On Thu, Aug 30, 2012 at 12:30 PM, Felix Krüger <[email protected]> wrote: > Thanks Greg.... > > On 30/08/2012 10:54, Greg Landrum wrote: >> Can you please do: >> ldd $RDBASE/rdkit/rdBase.so >> from within the same shell where you ran ctest and make sure that it's >> actually finding your python library and the boost libraries you >> built? > > The output here looks good, among others I find > libpython2.6.so.1.0 => /my/path/libpython2.6.so.1.0 > libboost_python.so.1.47.0 => /my/path/libboost_python.so.1.47.0 > (libboost_regex is not listed, but seems to be fine?)
Yes, that looks good. > >> The next tests are, from within that shell, to try the following: >> python -c 'from rdkit import rdBase' >> python -c 'from rdkit import Chem' > > This is interesting! The first command generates no output, the second > gives me the segmentation fault... So it's a problem with the numpy > version! Do you think there is any way to fix this without recompiling > python? It was convenient to use this system-wide version. Maybe it's > time to set up my own... You shouldn't need to rebuild it. This type of segfault normally comes about because you've linked against a different version of numpy than the one that you're currently using. When you ran cmake, it reported a location for numpy. You can see this via: grep -i numpy $RDBASE/build/CMakeCache.txt Make sure that version looks right and that it's the one you're actually using. You can check which one is being used like this: python -c 'import numpy;print numpy.__file__' Here's the output on one of the linux systems where I regularly build the RDKit : cix1:/scratch > grep -i numpy $RDBASE/build/CMakeCache.txt PYTHON_NUMPY_INCLUDE_PATH:PATH=/usr/prog/python/2.6.6_gnu/lib/python2.6/site-packages/numpy/core/include //Python numpy development package is available PYTHON_NUMPY_FOUND:INTERNAL=1 cix1:/scratch > python -c 'import numpy;print numpy.__file__' /usr/prog/python/2.6.6_gnu/lib/python2.6/site-packages/numpy/__init__.pyc notice how the .pyc file is in the same directory tree as the include directory. hopefully you'll notice some inconsistency here that can be fixed via your PYTHONPATH. out of curiousity: which version of redhat are you using? -greg ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
