[gmx-users] Regarding installation problem

[SOUVIK MONDAL]

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
-- 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.
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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