A GPU-based multi-resolution algorithm for simulation of seed dispersal

Jing FAN; Hai-feng JI; Xin-xin GUAN; Ying TANG

doi:10.1631/jzus.C1200147

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A GPU-based multi-resolution algorithm for simulation of seed dispersal

计算机与自动化 | Updated：2022-05-19

- A GPU-based multi-resolution algorithm for simulation of seed dispersal
- A GPU-based multi-resolution algorithm for simulation of seed dispersal
- 信息与电子工程前沿（英文） 2012年13卷第11期页码：816-827
- Affiliations：
  
  School of Computer Science and Technology, Zhejiang University of Technology, Hangzhou 310023, China
- Author bio：
  
  [ "Jing FAN, E-mail: fanjing@zjut.edu.cn" ]
  Ying TANG, E-mail: tangying@gmail.com
- Funds：
  
  Project supported by the National Natural Science Foundation of China (Nos. 61173097 and 61003265), the Natural Science Foundation of Zhejiang Province, China (No. Z1090459), the Science and Technology Planning Project of Zhejiang Province, China (No.2010C33046), and Tsinghua-Tencent Joint Laboratory for Internet Innovation Technology
- DOI：10.1631/jzus.C1200147
  中图分类号： TP391.9
- 收稿：2012-05-23，
  
  修回：2012-10-12，
  
  纸质出版：2012-11
- Accepted：
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A GPU-based multi-resolution algorithm for simulation of seed dispersal[J]. 信息与电子工程前沿（英文）, 2012,13(11):816-827.

Jing FAN, Hai-feng JI, Xin-xin GUAN, et al. A GPU-based multi-resolution algorithm for simulation of seed dispersal[J]. Frontiers of Information Technology & Electronic Engineering, 2012, 13(11): 816-827.
A GPU-based multi-resolution algorithm for simulation of seed dispersal[J]. 信息与电子工程前沿（英文）, 2012,13(11):816-827. DOI： 10.1631/jzus.C1200147.

Jing FAN, Hai-feng JI, Xin-xin GUAN, et al. A GPU-based multi-resolution algorithm for simulation of seed dispersal[J]. Frontiers of Information Technology & Electronic Engineering, 2012, 13(11): 816-827. DOI： 10.1631/jzus.C1200147.

摘要

Abstract

In forest dynamics models

the intensive computation and load involved in the simulation of seed dispersal can become unbearably huge for large-scale forest analysis. To solve this problem

we propose a multi-resolution algorithm to compute seed dispersal on GPU. By exploiting the computation parallelism of seed dispersal

the computation of the whole forest plot is divided into multiple small plot cells

which are computed independently by parallel threads on GPU. To further improve the calculation efficiency with limited threads scale for GPU computation

we propose a hierarchical method to cluster the plot cells into a multi-resolution form according to the biological curves of tree seed dispersal. Experimental results show that our algorithm not only greatly reduces computational time but also obtains comparably correct results as compared to the naive GPU algorithm

which makes it especially suitable for large-scale forest modeling.

关键词

Keywords

references

R. Astrup , , , D.K. Coates , , , E. Hall , , , A. Trowbridge . . Documentation for the SOTIE-ND SBS Research Parameter File Version 1.0. Natural Resources Research and Management Report, Bulkley Valley Centre . . Available from , , 2007 . . http://www.bvcentre.ca/files/SORTIE-ND_SBS_Research_Parameter_File_Version_1.0.pdf http://www.bvcentre.ca/files/SORTIE-ND_SBS_Research_Parameter_File_Version_1.0.pdf , , [Accessed on May 5, 2012] . .

J. Barnes , , , P. Hut . . A hierarchical O ( n log n ) force calculation algorithm . . Nature , , 1986 . . 324 ( ( 6096 ): ): 446 - - 449 . . DOI: 10.1038/324446a0 http://doi.org/10.1038/324446a0 . .

