Is there a particular reason you are installing the master branch and not the stable? If there is not a specific feature you need, you might try cloning the stable branch instead. Also do you know what compiler and version you are using?
On Thursday, February 7, 2019 at 3:43:04 PM UTC-7, Zidan Zhang wrote: > > Dear all, > > I am trying to install the newest version of VOTCA on cluster, the error > comes at the make step: > Scanning dependencies of target votca_tools_manpages > [ 0%] Built target votca_tools_manpages > Scanning dependencies of target gitversion > Current git revision is f00d0dd > [ 0%] Built target gitversion > Scanning dependencies of target votca_tools > [ 1%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/akimaspline.cc.o > [ 1%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/application.cc.o > [ 2%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/colors.cc.o > [ 3%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/correlate.cc.o > [ 3%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/crosscorrelate.cc.o > [ 4%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/cubicspline.cc.o > [ 5%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/datacollection.cc.o > [ 5%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/edge.cc.o > [ 6%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/edgecontainer.cc.o > [ 7%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/elements.cc.o > [ 7%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/globals.cc.o > [ 8%] Building CXX object > tools/src/libtools/CMakeFiles/votca_tools.dir/graph.cc.o > In file included from /usr/include/c++/4.8/algorithm:62:0, > from > /work/06148/vsc31483/software/votca_src/tools/src/libtools/graph.cc:20: > /usr/include/c++/4.8/bits/stl_algo.h: In instantiation of > ‘_RandomAccessIterator std::__unguarded_partition(_RandomAccessIterator, > _RandomAccessIterator, const _Tp&, _Compare) [with _RandomAccessIterator = > __gnu_cxx::__normal_iterator<std::pair<int, votca::tools::GraphNode>*, > std::vector<std::pair<int, votca::tools::GraphNode> > >; _Tp = > std::pair<int, votca::tools::GraphNode>; _Compare = bool (*)(std::pair<int, > votca::tools::GraphNode>&, std::pair<int, votca::tools::GraphNode>&)]’: > /usr/include/c++/4.8/bits/stl_algo.h:2296:78: required from > ‘_RandomAccessIterator > std::__unguarded_partition_pivot(_RandomAccessIterator, > _RandomAccessIterator, _Compare) [with _RandomAccessIterator = > __gnu_cxx::__normal_iterator<std::pair<int, votca::tools::GraphNode>*, > std::vector<std::pair<int, votca::tools::GraphNode> > >; _Compare = bool > (*)(std::pair<int, votca::tools::GraphNode>&, std::pair<int, > votca::tools::GraphNode>&)]’ > /usr/include/c++/4.8/bits/stl_algo.h:2337:62: required from ‘void > std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, > _Compare) [with _RandomAccessIterator = > __gnu_cxx::__normal_iterator<std::pair<int, votca::tools::GraphNode>*, > std::vector<std::pair<int, votca::tools::GraphNode> > >; _Size = long int; > _Compare = bool (*)(std::pair<int, votca::tools::GraphNode>&, > std::pair<int, votca::tools::GraphNode>&)]’ > /usr/include/c++/4.8/bits/stl_algo.h:5499:44: required from ‘void > std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = > __gnu_cxx::__normal_iterator<std::pair<int, votca::tools::GraphNode>*, > std::vector<std::pair<int, votca::tools::GraphNode> > >; _Compare = bool > (*)(std::pair<int, votca::tools::GraphNode>&, std::pair<int, > votca::tools::GraphNode>&)]’ > /work/06148/vsc31483/software/votca_src/tools/src/libtools/graph.cc:127:51: > required from here > /usr/include/c++/4.8/bits/stl_algo.h:2263:35: error: invalid > initialization of reference of type ‘std::pair<int, > votca::tools::GraphNode>&’ from expression of type ‘const std::pair<int, > votca::tools::GraphNode>’ > while (__comp(*__first, __pivot)) > ^ > /usr/include/c++/4.8/bits/stl_algo.h:2266:34: error: invalid > initialization of reference of type ‘std::pair<int, > votca::tools::GraphNode>&’ from expression of type ‘const std::pair<int, > votca::tools::GraphNode>’ > while (__comp(__pivot, *__last)) > ^ > tools/src/libtools/CMakeFiles/votca_tools.dir/build.make:205: recipe for > target 'tools/src/libtools/CMakeFiles/votca_tools.dir/graph.cc.o' failed > make[2]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/graph.cc.o] > Error 1 > CMakeFiles/Makefile2:217: recipe for target > 'tools/src/libtools/CMakeFiles/votca_tools.dir/all' failed > make[1]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/all] Error 2 > Makefile:129: recipe for target 'all' failed > make: *** [all] Error 2 > > Please let me know how I can fix it. Thanks in advance! > > Best regards, > Zidan > > The installation procedure is shown as following: > > git clone -b master --recursive https://github.com/votca/votca.git > > I passed through the cmake procedure with: > > cmake -DBUILD_CSGAPPS=ON -DCMAKE_INSTALL_PREFIX=/work/software/votca - > DWITH_GMX=ON -DGROMACS_INCLUDE_DIR=/work/software/gromacs/include - > DGROMACS_LIBRARY=/work/software/gromacs/lib64/libgromacs_mpi.so - > DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON -DEIGEN3_INCLUDE_DIR=/opt/apps/intel18/ > eigen/3.3.4/include/eigen3 -DBOOST_ROOT=/opt/apps/intel18/boost/1.64 .. > > -- The C compiler identification is GNU 4.8.5 > -- The CXX compiler identification is GNU 4.8.5 > -- 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 > -- Detecting C compile features > -- Detecting C compile features - 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 > -- Detecting CXX compile features > -- Detecting CXX compile features - done > -- Found Git: /opt/apps/git/2.19.1/bin/git (found version "2.19.1") > -- Looking for pthread.h > -- Looking for 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 > -- Boost version: 1.64.0 > -- Found the following Boost libraries: > -- program_options > -- filesystem > -- system > -- Found PkgConfig: /usr/bin/pkg-config (found version "0.28") > -- Checking for module 'fftw3' > -- Found fftw3, version 3.3.8 > -- Found FFTW3: > /opt/apps/intel18/cray_mpich_7_7/fftw3/3.3.8/lib/libfftw3.so > -- Looking for fftw_plan_r2r_1d in > /opt/apps/intel18/cray_mpich_7_7/fftw3/3.3.8/lib/libfftw3.so; > -- Looking for fftw_plan_r2r_1d in > /opt/apps/intel18/cray_mpich_7_7/fftw3/3.3.8/lib/libfftw3.so; - found > -- Looking for assert.h > -- Looking for assert.h - found > -- Looking for math.h > -- Looking for math.h - found > -- Looking for stdio.h > -- Looking for stdio.h - found > -- Looking for stdlib.h > -- Looking for stdlib.h - found > -- Looking for string.h > -- Looking for string.h - found > -- Looking for C++ include cmath > -- Looking for C++ include cmath - found > -- Looking for C++ include fstream > -- Looking for C++ include fstream - found > -- Looking for C++ include functional > -- Looking for C++ include functional - found > -- Looking for C++ include iostream > -- Looking for C++ include iostream - found > -- Looking for C++ include limits > -- Looking for C++ include limits - found > -- Looking for C++ include list > -- Looking for C++ include list - found > -- Looking for C++ include map > -- Looking for C++ include map - found > -- Looking for C++ include ostream > -- Looking for C++ include ostream - found > -- Looking for C++ include sstream > -- Looking for C++ include sstream - found > -- Looking for C++ include stack > -- Looking for C++ include stack - found > -- Looking for C++ include stdexcept > -- Looking