Can u tell what are compilers I need to up-to-date? ----- Original Message ----- From: "Mark Abraham" <mark.j.abra...@gmail.com> To: gmx-us...@gromacs.org Sent: Tuesday, February 23, 2016 4:50:52 PM Subject: Re: [gmx-users] Regarding installation problem
Hi, On Tue, Feb 23, 2016 at 11:54 AM SOUVIK MONDAL <m.sou...@iitkgp.ac.in> wrote: > After doing cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON > the output in that ternimal comes as follows > > - The C compiler identification is GNU 4.4.7 > -- The CXX compiler identification is GNU 4.4.7 > This compiler version was designed several years before your hardware model was released, so it will not work very well. Please get an up-to-date compiler for your distribution, as the install guide suggests :-) -- Check for working C compiler: /usr/bin/cc > -- Check for working C compiler: /usr/bin/cc -- works > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Detecting C compile features > -- Detecting C compile features - done > -- Check for working CXX compiler: /usr/bin/c++ > -- Check for working CXX compiler: /usr/bin/c++ -- works > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- Detecting CXX compile features > -- Detecting CXX compile features - done > -- Looking for NVIDIA GPUs present in the system > -- Could not detect NVIDIA GPUs > -- No compatible CUDA toolkit found (v4.0+), disabling native GPU > acceleration > -- 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 - AVX2_256 > -- 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_WARN > -- Performing Test CFLAGS_WARN - Success > -- Performing Test CFLAGS_WARN_EXTRA > -- Performing Test CFLAGS_WARN_EXTRA - Success > -- Performing Test CFLAGS_WARN_UNDEF > -- Performing Test CFLAGS_WARN_UNDEF - Success > -- Performing Test CFLAGS_WARN_REL > -- Performing Test CFLAGS_WARN_REL - Success > -- Performing Test CFLAGS_EXCESS_PREC > -- Performing Test CFLAGS_EXCESS_PREC - Failed > -- Performing Test CFLAGS_COPT > -- Performing Test CFLAGS_COPT - Success > -- Performing Test CFLAGS_NOINLINE > -- Performing Test CFLAGS_NOINLINE - Success > -- Performing Test CXXFLAGS_WARN > -- Performing Test CXXFLAGS_WARN - Success > -- Performing Test CXXFLAGS_WARN_EXTRA > -- Performing Test CXXFLAGS_WARN_EXTRA - Success > -- Performing Test CXXFLAGS_WARN_UNDEF > -- Performing Test CXXFLAGS_WARN_UNDEF - Success > -- Performing Test CXXFLAGS_WARN_REL > -- Performing Test CXXFLAGS_WARN_REL - Success > -- Performing Test CXXFLAGS_EXCESS_PREC > -- Performing Test CXXFLAGS_EXCESS_PREC - Failed > -- Performing Test CXXFLAGS_COPT > -- Performing Test CXXFLAGS_COPT - Success > -- Performing Test CXXFLAGS_NOINLINE > -- Performing Test CXXFLAGS_NOINLINE - Success > -- 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 > -- 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 pthread.h > -- Looking for 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 > -- 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. > Here's the diagnosis of the problem. But if you're anyway updating your infrastructure, get a new compiler first. Mark > Call Stack (most recent call first): > cmake/gmxManageSimd.cmake:285 > (gmx_give_fatal_error_when_simd_support_not_found) > CMakeLists.txt:645 (gmx_manage_simd) > > > -- Configuring incomplete, errors occurred! > See also "/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeOutput.log". > See also "/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeError.log". > > > ----- Original Message ----- > From: "Mark Abraham" <mark.j.abra...@gmail.com> > To: gmx-us...@gromacs.org > Sent: Tuesday, February 23, 2016 4:17:17 PM > Subject: Re: [gmx-users] Regarding installation problem > > Hi, > > Yes, I know. That's its job. The only likely relevant part is very near the > end. But first I wanted to see the terminal output - what you saw on the > screen when you ran cmake. > > 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. > -- > 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. -- 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.