化学系统随机模拟的全流水线FPGA体系结构

David B. Thomas, H. Amano
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引用次数: 8

摘要

化学系统的模拟使生物化学家能够理解单个分子的相互作用如何导致细胞和生物体水平的行为。当分子浓度非常小时,需要在蒙特卡罗模拟中对每一个化学相互作用进行建模,这带来了巨大的计算负担。本文提出了一种新的全流水线的化学模拟体系结构,它避免了传统的优化最小操作次数的方法,而是优化了吞吐量和并行性。我们表明,尽管这导致每个模拟步骤的渐近操作计数更高,但它允许更大程度的空间和管道并行性,并且增加的面积被更大的吞吐量所抵消。新架构在Virtex-6 SX475T上实现,对于少于64个反应的问题,可以维持每秒超过10亿个反应的速率。与现有中小型化学模型上的化学模拟器相比,新架构比运行在8核3.4GHz Core i7上的商业软件模拟器快30-100倍,比现有最好的FPGA模拟器快12-30倍。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
A fully pipelined FPGA architecture for stochastic simulation of chemical systems
Simulation of chemical systems allows bio-chemists to understand how the interactions of individual molecules can lead to cellular and organism level behaviour. When the concentration of moleculesis very small, it is necessary to model every single chemical interaction in a Monte-Carlo simulation, presenting a huge computational burden. This paper presents a new fully pipelined architecture for chemical simulation, which avoids the traditional approach of optimising for minimum operation count, and instead optimises for throughput and parallelism. We show that even though this leads to a higher asymptotic operation count per simulation step, it allows for a much greater degree of spatial and pipeline parallelism, and the increased area is offset by much greater throughput. The new architecture is implemented in a Virtex-6 SX475T and can sustain a rate of over 1 billion reactions per second for problems with less than 64 reactions. Compared against existing chemical simulators on small to medium size chemical models, the new architecture is 30-100 times faster than a commercial software simulator running on an 8-core 3.4GHz Core i7, and 12-30 times faster than the best existing FPGA simulators.
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