Dear Christoph, The OpenMPI problem has been solved by adding the full path of gfortran to f77 and fc in the $HOME/.spack/linux/compilers.yaml file. See https://github.com/LLNL/spack/issues/3146 <https://www.google.com/url?q=https%3A%2F%2Fgithub.com%2FLLNL%2Fspack%2Fissues%2F3146&sa=D&sntz=1&usg=AFQjCNFA_wE3tOYwe8kYGaL8yJHSsRw6WQ>
I am now able to install votca-csg@develop and votca-tools@develop. However, during the installation of csg package, the program will produce an error by saying something like "can not find libgromacs_d.so". This is because spack installed gromacs with enabled mpi but without double precision, thus the library name is libgromacs_mpi.so. When copy or rename this file to libgromacs_d.so, I am able to install the package without errors. But I don't know if this will harm the usage of csg or not since the library is not a double precision version. If it does not, a better way (I guess) to solve this problem might be add in the source code to let the program find either libgromacs_d.so, libgromacs_mpi.so or libgromacs_mpi_d.so, corresponding to different gromac versions. Another point is that I am wondering if it is possible to specify the library path in spack in case we need to use the packages outside spack, something like the -DCMAKE_PREFIX_PATH in cmake. Could you also add votca-ctp and its corresponding packages to spack? maybe also TXT2TAG as it is required in some packages in ctp. Thanks a lot With best regards, Shiyun 在 2017年6月18日星期日 UTC+8下午6:19:44，Shiyun Xiong写道： > > Dear Christoph, > > I found a discussion on this issue in spack at: > https://github.com/LLNL/spack/issues/3146 > I am not familiar with the solutions provided and I posted a further > question below the discussion. > > Best regards, > Shiyun > > 在 2017年6月17日星期六 UTC+8上午1:09:00，Christoph Junghans写道： >> >> 2017-06-16 5:55 GMT-06:00 Shiyun Xiong <[email protected]>: >> > Dear Christoph, >> > >> > Thanks a lot for your kind help. Yes, it does not matter the usage of >> the >> > software without installing the manual. I was just curious for that. >> > With the quota for the two paths in DCMAKE_PREFIX_PATH, it indeed works >> > without appearing the warnings. >> > The bug of spack has been reported. >> Thanks, can you also report the openmpi issue on Centos7. >> >> Thanks, >> >> Christoph >> > >> > Thanks again for the help! >> > >> > With best regards, >> > Shiyun >> > >> > 在 2017年6月15日星期四 UTC+8下午11:23:14，Christoph Junghans写道： >> >> >> >> 2017-06-15 6:50 GMT-06:00 Shiyun Xiong <[email protected]>: >> >> > Dear Christoph, >> >> > >> >> > Thanks a lot for you kind help. >> >> > >> >> > After many tryings, I am now able to install votca with build.sh >> except >> >> > the >> >> > manual. >> >> > So the problem should caused by the old versions of many softwares >> on >> >> > Centos >> >> > system. First I uninstalled gcc4.4.7 and deleted all files related >> to >> >> > all >> >> > gcc versions except 6.1.0. The binutils, fftw and cmake packages are >> >> > also >> >> > reinstalled with the latest version (important for gromacs). >> >> > Although votca is successfully installed, there are still several >> points >> >> > I >> >> > am not clear: >> >> > i) When installing the ctp-manual, an error "txt2tags wrote >> >> > /home/xiong/votca/ctp-manual/reference/programs/kmc_ru.tex >> >> > txt2tags: Error: Cannot read file: ctp_tools.t2t" >> >> That is a question for votca-ctp mailing list, but honestly you don't >> >> really need the manual to use ctp. >> >> And older version can be found in files section of: >> >> <http://www.votca.org/Documentation/charge-transport> >> >> >> >> > >> >> > ii) When install votca with the command >> >> > ./build.sh --prefix /usr/local/votca/ --dev tools csg kmc moo ctp >> >> > ctp-tutorials -DFFTW3_INCLUDE_DIR=/usr/local/fftw_shared/include/ >> >> > -DFFTW3_LIBRARY=/usr/local/fftw_shared/lib/libfftw3.so >> >> > -DGROMACS_INCLUDE_DIR=/usr/local/gromacs/include/ >> >> > -DGROMACS_LIBRARY=/usr/local/gromacs/lib64/libgromacs_mpi_d.so >> >> > it successfully compiled but gave a warning: >> >> > Manually-specified variables were not used by the >> >> > project: >> >> > FFTW3_INCLUDE_DIR >> >> > FFTW3_LIBRARY >> >> > GROMACS_INCLUDE_DIR >> >> > GROMACS_LIBRARY >> >> Well, FFTW3 variable are only needed to build tools and GROMACS >> >> variables are only needed to build csg. >> >> So, when building kmc moo ctp this warning will show up. >> >> You could build tools first and then csg and then the rest to avoid >> >> the warnings. >> >> >> >> > if I change the command to >> >> > ./build.sh --prefix /usr/local/votca/ --dev tools csg kmc moo ctp >> >> > ctp-tutorials >> >> > -DCMAKE_PREFIX_PATH=/usr/local/fftw_shared;/usr/local/gromacs/ >> >> I guess you forgot quotes around the two paths: >> >> ./build.sh --prefix /usr/local/votca/ --dev tools csg kmc moo ctp >> >> ctp-tutorials >> >> -DCMAKE_PREFIX_PATH="/usr/local/fftw_shared;/usr/local/gromacs/" >> >> >> >> > >> >> > It says "Could NOT find GROMACS (missing: GROMACS_LIBRARY >> >> > GROMACS_INCLUDE_DIR GROMACS_VERSION)" >> >> > but if I use the command: ./build.sh --prefix /usr/local/votca/ >> --dev >> >> > tools >> >> > csg kmc moo ctp ctp-tutorials >> -DCMAKE_PREFIX_PATH=/usr/local/fftw_shared >> >> > -DGROMACS_INCLUDE_DIR=/usr/local/gromacs/include/ >> >> > -DGROMACS_LIBRARY=/usr/local/gromacs/lib64/libgromacs_mpi_d.so >> >> > >> >> > the fftw problem can be solved but gromacs is still not used. >> >> > >> >> > iii) When using spack to install votca, it seems we need the GitHub >> >> > account >> >> > and passport of votca! >> >> No that is not true, votca is pull from the >> https://github.com/votca/tools >> >> (see >> >> >> >> < >> https://github.com/LLNL/spack/blob/develop/var/spack/repos/builtin/packages/votca-tools/package.py#L39>) >> >> >> >> which can be used anonymously (without an Github account). >> >> Again, this seems to be a bug in Spack, which you should report here: >> >> https://github.com/LLNL/spack/issues >> >> >> >> Honestly, if Votca-1.4 is enough for you, do: >> >> <https://github.com/votca/csg/wiki/Installing#centos-7> >> >> and install only votca-ctp and moo on top of it using build.sh. >> >> >> >> Christoph >> >> > >> >> > Thanks a lot >> >> > Best regards, >> >> > Shiyun >> >> > >> >> > >> >> > >> >> > 在 2017年6月13日星期二 UTC+8下午10:29:26，Christoph Junghans写道： >> >> >> >> >> >> 2017-06-12 6:46 GMT-06:00 Shiyun Xiong <[email protected]>: >> >> >> > 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 <[email protected]>: >> >> >> >> > 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 <[email protected]>: >> >> >> >> >> >> > 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 < >> [email protected]>: >> >> >> >> >> >> > 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 >> >> >> >> >> >> >> <[email protected]>: >> >> >> >> >> >> >> > 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 [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. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> >> >> 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. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> >> 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. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> 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. >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> 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. >> >> >> >> >> >> >> >> -- >> >> 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. >> >> >> >> -- >> 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.
