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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.?蛋白質(zhì)序列比對算
2、法在眾核結(jié)構(gòu)上的并行優(yōu)化1,2+1,211葉笑春,林偉,范東睿,張浩1(中國科學(xué)院計(jì)算技術(shù)研究所計(jì)算機(jī)體系結(jié)構(gòu)重點(diǎn)實(shí)驗(yàn)室,北京100190)2(中國科學(xué)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:在生物信息學(xué)中,蛋白質(zhì)序列比對是最為重要的算法之一,生物技術(shù)的發(fā)展使得已知的序列庫變得越來越龐大,這類算法本身又具有計(jì)算密集型的特點(diǎn),這導(dǎo)致進(jìn)行序列比對所消耗的時(shí)間也越來越長,目前的單核或者數(shù)量較少的多核系統(tǒng)均已經(jīng)難以滿足對計(jì)算速度的要求.Godson-T是一個(gè)包含諸多創(chuàng)新結(jié)構(gòu)的眾核平臺,在該系統(tǒng)
