I've seen this before. You should compile against the system Python. Your locally-compiled version was not compiled in a way consistent with linking against it (I don't know what options you should have used, but I recognise the symptoms).
To compile against the system Python, check your CMakeCache.txt for various Python related variables and define them at the command-line (something like PYTHON_INCLUDE, PYTHON_LIBRARY, PYTHON_EXECUTABLE). - Noel On 18 February 2013 10:52, Peter Maas <peter.m...@specs.net> wrote: > Dear All,**** > > ** ** > > I’m trying to install openbabel with python bindings on a 64 bits CentOS > release 5.9 (kernel 2.6.18-348.1.1.el5).**** > > ** ** > > I performed the following steps:**** > > (I also downloaded and unzipped the eigen2 package as shown in the cmake > line)**** > > ** ** > > tar zxf openbabel-2.3.2.tar.gz**** > > mkdir build**** > > cd build**** > > ** ** > > cmake ../openbabel-2.3.2 > -DEIGEN2_INCLUDE_DIR=/home/peter/lib/eigen-eigen-b23437e61a07 > -DPYTHON_BINDINGS=ON -DCMAKE_INSTALL_PREFIX=/home/peter/tools/openbabel > -DCMAKE_BUILD_TYPE=DEBUG**** > > ** ** > > make**** > > ** ** > > ** ** > > Now I’m getting an error which I can’t seem to fix:**** > > ** ** > > Linking CXX shared module ../lib/_openbabel.so**** > > /usr/bin/ld: /usr/local/lib/python2.6/config/libpython2.6.a(abstract.o): > relocation R_X86_64_32 against `a local symbol' can not be used when making > a shared object; recompile with -fPIC**** > > /usr/local/lib/python2.6/config/libpython2.6.a: could not read symbols: > Bad value**** > > collect2: ld returned 1 exit status**** > > make[2]: *** [lib/_openbabel.so] Error 1**** > > make[1]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2**** > > make: *** [all] Error 2**** > > ** ** > > Any suggestion would be appreciated.**** > > ** ** > > Thanks,**** > > ** ** > > Peter Maas**** > > ** ** > > ** ** > > ** ** > > ** ** > > ** ** > > ** ** > > ** ** > > [image: Specs] <http://www.specs.net/>**** > ------------------------------ > > Kluyverweg 6, 2629 HT Delft, The Netherlands *p* +31 15 2518139 *f* > +31 15 2518181 peter.m...@specs.net**** > > ** ** > > This message may contain privileged/confidential information and may be > subject to legal privilege. Access to this e-mail by anyone other than the > intended is unauthorised. If you have received this message in error, > please notify us and remove it from your system and note that you must not > copy, distribute or take any action in reliance on it. Unauthorized use or > disclosure of the contents of this message is not permitted and may be > unlawful. Specs/Compound Handling B.V. cannot accept responsibility for any > loss or damage arising from the use of this e-mail or its attachments.**** > > ** ** > > [image: > http://thinkbeforeprinting.org/struct/signature-1.gif]<http://thinkbeforeprinting.org/> > **** > > ** ** > > ** ** > > > ------------------------------------------------------------------------------ > The Go Parallel Website, sponsored by Intel - in partnership with Geeknet, > is your hub for all things parallel software development, from weekly > thought > leadership blogs to news, videos, case studies, tutorials, tech docs, > whitepapers, evaluation guides, and opinion stories. Check out the most > recent posts - join the conversation now. > http://goparallel.sourceforge.net/ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > >
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