Yeah, ours was a fluid dynamics problem that needed information from neighboring cells. So at some point there needed to be data moving between cells and that really killed performance. There was also a global value that need to be computed at each iteration that controlled the simulation speed to ensure the step sizes were not too big.

Also the file I/O was horribly slow. We where scaling and dumping raw data to files so what we could do post processing to make movies of the simulations.