Performance Limitation of Sequence Alignment on the NUMA-based Architecture

Abstract

In recent years NUMA architecture based on multicore system leads a mainstream solution to tackle the rapidly expanding computation in bioinformatics analysis. Sequence alignment is the most computing cost in the workflow of variant analysis in bioinformatics. Although parallel coding in sequence alignment could be few difficulties, approaching a good performance in such a system is complicated. This research explores the architecture bottlenecks we usually neglect in the implementation of bioinformatics computing, NUMA effect for instance. We exploit the scalability of threads in the sequence aligners to illustrate the problem and the significance of NUMA architecture in the multicore system. The preliminary results in the experiments display that sequence aligners cannot take advantage of NUMA-based multi-core architecture. The scalability of threads is deficient, even negative in time-cost at the case of large-scale genome data larger NUMA nodes.