
This Article  
 
Share  
Bibliographic References  
Add to:  
Digg Furl Spurl Blink Simpy Del.icio.us Y!MyWeb  
Search  
 
ASCII Text  x  
Guido Klingbeil, Radek Erban, Mike Giles, Philip K. Maini, "Fat versus Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions," IEEE Transactions on Parallel and Distributed Systems, vol. 23, no. 2, pp. 280287, February, 2012.  
BibTex  x  
@article{ 10.1109/TPDS.2011.157, author = {Guido Klingbeil and Radek Erban and Mike Giles and Philip K. Maini}, title = {Fat versus Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions}, journal ={IEEE Transactions on Parallel and Distributed Systems}, volume = {23}, number = {2}, issn = {10459219}, year = {2012}, pages = {280287}, doi = {http://doi.ieeecomputersociety.org/10.1109/TPDS.2011.157}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }  
RefWorks Procite/RefMan/Endnote  x  
TY  JOUR JO  IEEE Transactions on Parallel and Distributed Systems TI  Fat versus Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions IS  2 SN  10459219 SP280 EP287 EPD  280287 A1  Guido Klingbeil, A1  Radek Erban, A1  Mike Giles, A1  Philip K. Maini, PY  2012 KW  Parallel processing KW  compute unified device architecture (CUDA) KW  graphics processing unit (GPU). VL  23 JA  IEEE Transactions on Parallel and Distributed Systems ER   
[1] Nvidia CUDA Programming Guide, Version 2.1, NVIDIA Corporation, 2701 San Tomas Expressway, vol. 12, 2008.
[2] R. Erban, S. Chapman, I. Kevrekidis, and T. Vejchodsky, "Analysis of a Stochastic Chemical System Close to a Sniper Bifurcation of Its MeanField Model," SIAM J. Applied Math., vol. 70, no. 3, pp. 9841016, 2009.
[3] B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter, Molecular Biology of the Cell. Garland Science, 2007.
[4] F. Holstege, E. Jennings, J. Wyrick, T. Lee, C. Hengartner, M. Green, T. Golub, E. Lander, and R. Young, "Dissecting the Regulatory Circuitry of a Eukaryotic Genome," Cell, vol. 95, no. 5, pp. 717728, Nov. 1998.
[5] J. Hasty, D. McMillen, F. Isaacs, and J. Collins, "Computational Studies of Gene Regulatory Networks: In Numero Molecular Biology," Nature Rev. Genetics, vol. 2, no. 4, pp. 268279, Apr. 2001.
[6] T. Tian and K. Burrage, "Stochastic Models for Regulatory Networks of the Genetic Toggle Switch," Proc. Nat'l Academy of Sciences of USA, vol. 103, no. 22, pp. 83728377, 2006.
[7] G. Ewing, D. McNickle, and K. Pawlikowski, "Multiple Replications in Parallel: Distributed Generation of Data for Speeding up Quantitative Stochastic Simulation," Proc. Int'l Assoc. for Mathematics and Computers in Simulation (IMACS '97), pp. 397402, 1997.
[8] L. Dematte and T. Mazza, "On Parallel Stochastic Simulation of Diffusive Systems," Proc. Sixth Int'l Conf. Computational Methods in Systems Biology (CMSB '08), pp. 191210, 2008.
[9] T. Tian and K. Burrage, "Parallel Implementation of Stochastic Simulation for LargeScale Cellular Processes," Proc. Eighth Int'l Conf. High Performance Computing and Grid in AsiaPacific Region, vol. 0, pp. 621626, 2005.
[10] A. Snavely, L. Carter, J. Boisseau, A. Majumdar, K.S. Gatlin, N. Mitchell, J. Feo, and B. Koblenz, "MultiProcessor Performance on the Tera MTA," Proc. IEEE/ACM Conf. Supercomputing (SC '98), pp. 44, 1998.
[11] A. Agarwal, J. Kubiatowicz, D. Kranz, B. Lim, D. Yeung, G. D'souza, and M. Parkin, "Sparcle: An Evolutionary Processor Design for LargeScale Multiprocessors," IEEE Micro, vol. 13, no. 3, pp. 4861, June 1993.
[12] F. Irigoin and R. Triolet, "Supernode Partitioning," POPL '88: Proc. 15th ACM SIGPLANSIGACT Symp. Principles of Programming Languages, pp. 319329, 1988.
[13] D. Gillespie, "A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions," J. Computational Physics, vol. 22, pp. 403434, 1976.
[14] D. Gillespie, "Exact Stochastic Simulation of Coupled Chemical Reactions," J. Physical Chemistry, vol. 81, no. 25, pp. 23402361, 1977.
[15] M. Gibson and J. Bruck, "Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels," J. Physical Chemistry A, vol. 104, pp. 18761889, 2000.
[16] H. Li and L. Petzold, "Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems," technical report, Dept. of Computer Science, Univ. of California, http://www.cs.ucsb.edu/csepublications.php , 2006.
[17] Y. Cao, H. Li, and L. Petzold, "Efficient Formulation of the Stochastic Simulation Algorithm for Chemically Reacting Systems," J. Chemical Physics, vol. 121, no. 9, pp. 40594067, 2004.
[18] E. Lindholm, J. Nickolls, S. Oberman, and J. Montrym, "Nvidia Tesla: A Unified Graphics and Computing Architecture," IEEE CS Hot Chips, no. 19, pp. 3945, Mar./Apr. 2008.
[19] J. Nickolls, I. Buck, M. Garland, and K. Skadron, "Scalable Parallel Programming with CUDA," ACM Queue, vol. 6, no. 2, pp. 4053, Mar./Apr. 2008.
[20] P. Maciol and K. Banas, "Testing Tesla Architecture for Scientific Computing: The Performance of MatrixVector Product," Proc. Int'l Multiconf. Computer Science and Information Technology, vol. 3, pp. 285291, 2008.
[21] Nvidia Compute PTX: Parallel Thread Execution, ISA Version 1.4, NVIDIA Corporation, 2701 San Tomas Expressway, vol. 3, 2009.
[22] G.M. Amdahl, "Validity of the Single Processor Approach to Achieving Large Scale Computing Capabilities," AFIPS '67 : Proc. Apr. 1820, 1967, Spring Joint Computer Conf., pp. 483485, 1967.
[23] D. Gillespie, "Approximate Accelerated Stochastic Simulation of Chemically Reacting Systems," J. Chemical Physics, vol. 115, no. 4, pp. 17161733, 2001.
[24] J. Murray, Mathematical Biology 1: An Introduction, third ed. Springer Verlag, 2002.
[25] J. Vilar, H. Kueh, N. Barkai, and S. Leibler, "Mechanisms of NoiseResistance in Genetic Oscillators," Proc. Nat'l Academy of Sciences of USA, vol. 99, no. 9, pp. 59885992, 2002.
[26] D. Wilkinson, Stochastic Modelling for Systems Biology. Chapman & Hall/CRC, 2006.
[27] NVIDIA CUDA C Programming Best Practices Guide CUDA Toolkit 2.3, NVIDIA Corporation, 2701 San Tomas Expressway, July 2008.
[28] NVIDIAs Next Generation CUDA Compute Architecture: Fermi, NVIDIA Corporation, 2701 San Tomas Expressway, v 1.1, 2009.