[gmx-users] Regarding installation problem

Tue Feb 23 13:35:27 CET 2016

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modern hardware, which automatically means that everything is out of date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.souvik at iitkgp.ac.in>
wrote:

> Can u tell what are compilers I need to up-to-date?
>
> ----- Original Message -----
> From: "Mark Abraham" <mark.j.abraham at gmail.com>
> To: gmx-users at 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.souvik at 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.abraham at gmail.com>
> > To: gmx-users at 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
> >
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> >
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