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1、ISSN1000-9825,CODENRUXUEWE-mail:jos@iscas.ac.cnJournalofSoftware,Vol.21,No.12,December2010,pp.3094−3105http://www.jos.org.cndoi:10.3724/SP.J.1001.2010.03645Tel/Fax:+86-10-62562563©byInstituteofSoftware,theChineseAcademyofSciences.Allrightsreserved.∗蛋白质序列比对算
2、法在众核结构上的并行优化1,2+1,211叶笑春,林伟,范东睿,张浩1(中国科学院计算技术研究所计算机体系结构重点实验室,北京100190)2(中国科学院研究生院,北京100049)EfficientParallelizationandOptimizationofProteinSequenceComparisonAlgorithmonMany-CoreArchitecture1,2+1,211YEXiao-Chun,LINWei,FANDong-Rui,ZHANGHao1(KeyLaboratoryofCom
3、puterSystemandArchitecture,InstituteofComputingTechnology,TheChineseAcademyofSciences,Beijing100190,China)2(GraduateUniversity,TheChineseAcademyofSciences,Beijing100049,China)+Correspondingauthor:E-mail:yexiaochun@ict.ac.cnYeXC,LinW,FanDR,ZhangH.Efficientpa
4、rallelizationandoptimizationofproteinsequencecomparisonalgorithmonmany-corearchitecture.JournalofSoftware,2010,21(12):3094−3105.http://www.jos.org.cn/1000-9825/3645.htmAbstract:Inbioinformatics,aproteinsequencecomparisonbetweentwobanksisoneofmostimportantal
5、gorithms.Thesequencebanksizeisbecominglargerandlargerwiththedevelopmentofbiotechnology,whilethealgorithmisalsocomputationintensive.Thisleadstomoreandmoreconsumptiontimeandthesingleprocessorormulticoresystem,withonlyafewcores,arenotpowerfulenoughtoreachasati
6、sfyingspeednowadays.Godson-Tisanewkindofmany-corearchitecturewithlotsofnovelfeatures.TheparallelizationofaproteinsequencecomparisonalgorithmonGodson-Tisimplemented.Atthesametime,thealgorithmstructureandarchitecturefeaturesofGodson-Tarecombined,andsomeoptimi
7、zationinthreeaspectsaremade:synchronizationoverhead,memoryaccesscontention,andloadbalance.Theresultshowsthataclosetolinearspeedupisobtained,andtheperformanceismuchbetterthanthatoftheworkstationplatformbasedontheAMDOpteronprocessor.Keywords:sequencecompariso
8、nalgorithm;many-core;parallelization;optimization摘要:在生物信息学中,蛋白质序列比对是最为重要的算法之一,生物技术的发展使得已知的序列库变得越来越庞大,这类算法本身又具有计算密集型的特点,这导致进行序列比对所消耗的时间也越来越长,目前的单核或者数量较少的多核系统均已经难以满足对计算速度的要求.Godson-T是一个包含诸多创新结构的众核平台,在该系统