H. Bugmann . . A review of forest gap models . . Climate Change , , 2001 . . 51 ( ( 3/4 ): ): 259 - - 305 . . DOI: 10.1023/A:1012525626267 http://doi.org/10.1023/A:1012525626267 . .

J.S. Clark , , , M. Lewis , , , L. Horvath . . Invasion by extremes: population spread with variation in dispersal and reproduction . . Am. Nat. , , 2001 . . 157 ( ( 5 ): ): 537 - - 554 . . DOI: 10.1086/319934 http://doi.org/10.1086/319934 . .

Z.H. Du , , , Z.M. Yin , , , D.A. Bader . . A Tile-Based Parallel Viterbi Algorithm for Biological Sequence Alignment on GPU with CUDA . . IEEE Int. Symp. on Parallel & Distributed Processing Workshops and PhD Forum , , 2010 . . p.1 - - 8 . . DOI: 10.1109/IPDPSW.2010.5470903 http://doi.org/10.1109/IPDPSW.2010.5470903 . .

R. Gelbard , , , O. Goldman , , , I. Spiegler . . Investigating diversity of clustering methods: an empirical comparison . . Data. Knowl. Eng. , , 2007 . . 63 ( ( 1 ): ): 155 - - 166 . . DOI: 10.1016/j.datak.2007.01.002 http://doi.org/10.1016/j.datak.2007.01.002 . .

S. Govindarajan , , , M. Dietze , , , P.K. Agarwal , , , J. Clark . . A Scalable Simulator for Forest Dynamics . . Proc. 20th Annual Symp. on Computational Geometry , , 2004 . . p.106 - - 115 . . DOI: 10.1145/997817.997836 http://doi.org/10.1145/997817.997836 . .

S. Govindarajan , , , M.C. Dietze , , , P.K. Agarwal , , , J.S. Clark . . A scalable algorithm for dispersing population . . J. Intell. Inf. Syst. , , 2007 . . 29 ( ( 1 ): ): 39 - - 61 . . DOI: 10.1007/s10844-006-0030-z http://doi.org/10.1007/s10844-006-0030-z . .

T. Hamada , , , I. Titala . . The Chamomile Schema: an Optimized Algorithm for N -Body Simulations on Programmable Graphics Processing Units . . Available from , , 2007 . . http://arxiv.org/abs/astro-ph/0703100 http://arxiv.org/abs/astro-ph/0703100 , , [Accessed on June 25, 2012] . .

T. Hamada , , , T. Narumi , , , R. Yokota , , , K. Yasuola , , , K. Nitadori , , , M. Taiji . . 42 TFlops Hierarchical N -Body Simulations on GPUs with Applications in Both Astrophysics and Turbulence . . Proc. Conf. on High Performance Computing Networking, Storage and Analysis , , 2009 . . p.14 - - 20 . . DOI: 10.1145/1654059.1654123 http://doi.org/10.1145/1654059.1654123 . .

G. Kunstler , , , R.B. Allen , , , D.A. Coomes , , , C.D. Canham , , , E.F. Wright . . SORTIE/NZ Model Development . . Landcare Research New Zealand Ltd. Available from , , 2011 . . http://www.Landcareresearch.co.nz/publications/resear-chpubs/sortie_nz_model_dev.pdf http://www.Landcareresearch.co.nz/publications/resear-chpubs/sortie_nz_model_dev.pdf , , [Accessed on May 5, 2012] . .

P.T. Lepage , , , C.D. Canham , , , K.D. Coates , , , P. Bartemucci . . Seed abundance versus substrate limitation of seedling recruitment in northern temperate forests of British Columbia . . Can. J. Forest Res. , , 2000 . . 30 ( ( 3 ): ): 415 - - 427 . . DOI: 10.1139/x99-223 http://doi.org/10.1139/x99-223 . .

