2017-06-09 5:43 GMT-06:00 Shiyun Xiong <s.y.xiong...@gmail.com>: > Dear Christoph, > > Thanks for your suggestions and I am sorry for the late reply: I was > travelling last two weeks and were not able to try your suggestions. > > When running strings -a /path/to/libboost_program_options.so | grep GCC, I > got: > GCC_3.0 > GCC: (GNU) 4.4.7 20120313 (Red Hat 4.4.7-11) > GCC: (GNU) 6.1.0 > _Unwind_Resume@@GCC_3.0 > Does this means my boost is not installed by gcc-6.1? I don't why it shows > several versions of gcc. Even when I compile the boost with ./bootstrap.sh > --with-toolset=gcc, ./b2 --toolset=gcc-6.1.0, I got the same information. It seems like it is build with gcc-6.1, I guess.
> > Also, you recommended me to install boost in another directory, but in this > case, votca can not find the boost package even when I specified the path of > boost header files and libraries as I mention before. Do you have any ideas > on why this happens? It depends on your cmake version how to override the Boost search path, look for the documentation in the FindBoost.cmake coming with your cmake installation. The latest version uses BOOSTROOT or BOOST_ROOT: <https://gitlab.kitware.com/cmake/cmake/blob/master/Modules/FindBoost.cmake#L42> I am not 100% sure if these are cmake variables or just environment variables. As an alternative you could use CMAKE_PREFIX_PATH as well! > > The spack option has also been tried, while I also did not success to > install votca-csg. The corresponding on screen information and log files are > attached. Besides, it seems votca-ctp is not involved in spack (I tried to > append votca-ctp after the commend but it says it can not find the votca-ctp > package), while this is actually the one I needed. I can add votca-ctp to spack as well if needed. Any how you got hit by <https://github.com/votca/csg/issues/209> again: To overcome this install the development version using spack: $ spack install votca-csg@develop votca-tools@develop Christoph > > Your further help is greatly appreciated. > Best regards, > Shiyun > > > 在 2017年5月28日星期日 UTC+8上午5:24:27，Christoph Junghans写道： >> >> 2017-05-26 21:02 GMT-06:00 Shiyun Xiong <s.y.xi...@gmail.com>: >> > Dear Christoph, >> > >> > Thanks a lot for providing the solutions. >> > For the first point of using the system gcc and boost: my system gcc >> > (/usr/bin/gcc) version is 4.4.7 released in 2012, hence it is rather >> > old. >> > Also, I can not find (I don't know) where is the system boost header >> > files >> > although I can find the system boost library is in the /usr/lib64/ fold. >> > Most importantly, as mentioned in my first post, when the boost paths >> > are >> > specified during the votca installation, it says can not find the >> > required >> > boost package. As a result, I haven't try this solution! >> Yes, gcc-4.4.7 would also not support C++11, gcc-4.8 is the first one >> supporting enough of it to compile VOTCA. >> > >> > The second method of using another boost version with the same gcc >> > compiler >> > as votca: I actually using the default gcc to compile both Boost and >> > Votca >> > (which gcc --> /usr/local/bin/gcc gcc --version --> gcc (GCC) 6.1.0). >> > So >> > I think the gcc used to compile both BOOST and votca is the same. Using >> > the >> > default gcc, I now installed the BOOST 1.62.0 version. However, the >> > "undefined reference" error still appears. For gcc 6.1, I checked it >> > support >> > the c++11 standard. >> Something seems broken here, if you are lucky >> $ strings -a /path/to/libboost_program_options.so | grep GCC >> will reveal to you, which gcc was used to compile boost. >> >> But I would try to recompile boost in another directory using gcc-6.1 >> >> I recently added votca to spack, so you might have a chance to install >> it that way: >> <https://github.com/votca/csg/wiki/Installing#spack> >> >> Christoph >> > >> > For the third one: my system is Centos, it seems there is not votca >> > install. >> > >> > Best Regards, >> > Shiyun >> > >> > >> > 在 2017年5月27日星期六 UTC+8上午12:22:32，Christoph Junghans写道： >> >> >> >> 2017-05-26 4:23 GMT-06:00 Shiyun Xiong <s.y.xi...