[gmx-users] gmx 5.0 installation with cuda

[Raju]

Dear all,


I have installed cuda driver 7.0 in centos6.6 version has default gcc 4.4.7.


After the successful installation of cuda, i tried to install gmx 5.0.5 and found that gmx 5.0.5 version needs over gcc 4.6. 
Therefore, i updated gcc 4.4 to 4.7 through devtoolset. When i try to install the gmx through following commands i gets following errors. 


Kindly give a suggestion to rectify this problem. Thanks.


Cuda installed path
whereis cuda
cuda: /usr/local/cuda


gmx installation


[raju at ddteam build]$ gcc --version
gcc (GCC) 4.7.2 20121015 (Red Hat 4.7.2-5)
Copyright (C) 2012 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


[raju at ddteam build]$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_OPENMPI=ON -DGMX_GPU=ON
-- The C compiler identification is GNU 4.7.2
-- The CXX compiler identification is GNU 4.7.2
-- Check for working C compiler: /opt/centos/devtoolset-1.1/root/usr/bin/cc
-- Check for working C compiler: /opt/centos/devtoolset-1.1/root/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /opt/centos/devtoolset-1.1/root/usr/bin/c++
-- Check for working CXX compiler: /opt/centos/devtoolset-1.1/root/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Looking for NVIDIA GPUs present in the system
-- Number of NVIDIA GPUs detected: 1 
-- Found CUDA: /usr/local/cuda (found suitable version "7.0", minimum required is "4.0") 
-- 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_REL
-- Performing Test CFLAGS_WARN_REL - Success
-- Performing Test CFLAGS_WARN_UNINIT
-- Performing Test CFLAGS_WARN_UNINIT - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- 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_REL
-- Performing Test CXXFLAGS_WARN_REL - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- 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 - found
-- Looking for _aligned_malloc
-- Looking for _aligned_malloc - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - 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 sysconf
-- Looking for sysconf - found
-- Looking for rsqrt
-- Looking for rsqrt - not found
-- Looking for rsqrtf
-- Looking for rsqrtf - not found
-- Looking for sqrtf
-- Looking for sqrtf - not found
-- Looking for sqrt in m
-- Looking for sqrt in m - found
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - 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 include file pthread.h
-- Looking for include file 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
-- Performing Test CXXFLAG_FPIC
-- Performing Test CXXFLAG_FPIC - 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 - Success
-- 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 - Success
-- Performing Test C_SIMD_COMPILES_FLAG_march_core_avx2
-- Performing Test C_SIMD_COMPILES_FLAG_march_core_avx2 - Failed
-- Try C compiler AVX2 flag = [-mavx2]
-- Performing Test C_FLAG_mavx2
-- Performing Test C_FLAG_mavx2 - Success
-- Performing Test C_SIMD_COMPILES_FLAG_mavx2
-- Performing Test C_SIMD_COMPILES_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
-- Try C++ compiler AVX2 flag = [-march=core-avx2]
-- Performing Test CXX_FLAG_march_core_avx2
-- Performing Test CXX_FLAG_march_core_avx2 - Success
-- Performing Test CXX_SIMD_COMPILES_FLAG_march_core_avx2
-- Performing Test CXX_SIMD_COMPILES_FLAG_march_core_avx2 - Failed
-- Try C++ compiler AVX2 flag = [-mavx2]
-- Performing Test CXX_FLAG_mavx2
-- Performing Test CXX_FLAG_mavx2 - Success
-- Performing Test CXX_SIMD_COMPILES_FLAG_mavx2
-- Performing Test CXX_SIMD_COMPILES_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
CMake Error at cmake/gmxTestSimd.cmake:244 (message):
  Cannot find AVX2 compiler flag.  Use a newer compiler, or choose AVX SIMD
  (slower).
Call Stack (most recent call first):
  CMakeLists.txt:720 (gmx_test_simd)




-- Configuring incomplete, errors occurred!
See also "/home/raju/software/gromacs-5.0.5/build/CMakeFiles/CMakeOutput.log".
See also "/home/raju/software/gromacs-5.0.5/build/CMakeFiles/CMakeError.log".
[raju at ddteam build]$