I ended up not using yum to install Numpy - I installed it from source, which was only slightly painful.
>>> import platform; print platform.python_version() # /usr/local/lib/python2.7/platform.pyc matches /usr/local/lib/python2.7/platform.py import platform # precompiled from /usr/local/lib/python2.7/platform.pyc 2.7.0 >>> import numpy as N >>> a=N.random.randn(10, 10) >>> In /usr/lib64/ I can find some libpython2.4.so, libpython2.4.so.1.0 What should I do? On 22 February 2011 16:23, <[email protected]> wrote: > 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 <[email protected]> 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... > > > -- Jean-Paul Ebejer Early Stage Researcher InhibOx Ltd Pembroke House 36-37 Pembroke Street Oxford OX1 1BP UK (+44 / 0) 1865 262 034 This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. Any unauthorised dissemination or copying of this email or its attachments, and any use or disclosure of any information contained in them, is strictly prohibited and may be illegal. If you have received this email in error please notify the sender and delete all copies from your system. We and our group companies accept no liability or responsibility for personal emails or emails unconnected with our business. Internet communications including emails and access and use of web sites cannot be guaranteed to be secure or error free as information can be intercepted, corrupted, lost or arrive late. Furthermore, while we have taken steps to control the spread of viruses on our systems, we cannot guarantee that this email and any files transmitted with it are virus free. No liability is accepted for any errors, omissions, interceptions, corrupted mail, lost communications or late delivery arising as a result of receiving this message via the Internet or for any virus that may be contained in it.
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