Optimized parallel implementation of Gillespie's first reaction method on graphics processing units

Cristian Dittamo, Davide Cangelosi

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

Abstract

The simulation of chemical reacting systems is one of the most challenging topics in Systems Biology, due to their complexity and inherent randomness. The Gillespie's Stochastic Simulation Algorithm (SSA) is a standard algorithm to simulate well-stirred biochemical systems, but the computational burden makes this algorithm slow to compute for many realistic problems. Recent programmability improvements allow nongraphics applications to leverage the Graphics Processing Units' (GPUs) computational power. This paper describes practical issues arising by a parallel implementation on GPU technology, shows how to reduce the memory space required by one of the most known versions of SSA, and presents the application of the implemented algorithm to a test model.

Original languageEnglish
Title of host publicationProceedings - 2009 International Conference on Computer Modeling and Simulation, ICCMS 2009
Pages156-161
Number of pages6
DOIs
Publication statusPublished - 2009
Event2009 International Conference on Computer Modeling and Simulation, ICCMS 2009 - Macau, China
Duration: Feb 20 2009Feb 22 2009

Other

Other2009 International Conference on Computer Modeling and Simulation, ICCMS 2009
CountryChina
CityMacau
Period2/20/092/22/09

Fingerprint

Graphics processing unit
Data storage equipment
Systems Biology

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Computer Science Applications
  • Software

Cite this

Dittamo, C., & Cangelosi, D. (2009). Optimized parallel implementation of Gillespie's first reaction method on graphics processing units. In Proceedings - 2009 International Conference on Computer Modeling and Simulation, ICCMS 2009 (pp. 156-161). [4797374] https://doi.org/10.1109/ICCMS.2009.42

Optimized parallel implementation of Gillespie's first reaction method on graphics processing units. / Dittamo, Cristian; Cangelosi, Davide.

Proceedings - 2009 International Conference on Computer Modeling and Simulation, ICCMS 2009. 2009. p. 156-161 4797374.

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

Dittamo, C & Cangelosi, D 2009, Optimized parallel implementation of Gillespie's first reaction method on graphics processing units. in Proceedings - 2009 International Conference on Computer Modeling and Simulation, ICCMS 2009., 4797374, pp. 156-161, 2009 International Conference on Computer Modeling and Simulation, ICCMS 2009, Macau, China, 2/20/09. https://doi.org/10.1109/ICCMS.2009.42
Dittamo C, Cangelosi D. Optimized parallel implementation of Gillespie's first reaction method on graphics processing units. In Proceedings - 2009 International Conference on Computer Modeling and Simulation, ICCMS 2009. 2009. p. 156-161. 4797374 https://doi.org/10.1109/ICCMS.2009.42
Dittamo, Cristian ; Cangelosi, Davide. / Optimized parallel implementation of Gillespie's first reaction method on graphics processing units. Proceedings - 2009 International Conference on Computer Modeling and Simulation, ICCMS 2009. 2009. pp. 156-161
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