Hi Peter,
in case you really didn't want to use the python version originally
provided by your distribution, make sure that the version you are using was
configured at build time with --enable-shared (I think this is the likely
reason for the error you reported). You might also want to consider the
python26 package that is available from the EPEL repositories.
Best regards,
Riccardo
>
> On 19 February 2013 16:16, Peter Maas <peter.m...@specs.net> wrote:
>
>> Hi Noel,****
>>
>> ** **
>>
>> Then I did the right thing. I also checked whether the files python files
>> exists. Hell, I even reinstalled python which is kind of tricky because a
>> lot of tools are depending on it. ****
>>
>> Anyway, I’m getting the same results. It feels like a defeat but if you
>> would be so kind to take a look at the file I appreciate it very much.
>> Please find it attached.****
>>
>> ** **
>>
>> Thanks,****
>>
>> ** **
>>
>> 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/>****
>> ------------------------------
>>
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>> +31 15 2518181 peter.m...@specs.net****
>>
>> ****
>>
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>>
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