Thanks for letting us know how things turned out; it is interesting, though
I guess not 100% surprising that the system python doesn't work.
In any case: it's good to know for the next time the question comes up.
Glad you have a working rdkit build now,
-greg
On Sunday, June 24, 2012, Leonardo Trabuco wrote:
> On Sat, Jun 23, 2012 at 5:39 AM, Greg Landrum
> <greg.land...@gmail.com<javascript:;>>
> wrote:
> > Based on what I've been able to find on the 'net, the error is typical
> > for a version mismatch between the python you're using and the one
> > that boost was linked against. You can check this with ldd;
> > % ldd
> /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/boost/lib/libboost_python.so.1.49.0
>
> $ ldd
> /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/boost/lib/libboost_py
> thon.so.1.49.0
> linux-vdso.so.1 => (0x00007fff4d9fd000)
> libutil.so.1 => /lib64/libutil.so.1 (0x00002b8a43957000)
> libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b8a43b5b000)
> libdl.so.2 => /lib64/libdl.so.2 (0x00002b8a43d76000)
> librt.so.1 => /lib64/librt.so.1 (0x00002b8a43f7a000)
> libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00002b8a44184000)
> libm.so.6 => /lib64/libm.so.6 (0x00002b8a44484000)
> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b8a44707000)
> libc.so.6 => /lib64/libc.so.6 (0x00002b8a44916000)
> /lib64/ld-linux-x86-64.so.2 (0x0000003b69600000)
>
> I doesn't seem to show a linked python library...
>
> > If it is using the wrong version of python, I'm afraid you'll have to
> > re-build boost. There's documentation here that describes how to
> > ensure the correct python version is being used:
> >
> http://www.boost.org/doc/libs/1_49_0/libs/python/doc/building.html#python-configuration-parameters
>
> I realized that I built boost with the default python version in the
> system (2.4), so I followed the instructions from the link you sent
> above and re-built boost with python 2.6. But after re-building RDKit
> I get the same errors as before, and there are not changes to the
> output of ldd above.
>
> > An aside: my successful (and easy) build of the RDKit on CenOS 5.7
> > used a self-installed version of python 2.7. It's documented here:
> > http://code.google.com/p/rdkit/wiki/BuildingOnCentOS57
>
> Finally, I gave up on trying to get it to work with python 2.6 and
> followed your instructions for building it with 2.7. All tests pass
> now. Having RDKit with python 2.7 is even better for me, since I'll be
> able to run my code with the same python version across different
> platforms.
>
> Thank you very much for the help!
>
> Best,
> Leo
>
> --
> Leonardo Trabuco, Postdoctoral fellow (Russell group)
> CellNetworks, University of Heidelberg, Germany
> http://www.russelllab.org/people/leo/
>
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