I have no experience in this, and I'm afraid cannot help. Is there some reason you are avoiding using the system Python? It's included in all Linux distros and would resolve all of these issues.
- Noel On 20 February 2013 14:57, Peter Maas <peter.m...@specs.net> wrote: > Hi Noel,**** > > ** ** > > I think (not sure) I got a bit further.**** > > I’ve build python manually using the –fPIC option, which was suggested by > Greg (RDKit) in this forum: **** > > http://comments.gmane.org/gmane.science.chemistry.rdkit.user/6**** > > ** ** > > I ran into an additional problem which was fixed by a patch :**** > > > http://stackoverflow.com/questions/12573787/why-i-failed-to-build-sqlite3-when-build-python > **** > > ** ** > > Now Python seems to be OK.**** > > Unfortunately I got an different error but on the same action (sharing > openbabel.so):**** > > **** > > Linking CXX shared module ../lib/_openbabel.so**** > > /usr/local/lib/python2.7/config/libpython2.7.a(posixmodule.o): In function > `posix_forkpty':**** > > /home/peter/downloads/Python-2.7.3/./Modules/posixmodule.c:3816: undefined > reference to `forkpty'**** > > /usr/local/lib/python2.7/config/libpython2.7.a(posixmodule.o): In function > `posix_openpty':**** > > /home/peter/downloads/Python-2.7.3/./Modules/posixmodule.c:3756: undefined > reference to `openpty'**** > > 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**** > > ** ** > > ** ** > > ** ** > > I could even found less info on this one. Any clue? Did I get further or > into more problems?**** > > ** ** > > Cheers,**** > > ** ** > > Peter**** > > ** ** > > ** ** > > *From:* Noel O'Boyle [mailto:baoille...@gmail.com] > *Sent:* Tuesday, February 19, 2013 3:21 PM > > *To:* Peter Maas > *Cc:* openbabel-discuss@lists.sourceforge.net > *Subject:* Re: [Open Babel] install on Centos 64 bits**** > > ** ** > > By define at the command-line, I meant -DPYTHON_LIBRARY=wherever when > running cmake.**** > > Don't worry about the eigen3 warning. If Eigen3 is found, it uses that in > preference to Eigen2.**** > > Just a note, to force a Python rebuild, use "touch > src/scripts/openbabel-python.i".**** > > ** ** > > If you use "VERBOSE=1 make" you will see the command-line used to compile > the Python bindings.**** > > If you still can't figure it out, please attach your CMakeCache.txt.**** > > ** ** > > - Noel**** > > ** ** > > ** ** > > On 19 February 2013 13:38, Peter Maas <peter.m...@specs.net> wrote:**** > > 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**** > > **** > > **** > > **** > > **** > > **** > > **** > > **** > > [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**** > > **** > > ** ** >
<<image001.jpg>>
<<image002.gif>>
------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb
_______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
