{"id":"https://openalex.org/W2888836997","doi":"https://doi.org/10.1002/cpe.4522","title":"A multi\u2010GPU protein database search model with hybrid alignment manner on distributed GPU clusters","display_name":"A multi\u2010GPU protein database search model with hybrid alignment manner on distributed GPU clusters","publication_year":2018,"publication_date":"2018-04-20","ids":{"openalex":"https://openalex.org/W2888836997","doi":"https://doi.org/10.1002/cpe.4522","mag":"2888836997"},"language":"en","primary_location":{"id":"doi:10.1002/cpe.4522","is_oa":false,"landing_page_url":"https://doi.org/10.1002/cpe.4522","pdf_url":null,"source":{"id":"https://openalex.org/S11065456","display_name":"Concurrency and Computation Practice and Experience","issn_l":"1532-0626","issn":["1532-0626","1532-0634"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Concurrency and Computation: Practice and Experience","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048584674","display_name":"Wei Zhou","orcid":"https://orcid.org/0000-0001-7239-6321"},"institutions":[{"id":"https://openalex.org/I117331123","display_name":"Weifang Medical University","ror":"https://ror.org/03tmp6662","country_code":"CN","type":"education","lineage":["https://openalex.org/I117331123"]},{"id":"https://openalex.org/I66883779","display_name":"Weifang University","ror":"https://ror.org/01frp7483","country_code":"CN","type":"education","lineage":["https://openalex.org/I66883779"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wei Zhou","raw_affiliation_strings":["Network Information Center Weifang Medical University  Weifang China","Network Information Center Weifang Medical University Weifang China","Network Information Center, Weifang Medical University, Weifang, China","Wei Zhou, Network Information Center, Weifang Medical University, Weifang 261053, China"],"raw_orcid":"https://orcid.org/0000-0001-7239-6321","affiliations":[{"raw_affiliation_string":"Network Information Center Weifang Medical University  Weifang China","institution_ids":["https://openalex.org/I117331123"]},{"raw_affiliation_string":"Network Information Center Weifang Medical University Weifang China","institution_ids":["https://openalex.org/I117331123"]},{"raw_affiliation_string":"Network Information Center, Weifang Medical University, Weifang, China","institution_ids":["https://openalex.org/I117331123"]},{"raw_affiliation_string":"Wei Zhou, Network Information Center, Weifang Medical University, Weifang 261053, China","institution_ids":["https://openalex.org/I117331123","https://openalex.org/I66883779"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086671075","display_name":"Zhanxiu Cai","orcid":null},"institutions":[{"id":"https://openalex.org/I117331123","display_name":"Weifang Medical University","ror":"https://ror.org/03tmp6662","country_code":"CN","type":"education","lineage":["https://openalex.org/I117331123"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhanxiu Cai","raw_affiliation_strings":["School of Bioscience and Technology Weifang Medical University  Weifang China","School of Bioscience and Technology, Weifang Medical University, Weifang, China","School of Bioscience and Technology Weifang Medical University Weifang China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Bioscience and Technology Weifang Medical University  Weifang China","institution_ids":["https://openalex.org/I117331123"]},{"raw_affiliation_string":"School of Bioscience and Technology, Weifang Medical University, Weifang, China","institution_ids":["https://openalex.org/I117331123"]},{"raw_affiliation_string":"School of Bioscience and Technology Weifang Medical University Weifang China","institution_ids":["https://openalex.org/I117331123"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103029325","display_name":"Bo Lian","orcid":"https://orcid.org/0000-0002-2994-4633"},"institutions":[{"id":"https://openalex.org/I117331123","display_name":"Weifang Medical University","ror":"https://ror.org/03tmp6662","country_code":"CN","type":"education","lineage":["https://openalex.org/I117331123"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo Lian","raw_affiliation_strings":["School of Bioscience and Technology Weifang Medical University  Weifang China","School of Bioscience and Technology, Weifang Medical University, Weifang, China","School of Bioscience and Technology Weifang Medical University Weifang China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Bioscience and Technology Weifang Medical University  Weifang China","institution_ids":["https://openalex.org/I117331123"]},{"raw_affiliation_string":"School of Bioscience and Technology, Weifang Medical University, Weifang, China","institution_ids":["https://openalex.org/I117331123"]},{"raw_affiliation_string":"School of Bioscience and Technology Weifang Medical University Weifang China","institution_ids":["https://openalex.org/I117331123"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011333035","display_name":"Jincai Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I117331123","display_name":"Weifang Medical University","ror":"https://ror.org/03tmp6662","country_code":"CN","type":"education","lineage":["https://openalex.org/I117331123"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jincai Wang","raw_affiliation_strings":["Computer Staff Room Weifang Medical University  Weifang China","Computer Staff Room Weifang Medical University Weifang China","Computer Staff Room, Weifang Medical