Thanks a lot Christoph, everything just worked correctly. Best Regards, Shiyun
在 2017年6月21日星期三 UTC+8上午4:44:40，Christoph Junghans写道： > > 2017-06-20 11:08 GMT-06:00 Christoph Junghans <[email protected] > <javascript:>>: > > 2017-06-19 19:15 GMT-06:00 Shiyun Xiong <[email protected] > <javascript:>>: > >> 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 <[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] <javascript:>. > >> To post to this group, send email to [email protected] > <javascript:>. > >> 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 [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.