@gmail.com>: >> >> > Dear Christoph, >> >> > >> >> > I have install the latest BOOST version 1.64.0. However, I have >> >> > encountered >> >> > other errors: 'Make_array' is not a member of 'boost::serialization'. >> >> Yup, boost 1.64.0 has a bug (see here: >> >> <https://svn.boost.org/trac/boost/ticket/12516>), which has nothing to >> >> do with VOTCA. 1.64 is very new release and hence not very well >> >> tested. >> >> >> >> > In fact, I have used this version of BOOST at the beginning and this >> >> > error >> >> > occured. Denis suggested me to downgrade my boost version and I found >> >> > from >> >> > the votca website that 1.53 is a recommanded version. That's why I >> >> > used >> >> > 1.53 >> >> Ok, let me try to clarify. VOTCA works pretty much works with any gcc >> >> and boost version (except may the above mentioned boost-1.64.0). >> >> >> >> However, VOTCA (from version 1.4on ) uses C++-11 features and hence >> >> depends on C++-11 ABI. Unfortunately, <=gcc-4.9, gcc-5* and >=gcc-6 >> >> have 3 different C++-11 ABIs and hence you will get the "undefined >> >> reference" error from above when trying to link VOTCA against a boost, >> >> which was built with a different C++-11 ABI. >> >> >> >> There are multiple solutions to that issue: >> >> 1.) Use the system (NOT /usr/local) gcc and boost - usually the Linux >> >> distributions get their thing together nicely. >> >> 2.) Use a (non-buggy) boost version, which is compiled with SAME >> >> compiler as you are compiling VOTCA with. >> >> 3.) If you don't need the development version of VOTCA, just use the >> >> package, which comes with your linux distributions - OpenSuse, Fedora, >> >> Debian, Ubuntu have VOTCA packages. See >> >> <https://github.com/votca/csg/wiki/Installing> >> >> >> >> Christoph >> >> >> >> > >> >> > Attached are the on screen information and cmake error information. >> >> > Please >> >> > check it. Thank you so much! >> >> > >> >> > Best regards, >> >> > Shiyun >> >> > >> >> > >> >> > 在 2017年5月24日星期三 UTC+8下午9:53:25，Christoph Junghans写道： >> >> >> >> >> >> 2017-05-24 2:00 GMT-06:00 Bensen-zjg Zhang <zhang...@gmail.com>: >> >> >> > Dear VOTCA developers and users, >> >> >> > >> >> >> > >> >> >> > I am trying to install the VOTCA software with build.sh on Centos >> >> >> > system >> >> >> > but >> >> >> > encountered some errors. Before install votca, I have installed >> >> >> > all >> >> >> > the >> >> >> > dependencies: Boost, Git, GSL, FFTW3, EXPAT, PkgConfig, SQLITE3, >> >> >> > Doxygen, >> >> >> > Gromacs. The gcc version is 6.1.0 and the current boost version is >> >> >> > 1.53.0. >> >> >> > The installation command I used is: >> >> >> > >> >> >> > ./build.sh --prefix /usr/local/votca/ >> >> >> > -DFFTW3_INCLUDE_DIR=/usr/local/fftw_shared/include/ >> >> >> > -DFFTW3_LIBRARY=/usr/local/fftw_shared/lib/libfftw3.so --dev tools >> >> >> > csg >> >> >> > kmc >> >> >> > moo ctp ctp-tutorials ctp-manual >> >> >> > >> >> >> > With this building command, I got the following error information: >> >> >> > /usr/local/lib/libboost_program_options.so: undefined reference to >> >> >> > `std::__cxx11::basic_string<char, std::char_traits<char>, >> >> >> > std::allocator<char> >::~basic_string()@GLIBCXX_3.4.21' >> >> >> Errors like these usually mean your boost has been compiled with an >> >> >> older (ABI-incompatible) version of gcc. >> >> >> (I am guessing so, as you are using gcc-6.1 which relatively recent, >> >> >> while boost-1.53 is actually more than 4 years old.) >> >> >> >> >> >> See the troubleshooting block of >> >> >> >> >> >> >> >> >> >> >> >> https://gcc.gnu.org/onlinedocs/gcc-5.2.0/libstdc++/manual/manual/using_dual_abi.html >> >> >> for details. >> >> >> >> >> >> Just install a newer version of boost using your gcc-6.1 and have >> >> >> VOTCA compile against that one. >> >> >> >> >> >> Christoph >> >> >> >> >> >> >> >> >> >> >> >> > /usr/local/lib/libboost_program_options.so: undefined reference to >> >> >> > `std::logic_error::logic_error(std::__cxx11::basic_string<char, >> >> >> > std::char_traits<char>, std::allocator<char> > >> >> >> > const&)@GLIBCXX_3.4.21' >> >> >> > /usr/local/lib/libboost_program_options.so: undefined reference to >> >> >> > `std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, >> >> >> > std::allocator<wchar_t> >::~basic_string()@GLIBCXX_3.4.21' >> >> >> > /usr/local/lib/libboost_program_options.so: undefined reference to >> >> >> > `operator >> >> >> > delete(void*, unsigned long)@CXXABI_1.3.9' >> >> >> > /usr/local/lib/libboost_program_options.so: undefined reference to >> >> >> > `std::__cxx11::basic_string<char, std::char_traits<char>, >> >> >> > std::allocator<char> >::_M_replace(unsigned long, unsigned long, >> >> >> > char >> >> >> > const*, unsigned long)@GLIBCXX_3.4.21' >> >> >> > /usr/local/lib/libboost_program_options.so: undefined reference to >> >> >> > `std::__cxx11::basic_string<char, std::char_traits<char>, >> >> >> > std::allocator<char> >::find(char const*, unsigned long, unsigned >> >> >> > long) >> >> >> > const@GLIBCXX_3.4.21' >> >> >> > /usr/local/lib/libboost_filesystem.so: undefined reference to >> >> >> > `std::__cxx11::basic_string<char, std::char_traits<char>, >> >> >> > std::allocator<char> >::rfind(char, unsigned long) >> >> >> > const@GLIBCXX_3.4.21' >> >> >> > collect2: ld returned 1 exit status >> >> >> > make[2]: *** [src/tools/votca_property] Error 1 >> >> >> > make[1]: *** [src/tools/CMakeFiles/votca_property.dir/all] Error 2 >> >> >> > make: *** [all] Error 2 >> >> >> > >> >> >> > When searching from the previous discussions, I found that I may >> >> >> > need >> >> >> > to >> >> >> > specify the Boost path. As a result, I tried: >> >> >> > >> >> >> > ./build.sh --prefix /usr/local/votca/ >> >> >> > -DFFTW3_INCLUDE_DIR=/usr/local/fftw_shared/include/ >> >> >> > -DFFTW3_LIBRARY=/usr/local/fftw_shared/lib/libfftw3.so >> >> >> > -DBoost_INCLUDE_DIR=/usr/local/include/boost/ >> >> >> > >> >> >> > >> >> >> > >> >> >> > -DBoost_PROGRAM_OPTIONS_LIBRARY=/usr/local/lib/libboost_program_options.so >> >> >> > -DBoost_FILESYSTEM_LIBRARY=/usr/local/lib/libboost_filesystem.so >> >> >> > --dev >> >> >> > tools >> >> >> > csg kmc moo ctp ctp-tutorials ctp-manual >> >> >> > >> >> >> > >> >> >> > This time, votca can not find the boost package? I have no idea >> >> >> > why >> >> >> > it >> >> >> > can >> >> >> > not find boost since I have specified the path to it! >> >> >> > For more information, I have attached the entire on screen printed >> >> >> > information and the cmake error file. The file names with >> >> >> > "_noBoostPath" >> >> >> > correspond to the first building command (no boost path is >> >> >> > specified) >> >> >> > while >> >> >> > the file names with "_withBoostPath" correspond to the second >> >> >> > building >> >> >> > command. >> >> >> > >> >> >> > By the way, when using the second building command, votca find >> >> >> > both >> >> >> > GSL >> >> >> > and >> >> >> > MKL libraries, so I have also tried to disable the mkl library >> >> >> > with >> >> >> > -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON, but not change happens. >> >> >> > >> >> >> > Thank you very much for your kind help! >> >> >> > With best regards, >> >> >> > Shiyun >> >> >> > >> >> >> > -- >> >> >> > 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+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+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. 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