J. Lin , , , M. Tang , , , R.F. Tong . . GPU accelerated biological sequence alignment . . J. Comput.-Aided Des. Comput. Graph. , , 2010 . . 22 ( ( 3 ): ): 420 - - 427 . . . .

J. Mielikainen , , , B. Huang , , , H.L.A. Huang . . GPU-accelerated multi-profile radiative transfer model for the infrared atmospheric sounding Interferometer . . IEEE J. Sel. Topics Appl. Earth Observ. Remote Sens. , , 2011 . . 4 ( ( 3 ): ): 691 - - 700 . . DOI: 10.1109/JSTARS.2011.2159195 http://doi.org/10.1109/JSTARS.2011.2159195 . .

J. Nickolls , , , I. Buck , , , M. Garland , , , K. Skadron . . Scalable parallel programming with CUDA . . Queue , , 2008 . . 6 ( ( 2 ): ): 40 - - 53 . . DOI: 10.1145/1365490.1365500 http://doi.org/10.1145/1365490.1365500 . .

Corporation NVIDIA . . CUDA Programming Guide, Version 33.0. NVIDIA Corporation . . Available from , , 2007 . . http://developer.nvidia.com/nvidia-gpu-programming-guide http://developer.nvidia.com/nvidia-gpu-programming-guide , , [Accessed on May 5, 2012] . .

L. Nyland , , , M. Harris , , , J. Prins . . Fast N -Body Simulation with CUDA . . In : Nguyen, H. (Ed.), GPU Gems 3. Addison-Wesley, London , , 2007 . . p.677 - - 795 . . . .

S.W. Pacala , , , C.D. Canham , , , J.A.Jr. Silander . . Forest models defined by field measurements:I . . The design of a northeastern forest simulator. Can. J. Forest Res. , , 1993 . . 23 ( ( 10 ): ): 1980 - - 1988 . . DOI: 10.1139/x93-249 http://doi.org/10.1139/x93-249 . .

S. Ryoo , , , C.I. Rodrigues , , , S.S. Banghsorkhi , , , S.S. Stone , , , D.B. Kirk , , , W.W. Hwu . . Optimization Principles and Application Performance Evaluation of a Multithreaded GPU Using CUDA . . Proc. 13th ACM SIGPLAN Symp. on Principles and Practice of Parallel Programming , , 2008 . . p.73 - - 82 . . DOI: 10.1145/1345206.1345220 http://doi.org/10.1145/1345206.1345220 . .

J.E. Stone , , , J.C. Phillips , , , P.L. Freddolino , , , D.J. Hardy , , , L.G. Tra-buco , , , K. Schulten . . Accelerating molecular modeling applications with graphics processors . . J. Comput. Chem. , , 2007 . . 28 ( ( 16 ): ): 2618 - - 2640 . . DOI: 10.1002/jcc.20829 http://doi.org/10.1002/jcc.20829 . .

Y. Tang , , , X.X. Guan , , , J. Fan . . Design and Implementa-tion of Seeds Dispersion on Graphic Processor Unit . . Proc. 10th Int. Conf. on Virtual Reality Continuum and Its Applications in Industry , , 2011 . . p.403 - - 406 . . DOI: 10.1145/2087756.2087828 http://doi.org/10.1145/2087756.2087828 . .

Y.J. Xia , , , L. Kuang , , , X.M. Li . . Accelerating geospatial analysis on GPUs using CUDA . . J. Zhejiang Univ.-Sci. C (Comput. & Electron.) , , 2011 . . 12 ( ( 12 ): ): 990 - - 999 . . DOI: 10.1631/jzus.C1100051 http://doi.org/10.1631/jzus.C1100051 . .

S. Zhang , , , Y.L. Chu , , , K.Y. Zhao , , , Y.B. Zhang . . High Performance GPU Computing of CUDA . . China Water Publishing House, Beijing, China , , 2009 . . p.155 - - 157 . . . .

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