曙光4000H生物信息处理专用计算机的高性能算法研究  

Research on the High Performance Algorithms of Dawning 4000H Bioinformatics Specific Machine

作　　者：冯圣中[1] 谭光明[1] 徐琳[1] 孙凝晖[1] 徐志伟[1] 

机构地区：[1]中国科学院计算技术研究所,北京100080

出　　处：《计算机研究与发展》2005年第6期1053-1058,共6页Journal of Computer Research and Development

基　　金：国家自然科学基金项目(60372040);中国科学院重大创新工程基金项目(KSCX2SW233)

摘　　要：曙光4000H生物信息处理专用计算机基于现代计算机体系结构和可重构计算器件,分别通过IO延迟隐藏、细粒度并行以及并行流水等技巧优化设计了BLAST、动态规划、RNA二级结构预测等有代表性的3类算法,并开发C模拟器进行了性能评价,结果表明,上述算法大幅度提高了计算机处理能力.The bioinformatics specific supercomputer is the key project supported by the Knowledge Innovation Program of CAS. The challenge is to accelerate the important core algorithms of bioinformation processing based on the modern computer system architecture and reconfigurable computing chip, and reach tens of times improvement. In this paper, the three typical algorithms, BLAST, dynamic programming, and Zuker-RNA secondary structure prediction, are optimized with hiding I?O latency, fine granularity paralleling, and pipeline paralleling, and C simulators are developed to evaluate the performance of those algorithms. The results show the performance can be improved efficiently by the special machine.

关 键 词：可重构计算 生物信息学 高性能计算 

分 类 号：TP301.6[自动化与计算机技术—计算机系统结构]