University, Weifang, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Staff Room Weifang Medical University  Weifang China","institution_ids":["https://openalex.org/I117331123"]},{"raw_affiliation_string":"Computer Staff Room Weifang Medical University Weifang China","institution_ids":["https://openalex.org/I117331123"]},{"raw_affiliation_string":"Computer Staff Room, Weifang Medical University, Weifang, China","institution_ids":["https://openalex.org/I117331123"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101040780","display_name":"Jianping Ma","orcid":null},"institutions":[{"id":"https://openalex.org/I117331123","display_name":"Weifang Medical University","ror":"https://ror.org/03tmp6662","country_code":"CN","type":"education","lineage":["https://openalex.org/I117331123"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianping Ma","raw_affiliation_strings":["Division of Human Resources Weifang Medical University  Weifang China","Division of Human Resources, Weifang Medical University, Weifang, China","Division of Human Resources Weifang Medical University Weifang China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Human Resources Weifang Medical University  Weifang China","institution_ids":["https://openalex.org/I117331123"]},{"raw_affiliation_string":"Division of Human Resources, Weifang Medical University, Weifang, China","institution_ids":["https://openalex.org/I117331123"]},{"raw_affiliation_string":"Division of Human Resources Weifang Medical University Weifang China","institution_ids":["https://openalex.org/I117331123"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081387353","display_name":"Bin Sun","orcid":null},"institutions":[{"id":"https://openalex.org/I117331123","display_name":"Weifang Medical University","ror":"https://ror.org/03tmp6662","country_code":"CN","type":"education","lineage":["https://openalex.org/I117331123"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bin Sun","raw_affiliation_strings":["Network Information Center Weifang Medical University  Weifang China","Network Information Center Weifang Medical University Weifang China","Network Information Center, Weifang Medical University, Weifang, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Network Information Center Weifang Medical University  Weifang China","institution_ids":["https://openalex.org/I117331123"]},{"raw_affiliation_string":"Network Information Center Weifang Medical University Weifang China","institution_ids":["https://openalex.org/I117331123"]},{"raw_affiliation_string":"Network Information Center, Weifang Medical University, Weifang, China","institution_ids":["https://openalex.org/I117331123"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083473626","display_name":"Qian Yu","orcid":null},"institutions":[{"id":"https://openalex.org/I117331123","display_name":"Weifang Medical University","ror":"https://ror.org/03tmp6662","country_code":"CN","type":"education","lineage":["https://openalex.org/I117331123"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qian Yu","raw_affiliation_strings":["Network Information Center Weifang Medical University  Weifang China","Network Information Center Weifang Medical University Weifang China","Network Information Center, Weifang Medical University, Weifang, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Network Information Center Weifang Medical University  Weifang China","institution_ids":["https://openalex.org/I117331123"]},{"raw_affiliation_string":"Network Information Center Weifang Medical University Weifang China","institution_ids":["https://openalex.org/I117331123"]},{"raw_affiliation_string":"Network Information Center, Weifang Medical University, Weifang, China","institution_ids":["https://openalex.org/I117331123"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5048584674"],"corresponding_institution_ids":["https://openalex.org/I117331123","https://openalex.org/I66883779"],"apc_list":{"value":4740,"currency":"USD","value_usd":4740},"apc_paid":null,"fwci":0.2783,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.57588827,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"30","issue":"18","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9973000288009644,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.9165497422218323},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.6977716684341431},{"id":"https://openalex.org/keywords/gpu-cluster","display_name":"GPU cluster","score":0.693581223487854},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.6928262710571289},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5706357955932617},{"id":"https://openalex.org/keywords/message-passing-interface","display_name":"Message Passing Interface","score":0.5685358047485352},{"id":"https://openalex.org/keywords/workload","display_name":"Workload","score":0.4698300063610077},{"id":"https://openalex.org/keywords/cluster","display_name":"Cluster (spacecraft)","score":0.44839537143707275},{"id":"https://openalex.org/keywords/graphics-processing-unit","display_name":"Graphics processing unit","score":0.43439802527427673},{"id":"https://openalex.org/keywords/message-passing","display_name":"Message passing","score":0.43238168954849243},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4183065593242645},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3398836851119995},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.14979076385498047}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.9165497422218323},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.6977716684341431},{"id":"https://openalex.org/C2781335571","wikidata":"https://www.wikidata.org/wiki/Q2633544","display_name":"GPU