Use -lboost_python3 instead of -lboost_python for python3
When setting the python interpreter using the environment to /usr/bin/python3, the compiler flags are not set the more appropriate lboost_python3.
export PYTHON=/usr/bin/python3
./configure
The build it self appears happy, but on import python3 will exit with with a symbol lookup error:
symbol lookup error: /lib64/python3.4/site-packages/graph_tool/libgraph_tool_core.so: undefined symbol: _ZN5boost6python6detail11init_moduleER11PyModuleDefPFvvE
Compiling with the -lboost_python3 flags will produce a working build.