Computer Engineering & Science ›› 2024, Vol. 46 ›› Issue (12): 2117-2127.
• High Performance Computing • Previous Articles Next Articles
WANG Qiang,SUN Yan-jie,QI Xing-yun,XU Jia-qing
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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)
WANG Qiang, SUN Yan-jie, QI Xing-yun, XU Jia-qing. Bowtie 2-NUMA: Gene sequence alignment application with NUMA architecture adaptability[J]. Computer Engineering & Science, 2024, 46(12): 2117-2127.
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URL: http://joces.nudt.edu.cn/EN/
http://joces.nudt.edu.cn/EN/Y2024/V46/I12/2117