[gmx-users] Regarding installation problem

Tue Feb 23 12:21:07 CET 2016

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
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