[gmx-users] Gromacs 5.0.4 Installation error

[Sarath Kumar Baskaran]

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.*