2017-06-12 6:46 GMT-06:00 Shiyun Xiong <s.y.xiong...@gmail.com>: > Dear Christoph, > > Thanks so much for your kind help. Sorry I still have problems. > When using the develop version, there is an error when installing the > openmpi package. It seems that the gcc version it used is not my default > version of 6.1.0 but 4.4.7. Even though I replace the /usr/bin/gcc with my > 6.1.0 version, the same thing happens. The on screen file and the log file > is attached. > > On the other hand, I am also trying to install votca in another cluster > (RedHat). I first installed gcc-6.3.0 and set it as the default gcc version. > However, when I use spack to intall votca, it also stoped on openmpi > installation again. But on this cluster, it says can not find the Fortran > compile! When installing gcc, I have enable the fortran language and also > linked gfortran to /usr/bin/gfortran. When using "gfortran --version" and > "gcc --version", it does appear the correct version I installed. I don't > know why this happens. I have also attached the on screen information as > onScreenInfo_Redhat.txt. The log file is empty so I did not attached it. If it fails building OpenMPI, that is really more a question for the spack mailing list: <https://groups.google.com/d/forum/spack> or its issue tracker: <https://github.com/LLNL/spack/issues>
Christoph > > THanks a lot. > Shiyun > > 在 2017年6月9日星期五 UTC+8下午10:59:47，Christoph Junghans写道： >> >> 2017-06-09 5:43 GMT-06:00 Shiyun Xiong <s.y.xi...@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+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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