cluster","level":3,"score":0.693581223487854},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.6928262710571289},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5706357955932617},{"id":"https://openalex.org/C166782233","wikidata":"https://www.wikidata.org/wiki/Q127879","display_name":"Message Passing Interface","level":3,"score":0.5685358047485352},{"id":"https://openalex.org/C2778476105","wikidata":"https://www.wikidata.org/wiki/Q628539","display_name":"Workload","level":2,"score":0.4698300063610077},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.44839537143707275},{"id":"https://openalex.org/C2779851693","wikidata":"https://www.wikidata.org/wiki/Q183484","display_name":"Graphics processing unit","level":2,"score":0.43439802527427673},{"id":"https://openalex.org/C854659","wikidata":"https://www.wikidata.org/wiki/Q1859284","display_name":"Message passing","level":2,"score":0.43238168954849243},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4183065593242645},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3398836851119995},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.14979076385498047},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1002/cpe.4522","is_oa":false,"landing_page_url":"https://doi.org/10.1002/cpe.4522","pdf_url":null,"source":{"id":"https://openalex.org/S11065456","display_name":"Concurrency and Computation Practice and Experience","issn_l":"1532-0626","issn":["1532-0626","1532-0634"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Concurrency and Computation: Practice and Experience","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8686087829","display_name":null,"funder_award_id":"ZR2015CL020","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"}],"funders":[{"id":"https://openalex.org/F4320324174","display_name":"Natural Science Foundation of Shandong Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1558365920","https://openalex.org/W1762731526","https://openalex.org/W1886151154","https://openalex.org/W1955619021","https://openalex.org/W1991467930","https://openalex.org/W1995106824","https://openalex.org/W2000335122","https://openalex.org/W2013733655","https://openalex.org/W2024122052","https://openalex.org/W2028499920","https://openalex.org/W2044338118","https://openalex.org/W2049349724","https://openalex.org/W2065461987","https://openalex.org/W2068448872","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2105672886","https://openalex.org/W2133540884","https://openalex.org/W2152706101","https://openalex.org/W2156931339","https://openalex.org/W2158714788","https://openalex.org/W2605274051","https://openalex.org/W2980128339","https://openalex.org/W3138798301"],"related_works":["https://openalex.org/W2124048060","https://openalex.org/W1902983110","https://openalex.org/W2378910916","https://openalex.org/W4386915331","https://openalex.org/W2116006827","https://openalex.org/W2056717482","https://openalex.org/W2030707850","https://openalex.org/W2393490604","https://openalex.org/W2062632752","https://openalex.org/W2808583214"],"abstract_inverted_index":{"Summary":[0],"In":[1,33,151],"computational":[2],"biology,":[3],"technologies":[4],"of":[5,56,71,89,163],"protein":[6,41],"database":[7,18,42],"search":[8,23,43],"become":[9],"more":[10,12],"and":[11,66,73,127,145],"indispensable":[13],"for":[14],"researchers.":[15],"As":[16],"the":[17,22,76,87,96,152,154,171,183,188],"size":[19],"rapidly":[20],"grows,":[21],"complexity":[24],"is":[25,83,119,135,156],"improving,":[26],"leading":[27],"to":[28,85,98,115,124,179],"an":[29,113],"excessively":[30],"long":[31],"runtime.":[32],"this":[34],"paper,":[35],"we":[36],"provide":[37],"a":[38,159,176],"novel":[39],"parallel":[40,133,143],"model":[44,52,97,123,155,173],"based":[45],"on":[46,158],"distributed":[47],"GPU":[48],"clusters.":[49],"The":[50,79,132,167],"proposed":[51,172],"targets":[53],"clusters":[54],"composed":[55,162],"personal":[57,165],"computers":[58],"equipped":[59],"with":[60,101,105,137],"graphic":[61],"processing":[62],"unit":[63],"(GPU)":[64],"cards":[65],"can":[67,174],"employ":[68],"computing":[69],"power":[70],"GPUs":[72],"CPUs":[74],"in":[75,121],"cluster":[77,103,161],"nodes.":[78],"workload":[80],"distribution":[81],"strategy":[82],"designed":[84],"take":[86],"performance":[88],"each":[90],"node":[91],"into":[92],"account,":[93],"which":[94],"enables":[95],"work":[99],"well":[100],"inhomogeneous":[102],"nodes":[104],"different":[106],"hardware":[107],"configurations.":[108],"A":[109],"hybrid":[110],"alignment":[111],"approach,":[112],"extension":[114],"our":[116,122],"previous":[117],"work,":[118],"used":[120],"make":[125],"global":[126],"local":[128],"alignments":[129],"done":[130],"concurrently.":[131],"program":[134],"realized":[136],"compute":[138],"unified":[139],"device":[140],"architecture":[141],"(CUDA)":[142],"framework":[144],"Microsoft":[146],"message":[147],"passing":[148],"interface":[149],"(MS\u2010MPI).":[150],"experiment,":[153],"tested":[157],"small":[160],"three":[164],"computers.":[166],"results":[168],"show":[169],"that":[170],"achieve":[175],"speedup":[177],"up":[178],"159.89":[180],"times":[181],"over":[182],"serial":[184],"counterpart":[185],"when":[186],"searching":[187],"Swiss\u2010Prot":[189],"database.":[190]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
