Parallel coprocessor architectures for molecular dynamics simulation: a case study in design space exploration

The purpose of the paper is to describe a new semi-automated design space exploration method based on genetic programming. A new control/dataflow specification method is proposed as well as appropriate models for hardware parts and algorithms. With this method we are able to test many different hardware architectures and algorithms against cost, speed, computation time and other constraints within a very short time. The remaining manual work is to exploit the model parameters of the components of the architecture and the algorithm. In contrast to other approaches our method is suited for embedded and distributed systems. The method, models and application are explained in detail by means of a comprehensive case study.