Igor,I am very happy to hear that the script is helpful. And, yes, installation on CentOS 5.5 is a pain. The problem actually resides in the fact that the major CentOS and RHEL releases are very dated once they are released. GCC is my biggest complaint as the standard version on the current CentOS is known to have a major bug that causes the Boost compile and therefore RDKit compile to fail. I believe that the new RHEL 6 is somewhat better - based on Fedora 12 and 13 - and the upcoming CentOS 6 will obviously be better as well. Unfortunately, this is what we have to work with. Alternatively, I have also installed RDKit on Fedora 14 with no need for any updates to any other package. One step and I was done. The good news is that future releases of RDKit should go somewhat painlessly. I was able to install the current beta package by simply compiling the RDKit code. After 2 minutes of hands on time, 15 minutes of waiting, and RDKit was up and running.
If you run into any problems, please post them so that we can (hopefully) help and others can benefit in the future.
-Kirk On Jan 6, 2011 10:11am, "Igor Filippov [Contr]" <[email protected]> wrote:
Dear Kirk,
Thank you so much! I'm in the process of compiling gcc-4.5.1 right now,
having got gmp, mpc, and mpfr built with the older version of gcc.
Your instructions have to be preserved for the others, I can't believe
I'm the only one using CentOs/RHEL on a server/compute node.
Greg, don't take it as a slam but compiling the Linux kernel is a walk
in a park compared to a recent RDkit. I'm working on it second day and
I'm barely half-way through the process of installing dependencies. Even
without python the version of gcc which comes with CentOs 5 (4.1.2)
cannot compile RDKit.
On the other hand the RPM packages for Fedora have been painless to
install, how nice it would be to have the RDKit RPMs for CentOs!
Best,
Igor
On Wed, 2011-01-05 at 17:41 -0500, Robert DeLisle wrote:
> I have been able to reproducibly build RDKit on CentOS 5.5, but it
> required a significant amount of updating of the build components.
> The attached walk-through script should get you there. I do not
> recall ever seeing that particular error, however.
>
> -Kirk
>
>
>
>
> On Wed, Jan 5, 2011 at 1:15 PM, Igor Filippov [Contr]
> [email protected]> wrote:
> Dear All,
>
> Has anyone successfully compiled RDKit on CentOs 5? I'm
> running into the
> following error message:
> [ 15%] Building CXX object
>
> Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o
>
> /root/RDKit_2010_09_1/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:14:31: error: numpy/arrayobject.h: No such file or directory
>
> On CentOs 5 arrayobject.h is part of python-numeric package
> and it's
> located in:
> /usr/include/python2.4/Numeric/arrayobject.h
>
> I'm attempting to compile RDKit_2010_09_1, using boost version
> 1.39.0,
> x86_64 system.
>
> Regards,
> Igor
>
>
>
>
>
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