Hi all,
I am trying to compile RDKit using self-compiled cmake, Python, Boost
and numpy dependencies.
All seems to compile and install fine. However,
tiresias ~/autobuild/build-koala-like> python
Python 2.7 (r27:82500, Feb 1 2012, 09:30:41)
[GCC 4.6.1 20110908 (Red Hat 4.6.1-9)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from rdkit import Chem
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File
"/home/paule/autobuild/Linux-release-python/lib/python2.7/site-packages/rdkit/Chem/__init__.py",
line 18, in <module>
from rdkit import rdBase
ImportError: /usr/lib64/libboost_python-mt.so.1.46.0: undefined symbol:
PyUnicodeUCS4_FromEncodedObject
>>>
OK, So I guess that this is related to:
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found PythonLibs: /usr/lib64/libpython2.7.so
^^^^^^^^^^^^^^^^^^^^^^^^^^ This is not what I want.
-- Found PythonInterp:
/home/paule/autobuild/Linux-release-python/bin/python (found version "2.7")
-- Boost version: 1.48.0
-- Found the following Boost libraries:
-- python
Python Install directory
/home/paule/autobuild/Linux-release-python/lib/python2.7/site-packages
It is not clear to me how to tell RDKit's configuration step to use the
python libs that I have compiled.
CMakeCache.txt says:
//Path to a file.
Boost_INCLUDE_DIR:PATH=/home/paule/autobuild/Linux-release-python/include
//Boost library directory
Boost_LIBRARY_DIRS:FILEPATH=/usr/lib64
//The Boost PYTHON library
Boost_PYTHON_LIBRARY:FILEPATH=/usr/lib64/libboost_python-mt.so
//Boost python library (debug)
Boost_PYTHON_LIBRARY_DEBUG:FILEPATH=/usr/lib64/libboost_python-mt.so
//Boost python library (release)
Boost_PYTHON_LIBRARY_RELEASE:FILEPATH=/usr/lib64/libboost_python-mt.so
(etc) all pointing to /usr/lib64 versions...
It The RightWay to specify each of these things on the command line for
cmake?
I see in CMakeLists.txt, there is:
# pull in python:
find_package(PythonLibs)
But there my detective skills come to an end... I don't know what this
is doing.
RDBASE is /home/paule/autobuild/Linux-release-python
PYTHONPATH is $RDBASE
LD_LIBRARY_PATH is $RDBASE/lib
and my python libs are indeed in $RDBASE/lib
Thanks for your advice,
Paul.
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