for C++ include stdexcept - found > -- Looking for C++ include string > -- Looking for C++ include string - found > -- Looking for C++ include vector > -- Looking for C++ include vector - found > -- Looking for sqrt in m > -- Looking for sqrt in m - found > -- Found EXPAT: /usr/lib64/libexpat.so (found version "2.1.0") > -- Checking for module 'sqlite3' > -- Found sqlite3, version 3.8.10.2 > -- Found SQLITE3: /usr/lib64/libsqlite3.so > -- Performing Test HAVE_AIX > -- Performing Test HAVE_AIX - Failed > -- Found Doxygen: /usr/bin/doxygen (found version "1.8.6") found > components: doxygen dot > -- Could NOT find TXT2TAGS (missing: TXT2TAGS_EXECUTABLE) > txt2tags not found, help cmake to find it by setting TXT2TAGS_EXECUTABLE > -- Found UnixCommands: /bin/bash > -- Boost version: 1.64.0 > -- Found the following Boost libraries: > -- program_options > -- filesystem > -- system > -- Checking for module 'libvotca_tools' > -- No package 'libvotca_tools' found > -- Found VOTCA_TOOLS: votca_tools > -- Checking for module 'libgromacs_d' > -- No package 'libgromacs_d' found > -- Checking for module 'libgromacs' > -- No package 'libgromacs' found > -- Looking for c++ gmx_version in > /work/06148/vsc31483/software/gromacs/lib64/libgromacs_mpi.so > -- Looking for c++ gmx_version in > /work/06148/vsc31483/software/gromacs/lib64/libgromacs_mpi.so - found > -- Looking for c++ gmx_is_single_precision in > /work/06148/vsc31483/software/gromacs/lib64/libgromacs_mpi.so > -- Looking for c++ gmx_is_single_precision in > /work/06148/vsc31483/software/gromacs/lib64/libgromacs_mpi.so - found > -- Looking for c++ gmx_is_double_precision in > /work/06148/vsc31483/software/gromacs/lib64/libgromacs_mpi.so > -- Looking for c++ gmx_is_double_precision in > /work/06148/vsc31483/software/gromacs/lib64/libgromacs_mpi.so - not found > -- Found GROMACS: > /work/06148/vsc31483/software/gromacs/lib64/libgromacs_mpi.so (found > suitable version "20180004", minimum required is "20160000") > -- Looking for C++ include algorithm > -- Looking for C++ include algorithm - found > -- Looking for C++ include iomanip > -- Looking for C++ include iomanip - found > -- Looking for C++ include numeric > -- Looking for C++ include numeric - found > -- Looking for C++ include cstdlib > -- Looking for C++ include cstdlib - found > -- HDF5: Using hdf5 compiler wrapper to determine C configuration > -- Found HDF5: > /opt/apps/intel18/hdf5/1.8.21/x86_64/lib/libhdf5.so;/opt/apps/intel18/hdf5/1.8.21/x86_64/lib/libsz.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so > > (found version "1.8.21") found components: C > -- Could NOT find GMX (missing: GMX_EXECUTABLE) > -- Boost version: 1.64.0 > -- Found the following Boost libraries: > -- program_options > -- Checking for module 'libvotca_tools' > -- No package 'libvotca_tools' found > -- Checking for module 'libvotca_csg' > -- No package 'libvotca_csg' found > -- Found VOTCA_CSG: votca_csg > -- Could NOT find CLANG_FORMAT (missing: CLANG_FORMAT_EXECUTABLE) > -- The following OPTIONAL packages have been found: > > * Git > * FFTW3 > * EXPAT > * UnixCommands > * HDF5 > * PkgConfig > * Doxygen > > -- The following REQUIRED packages have been found: > > * Threads > * GROMACS (required version >= 20160000) > * Boost (required version >= 1.57.0) > * Eigen3 (required version >= 3.3.0) > * SQLITE3 > * VOTCA_TOOLS > * VOTCA_CSG > > -- The following OPTIONAL packages have not been found: > > * TXT2TAGS > > -- Configuring done > -- Generating done > -- Build files have been written to: > /work/06148/vsc31483/software/votca_src/build > -- You received this message because you are subscribed to the Google Groups "votca" group. 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