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.
Simply said, though Hadoop may solve your problem here, its not the right tool for your purpose.
I see a number of answers here that basically are saying, "no, you shouldn't use Hadoop for simulations because it wasn't built for simulations." I believe this is a rather short sighted view and would be akin to someone saying in 1985, "you can't use a PC for word processing, PCs are for spreadsheets!"
Hadoop is a fantastic framework for construction of a simulation engine. I've been using it for this purpose for months and have had great success with small data / large computation problems. Here's the top 5 reasons I migrated to Hadoop for simulation (using R as my language for simulations, btw):
While you might be able to get by using MapReduce with Hadoop, it seems like what you're doing might be better suited for a grid/job scheduler such as Condor or Sun Grid Engine. Hadoop is more suited for doing something where you take a single (very large) input, split it into chunks for your worker machines to process, and then reduce it to produce an output.
Since you are already using Java, I suggest taking a look at GridGain which, I think, is particularly well suited to your problem.