Hi Noel,
Thanks for your suggestion. I checked the variables in CMakeCache.txt and all are pointing to the right (system) Python. If set the parameters as environmental setting and redid everything but the same error comes up. I'm not sure what you mean by "define them at the command-line" Do you mean at the cmake command line or the make command line. Something else I noticed. The documentation says you need to install eigen2. CMake give this warning (while I've eigen2 in the command line): Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) So should I install Eigen3 as well? Thanks, Peter From: Noel O'Boyle [mailto:baoille...@gmail.com] Sent: Monday, February 18, 2013 12:26 PM To: Peter Maas Cc: openbabel-discuss@lists.sourceforge.net Subject: Re: [Open Babel] install on Centos 64 bits 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 <http://www.specs.net/> Specs _____ Kluyverweg 6, 2629 HT Delft, The Netherlands p +31 15 2518139 f +31 15 2518181 <http://peter.m...@specs.net> 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. <http://thinkbeforeprinting.org/> http://thinkbeforeprinting.org/struct/signature-1.gif ---------------------------------------------------------------------------- -- 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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