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并行 MapReduce:利用并行执行策略最大化云资源利用率和提升性能。

Parallel MapReduce: Maximizing Cloud Resource Utilization and Performance Improvement Using Parallel Execution Strategies.

机构信息

Department of Smart Computing, Kyungdong University, Global Campus, 46 4-gil, Gosung, Gangwondo 24764, Republic of Korea.

Faculty of Computer and Information Technology, Al-Madinah International University, 2 Jalan Tengku Ampuan Zabedah E/9E, 40100 Shah Alam, Selangor, Malaysia.

出版信息

Biomed Res Int. 2018 Oct 17;2018:7501042. doi: 10.1155/2018/7501042. eCollection 2018.

DOI:10.1155/2018/7501042
PMID:30417014
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6207866/
Abstract

MapReduce is the preferred cloud computing framework used in large data analysis and application processing. MapReduce frameworks currently in place suffer performance degradation due to the adoption of sequential processing approaches with little modification and thus exhibit underutilization of cloud resources. To overcome this drawback and reduce costs, we introduce a Parallel MapReduce () framework in this paper. We design a novel parallel execution strategy of Map and Reduce worker nodes. Our strategy enables further performance improvement and efficient utilization of cloud resources execution of Map and Reduce functions to utilize multicore environments available with computing nodes. We explain in detail makespan modeling and working principle of the framework in the paper. Performance of is compared with Hadoop through experiments considering three biomedical applications. Experiments conducted for BLAST, CAP3, and DeepBind biomedical applications report makespan time reduction of 38.92%, 18.00%, and 34.62% considering the framework against Hadoop framework. Experiments' results prove that the cloud computing platform proposed is robust, cost-effective, and scalable, which sufficiently supports diverse applications on public and private cloud platforms. Consequently, overall presentation and results indicate that there is good matching between theoretical makespan modeling presented and experimental values investigated.

摘要

MapReduce 是大数据分析和应用处理中首选的云计算框架。现有的 MapReduce 框架由于采用了几乎没有修改的顺序处理方法,因此性能下降,从而导致云资源未得到充分利用。为了克服这一缺点并降低成本,我们在本文中引入了一种并行 MapReduce () 框架。我们设计了一种新颖的 Map 和 Reduce 工作节点的并行执行策略。我们的策略通过利用计算节点上可用的多核环境,进一步提高了 Map 和 Reduce 功能的性能和云资源的有效利用。本文详细说明了 框架的完成时间建模和工作原理。通过考虑三个生物医学应用程序,通过实验将 与 Hadoop 进行了性能比较。针对 BLAST、CAP3 和 DeepBind 生物医学应用程序的实验报告显示,与 Hadoop 框架相比,考虑到 框架,完成时间分别减少了 38.92%、18.00%和 34.62%。实验结果证明,所提出的 云计算平台具有稳健性、成本效益和可扩展性,足以在公共和私有云平台上支持各种应用程序。因此,总体表现和结果表明,所提出的理论完成时间建模与所研究的实验值之间存在很好的匹配。

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本文引用的文献

1
Long Read Alignment with Parallel MapReduce Cloud Platform.使用并行MapReduce云平台进行长读段比对
Biomed Res Int. 2015;2015:807407. doi: 10.1155/2015/807407. Epub 2015 Dec 29.
2
Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning.通过深度学习预测 DNA 和 RNA 结合蛋白的序列特异性。
Nat Biotechnol. 2015 Aug;33(8):831-8. doi: 10.1038/nbt.3300. Epub 2015 Jul 27.
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Translational biomedical informatics in the cloud: present and future.云环境下的转化医学信息学:现状与未来。
Biomed Res Int. 2013;2013:658925. doi: 10.1155/2013/658925. Epub 2013 Mar 17.
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Now and next-generation sequencing techniques: future of sequence analysis using cloud computing.现在和下一代测序技术:使用云计算进行序列分析的未来。
Front Genet. 2012 Dec 11;3:280. doi: 10.3389/fgene.2012.00280. eCollection 2012.
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CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping.CloudAligner:一种基于MapReduce的快速且功能齐全的序列映射工具。
BMC Res Notes. 2011 Jun 6;4:171. doi: 10.1186/1756-0500-4-171.
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Cloud-scale RNA-sequencing differential expression analysis with Myrna.利用 Myrna 进行云规模 RNA-seq 差异表达分析。
Genome Biol. 2010;11(8):R83. doi: 10.1186/gb-2010-11-8-r83. Epub 2010 Aug 11.
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Cloud computing for comparative genomics.云计算在比较基因组学中的应用。
BMC Bioinformatics. 2010 May 18;11:259. doi: 10.1186/1471-2105-11-259.
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The case for cloud computing in genome informatics.云计算在基因组信息学中的应用。
Genome Biol. 2010;11(5):207. doi: 10.1186/gb-2010-11-5-207. Epub 2010 May 5.
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Searching for SNPs with cloud computing.利用云计算搜索 SNP。
Genome Biol. 2009;10(11):R134. doi: 10.1186/gb-2009-10-11-r134. Epub 2009 Nov 20.
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Cloud computing: a new business paradigm for biomedical information sharing.云计算:生物医学信息共享的新业务模式。
J Biomed Inform. 2010 Apr;43(2):342-53. doi: 10.1016/j.jbi.2009.08.014. Epub 2009 Aug 26.