have written a stochastic simulation in Java, which loads data from a few CSV files on disk (totaling about 100MB) and writes results to another output file (not much data, just
Hadoop can be made to perform your simulation if you already have a Hadoop cluster, but it's not the best tool for the kind of application you are describing. Hadoop is built to make working on big data possible, and you don't have big data -- you have big computation.
I like Gearman (http://gearman.org/) for this sort of thing.