Cross Layer Design Using HW/SW Co-Design and HLS to Accelerate Chaining in Genomic Analysis

被引：0

作者：

Liyanage, Kisaru ^{[1
]}

Gamaarachchi, Hasindu ^{[1
,2
]}

Ragel, Roshan ^{[3
]}

Parameswaran, Sri ^{[1
]}

机构：

[1] UNSW Sydney, Sch Comp Sci & Engn, Sydney, NSW 2052, Australia

[2] Garvan Inst Med Res, Kinghorn Ctr Clin Genom, Darlinghurst, NSW 2010, Australia

[3] Univ Peradeniya, Dept Comp Engn, Peradeniya, Sri Lanka

来源：

IEEE TRANSACTIONS ON COMPUTER-AIDED DESIGN OF INTEGRATED CIRCUITS AND SYSTEMS | 2023年 / 42卷 / 09期

关键词：

Chaining; DNA sequence alignment; energy-efficient; FPGA acceleration; minimap2;

D O I：

10.1109/TCAD.2023.3236559

中图分类号：

TP3 [计算技术、计算机技术];

学科分类号：

0812 ;

摘要：

DNA sequence analysis is a computationally intensive task. Minimap2 is a state-of-the-art software tool for third-generation sequence analysis workflow. Nearly 50% of Minimap2's computation time is spent on what is known as the chaining step. In this article, the chaining step is accelerated using a novel heterogeneous computing system combining an Intel FPGA-based hardware accelerator and a CPU (using high-level synthesis for the FPGA and multithreaded software for the CPU). The system in this article is capable of handling large-realistic workloads and achieves up to similar to 1.35x performance improvement over the software solution running on an Intel CPU with SIMD intrinsics (Intel's latest AVX-512) while consuming similar to 27 % less energy. When compared to the software solution running on the CPU without SIMD intrinsics, the system performs similar to 1.9x faster while consuming similar to 38% less energy. Importantly, this work also ensures that the accuracy of the output generated is not compromised for the speed-up gained (this work only has an error rate of less than 10(-6)% compared to 26% in previous FPGA-based chaining step accelerator).

引用

页码：2924 / 2937

页数：14