Oh got it. Thanks for the help. On Wednesday, December 16, 2015 at 10:08:46 AM UTC-6, Christoph Junghans wrote: > > 2015-12-16 7:10 GMT-07:00 Bijay Shrestha <bijay.s...@selu.edu > <javascript:>>: > > 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) > That is a problem in Gromacs, not VOTCA. Gromacs needs a single > precision version of fftw (unless you build a double precision version > of gromacs using GMX_DOUBLE=ON). However VOTCA needs a double > precision version of fftw. > > In Ubuntu 14.04 both of them are part of the libfftw3-dev package, > which also contain the headers you will need. > > Also you actually don't need to build gromacs, just install the > gromacs-dev package on Ubuntu. > > (see here https://github.com/votca/csg/wiki/Dependencies for details) > > Christoph > > > > > > > -- 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 <bijay.s...@selu.edu>: > >> > 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 votca+un...@googlegroups.com. > >> > To post to this group, send email to vo...@googlegroups.com. > >> > 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 votca+un...@googlegroups.com <javascript:>. > > To post to this group, send email to vo...@googlegroups.com > <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 >
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