Communication Requirements for FPGA-Centric Molecular Dynamics

FPGA-centric clusters use FPGAs for both computation and communication and thereby address three fundamental problems of future High Performance Clusters: efficient use of silicon, power, and removing communication bottlenecks. In this study we report on the plausibility of using such clusters for Molecular Dynamics simulations, in particular by determining the communication requirements for such a cluster. We begin by reviewing MD on a single FPGA-based node and use that performance to determine the time budget for the communication. We then characterize the data communication characteristics for a production MD code (NAMD) in two ways: analytically and by instrumenting the code. We apply this information to clusters of various sizes and node complexity. The conclusion is that a cluster with 256 FPGAs distributed in 64 nodes is appropriately provisioned, even for modest simulations, with a bidirectional 3D torus where each link consists of 1-2 of an FPGAs serial ports. Keywords-High Performance Reconfigurable Computing; Molecular Dynamics; FPGA-Centric Compute Clusters