[gmx-users] Gromacs 5.0.4 Installation error

Fri Apr 24 13:31:53 CEST 2015

Hi,

This can't happen with a correct toolchain and unmodified source files. I
think you should unpack the tarball fresh and try again.

Mark

On Wed, Apr 22, 2015 at 2:46 PM, Sarath Kumar Baskaran <
bskumar.tech at gmail.com> wrote:

> Hi all,
>
> While Trying to install GROMACS 5.0.4 with the following compiling
> arguments,
> during make i am getting the following error,
>  I dont know how to solve it
> Please help me
>
> *# cmake .. -DGMX_THREAD_MPI=ON
> -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-5.0.4-gpu -DGMX_GPU=ON
> -DGMX_BUILD_OWN_FFTW=ON -DGMX_DEFAULT_SUFFIX=OFF
> -DGMX_BINARY_SUFFIX="-5.0.4-gpu" -DGMX_LIBS_SUFFIX="-5.0.4-gpu"
> -DGMX_PREFER_STATIC_LIBS=ON -DBUILD_SHARED_LIBS=OFF*
>
> -- The C compiler identification is GNU 4.8.3
> -- The CXX compiler identification is GNU 4.8.3
> -- 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
> -- 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
> -- 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 - SSE4.1
> -- 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 C++ include regex
> -- Looking for C++ include regex - not 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
> -- Found LibXml2: /usr/lib64/libxml2.a (found version "2.9.1")
> -- Looking for xmlTextWriterEndAttribute in /usr/lib64/libxml2.a
> -- Looking for xmlTextWriterEndAttribute in /usr/lib64/libxml2.a - not
> 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
> -- Boost version: 1.54.0
> CMake Warning at CMakeLists.txt:601 (message):
>   libxml2 not found.  Will build GROMACS without unit-tests.  This is not
>   recommended, because the unit-tests help to verify that GROMACS functions
>   correctly.  Most likely you are missing the libxml2-dev(el) package.
> After
>   you installed it, set GMX_BUILD_UNITTESTS=ON.
>
>
> -- Looking for zlibVersion in /usr/lib64/libz.so
> -- Looking for zlibVersion in /usr/lib64/libz.so - found
> -- 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
> -- Checking for system XDR support
> -- Checking for system XDR support - present
> -- Try C compiler SSE4.1 flag = [-msse4.1]
> -- Performing Test C_FLAG_msse4_1
> -- Performing Test C_FLAG_msse4_1 - Success
> -- Performing Test C_SIMD_COMPILES_FLAG_msse4_1
> -- Performing Test C_SIMD_COMPILES_FLAG_msse4_1 - Success
> -- Try C++ compiler SSE4.1 flag = [-msse4.1]
> -- Performing Test CXX_FLAG_msse4_1
> -- Performing Test CXX_FLAG_msse4_1 - Success
> -- Performing Test CXX_SIMD_COMPILES_FLAG_msse4_1
> -- Performing Test CXX_SIMD_COMPILES_FLAG_msse4_1 - Success
> -- Enabling SSE4.1 SIMD instructions
> -- Performing Test _callconv___vectorcall
> -- Performing Test _callconv___vectorcall - Failed
> -- Performing Test _callconv___regcall
> -- Performing Test _callconv___regcall - Failed
> -- Performing Test _callconv_
> -- Performing Test _callconv_ - Success
> -- The GROMACS-managed build of FFTW 3 will configure with the following
> optimizations: --enable-sse2
> -- Using external FFT library - FFTW3
> -- Looking for sgemm_
> -- Looking for sgemm_ - found
> -- A library with BLAS API found.
> -- Looking for cheev_
> -- Looking for cheev_ - not found
> -- A library with LAPACK API not found. Please specify library location.
> -- Using GROMACS built-in LAPACK.
> -- Checking for dlopen
> -- Performing Test HAVE_DLOPEN
> -- Performing Test HAVE_DLOPEN - Success
> -- Checking for dlopen - found
> -- Using manually set binary suffix: "-5.0.4-gpu"
> -- Using manually set library suffix: "-5.0.4-gpu"
> -- Could NOT find Pandoc (missing:  PANDOC_EXECUTABLE)
> -- Found PythonInterp: /usr/bin/python (found version "2.7.5")
> -- Check if the system is big endian
> -- Searching 16 bit integer
> -- Using unsigned short
> -- Check if the system is big endian - little endian
> -- Looking for inttypes.h
> -- Looking for inttypes.h - found
> -- Performing Test HAS_NO_UNUSED_PARAMETER
> -- Performing Test HAS_NO_UNUSED_PARAMETER - Success
> -- Performing Test HAS_NO_DEPRECATED_REGISTER
> -- Performing Test HAS_NO_DEPRECATED_REGISTER - Success
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /usr/local/src/gromacs-5.0.4/build-cpu
>
> *# make -j 4*
> ...................
> [ 42%] Building CXX object
>
> src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o
>
> /usr/local/src/gromacs-5.0.4/src/gromacs/analysisdata/modules/histogram.cpp:127:33:
> error: macro "GMX_RELEASE_ASSERT" requires 2 arguments, but only 1 given
>          GMX_RELEASE_ASSERT(isDef)ned(settings.binWidth_) ||
> settings.binCount_ > 0,
>                                  ^
> [ 42%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o
>
> /usr/local/src/gromacs-5.0.4/src/gromacs/analysisdata/modules/histogram.cpp:
> In constructor
> ‘gmx::AnalysisHistogramSettings::AnalysisHistogramSettings(const
> gmx::AnalysisHistogramSettingsInitializer&)’:
>
> /usr/local/src/gromacs-5.0.4/src/gromacs/analysisdata/modules/histogram.cpp:127:9:
> error: ‘GMX_RELEASE_ASSERT’ was not declared in this scope
>          GMX_RELEASE_ASSERT(isDef)ned(settings.binWidth_) ||
> settings.binCount_ > 0,
>          ^
>
> /usr/local/src/gromacs-5.0.4/src/gromacs/analysisdata/modules/histogram.cpp:127:34:
> error: expected ‘;’ before ‘ned’
>          GMX_RELEASE_ASSERT(isDef)ned(settings.binWidth_) ||
> settings.binCount_ > 0,
>                                   ^
> make[2]: ***
>
> [src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs....
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
>
>
> *Yours Sincerely,*
>
>
> *B. Sarath Kumar,*
> *PhD Student**,*
> *Centre for Biotechnology,*
> *Anna University, Chennai-25.*
> --
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