I apologize for that doulbe post before - itchy send finger.
Here's the specific error I'm getting after the build process has otherwise
succeded.
>>> from rdkit import Chem
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/opt/RDKit_svn_20101115/rdkit/Chem/__init__.py", line 18, in
<module>
from rdkit import rdBase
ImportError: /usr/lib64/libboost_python.so.2: undefined symbol:
Py_InitModule4
On Tue, Nov 16, 2010 at 3:04 PM, Robert DeLisle <[email protected]> wrote:
>
>
> ---------- Forwarded message ----------
> From: Robert DeLisle <[email protected]>
> Date: Tue, Nov 16, 2010 at 3:03 PM
> Subject: Re: Re: [Rdkit-discuss] Building RDKit on CentOS 5
> To: Greg Landrum <[email protected]>, Robert DeLisle <
> [email protected]>
>
>
> 'm sorry for the slow response. Busy day.
>
> For this install, I started on a CentOS 5.5 system that was up to date with
> all package upgrades. Following is what I've done so far:
>
> installed blas, blas-devel, lapack, lapack-devel through yum
>
> I had problems in the past with the standard GCC package on CentOS which is
> version 4.1.2, so I rebuilt the GCC 4.4.5 package and included mpfr 2.4.1
>
> Installed cmake 2.8.2
> Installed flex 2.5.35
>
> CentOS's Python installation is v2.4.1, so I built and installed 2.7. Due
> to errors found later in the process, I built this with the -fPIC switch and
> also enabled Unicode UCS4 support
>
> ./configure CFLAGS=-fPIC --enable-unicode=ucs4
>
> Built and installed NumPy 1.5.0
>
> Boost on CentOS 5.5 is v1.33, so I built and installed boost 1.44 with the
> following commands:
>
> ./bootstrap.sh --with-libraries=python,regex
> ./bjam address-model=64 install
>
>
> Finally, with RDKit I have $LD_LIBRARY_PATH set with /usr/local/lib first
> to avoid conflicts with the system packages. GCC and Python are both in
> /usr/local and these are the instances referred to by my user and root. For
> RDKit, the following commands were done:
>
> cmake -DBoost_USE_STATIC_LIBS=OFF -DBOOST_ROOT=/usr/local ..
> make
> make install
>
>
>
> I have also installed FreeType2 and PIL - both seem fine with Python 2.7.
> I attempted aggdraw, but the self-test seem to always give me a Segmentation
> Fault. I found that I can build aggdraw using the code as-is as long as I
> include CFLAGS="-fpermissive", or there is a one line code change that makes
> the compiler happy on 64-bit. Either way I still get the seg fault upon
> testing.
>
>
> Regarding RDKit, the first group of errors I received consisted of that
> requiring Python be built with -fPIC and what seems to be the typical
> USE_STATIC_LIBS error.
>
> Initially, an -fPIC error would occur around 87% which was not cured by the
> Python rebuild or any other modification. I found that by switching to the
> SVN code, the problem was solved. Upon inspecting the errors logs, it
> appeared that the build process was always referring to the system Boost
> install and not my new install despite having set -DBOOST_ROOT correctly.
>
> Currently, the build goes to completion but upon issuing 'from rdkit import
> Chem' wihtin Python 2.7, I get an error related to Py_InitModule4 not being
> defined. From a little Google searching for Py_InitModule4 the only thing
> I've seen thus far is a conflict in various packages on code built on 32-bit
> or 64-bit systems. It seems that this name has been renamed to
> Py_InitModule4_64 on 64-bit systems but that change may not be reflected in
> all code necessary. It seemed a widespread problem and not specific to any
> one application or library, which makes me think it is something in a Python
> include file.
>
> I appreciate any help that anyone can provide. Please let me know if I
> need to clarify or add any details.
>
> -Kirk
>
>
>
>
>
>
> On Mon, Nov 15, 2010 at 10:11 PM, <[email protected]> wrote:
>
>> No, I made sure to include the address-model=64 switch to bjam.
>>
>> Tomorrow when I get in I'll update the thread with all the steps I've
>> followed.
>>
>> -Kirk
>>
>>
>>
>>
>> On Nov 15, 2010 9:52pm, Greg Landrum <[email protected]> wrote:
>> > Kirk,
>> >
>> >
>> >
>> > On Tue, Nov 16, 2010 at 12:38 AM, Robert DeLisle [email protected]>
>> wrote:
>> >
>> > > Yes, that is also true.
>> >
>> > >
>> >
>> > > The error in my most recent messages stems from the default build of
>> Python
>> >
>> > > supporst Unicode UCS2, but apparently boost expects UCS4. A rebuild
>> of
>> >
>> > > Python with UCS4 enabled fixed that problem.
>> >
>> > >
>> >
>> > > Now I get a similar error related to Py_InitModule4 not being
>> defined. From
>> >
>> > > what I can find, this is a 32-bit - 64-bit problem in which this was
>> defined
>> >
>> > > as Py_InitModule4_64 in the 64-bit Python libraries but that change
>> may not
>> >
>> > > have cascaded to all necessary parts of the build process. Most of
>> the
>> >
>> > > changes involve some substantial changes to the accessing code, but
>> I'm
>> >
>> > > still looking for a better option.
>> >
>> >
>> >
>> > Could it be that the boost libraries you are using were not built in
>> >
>> > 64bit mode? I've managed to force a 64bit build in the past with the
>> >
>> > following command line:
>> >
>> > ./bjam address-model=64 cflags=-fPIC cxxflags=-fPIC install
>> >
>> >
>> >
>> > Best Regards,
>> >
>> > -greg
>> >
>>
>
>
>
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