Dear all,
I am having difficulties installing RDKIT on a Centos 5.6 (with python
bindings).
I compiled and installed the latest numpy, boost and cmake version from their
sources (I had also tried using
the versions available through "yum" - which are quite old compared to the most
up-to-date version). I updated
LD_LIBRARY_PATH to include the boost libraries and compiled RDKIT as mentioned
in the installation instruction,
which finishes without a single error. However, when I run "make test" I get a
lot of seg-faults (only with "py"thon
tests):
Start 1: testDict
1/76 Test #1: testDict ......................... Passed 0.00 sec
Start 2: testDataStructs
2/76 Test #2: testDataStructs .................. Passed 0.01 sec
Start 3: pyBV
3/76 Test #3: pyBV .............................***Exception: SegFault 0.02
sec
Start 4: pyDiscreteValueVect
4/76 Test #4: pyDiscreteValueVect ..............***Exception: SegFault 0.07
sec
Start 5: pySparseIntVect
5/76 Test #5: pySparseIntVect ..................***Exception: SegFault 0.02
sec
Start 6: testTransforms
6/76 Test #6: testTransforms ................... Passed 0.01 sec
Start 7: testGrid
7/76 Test #7: testGrid ......................... Passed 0.04 sec
..
..
.. one of the python tests pass:
Start 15: pyDistGeom
15/76 Test #15: pyDistGeom ....................... Passed 0.10 sec
and at test 44 - it basically freezes ("Start 44: pyPartialCharges"). If I
start python (2.4) and try to import rdkit
it crashes with a seg-fault, in python2.6 I get:
>>> from rdkit import Chem
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/dey/Downloads/RDKit_2012_06_1/rdkit/Chem/__init__.py", line 18,
in <module>
from rdkit import rdBase
ImportError: /usr/local/lib/libboost_python.so.1.50.0: undefined symbol:
Py_InitModule4
My gcc version is 4.1.2, I also tried compiling with a newer version of the gnu
compiler , which did not help either
(using -DCMAKE_C_COMPILER=gcc44 -DCMAKE_CXX_COMPILER=g++44 )
I am aware that people have reported similar issues, but in my case I was not
able to trace the problem back to
my installed cmake version - any tips would be greatly appreciated.
cheers
Fabian
ps: when issuing "cmake .. " I get
-- Found the following Boost libraries:
-- regex
but not python (although boost was configured and built with "./bootstrap.sh
--with-libraries=regex,python" could this be
an issue ??)
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