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Towards production FPGA-accelerated molecular dynamics: Progress and challenges

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2 Author(s)
Matt Chiu ; Computer Architecture and Automated Design Laboratory, Department of Electrical and Computer Engineering, Boston University; Boston, MA 02215 ; Martin C. Herbordt

Recent work in the FPGA acceleration of molecular dynamics simulation has shown that including on-the-fly neighbor list calculation (particle filtering) in the device has the potential for an 80× per core speed-up over the CPU-based reference code and so to make the approach competitive with other computing technologies. In this paper we report on progress and challenges in advancing this work towards the creation of a production system, especially one capable of running on a large-scale system such as the Novo-G. The current version consists of an FPGA-accelerated NAMD-lite running on a PC with a Gidel PROCStar III. The most important implementation issues include software integration, handling exclusion, and modifying the force pipeline. In the last of these we have added support for Particle-Mesh-Ewald and augmented the Lennard-Jones calculation with a switching function. In experiments, we find that energy stability so far appears to be acceptable, but that longer simulations are needed. Due primarily to the added complexity of the force pipelines, performance is somewhat diminished from the previous study; we find, however, that porting to a newer (existing) device will more than compensate for this loss.

Published in:

2010 FOURTH INTERNATIONAL WORKSHOP ON HIGH-PERFORMANCE RECONFIGURABLE COMPUTING TECHNOLOGY AND APPLICATIONS (HPRCTA)

Date of Conference:

14-14 Nov. 2010