Hi, That's still going to need an updated binutils, though.
Mark On Tue, Feb 23, 2016 at 3:40 PM Szilárd Páll <pall.szil...@gmail.com> wrote: > AVX is supported even by gcc 4.4.7 (although admittedly I'm not sure if > it's functional), so you may want to try -DGMX_SIMD=AVX_256, that will > waste your hardware a bit less. > > -- > Szilárd > > On Tue, Feb 23, 2016 at 3:02 PM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > You can probably use any GROMACS version, if you want it to run slowly > and > > generate less science for you. Just use cmake -DGMX_SIMD=SSE4.1. > > > > Mark > > > > On Tue, Feb 23, 2016 at 2:47 PM SOUVIK MONDAL <m.sou...@iitkgp.ac.in> > > wrote: > > > > > Which version of gromacs will be suitable for gcc version 4.4.7? > > > > > > > > > > > > ----- Original Message ----- > > > From: "Mark Abraham" <mark.j.abra...@gmail.com> > > > To: gmx-us...@gromacs.org > > > Sent: Tuesday, February 23, 2016 6:05:13 PM > > > Subject: Re: [gmx-users] Regarding installation problem > > > > > > Hi, > > > > > > The simplest thing is to get the latest version of gcc that your > > operating > > > system (e.g. Linux distribution) supports. Sadly, people often sell > > compute > > > systems based on "mature, stable, reliable" versions of software, but > > with > > > modern hardware, which automatically means that everything is out of > date > > > and their users have to do all of this useless work. But do talk to > your > > > system administrators to get some up to date tools installed for you. > > > > > > Mark > > > > > > On Tue, Feb 23, 2016 at 12:55 PM SOUVIK MONDAL <m.sou...@iitkgp.ac.in> > > > wrote: > > > > > > > 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. > > > > > > > -- > > > 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. -- 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.