On Thu, Feb 7, 2019 at 9:12 PM Zidan Zhang <[email protected]> wrote: > > > Dear Joshua, > > Problem solved by adding -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc. I think the original issue was a combination of an old gcc (4.8.5 - currently is version 8) and relatively new boost (1.64). By using a relatively new intel compiler (18.0.2), you just worked around the issue.
You should update your gcc as the intel compiler internally uses header from (your old) gcc. Christoph > > I am using intel 18.0.2 compiler. > > There is no particular reason, I am testing a function by comparing stable > and master, the previous stable version (1.5) was installed by another user > in the group (at least 1 year ago), he also installed a developer version, > there is a small difference between these two, so I am checking it. > > Thank you so much for your time! > > Best regards, > Zidan > > On Thursday, 7 February 2019 16:55:07 UTC-6, Joshua Brown wrote: >> >> 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. > 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. -- 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.
