2017-06-20 11:08 GMT-06:00 Christoph Junghans <jungh...@votca.org>: > 2017-06-19 19:15 GMT-06:00 Shiyun Xiong <s.y.xiong...@gmail.com>: >> 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> It got merged, so just update your spack version and it should work!
Christoph > > 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 <s.y.xi...@gmail.com>: >>>> > 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 <s.y.xi...@gmail.com>: >>>> >> > 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 <s.y.xi...@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+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 -- 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.
