PNNL

Abstract

Long timescale Molecular Dynamics (MD) simulation of small molecules is crucial in drug design and basic science. To accelerate a small data set that is executed for a large number of iterations, high-efficiency is crucial. Recent work has demonstrated that among COTS devices only FPGA-centric clusters can scale beyond a few processors for relevant targets. The problem addressed here is that, as the number of on-chip processors has increased from fewer than 10 into hundreds, previous routing solutions are no longer viable. We find, however, that through various design innovations maintaining high efficiency can be maintained. These include replacing the previous broadcast networks with ring-routing and then augmenting the rings with out-of-order and caching mechanisms. Others are adding a level of hierarchical filtering and memory recycling. Two novel optimized architectures emerge, together with a number of variations. These are validated, analyzed, and evaluated. We find that in the domain of interest speed-ups over GPUs are achieved. The potential impact is that this system promises to be the basis for long timescale MD with a commodity cluster.