Efficient scheduling of rate law functions for ODE-based multimodel biochemical simulation on an FPGA

Naoki Iwanagra, Yuichiro Shibata, Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Tomonori Fukushima, Hideharu Amano, Akira Funahashi, Noriko Hiroi, Hiroaki Kitano, Kiyoshi Oguri

Research output: Chapter in Book/Report/Conference proceedingConference contribution

10 Citations (Scopus)

Abstract

A reconfigurable biochemical simulator by solving ordinary differential equations has received attention as a personal high speed environment for biochemical researchers. For efficient use of the reconfigurable hardware, static scheduling of high-throughput arithmetic pipeline structures is essential. This paper shows and compares some scheduling alternatives, and analyzes the tradeoffs between performance and hardware amount. Through the evaluation, it is shown that the sharing first scheduling reduces the hardware cost by 33.8% in average, with the up to 11.5% throughput degradation. Effects of sharing of rate law functions are also analyzed.

Original languageEnglish
Title of host publicationProceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL
Pages666-669
Number of pages4
Volume2005
DOIs
Publication statusPublished - 2005
Event2005 International Conference on Field Programmable Logic and Applications, FPL - Tampere, Finland
Duration: 2005 Aug 242005 Aug 26

Other

Other2005 International Conference on Field Programmable Logic and Applications, FPL
CountryFinland
CityTampere
Period05/8/2405/8/26

Fingerprint

Field programmable gate arrays (FPGA)
Scheduling
Throughput
Hardware
Reconfigurable hardware
Ordinary differential equations
Pipelines
Simulators
Degradation
Costs

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Iwanagra, N., Shibata, Y., Yoshimi, M., Osana, Y., Iwaoka, Y., Fukushima, T., ... Oguri, K. (2005). Efficient scheduling of rate law functions for ODE-based multimodel biochemical simulation on an FPGA. In Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL (Vol. 2005, pp. 666-669). [1515809] https://doi.org/10.1109/FPL.2005.1515809

Efficient scheduling of rate law functions for ODE-based multimodel biochemical simulation on an FPGA. / Iwanagra, Naoki; Shibata, Yuichiro; Yoshimi, Masato; Osana, Yasunori; Iwaoka, Yow; Fukushima, Tomonori; Amano, Hideharu; Funahashi, Akira; Hiroi, Noriko; Kitano, Hiroaki; Oguri, Kiyoshi.

Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL. Vol. 2005 2005. p. 666-669 1515809.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Iwanagra, N, Shibata, Y, Yoshimi, M, Osana, Y, Iwaoka, Y, Fukushima, T, Amano, H, Funahashi, A, Hiroi, N, Kitano, H & Oguri, K 2005, Efficient scheduling of rate law functions for ODE-based multimodel biochemical simulation on an FPGA. in Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL. vol. 2005, 1515809, pp. 666-669, 2005 International Conference on Field Programmable Logic and Applications, FPL, Tampere, Finland, 05/8/24. https://doi.org/10.1109/FPL.2005.1515809
Iwanagra N, Shibata Y, Yoshimi M, Osana Y, Iwaoka Y, Fukushima T et al. Efficient scheduling of rate law functions for ODE-based multimodel biochemical simulation on an FPGA. In Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL. Vol. 2005. 2005. p. 666-669. 1515809 https://doi.org/10.1109/FPL.2005.1515809
Iwanagra, Naoki ; Shibata, Yuichiro ; Yoshimi, Masato ; Osana, Yasunori ; Iwaoka, Yow ; Fukushima, Tomonori ; Amano, Hideharu ; Funahashi, Akira ; Hiroi, Noriko ; Kitano, Hiroaki ; Oguri, Kiyoshi. / Efficient scheduling of rate law functions for ODE-based multimodel biochemical simulation on an FPGA. Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL. Vol. 2005 2005. pp. 666-669
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