Hi Christoph,
That worked, thanks. Now ccmake ends without a problem. But make process
terminates with:
/[ 67%] Building CXX object
src/libcsg/CMakeFiles/votca_csg.dir/modules/io/xmltopologyreader.cc.o/
/Linking CXX static library libvotca_csg.a/
/[ 67%] Built target votca_csg/
/Scanning dependencies of target csg_density/
/[ 69%] Building CXX object
src/tools/CMakeFiles/csg_density.dir/csg_density.cc.o/
/Linking CXX executable csg_density/
//home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.a(property.cc.o):
In function
`votca::tools::load_property_from_xml(votca::tools::Property&,
std::basic_string<char, std::char_traits<char>, std::allocator<char>
>)':/
/property.cc:(.text+0x10e): undefined reference to `XML_ParserCreate'/
/property.cc:(.text+0x127): undefined reference to
`XML_UseParserAsHandlerArg'/
/property.cc:(.text+0x144): undefined reference to
`XML_SetElementHandler'/
/property.cc:(.text+0x151): undefined reference to
`XML_SetCharacterDataHandler'/
/property.cc:(.text+0x4db): undefined reference to `XML_SetUserData'/
/property.cc:(.text+0x563): undefined reference to `XML_Parse'/
/property.cc:(.text+0x648): undefined reference to `XML_GetErrorCode'/
/property.cc:(.text+0x64f): undefined reference to `XML_ErrorString'/
/property.cc:(.text+0x65a): undefined reference to
`XML_GetCurrentLineNumber'/
//home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.a(parsexml.cc.o):
In function `votca::tools::ParseXML::Open(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)':/
/parsexml.cc:(.text+0x1fc): undefined reference to `XML_ParserCreate'/
/parsexml.cc:(.text+0x215): undefined reference to
`XML_UseParserAsHandlerArg'/
/parsexml.cc:(.text+0x232): undefined reference to
`XML_SetElementHandler'/
/parsexml.cc:(.text+0x31b): undefined reference to `XML_SetUserData'/
/parsexml.cc:(.text+0x3c3): undefined reference to `XML_Parse'/
/parsexml.cc:(.text+0x46c): undefined reference to `XML_GetErrorCode'/
/parsexml.cc:(.text+0x473): undefined reference to `XML_ErrorString'/
/parsexml.cc:(.text+0x480): undefined reference to
`XML_GetCurrentLineNumber'/
/collect2: ld returned 1 exit status/
/make[2]: *** [src/tools/csg_density] Error 1/
/make[1]: *** [src/tools/CMakeFiles/csg_density.dir/all] Error 2/
/make: *** [all] Error 2/
What may cause this problem? I thought maybe it has something to do with
static vs. shared so I tried an installation with turning the shared
library on.
When I try to build csg using the command:
/ccmake
-DFFTW3_INCLUDE_DIR=/home/cdalgicdir/progs/fftw-3.2.2-votca/include
-DFFTW3_LIBRARY=/home/cdalgicdir/progs/fftw-3.2.2-votca/lib/libfftw3.so
-DGSL_INCLUDE_DIR=/home/cdalgicdir/progs/gsl-1.14/include
-DGSL_LIBRARY=/home/cdalgicdir/progs/gsl-1.14/lib/libgsl.so
-DCBLAS_LIBRARY=/home/cdalgicdir/progs/gsl-1.14/lib/libgslcblas.so
-DCMAKE_INSTALL_PREFIX=/home/cdalgicdir/progs/votca/votca-1.2/
-DBoost_INCLUDE_DIR=/home/cdalgicdir/progs/boost-1.46.1/include/
-DBoost_LIBRARY=/home/cdalgicdir/progs/boost-1.46.1/lib/libboost_filesystem.so
-DBoost_PROGRAM_OPTIONS_LIBRARY=/home/cdalgicdir/progs/boost-1.46.1/lib/libboost_program_options.so
-DWITH_SQLITE3=OFF -DGMX_INCLUDE_DIR=$HOME/progs/gromacs-4.5.3/include
-DGMX_LIBRARY="$HOME/progs/gromacs-4.5.3/lib/libgmx.a;/usr/lib64/libpthread.so;/usr/lib64/libdl.so;/usr/lib64/libm.so"
*-DVOTCA_TOOLS_LIBRARY='/home/cdalgicdir/progs/gsl-1.14/lib/libgsl.so;/home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so;/home/cdalgicdir/progs/gsl-1.14/lib/libgslcblas.so;/usr/lib64/libm.so;/home/cdalgicdir/progs/fftw-3.2.2-votca/lib/libfftw3.so.3;/home/cdalgicdir/progs/gromacs-4.5.3/lib/libgmx.a'*
