Discrete EventSimulation ofMolecular Dynamics withConfigurable Logic
Martin Herbordt · 2007
Molecular dynamics simulation basedon discrete eventsimulation (DMD)isemerging asan alternative totime-step driven molecular dynamics (MD).DMD usessimplified discretized models, en- abling simulations tobeadvanced byevent, witha resulting performance increase ofseveral orders ofmag- nitude. Evenso,DMD iscomputebound.More- over, unlike MD,causality issues makeDMD difficult toscale, withO( p)beingthebestsofarachieved. We findthatFPGAsareextremely wellsuited toac- celerating DMD. Thechaotic execution, whichresults inthere beingvirtually noprediction window, isover- comewithalongprocessing pipeline augmented with associative structures analogous tothose usedinCPU reorder buffers. Ourprimary result isamicroarchitec- tureforDMD thatprocesses events withathroughput equal toasmall multiple oftheFPGA'sclock, resulting inahundred-fold speed-up overserial implementations.