The acceleration of molecular dynamics (MD) simulations using high-performance reconfigurable computing (HPRC) has been much studied. Given the intense competition from multicore and GPUs, there is now a question whether MD on HPRC can be competitive. We concentrate here on the MD kernel computation: determining the short-range force between particle pairs. In one part of the study, we systematically explore the design space of the force pipeline with respect to arithmetic algorithm, arithmetic mode, precision, and various other optimizations. We examine simplifications and find that some have little effect on simulation quality. In the other part, we present the first FPGA study of the filtering of particle pairs with nearly zero mutual force, a standard optimization in MD codes. There are several innovations, including a novel partitioning of the particle space, and new methods for filtering and mapping work onto the pipelines. As a consequence, highly efficient filtering can be implemented with only a small fraction of the FPGA’s resources. Overall, we find that, for an Altera Stratix-III EP3ES260, 8 force pipelines running at nearly 200 MHz can fit on the FPGA, and that they can perform at 95% efficiency. This results in an 80-fold per core speed-up for the short-range force, which is likely to make FPGAs highly competitive for MD.

中文翻译：

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高性能可重构计算系统的分子动力学模拟

使用高性能可重构计算 (HPRC) 加速分子动力学 (MD) 模拟已得到大量研究。鉴于来自多核和 GPU 的激烈竞争，现在存在一个问题，即 HPRC 上的 MD 是否具有竞争力。我们在这里专注于 MD 核计算：确定粒子对之间的短程力。在研究的一部分中，我们从算术算法、算术模式、精度和其他各种优化方面系统地探索了力管道的设计空间。我们检查了简化，发现有些简化对模拟质量影响不大。在另一部分中，我们介绍了第一个 FPGA 研究，即过滤具有几乎为零的互力的粒子对，这是 MD 代码中的标准优化。有几项创新，包括粒子空间的新分区，以及用于过滤和映射工作到管道上的新方法。因此，只需 FPGA 资源的一小部分就可以实现高效滤波。总的来说，我们发现，对于 Altera Stratix-III EP3ES260，运行在近 200 MHz 的 8 个强制流水线可以安装在 FPGA 上，并且它们可以以 95% 的效率运行。这导致短程力的每个内核加速了 80 倍，这很可能使 FPGA 对 MD 具有很强的竞争力。并且它们可以以 95% 的效率运行。这导致短程力的每个内核加速了 80 倍，这很可能使 FPGA 对 MD 具有很强的竞争力。并且它们可以以 95% 的效率运行。这导致短程力的每个内核加速了 80 倍，这很可能使 FPGA 对 MD 具有很强的竞争力。