• 中国计算机学会会刊
  • 中国科技核心期刊
  • 中文核心期刊

Computer Engineering & Science ›› 2024, Vol. 46 ›› Issue (12): 2117-2127.

• High Performance Computing • Previous Articles     Next Articles

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

WANG Qiang,SUN Yan-jie,QI Xing-yun,XU Jia-qing   

  1. (College of Computer Science and Technology,National University of Defense Technology,Changsha 410073,China)
  • Received:2023-03-29 Revised:2023-10-17 Accepted:2024-12-25 Online:2024-12-25 Published:2024-12-23

Abstract: 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.


Key words: non-uniform memory access (NUMA), Bowtie 2, adaptive optimization, computer architecture, memory bandwidth, last level cache (LLC)