GPU加速窦房结计算机仿真的实现及优化

张虹; 郑霄; 赵丹

doi:10.7652/xjtuxb201407011

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GPU加速窦房结计算机仿真的实现及优化

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- GPU加速窦房结计算机仿真的实现及优化
- Implementation and Optimization of Computer Simulations with GPU Acceleration for Sino-Atrial Nodes
- 西安交通大学学报 2014年48卷第7期页码：60-64
- 作者机构：
  
  西安交通大学电气工程学院,西安,710049
- 作者简介：
- 基金信息：
  
  : 2014-01-15。作者简介: 张虹(1969—),女,副教授。基金项目: 国家自然科学基金资助项目(81271661);教育部回国留学基金资助项目(第40批);中央高校基本科研业务费专项资金项目(xjj2011087)
- DOI：10.7652/xjtuxb201407011
  中图分类号： TP391.9
- 网络首发：2014-07-10，
  
  纸质出版：2014
- 稿件说明：
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张虹, 郑霄, 赵丹. GPU加速窦房结计算机仿真的实现及优化[J]. 西安交通大学学报, 2014,48(7):60-64.

Implementation and Optimization of Computer Simulations with GPU Acceleration for Sino-Atrial Nodes[J]. 2014, 48(7): 60-64.
张虹, 郑霄, 赵丹. GPU加速窦房结计算机仿真的实现及优化[J]. 西安交通大学学报, 2014,48(7):60-64. DOI： 10.7652/xjtuxb201407011.

Implementation and Optimization of Computer Simulations with GPU Acceleration for Sino-Atrial Nodes[J]. 2014, 48(7): 60-64. DOI： 10.7652/xjtuxb201407011.

摘要

针对窦房结电生理计算机仿真运算量巨大、耗时长的问题

提出了基于高性能图形处理单元(GPU)实现并行计算及优化的方法。首先考虑窦房结细胞中央和边缘的差异

构建了一维非匀质窦房结组织模型; 利用算子分裂方法使模型的解算任务具备并行性。根据具体解算过程提出了三种并行化策略

并对其中耗时最短的策略从线程块设置、数据交换频率以及存储模式等方面进行了进一步优化。结果表明:对于500个细胞的仿真

CUDA程序较串行程序的执行时间下降了60%

进一步优化后

CUDA程序的执行时间可下降84%; 窦房结组织越大

GPU的加速效果越明显。结果验证了GPU加速解算方法可显著提高窦房结模型的解算速度

降低实际执行时间。

Abstract

A parallel computation method with its optimization based on graphic processing unit(GPU)is proposed to improve the problem that the electrophysiological simulations for sino-atrial nodes(SAN)needs large amount of calculation and time consumption. A one-dimensional inhomogeneous model for tissue of SAN is established by considering the difference of properties in the central and the edge of SAN cell. Then

the calculation of the model is parallelly performed by using the operator splitting method. Three parallelization strategies are put forward based on the calculation process. The strategy with the shortest running time is further optimized by considering the block size

the data transfer and data partitioning across various memories. Simulation results with 500 cells show that

compared with a serial program

the execution time of the non-optimized CUDA program decreases by about 60%

and the execution time further reduces to 84% when the CUDA program is optimized. It is also observed that the larger the tissue is

the more significant the acceleration effect of GPU is. It can be concluded that the proposed GPU accelerating method significantly speeds up the computation of SAN tissue model and decreases the execution time.

关键词

Keywords

references

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