基于Minimap2的第三代基因组测序高效CPU-FPGA异构加速系统

IF 4.9 2区 工程技术 Q2 ENGINEERING, ELECTRICAL & ELECTRONIC
Jialei Sun;Lingyi Liu;Kunyue Li;Shuaipeng Li;Sai Gao;Zizheng Dong;Jianfei Jiang;Fangzhen Wu
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引用次数: 0

摘要

Minimap2已成为广泛使用的第三代长读基因组测序软件。由于长读序列的数据处理越来越复杂,这种分析计算量大、能耗高。本文介绍了一种针对Minimap2的端到端CPU-FPGA异构加速系统,该系统以链式操作为核心,多线程软件位于CPU上,链式操作的多内核加速器位于FPGA上。此概要可以容纳现代cpu的高线程数,以最大限度地提高性能和能源效率。硬件高效的内核设计、软硬件协同优化和内存访问融合技术已被应用于以更低的功耗实现更高的计算性能。与软件相比,该方案最多可实现2.01美元的加速度,与基线相比,最多可实现1.65美元的加速度,与软件相比,EDP降低72%,与基线相比,EDP降低59%,优于最先进的设计。我们的加速系统的代码可以在GitHub上获得,以及FPGA比特流。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
An Energy-Efficient CPU–FPGA Heterogeneous Acceleration System for Third-Generation Genomic Sequencing Based on Minimap2
Minimap2 has become a widely used software for third-generation long-read genomic sequencing. Due to the increasing complexity of data processing with long-read sequences, the analysis is computationally intensive and energy-consuming. This brief presents an end-to-end CPU-FPGA heterogeneous acceleration system for Minimap2 focusing on chaining operation, in which multi-threaded software is on the CPU, and a multi-kernel accelerator for chaining operation is on the FPGA. This brief can hold the high thread number of modern CPUs to maximize performance and energy efficiency. Hardware-efficient kernel design, software-hardware co-optimization, and memory access fusion techniques have been applied to achieve higher computational performance with less power consumption. This brief achieves at most $2.01\times $ acceleration against software and $1.65\times $ against the baseline, and EDP reduction of 72% against software and 59% against the baseline, outperforming state-of-the-art designs. The code of our acceleration system is available on GitHub, together with FPGA bitstream.
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来源期刊
IEEE Transactions on Circuits and Systems II: Express Briefs
IEEE Transactions on Circuits and Systems II: Express Briefs 工程技术-工程:电子与电气
CiteScore
7.90
自引率
20.50%
发文量
883
审稿时长
3.0 months
期刊介绍: TCAS II publishes brief papers in the field specified by the theory, analysis, design, and practical implementations of circuits, and the application of circuit techniques to systems and to signal processing. Included is the whole spectrum from basic scientific theory to industrial applications. The field of interest covered includes: Circuits: Analog, Digital and Mixed Signal Circuits and Systems Nonlinear Circuits and Systems, Integrated Sensors, MEMS and Systems on Chip, Nanoscale Circuits and Systems, Optoelectronic Circuits and Systems, Power Electronics and Systems Software for Analog-and-Logic Circuits and Systems Control aspects of Circuits and Systems.
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