./
I get,
Error output:
/
/
/CMake Error at CMakeModules/FindVOTCA_TOOLS.cmake:61 (message):/
/ Could not find votca::tools::ToolsVersionStr in/
/
/home/cdalgicdir/progs/gsl-1.14/lib/libgsl.so;/home/cdalgicdir/progs/votca/votca-1./
/
2/lib/libvotca_tools.so;/home/cdalgicdir/progs/gsl-1.14/lib/libgslcblas.so;/usr/lib/
/
64/libm.so;/home/cdalgicdir/progs/fftw-3.2.2-votca/lib/libfftw3.so.3;/home/cdalgicd/
/ ir/progs/gromacs-4.5.3/lib/libgmx.a,/
/ take look at the error message in/
/
/home/cdalgicdir/progs/tars/votca-csg-1.2/CMakeFiles/CMakeError.log
to find/
/ out what was going wrong. If you don't have pkg-config
installed you will/
/ most likely have to set VOTCA_TOOLS_LIBRARY by hand and include
all it's/
/ deps in there (i.e./
/
-DVOTCA_TOOLS_LIBRARY='/path/to/libvotca_tools.so;/path/to/libgsl.so;/path/to/libm./
/ so')/
/ !/
/ Call Stack (most recent call first):/
/ CMakeLists.txt:67 (find_package)/
Error log:
/Determining if the function ToolsVersionStr exists in the
/home/cdalgicdir/progs/gsl-1.14/lib/libgsl.so;/home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so;/home/cdalgicdir/progs/gsl-1.14/lib/libgslcblas.so;/usr/lib64/libm.so;/home/cdalgicdir/progs/fftw-3.2.2-votca/lib/libfftw3.so.3;/home/cdalgicdir/progs/gromacs-4.5.3/lib/libgmx.a
failed with the following output:/
/Change Dir:
/home/cdalgicdir/progs/tars/votca-csg-1.2/CMakeFiles/CMakeTmp/
/Run Build Command:/usr/bin/gmake "cmTryCompileExec/fast"/
//usr/bin/gmake -f CMakeFiles/cmTryCompileExec.dir/build.make
CMakeFiles/cmTryCompileExec.dir/build/
/gmake[1]: Entering directory
`/home/cdalgicdir/progs/tars/votca-csg-1.2/CMakeFiles/CMakeTmp'/
//home/cdalgicdir/progs/cmake-2.8.4/bin/cmake -E
cmake_progress_report
/home/cdalgicdir/progs/tars/votca-csg-1.2/CMakeFiles/CMakeTmp/CMakeFiles
1/
/Building CXX object
CMakeFiles/cmTryCompileExec.dir/TestVotcaToolsVersion.cxx.o/
//usr/bin/c++ -DCHECK_FUNCTION_EXISTS=ToolsVersionStr -o
CMakeFiles/cmTryCompileExec.dir/TestVotcaToolsVersion.cxx.o -c
/home/cdalgicdir/progs/tars/votca-csg-1.2/CMakeModules/TestVotcaToolsVersion.cxx/
/Linking CXX executable cmTryCompileExec/
//home/cdalgicdir/progs/cmake-2.8.4/bin/cmake -E cmake_link_script
CMakeFiles/cmTryCompileExec.dir/link.txt --verbose=1/
//usr/bin/c++ -DCHECK_FUNCTION_EXISTS=ToolsVersionStr
CMakeFiles/cmTryCompileExec.dir/TestVotcaToolsVersion.cxx.o -o
cmTryCompileExec -rdynamic
/home/cdalgicdir/progs/gsl-1.14/lib/libgsl.so
/home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so
/home/cdalgicdir/progs/gsl-1.14/lib/libgslcblas.so -lm
/home/cdalgicdir/progs/fftw-3.2.2-votca/lib/libfftw3.so.3
/home/cdalgicdir/progs/gromacs-4.5.3/lib/libgmx.a
-Wl,-rpath,/home/cdalgicdir/progs/gsl-1.14/lib:/home/cdalgicdir/progs/votca/votca-1.2/lib
/
//usr/bin/ld: warning: libboost_program_options.so.1.46.1, needed by
/home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so, not
found (try using -rpath or -rpath-link)/
//home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so:
undefined reference to
`boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::basic_string<char,
std::char_traits<char>, std::allocator<char> >,
std::basic_string<char, std::char_traits<char>, std::allocator<char>
> >, std::basic_string<char, std::char_traits<char>,
std::allocator<char> > const&>)'/
//home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so:
undefined reference to
`boost::program_options::variables_map::variables_map()'/
