Are you sure that your NumPy installation is going to the correct Python
instance? I see from the logs that you have Python 2.7 installed, or at
least that is what cmake is finding at /usr/local/lib. You use yum to
install NumPy, but the standard installation of Python on CentOS 5.x is 2.4
and it is located in /usr/lib. Which version of Python has NumPy?
-Kirk
On Feb 22, 2011 9:14am, JP <jeanpaul.ebe...@inhibox.com> wrote:
I've installed Atlas, Numpy, Boostand everything works fine until I try:
cmake .. -DBOOST_ROOT=/share/apps/boost_1_45_0/
sudo make VERBOSE=1
At which point everything fails as follows::
[ 3%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o
cd /share/apps/RDKit_2010_12_1/build/Code/RDBoost && /usr/bin/c++
-DRDBoost_EXPORTS -O3 -DNDEBUG -fPIC -I/usr/local/include/python2.7
-I/usr/local/lib/python2.7/site-packages/numpy/core/include
-I/share/apps/boost_1_45_0/include -I/share/apps/RDKit_2010_12_1/Code
-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -o
CMakeFiles/RDBoost.dir/Wrap.cpp.o -c
/share/apps/RDKit_2010_12_1/Code/RDBoost/Wrap.cpp
Linking CXX shared library ../../lib/libRDBoost.so
cd /share/apps/RDKit_2010_12_1/build/Code/RDBoost && /usr/local/bin/cmake
-E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -O3 -DNDEBUG -shared -Wl,-soname,libRDBoost.so.1
-o ../../lib/libRDBoost.so.1.2010.12.1 CMakeFiles/RDBoost.dir/Wrap.cpp.o
-L/usr/local/lib/libpython2.7.a -L/share/apps/boost_1_45_0/lib
/usr/local/lib/libpython2.7.a
/share/apps/boost_1_45_0/lib/libboost_python.so
-Wl,-rpath,/usr/local/lib/libpython2.7.a:/share/apps/boost_1_45_0/lib:
/usr/bin/ld: /usr/local/lib/libpython2.7.a(exceptions.o): relocation
R_X86_64_32 against `_Py_NoneStruct' can not be used when making a shared
object; recompile with -fPIC
/usr/local/lib/libpython2.7.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[2]: *** [lib/libRDBoost.so.1.2010.12.1] Error 1
make[2]: Leaving directory `/share/apps/RDKit_2010_12_1/build'
make[1]: *** [Code/RDBoost/CMakeFiles/RDBoost.dir/all] Error 2
make[1]: Leaving directory `/share/apps/RDKit_2010_12_1/build'
make: *** [all] Error 2
Note that all env variables have been set:
[jpebe@caio build]$ echo $LD_LIBRARY_PATH
/share/apps/boost_1_45_0/lib:/share/apps/openbabel-2.3.0/lib:/usr/lib64/atlas/sse2:/share/apps/RDKit_2010_12_1/lib:/opt/gridengine/lib/lx26-amd64
Any ideas? I spent the whole day on this...
And its freaking me out...
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