2014-05-21 6:13 GMT-06:00 Jan Michael Carrillo <[email protected]>: > Here is the clang version: > $ clang --version > Apple clang version 4.1 (tags/Apple/clang-421.11.66) (based on LLVM 3.1svn) > Target: x86_64-apple-darwin12.5.0 > Thread model: posix clang-3.1, I have tested that. However it seems the linker works different (different DSO policy)
> > I did "--do-update" and the installation went further than the previous one > and I get a new set of errors: > > Linking CXX shared library libvotca_csg.dylib > Undefined symbols for architecture x86_64: > "boost::system::system_category()", referenced from: > __GLOBAL__I_a in dlpolytopologyreader.cc.o > __GLOBAL__I_a in dlpolytrajectoryreader.cc.o > __GLOBAL__I_a in dlpolytrajectorywriter.cc.o > "boost::system::generic_category()", referenced from: > __GLOBAL__I_a in dlpolytopologyreader.cc.o > __GLOBAL__I_a in dlpolytrajectoryreader.cc.o > __GLOBAL__I_a in dlpolytrajectorywriter.cc.o > "boost::filesystem::path::parent_path() const", referenced from: > votca::csg::DLPOLYTopologyReader::ReadTopology(std::string, > votca::csg::Topology&) in dlpolytopologyreader.cc.o > votca::csg::DLPOLYTrajectoryReader::Open(std::string const&) in > dlpolytrajectoryreader.cc.o > votca::csg::DLPOLYTrajectoryWriter::Open(std::string, bool) in > dlpolytrajectorywriter.cc.o > "boost::filesystem::path::stem() const", referenced from: > votca::csg::DLPOLYTopologyReader::ReadTopology(std::string, > votca::csg::Topology&) in dlpolytopologyreader.cc.o > votca::csg::DLPOLYTrajectoryReader::Open(std::string const&) in > dlpolytrajectoryreader.cc.o > votca::csg::DLPOLYTrajectoryWriter::Open(std::string, bool) in > dlpolytrajectorywriter.cc.o > "boost::filesystem::path::extension() const", referenced from: > votca::csg::DLPOLYTrajectoryReader::Open(std::string const&) in > dlpolytrajectoryreader.cc.o > votca::csg::DLPOLYTrajectoryWriter::Open(std::string, bool) in > dlpolytrajectorywriter.cc.o > ld: symbol(s) not found for architecture x86_64 > clang: error: linker command failed with exit code 1 (use -v to see > invocation) > make[2]: *** [src/libcsg/libvotca_csg.3.dylib] Error 1 > make[1]: *** [src/libcsg/CMakeFiles/votca_csg.dir/all] Error 2 > make: *** [all] Error 2 I updated csg in the same way, have another go with "--do-update" Christoph > > > On Wednesday, May 21, 2014 12:01:54 AM UTC-4, Christoph Junghans wrote: >> >> 2014-05-20 13:46 GMT-06:00 Jan Michael Carrillo <[email protected]>: >> > otool -L /usr/local/lib/libboost_filesystem-mt.dylib >> > /usr/local/lib/libboost_filesystem-mt.dylib: >> > /usr/local/lib/libboost_filesystem-mt.dylib (compatibility version >> > 0.0.0, >> > current version 0.0.0) >> > /usr/local/lib/libboost_system-mt.dylib (compatibility version 0.0.0, >> > current version 0.0.0) >> > /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version >> > 56.0.0) >> > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version >> > 169.3.0) >> So obviously libboost_filesystem-mt.dylib loads libboost_system-mt.dylib. >> That is a bit confusing. >> >> Which version of clang is that? ($ clang --version) >> >> I pushed a change to the tools repository, maybe that one helps.(add >> "--do-update" to your build.sh command line to get it.) >> >> > >> > On Tuesday, May 20, 2014 3:37:48 PM UTC-4, Christoph Junghans wrote: >> >> >> >> 2014-05-20 12:22 GMT-06:00 Jan Michael Carrillo <[email protected]>: >> >> > Here it is: >> >> > >> >> > Boost_DIR:PATH=Boost_DIR-NOTFOUND >> >> > >> >> > >> >> > Boost_FILESYSTEM_LIBRARY:FILEPATH=/usr/local/lib/libboost_filesystem-mt.dylib >> >> Ok can you run >> >> $ otool -L /usr/local/lib/libboost_filesystem-mt.dylib >> >> and see if libboost_system-mt.dylib shows up. >> >> >> >> > >> >> > >> >> > Boost_FILESYSTEM_LIBRARY_DEBUG:FILEPATH=/usr/local/lib/libboost_filesystem-mt.dylib >> >> > >> >> > >> >> > Boost_FILESYSTEM_LIBRARY_RELEASE:FILEPATH=/usr/local/lib/libboost_filesystem-mt.dylib >> >> > Boost_INCLUDE_DIR:PATH=/usr/local/include >> >> > Boost_LIBRARY_DIRS:FILEPATH=/usr/local/lib >> >> > >> >> > >> >> > Boost_PROGRAM_OPTIONS_LIBRARY:FILEPATH=/usr/local/lib/libboost_program_options-mt.dylib >> >> > >> >> > >> >> > Boost_PROGRAM_OPTIONS_LIBRARY_DEBUG:FILEPATH=/usr/local/lib/libboost_program_options-mt.dylib >> >> > >> >> > >> >> > Boost_PROGRAM_OPTIONS_LIBRARY_RELEASE:FILEPATH=/usr/local/lib/libboost_program_options-mt.dylib >> >> > Boost_FILESYSTEM_FOUND:INTERNAL=ON >> >> > Boost_FILESYSTEM_LIBRARY-ADVANCED:INTERNAL=1 >> >> > Boost_FILESYSTEM_LIBRARY_DEBUG-ADVANCED:INTERNAL=1 >> >> > Boost_FILESYSTEM_LIBRARY_RELEASE-ADVANCED:INTERNAL=1 >> >> > Boost_INCLUDE_DIR-ADVANCED:INTERNAL=1 >> >> > Boost_LIBRARY_DIRS-ADVANCED:INTERNAL=1 >> >> > Boost_LIB_VERSION:INTERNAL=1_52 >> >> > Boost_PROGRAM_OPTIONS_FOUND:INTERNAL=ON >> >> > Boost_PROGRAM_OPTIONS_LIBRARY-ADVANCED:INTERNAL=1 >> >> > Boost_PROGRAM_OPTIONS_LIBRARY_DEBUG-ADVANCED:INTERNAL=1 >> >> > Boost_PROGRAM_OPTIONS_LIBRARY_RELEASE-ADVANCED:INTERNAL=1 >> >> > Boost_VERSION:INTERNAL=105200 >> >> > >> >> > Jan-Michael >> >> > >> >> > On Tuesday, May 20, 2014 2:14:40 PM UTC-4, Christoph Junghans wrote: >> >> >> >> >> >> 2014-05-20 11:50 GMT-06:00 Jan Michael Carrillo <[email protected]>: >> >> >> > Thanks for the speedy reply. >> >> >> > >> >> >> > My OS is OS X 10.8.5 >> >> >> > I got boost from Mac homebrew and its version is 1.52.0 >> >> >> > I looked at the lib directory where boost was installed and it has >> >> >> > both >> >> >> > .dylib and .a >> >> >> Ok, can you do >> >> >> $grep -i ^Boost tools/CMakeCache.txt >> >> >> >> >> >> I just want to know if cmake uses .dylib or .a >> >> >> >> >> >> Christoph >> >> >> >> >> >> > >> >> >> > Jan-Michael >> >> >> > >> >> >> > >> >> >> > On Tuesday, May 20, 2014 12:58:06 PM UTC-4, Christoph Junghans >> >> >> > wrote: >> >> >> >> >> >> >> >> Hi and welcome, >> >> >> >> >> >> >> >> 2014-05-20 10:40 GMT-06:00 Jan Michael Carrillo >> >> >> >> <[email protected]>: >> >> >> >> > Hi, >> >> >> >> > >> >> >> >> > I can easily install votca using this script: >> >> >> >> > >> >> >> >> > prefix=/Users/mydir/Installers/VOTCA >> >> >> >> > mkdir -p ${prefix}/src >> >> >> >> > cd ${prefix}/src >> >> >> >> > wget http://votca.googlecode.com/hg/build.sh >> >> >> >> > chmod +x build.sh >> >> >> >> > ./build.sh --prefix ${prefix} --minimal -DWITH_FFTW=ON >> >> >> >> > -DWITH_GSL=ON >> >> >> >> > tools >> >> >> >> > csg >> >> >> >> > >> >> >> >> > However, If I add the --dev option such that >> >> >> >> > ./build.sh --prefix ${prefix} --dev --minimal -DWITH_FFTW=ON >> >> >> >> > -DWITH_GSL=ON >> >> >> >> > tools csg >> >> >> >> > I get the error: >> >> >> >> > >> >> >> >> > Linking CXX shared library libvotca_tools.dylib >> >> >> >> > Undefined symbols for architecture x86_64: >> >> >> >> > "boost::system::system_category()", referenced from: >> >> >> >> > __GLOBAL__I_a in application.cc.o >> >> >> >> > "boost::system::generic_category()", referenced from: >> >> >> >> > __GLOBAL__I_a in application.cc.o >> >> >> >> > ld: symbol(s) not found for architecture x86_64 >> >> >> >> > clang: error: linker command failed with exit code 1 (use -v to >> >> >> >> > see >> >> >> >> > invocation) >> >> >> >> > make[2]: *** [src/libtools/libvotca_tools.3.dylib] Error 1 >> >> >> >> > make[1]: *** [src/libtools/CMakeFiles/votca_tools.dir/all] >> >> >> >> > Error 2 >> >> >> >> > make: *** [all] Error 2 >> >> >> >> Can you give us a bit more information? >> >> >> >> >> >> >> >> What version of boost is that? Is it static or shared (.a or >> >> >> >> .dylib >> >> >> >> files)? >> >> >> >> What operating system is that? >> >> >> >> >> >> >> >> VOTCA isn't using libboost_system, but I have the suspicion that >> >> >> >> it >> >> >> >> gets pulled in by libboost_filesystem. >> >> >> >> >> >> >> >> Christoph >> >> >> >> > >> >> >> >> > My goal is to use votca with LAMMPS. >> >> >> >> > >> >> >> >> > Thanks, >> >> >> >> > >> >> >> >> > Jan-Michael >> >> >> >> > >> >> >> >> > >> >> >> >> > -- >> >> >> >> > 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 http://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 http://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 http://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 http://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 http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. 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