Dear Hoshua, Problem solved by adding -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc.
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 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.
