executable did not build - perhaps update > the binutils package > CMake Error at cmake/gmxManageSimd.cmake:67 (message): > Found a compiler flag for AVX2 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:285 > (gmx_give_fatal_error_when_simd_support_not_found) > CMakeLists.txt:648 (gmx_manage_simd) > > > -- Configuring incomplete, errors occurred! > See also > "/root/gromacs_source/gromacs-5.1.3/build/CMakeFiles/CMakeOutput.log". > See also > "/root/gromacs_source/gromacs-5.1.3/build/CMakeFiles/CMakeError.log". > > > --------------------------------------------------------------------------------------- > > How to resolve this error? > > Best, > Atila > -- > 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.
