Greg and JP,
For my own education, could this be related to having upgraded GCC through
the CentOS install instructions, but using the old Python? The new version
of RDKit would have been built with the newer GCC but the old Python may not
refer to the correct libraries?
Or am I mixing concepts here?
-Kirk
On Fri, Jun 10, 2011 at 1:30 PM, Greg Landrum <[email protected]>wrote:
> Hi
>
> On Friday, June 10, 2011, JP <[email protected]> wrote:
> > I am installing the brand new RDKit (2011_03_2) on CentOS (lol!) on a
> Friday evening (6.54pm here in Oxford)... So I probably deserve the misery
> of the following.
>
> Nobody deserves the misery of working with Centos. ;-)
>
> > I have already gone through the whole RDKit on Centos installation
> procedure and pain on other machines and I now am undaunted by it. Bring it
> on.
>
> Good attitude!
>
> >
> > Still I installed everything (almost) according to the book (
> http://code.google.com/p/rdkit/wiki/BuildingOnCentOS) with the exception
> that I stuck to Python 2.4.3 (Python 2.7, doesn't play nicely with Rocks)
> >
> >
> > And I get this anti-fancy error message
> >>>> from rdkit import ChemTraceback (most recent call last): File
> "<stdin>", line 1, in ?
> >
> > File "/share/apps/RDKit_2011_03_2/rdkit/Chem/__init__.py", line 18, in
> ? from rdkit import rdBaseImportError: /usr/lib64/libstdc++.so.6: version
> `GLIBCXX_3.4.9' not found (required by
> /share/apps/RDKit_2011_03_2/rdkit/rdBase.so)
>
> That is a glibc problem. It means that you are using something that
> has been built with a version of g++ that is more modern than the
> version of libstdc++ (I think) that is being found. You might want to
> google around a little bit for the error message in combination with
> centos and see what you can find. Believe it or not, this doesn't have
> much to do with the rdkit.
>
> -greg
>
> >
> >
> > Any ideas?
> > [jp@xxx build]$ echo
> $LD_LIBRARY_PATH/share/apps/RDKit_2011_03_2/lib:/share/apps/boost_1_46_1/lib:/opt/gridengine/lib/lx26-amd64:/share/apps/openbabel/lib:/usr/local/lib:/share/apps/openbabel/lib:
> >
> >
> > [jp@xxx build]$ echo $PYTHONPATH :/share/apps/RDKit_2011_03_2
> > [jp@xxx build]$ echo $RDBASE /share/apps/RDKit_2011_03_2
> >
> >
> > Any sympathy will be greatly appreciated.
> > CheersJP
> >
>
>
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