FPGA-based supercomputing: an implementation for molecular dynamics

Current high-performance supercomputing applications are typically implemented on large-scale general-purpose distributed or multiprocessing systems often based on commodity microprocessors. FPGAs have now reached a level of sophistication that they too could be used for such applications. We explore the feasibility of using FPGAs to implement large-scale application-specific computations by way of a case study that implements a novel Molecular Dynamics system. The system has been designed such that it is scalable and parallelizable. On the Transmogrifier 3, the system performs calculations on an 8,192 particle system in 37 seconds at 26MHz. This implementation shows that by scaling to more modern parts running at 100MHz and using a better architecture, a speedup of over 20x can be achieved compared to a state-of-the-art microprocessor. This can also be achieved at less cost, using less power and taking less space than a standard microprocessor-based system, while maintaining the computational precision required.