Paper Abstract and Keywords |
Presentation |
2007-11-22 13:25
Evaluation of a Data-Driven Architecture for a Stochastic Biochemical Simulator on an FPGA Masato Yoshimi, Yuri Nishikawa, Toshinori Kojima, Yasunori Osana, Akira Funahashi (Keio Univ.), Noriko Hiroi (EMBL-EBI), Yuichiro Shibata, Hideki Yamada (Nagasaki Univ.), Hiroaki Kitano (JST), Hideharu Amano (Keio Univ.) RECONF2007-50 |
Abstract |
(in Japanese) |
(See Japanese page) |
(in English) |
This paper studies several designs of network-based FPGA implementation of a stochastic simulation algorithm called the Next Reaction Method. Whole procedure of the algorithm is divided into several subdivisions which will be implemented as independent modules, and they are connected with configurable interconnection networks so as to provide high throughput. Area and throughput were measured for each type of network configuration, as well as studying each cause of bottleneck. By performing a multi-threading simulation, maximum of 3.6 times speedup was obtained compared to an execution on Xeon 3.20 GHz. Although current designs did not achieve significant speedup, performance analysis study of each network configuration suggested capability of throughput enhancement. |
Keyword |
(in Japanese) |
(See Japanese page) |
(in English) |
Data-transfer network / Data-driven / FPGA / stochastic biochemical simulation / On-chip network / / / |
Reference Info. |
IEICE Tech. Rep., vol. 107, no. 342, RECONF2007-50, pp. 43-48, Nov. 2007. |
Paper # |
RECONF2007-50 |
Date of Issue |
2007-11-15 (RECONF) |
ISSN |
Print edition: ISSN 0913-5685 Online edition: ISSN 2432-6380 |
Copyright and reproduction |
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RECONF2007-50 |
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