An FPGA Implementation of High Throughput Stochastic Simulator for Large-Scale Biochemical Systems
An FPGA Implementation of High Throughput Stochastic Simulator for Large-Scale Biochemical Systems
复制标题
大规模生化系统高通量随机模拟器的 FPGA 实现
DOI：
10.1109/fpl.2006.311218
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发表时间：
2006
期刊：
影响因子：
--
通讯作者：
H. Amano
中科院分区：
文献类型：
--
作者：
Masato Yoshimi;Yasunori Osana;Y. Iwaoka;Yuri Nishikawa;Toshinori Kojima;Akira Funahashi;N. Hiroi;Yuichiro Shibata;Naoki Iwanaga;H. Kitano;H. Amano
生化系统的随机模拟已经成为将生命过程作为系统研究的主要手段之一，但由于其巨大的计算代价，模拟的进行是一个计算挑战。本文介绍了一种称为“第一反应法”的随机模拟算法在基于现场可编程门阵列的生化模拟器上的实现和评价。它通过(1)连续地将数据投放到深度流水线浮点运算单元中，以及(2)通过分布多个用于并行执行的模拟器来实现高吞吐量。在一个基于FPGA的仿真平台Rec-SiP2上的测试结果表明，即使在大规模生化系统中，该仿真器的性能也比在至强2.80 GHz上执行的性能高出约80倍
Stochastic simulation of biochemical systems has become one of major approaches to study life processes as system, yet is a computational challenge to run the simulation due to its vast calculation cost. This paper shows the implementation and evaluation of a stochastic simulation algorithm (SSA) called "first reaction method" on an FPGA-based biochemical simulator. It achieves high throughput by (1) consecutively throwing data into deeply-pipelined floating point arithmetic units, and (2) by distributing multiple simulators for parallel execution. As the result of evaluation on an FPGA-based simulation platform called ReC-SiP2, the simulator outperforms execution on Xeon 2.80 GHz by approximately 80 times, even with large-scale biochemical systems
影响因子：
5.8
作者：
Takahashi, K;Kaizu, K;Tomita, M
通讯作者：
Tomita, M