Here is the output that I get. This is VOTCA build.sh, version 2.0.2 Install prefix is '/home/bskrb/votca' Using 5 jobs for make/ninja Working on gromacs Source dir (gromacs) is already there - skipping checkout updating git repository gromacs from origin/release-5-0 We are on branch release-5-0 remote: Counting objects: 644, done. remote: Compressing objects: 100% (416/416), done. remote: Total 644 (delta 599), reused 262 (delta 228) Receiving objects: 100% (644/644), 301.27 KiB | 314.00 KiB/s, done. Resolving deltas: 100% (599/599), completed with 267 local objects. >From git://git.gromacs.org/gromacs 099ab22..1833adf alexandria -> origin/alexandria 92bb11e..5a7bb7e master -> origin/master Already up-to-date. cmake -DCMAKE_INSTALL_PREFIX='/home/bskrb/votca' -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON . -- 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 - AVX_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/lib/i386-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/i386-linux-gnu/libz.so - found -- Could NOT find LibXml2 (missing: LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR) -- 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 -- Found Git: /usr/bin/git (found version "1.9.1") -- 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. CMake Warning at CMakeLists.txt:619 (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.
-- 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 AVX (256 bit) flag = [-mavx] -- Performing Test C_FLAG_mavx -- Performing Test C_FLAG_mavx - Success -- Performing Test C_SIMD_COMPILES_FLAG_mavx -- Performing Test C_SIMD_COMPILES_FLAG_mavx - Success -- Try C++ compiler AVX (256 bit) flag = [-mavx] -- Performing Test CXX_FLAG_mavx -- Performing Test CXX_FLAG_mavx - Success -- Performing Test CXX_SIMD_COMPILES_FLAG_mavx -- Performing Test CXX_SIMD_COMPILES_FLAG_mavx - Success -- Checking for gcc AVX maskload bug -- Checking for gcc AVX maskload bug - not present -- Enabling 256-bit AVX 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 -- checking for module 'fftw3f' -- package 'fftw3f' not found -- pkg-config could not detect fftw3f, trying generic detection Could not find fftw3f library named libfftw3f, please specify its location in CMAKE_PREFIX_PATH or FFTWF_LIBRARY by hand (e.g. -DFFTWF_LIBRARY='/path/to/libfftw3f.so') CMake Error at cmake/gmxManageFFTLibraries.cmake:82 (MESSAGE): Cannot find FFTW 3 (with correct precision - libfftw3f for mixed-precision GROMACS or libfftw3 for double-precision GROMACS). Either choose the right precision, choose another FFT(W) library (-DGMX_FFT_LIBRARY), enable the advanced option to let GROMACS build FFTW 3 for you (-GMX_BUILD_OWN_FFTW=ON), or use the really slow GROMACS built-in fftpack library (-DGMX_FFT_LIBRARY=fftpack). Call Stack (most recent call first): CMakeLists.txt:751 (include) -- Configuring incomplete, errors occurred! See also "/home/bskrb/votca/src/gromacs/CMakeFiles/CMakeOutput.log". See also "/home/bskrb/votca/src/gromacs/CMakeFiles/CMakeError.log". On Tuesday, December 15, 2015 at 10:47:06 AM UTC-6, Christoph Junghans wrote: > > HI, > > can you post the output cmake is producing? > > And yep, Ubuntu 14.04 is basically the last release, which doesn't > have a votca package. 14.10/15.04/15.10 have it! > > Cheers, > > Christoph > > 2015-12-15 7:21 GMT-07:00 Bijay Shrestha <[email protected] > <javascript:>>: > > Dear VOTCA users, > > Our research team is using GROMACS for the MD simulation. Now > we > > are planning to implement VOTCA for our coarse-graining analysis. During > our > > installation, we encountered many issues. We are using Ubuntu 14.0.4 LTS > and > > GROMACS v5.0.7 for the MD. We tried different methods for the > installation. > > We followed the instruction on handout from votca.org by downloading > from > > the git. It gives error report log files which I have attached in this > > email. We also tried installing from apt-get but it says unable to > locate > > the package. Could you help us to resolve the problem? Thank you. Have a > > great day! > > > > -- > > You received this message because you are subscribed to the Google > Groups > > "votca" group. > > To unsubscribe from this group and stop receiving emails from it, send > an > > email to [email protected] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > Visit this group at https://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/d/optout. > > > > -- > Christoph Junghans > Web: http://www.compphys.de > -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
