This was proved to be a very difficult task since a lot of tools were required to be re-compiled for the custom built python. I documented the sequence of tools required to be re-built below :
All the newly compiled binaries/headers/libraries will be set to put in /opt/local
1. Compile python 2.7.2 with shared library enabled.
./configure --prefix=/opt/local --enable-shared
2. Setup environment variables
edit ~/.bashrc export PATH=/opt/local/bin:$PATH export LD_LIBRARY_PATH=/opt/local/lib:$LD_LIBRARY_PATH export PYTHONPATH=/opt/local/lib/python2.7/site-packages:$PYTHONPATH
3. Compile LAPACK
(make sure fortran compiler is installed) wget http://www.netlib.org/lapack/lapack.tgz tar xzvf lapack.tgz cp -vf make.inc.example make.inc vi make.inc # OPTS = -O2 -fPIC -m64 # NOOPT = -O0 -fPIC -m64 #the -m64 flags build 64-bit code (nothing for 32bit) cd ~/src/lapack-3.4.0/SRC make lib cp libtmglib.a /opt/local/lib cp liblapack.a /opt/local/lib
4. Compile ATLAS
wget http://sourceforge.net/projects/math-atlas/files/Stable/3.8.2/atlas3.8.2.tar.gz tar zxvf atlas3.8.2.tar.gz mkdir ATLAS_BUILD cd ATLAS_BUILD /usr/bin/cpufreq-selector -g performance (turn off CPU Throttling for CentOS) /root/src/ATLAS/configure -Fa alg -fPIC --prefix=/opt/local \ --with-netlib-lapack=/opt/local/lib/liblapack.a make make check make ptcheck make time make install cd lib make shared make ptshared cp -vf *.so *.a /opt/local/lib
5. numpy
wget http://voxel.dl.sourceforge.net/sourceforge/numpy/numpy-1.6.1.tar.gz tar xzvf numpy-1.6.1.tar.gz cd ~/src/numpy-1.6.1 rm -rvf build cp -vf site.cfg.example site.cfg vi site.cfg [DEFAULT] library_dirs = /opt/local/lib include_dirs = /opt/local/include [blas_opt] libraries = ptf77blas, ptcblas, atlas [lapack_opt] libraries = lapack, ptf77blas, ptcblas, atlas python setup.py build --fcompiler=gnu95 python setup.py install --prefix=/opt/local # verify install (cd ~/ && python -c "import numpy; \ assert numpy.dot.__module__ == 'numpy.core._dotblas'; \ from numpy.linalg import lapack_lite")
6. scipy
wget http://voxel.dl.sourceforge.net/sourceforge/scipy/scipy-0.10.1.tar.gz tar xzvf scipy-0.10.1.tar.gz rm -rvf build python setup.py build python setup.py install --prefix=/opt/local # verify install (cd ~/ && python -c "from scipy import linalg")
7. boost library (we need boost library 1.42 as required by graph tool later)
get boost 1.42 from http://www.boost.org/users/history/version_1_42_0.html edit bootstrap.sh PREFIX=/opt/local EPREFIX= LIBDIR=/opt/local/lib INCLUDEDIR= LIBS="" PYTHON=/opt/local/bin/python ./bootstrap.sh ./bjam ./bjam install --prefix=/opt/local (move/remove the system boost header in /usr/include to make sure the later package will find and use the updated boost header and libraries)
8. CGAL
get CGAL from here cmake . -DCMAKE_INSTALL_PREFIX=/opt/local -DBUILD_SHARED_LIBS=TRUE \ -DCGAL_CXX_FLAGS=-I/opt/local/include \ -DCGAL_SHARED_LINKER_FLAGS=-L/opt/local/lib make make install
9. graph-tool (require gcc 4.2 or above and boost 1.42 or above)
get graph-tool from here export CFLAGS=-I/opt/local/include export CPPFLAGS=-I/opt/local/include export CXXFLAGS=-I/opt/local/include export LDFLAGS=-L/opt/local/lib export CC=gcc44 (centos 5 only) export CXX=g++44 (centos 5 only) ./configure --prefix=/opt/local --with-boost=/opt/local make (this require around 100min. for Core 2 Quad Q9400 2.66hz 4GB RAM computer) make install
10. Compile a custom swig for graphviz-python, otherwise the compile of graphviz will fail later
get swig source from http://www.swig.org/download.html export CFLAGS=-I/opt/local/include export CPPFLAGS=-I/opt/local/include export CXXFLAGS=-I/opt/local/include export LDFLAGS=-L/opt/local/lib ./configure --prefix=/opt/local make make install
11. Compile graphviz to get the graphviz-python (gv) module for our custom built python. It is needed by graph-tool
get graphviz source from http://www.graphviz.org/Download_source.php export CFLAGS=-I/opt/local/include export CPPFLAGS=-I/opt/local/include export CXXFLAGS=-I/opt/local/include export LDFLAGS=-L/opt/local/lib ./configure --prefix=/opt/local --enable-shared --enable-python=yes --enable-php=no \ --enable-tcl=no --enable-perl=no make make install
12. python-igraph
wget http://switch.dl.sourceforge.net/sourceforge/igraph/igraph-0.5.4.tar.gz wget http://pypi.python.org/packages/source/p/python-igraph/python-igraph-0.5.4.tar.gz tar xzf python-igraph-0.5.4.tar.gz tar xzf igraph-0.5.4.tar.gz cd igraph-0.5.4 export CPPFLAGS=-I/opt/local/include export CXXFLAGS=-I/opt/local/include export LDFLAGS=-L/opt/local/lib ./configure --prefix=/opt/local make make install cd python-igraph-0.5.4 python setup.py install
13. Compile pycairo [optional for some function of python-igraph]
make sure cairo and cairo-devel packages are installed get pycairo-1.2.2.tar.gz from http://cairographics.org/releases/ (Pls note that if you get a newer version of pycairo which require a newer rversion of cairo library, you may need to recompile the cairo library from source) ./configure --prefix=/opt/local make make install
14. fix graph-tool cannot find gvc library when it’s installed in a non-standard location
edit /opt/local/lib/python2.7/site-packages/graph_tool /draw/__init__.py
#libname = ctypes.util.find_library("gvc")
#if libname is None:
# raise OSError()
libgv = ctypes.CDLL("libgvc.so")
# libgv = ctypes.CDLL(libname)
Reference : https://projects.skewed.de/graph-tool/ticket/100
16. Compile matplotlib
Get the source from http://matplotlib.sourceforge.net/ python setup.py build python setup.py install
17. test code
#!/opt/local/bin/python from igraph import * g = Graph.Kautz(m=3, n=2) adj = g.get_adjacency() fig = Plot(bbox=(480, 480)) fig.add(g, layout="fr", vertex_label=None) fig.add(adj, bbox=(360, 0, 480, 120), grid_width=0, opacity=0.7) fig.show()
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