Multithreaded programming is not for the feint of heart. That being said you're using a program which does not support multiple cores. Simulation scripting is very different from a compiled language (e.g. C) where a programmer can use libraries (pthreads, openmp, openmpi, etc) to multi-thread and manage the threads. Since threaded programming is outside of the scope of your question I'll skip that as it doesn't apply here.
Looking at the Geant 4 website you provided I gather the program is currently single threaded. However, their planned features for 2013
state multi-threading (i.e. using multiple cores) is a goal. You'll have to contact the original developers to find out more information about it as I've just gleaned this from their website after a quick viewing.