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With advances in reconfigurable hardware, especially field-programmable gate arrays (FPGAs), it has become possible to use reconfigurable hardware to accelerate complex applications, such as those in scientific computing. There has been a resulting development of reconfigurable computers--computers which have both general purpose processors and reconfigurable hardware, as well as memory and high-performance interconnection networks. In this paper, we describe the acceleration of molecular dynamics simulation with reconfigurable computers. We evaluate several design alternatives for the reconfigurable computer implementation. We show that a single node accelerated with reconfigurable hardware--utilizing fine-grained parallelism in the reconfigurable hardware design--is able to achieve a speed-up of about 2X over the corresponding software-only simulation. We then parallelize the application and study the effect of acceleration on performance and scalability. Specifically, we study strong scaling in which the problem size is fixed. We find that the unaccelerated version actually scales better because it spends more time in computation than the accelerated version does. However, we also find that a cluster of P accelerated nodes gives better performance than a cluster of 2P unaccelerated nodes.
Reconfigurable hardware, Distributed architectures, Physics, Chemistry

V. K. Prasanna, F. Trouw, M. B. Gokhale and R. Scrofano, "Accelerating Molecular Dynamics Simulations with Reconfigurable Computers," in IEEE Transactions on Parallel & Distributed Systems, vol. 19, no. , pp. 764-778, 2007.
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