Dear Christoph, Yes, you are correct, I load boost, eigen3 and fftw3 from the intel modules on the cluster (/opt/apps/intel18/modulefiles), so in my case I should use intel18 compiler.
Thank you so much for your time. Best regards, Zidan On Saturday, 9 February 2019 10:07:57 UTC-6, Christoph Junghans wrote: > > On Thu, Feb 7, 2019 at 9:12 PM Zidan Zhang <[email protected] > <javascript:>> 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] <javascript:>. > > To post to this group, send email to [email protected] > <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 > -- 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.
