An Efficient GPU Implementation for Large Scale Individual-Based Simulation of Collective Behavior

Erra, Ugo; Frola, Bernardino; Scarano, Vittorio; Couzin, Iain D.

An Efficient GPU Implementation for Large Scale Individual-Based Simulation of Collective Behavior

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Date

2009

Authors

Erra, Ugo

Frola, Bernardino

Scarano, Vittorio

Couzin, Iain D.

DOI (citable link)

10.1109/HiBi.2009.11

Collections

Biologie

Publication type

Contribution to a conference collection

Publication status

Published

Published in

2009 International Workshop on High Performance Computational Systems Biology : (HiBi 2009) ; Trento, Italy, 14 - 16 October 2009. - Piscataway, NJ : IEEE, 2009. - pp. 51-58. - ISBN 978-0-7695-3809-9

Abstract

In this work we describe a GPU implementation for an individual-based model for fish schooling. In this model each fish aligns its position and orientation with an appropriate average of its neighbors' positions and orientations. This carries a very high computational cost in the so-called nearest neighbors search. By leveraging the GPU processing power and the new programming model called CUDA we implement an efficient framework which permits to simulate the collective motion of high-density individual groups. In particular we ...

Subject (DDC)

570 Biosciences, Biology

Keywords

large scale simulation, gpu, individual-based model

Conference

High Performance Computational Systems Biology, Oct 14, 2009 - Aug 16, 2017, Trento, Italy

Cite This

ISO 690

ERRA, Ugo, Bernardino FROLA, Vittorio SCARANO, Iain D. COUZIN, 2009. An Efficient GPU Implementation for Large Scale Individual-Based Simulation of Collective Behavior. High Performance Computational Systems Biology. Trento, Italy, Oct 14, 2009 - Aug 16, 2017. In: 2009 International Workshop on High Performance Computational Systems Biology : (HiBi 2009) ; Trento, Italy, 14 - 16 October 2009. Piscataway, NJ:IEEE, pp. 51-58. ISBN 978-0-7695-3809-9. Available under: doi: 10.1109/HiBi.2009.11

BibTex

@inproceedings{Erra2009Effic-39873,
  year={2009},
  doi={10.1109/HiBi.2009.11},
  title={An Efficient GPU Implementation for Large Scale Individual-Based Simulation of Collective Behavior},
  isbn={978-0-7695-3809-9},
  publisher={IEEE},
  address={Piscataway, NJ},
  booktitle={2009 International Workshop on High Performance Computational Systems Biology : (HiBi 2009) ; Trento, Italy, 14 - 16 October 2009},
  pages={51--58},
  author={Erra, Ugo and Frola, Bernardino and Scarano, Vittorio and Couzin, Iain D.}
}

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