Bowtie 2-NUMA:具有NUMA体系结构适应性的基因序列比对应用  

Bowtie 2-NUMA:Gene sequence alignment application with NUMA architecture adaptability

作　　者：王强[1] 孙彦洁 齐星云[1] 徐佳庆[1] WANG Qiang;SUN Yan-jie;QI Xing-yun;XU Jia-qing(College of Computer Science and Technology,National University of Defense Technology,Changsha 410073,China)

机构地区：[1]国防科技大学计算机学院,湖南长沙410073

出　　处：《计算机工程与科学》2024年第12期2117-2127,共11页Computer Engineering & Science

基　　金：国家重点研发计划(2021YFB0300101)。

摘　　要：Bowtie 2作为生物信息领域使用最广泛的二代测序软件之一,具有计算密集的特点。如何根据多核平台的体系结构进行适应性优化以提高并行效率,成为亟待解决的问题。首先分析了非一致性访存架构的多样性,以及Bowtie 2在多种非一致性访存架构下内存访问拥塞和最后一级缓存命中率低的结构性瓶颈。然后,基于Bowtie 2在不同非一致性访存平台的表现特点,在复制索引、内存分配以及数据划分3个方面进行优化,提出了Bowtie 2-NUMA。最后,通过实验表明,Bowtie 2-NUMA面向不同计算平台,能够基于体系结构进行适应性优化,实现并行效率的提升。Bowtie 2,as one of the most widely used second-generation sequencing software in the field of bioinformatics,is characterized by its computational intensity.How to conduct adaptive optimization based on the architecture of multi-core platforms to improve parallel efficiency has become an urgent problem to be solved.This paper first analyzes the diversity of non-uniform memory access(NUMA)architectures and the structural bottlenecks of Bowtie 2 under various NUMA architectures,including memory access congestion and low last level cache hit rates.Then,based on the performance characteristics of Bowtie 2 on different NUMA platforms,optimizations are carried out in three aspects:index replication,memory allocation,and data partitioning,leading to the proposal of Bowtie 2-NUMA.Finally,experiments show that Bowtie 2-NUMA can achieve adaptive optimization based on the architecture for different computing platforms,thereby improving parallel efficiency.

关 键 词：非一致性访存 Bowtie 2 适应性优化 体系结构 内存带宽 最后一级缓存 

分 类 号：TP303[自动化与计算机技术—计算机系统结构]