2017-06-19 19:15 GMT-06:00 Shiyun Xiong <[email protected]>: > 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 > > 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. Oh, votca-csg should actually depend on a non-mpi version of gromacs, here is a fix: <https://github.com/LLNL/spack/pull/4556/commits/205e2a1fb8ef5eca3710a8381a58507a7035ef6d>
> > 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. Yeah, just use the path from "spack find -p votca-csg@develop". > > Could you also add votca-ctp and its corresponding packages to spack? maybe > also TXT2TAG as it is required in some packages in ctp. I add the votca-ctp in this pull request to spack: <https://github.com/LLNL/spack/pull/4556> Christoph > > 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. -- 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.
