Peter Luk's Blog

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()