[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

[Atila Petrosian]

Dear gromacs users,

I am using Rocks cluster system with following info:

Rocks 6.2
CentOS 6.6
Cuda 7.5 and 8
gcc 4.4.7

I am installing gromacs-5.1.3. I used following command:

cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=ON
-DGMX_MPI=ON -DGMX_GPU=ON

But I encountered with error. The last lines are as follows:

------------------------------------------------------------------------------------------
-- 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
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Found MPI_C:
/opt/openmpi/lib/libmpi.so;/usr/lib64/libibverbs.so;/usr/lib64/libdat.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so
-- Found MPI_CXX:
/opt/openmpi/lib/libmpi_cxx.so;/opt/openmpi/lib/libmpi.so;/usr/lib64/libibverbs.so;/usr/lib64/libdat.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- 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 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:648 (gmx_manage_simd)


-- Configuring incomplete, errors occurred!
See also
"/root/gromacs_source/gromacs-5.1.3/build/CMakeFiles/CMakeOutput.log".
See also
"/root/gromacs_source/gromacs-5.1.3/build/CMakeFiles/CMakeError.log".

---------------------------------------------------------------------------------------

How to resolve this error?

Best,
Atila