2015-12-16 7:10 GMT-07:00 Bijay Shrestha <bijay.shres...@selu.edu>: > 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+unsubscr...@googlegroups.com. > To post to this group, send email to votca@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+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
