Bowtie 2-NUMA:Gene sequence alignment application with NUMA architecture adaptability
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 optimi-zation 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.
万方数据
维普
