Compilation was successful. Thanks! Jan-Michael
On Wednesday, May 21, 2014 10:57:17 AM UTC-4, Christoph Junghans wrote: > > 2014-05-21 6:13 GMT-06:00 Jan Michael Carrillo > <[email protected]<javascript:>>: > > > 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] <javascript:>. > > To post to this group, send email to [email protected]<javascript:>. > > > 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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