//home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so:
undefined reference to
`boost::program_options::options_description::add_options()'/
//home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so:
undefined reference to
`boost::program_options::detail::cmdline::cmdline(std::vector<std::basic_string<char,
std::char_traits<char>, std::allocator<char> >,
std::allocator<std::basic_string<char, std::char_traits<char>,
std::allocator<char> > > > const&)'/
//home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so:
undefined reference to
`boost::program_options::store(boost::program_options::basic_parsed_options<char>
const&, boost::program_options::variables_map&, bool)'/
//home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so:
undefined reference to
`boost::program_options::detail::cmdline::set_options_description(boost::program_options::options_description
const&)'/
//home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so:
undefined reference to
`boost::program_options::options_description::m_default_line_length'/
//home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so:
undefined reference to
`boost::program_options::detail::cmdline::style(int)'/
//home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so:
undefined reference to `boost::program_options::detail::cmdline::run()'/
//home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so:
undefined reference to
`boost::program_options::options_description::options_description(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&, unsigned int,
unsigned int)'/
//home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so:
undefined reference to
`boost::program_options::to_internal(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)'/
//home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so:
undefined reference to
`boost::program_options::operator<<(std::basic_ostream<char,
std::char_traits<char> >&,
boost::program_options::options_description const&)'/
//home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so:
undefined reference to
`boost::program_options::options_description_easy_init::operator()(char
const*, char const*)'/
//home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so:
undefined reference to
`boost::program_options::options_description::add(boost::program_options::options_description
const&)'/
//home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so:
undefined reference to
`boost::program_options::options_description::options_description(unsigned
int, unsigned int)'/
//home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so:
undefined reference to
`boost::program_options::notify(boost::program_options::variables_map&)'/
//home/cdalgicdir/progs/votca/votca-1.2/lib/libvotca_tools.so:
undefined reference to `vtable for
boost::program_options::variables_map'/
/collect2: ld returned 1 exit status/
/gmake[1]: *** [cmTryCompileExec] Error 1/
/gmake[1]: Leaving directory
`/home/cdalgicdir/progs/tars/votca-csg-1.2/CMakeFiles/CMakeTmp'/
/gmake: *** [cmTryCompileExec/fast] Error 2/
Any ideas?
Thanks,
Cahit
On 07/01/2011 01:15 PM, Christoph Junghans wrote:
However libgmx also depends on libpthread and libdl, but libpthread
and libdl don't show up in the output of pkg-config (run pkg-config
--libs libgmx). That is why the undefined reference appear. So this is
actually a bug in gromacs autotools build system.
To workaround that issue, just add libpthread and libdl by hand to
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