耗散粒子动力学平衡并行算法的实现

赵英;佟林

北京化工大学学报(自然科学版) ›› 2012, Vol. 39 ›› Issue (4) : 111-116.

PDF(1280 KB)
欢迎访问北京化工大学学报(自然科学版),今天是 2025年7月13日 星期日
Email Alert  RSS
PDF(1280 KB)
北京化工大学学报(自然科学版) ›› 2012, Vol. 39 ›› Issue (4) : 111-116.
机电工程和信息科学

耗散粒子动力学平衡并行算法的实现

  • 赵英;佟林
作者信息 +

Balance parallelization of dissipative particle dynamics simulation

  • ZHAO Ying;TONG Lin
Author information +
文章历史 +

摘要

提出了一种耗散粒子动力学(DPD)的平衡并行(BPDPD)算法,解决了传统DPD程序计算时间过长的问题。通过动态的划分模拟空间实现了节点间的负载均衡,并且运用子节点数据本地重建机制有效减少了节点通信的数据量。对锚定蛋白质的聚集做了模拟,实验结果显示,该算法有效的减少DPD模拟的时间,并在10节点的集群上得到了6.3的加速比。

Abstract

In this paper, a balance parallelization method for dissipative particle dynamics (BPDPD) simulation is presented. By dynamically calculating the range of each computed node, the load of the cluster becomes balanced, and by means of data rebuilding, the amount of communication data is also reduced. An anchored protein gathering problem was simulated in BPDPD and showed that the BPDPD can effectively reduce the computing time and afford a speed-up ratio of 6.3 on a cluster with ten nodes.

引用本文

导出引用
赵英;佟林. 耗散粒子动力学平衡并行算法的实现[J]. 北京化工大学学报(自然科学版), 2012, 39(4): 111-116
ZHAO Ying;TONG Lin. Balance parallelization of dissipative particle dynamics simulation[J]. Journal of Beijing University of Chemical Technology, 2012, 39(4): 111-116

参考文献

[1] Pan H, Ng T Y, Li H, et al. Dissipative particle dynamics simulation of entropic trapping for DNA separation[J]. Sensors and Actuators A: Physical, 2010, 157(2): 328-335.
[2]Pivkin I V, Richardson P D, Karniadakis G E. Effect of red blood cells on platelet aggregation[J]. IEEE Engineering in Medicine and Biology Magazine, 2009, 28(2): 32-37.
[3]Sims J S, Martys N. Simulation of sheared suspensions with a parallel implementation of QDPD[J]. Journal of Research of the National Institute of Standards and Technology, 2004, 109(2): 267-277.
[4]Yue Y, Zhao Y, You G H, et al. Parallelization of dissipative particle dynamics simulation[C]∥2009 International Joint Conference on Computational Sciences and Optimization, IEEE Computer Society, 2009: 18-22.
[5]Groot R D, Warren P B. Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation[J]. J Chem Phys, 1997, 107(11): 4423-4435.
PDF(1280 KB)

Accesses

Citation

Detail

段落导航
相关文章

/