{"id":"https://openalex.org/W2116567188","doi":"https://doi.org/10.1145/2555243.2555280","title":"Fine-grain parallel megabase sequence comparison with multiple heterogeneous GPUs","display_name":"Fine-grain parallel megabase sequence comparison with multiple heterogeneous GPUs","publication_year":2014,"publication_date":"2014-02-06","ids":{"openalex":"https://openalex.org/W2116567188","doi":"https://doi.org/10.1145/2555243.2555280","mag":"2116567188"},"language":"en","primary_location":{"id":"doi:10.1145/2555243.2555280","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2555243.2555280","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 19th ACM SIGPLAN symposium on Principles and practice of parallel programming","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/2117/23094","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058639233","display_name":"Edans F. O. Sandes","orcid":"https://orcid.org/0000-0001-9502-7799"},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Edans F. de O. Sandes","raw_affiliation_strings":["University of Brasilia, Brasilia, Brazil"],"affiliations":[{"raw_affiliation_string":"University of Brasilia, Brasilia, Brazil","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017532574","display_name":"Guillermo Miranda","orcid":null},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]},{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Guillermo Miranda","raw_affiliation_strings":["Barcelona Supercomputing Center, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005717412","display_name":"Alba Cristina Magalh\u00e3es Alves de Melo","orcid":"https://orcid.org/0000-0001-5191-5209"},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Alba C.M.A. Melo","raw_affiliation_strings":["University of Brasilia, Brasilia, Brazil"],"affiliations":[{"raw_affiliation_string":"University of Brasilia, Brasilia, Brazil","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074097057","display_name":"Xavier Martorell","orcid":"https://orcid.org/0000-0002-0417-3430"},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Xavier Martorell","raw_affiliation_strings":["Barcelona Supercomputing Center, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075755125","display_name":"Eduard Ayguad\u00e9","orcid":"https://orcid.org/0000-0002-5146-103X"},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]},{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Eduard Ayguade","raw_affiliation_strings":["Barcelona Supercomputing Center, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5058639233"],"corresponding_institution_ids":["https://openalex.org/I150729083"],"apc_list":null,"apc_paid":null,"fwci":0.7116,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.70680012,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"383","last_page":"384"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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":0.9991000294685364,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9979000091552734,"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":0.7777116298675537},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.758248507976532},{"id":"https://openalex.org/keywords/overhead","display_name":"Overhead (engineering)","score":0.6952119469642639},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5762576460838318},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5387265682220459},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4189297556877136},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.3774380385875702},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.299696147441864},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14816394448280334},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.097291499376297},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09698709845542908}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7777116298675537},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.758248507976532},{"id":"https://openalex.org/C2779960059","wikidata":"https://www.wikidata.org/wiki/Q7113681","display_name":"Overhead (engineering)","level":2,"score":0.6952119469642639},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5762576460838318},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5387265682220459},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4189297556877136},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.3774380385875702},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.299696147441864},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14816394448280334},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.097291499376297},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09698709845542908}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1145/2555243.2555280","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2555243.2555280","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 19th ACM SIGPLAN symposium on Principles and practice of parallel programming","raw_type":"proceedings-article"},{"id":"pmh:oai:upcommons.upc.edu:2117/23094","is_oa":true,"landing_page_url":"http://hdl.handle.net/2117/23094","pdf_url":null,"source":{"id":"https://openalex.org/S4377196262","display_name":"UPCommons institutional repository (Universitat Polit\u00e8cnica de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9617848","host_organization_name":"Universitat Polit\u00e8cnica de Catalunya","host_organization_lineage":["https://openalex.org/I9617848"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/conferenceObject"},{"id":"pmh:oai:upcommons.upc.edu:2117/27492","is_oa":true,"landing_page_url":"http://hdl.handle.net/2117/27492","pdf_url":null,"source":{"id":"https://openalex.org/S4377196262","display_name":"UPCommons institutional repository (Universitat Polit\u00e8cnica de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9617848","host_organization_name":"Universitat Polit\u00e8cnica de Catalunya","host_organization_lineage":["https://openalex.org/I9617848"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:upcommons.upc.edu:2117/23094","is_oa":true,"landing_page_url":"http://hdl.handle.net/2117/23094","pdf_url":null,"source":{"id":"https://openalex.org/S4377196262","display_name":"UPCommons institutional repository (Universitat Polit\u00e8cnica de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9617848","host_organization_name":"Universitat Polit\u00e8cnica de Catalunya","host_organization_lineage":["https://openalex.org/I9617848"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/conferenceObject"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320321505","display_name":"Generalitat de Catalunya","ror":"https://ror.org/01bg62x04"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":5,"referenced_works":["https://openalex.org/W1986228396","https://openalex.org/W2087064593","https://openalex.org/W2098232690","https://openalex.org/W2108215151","https://openalex.org/W6675949863"],"related_works":["https://openalex.org/W4231775656","https://openalex.org/W2046435967","https://openalex.org/W2383646825","https://openalex.org/W2371018915","https://openalex.org/W2354191502","https://openalex.org/W1972225038","https://openalex.org/W3134658850","https://openalex.org/W2355938171","https://openalex.org/W2780079842","https://openalex.org/W2952348651"],"abstract_inverted_index":{"This":[0],"paper":[1],"proposes":[2],"and":[3],"evaluates":[4],"a":[5,29,47,70],"parallel":[6],"strategy":[7],"to":[8,43,74],"execute":[9],"the":[10,26,44,53],"exact":[11],"Smith-Waterman":[12],"(SW)":[13],"algorithm":[14],"for":[15],"megabase":[16],"DNA":[17],"sequences":[18],"in":[19],"heterogeneous":[20,85],"multi-GPU":[21],"platforms.":[22],"In":[23],"our":[24],"strategy,":[25],"computation":[27],"of":[28,60,72,78],"single":[30],"huge":[31],"SW":[32],"matrix":[33],"is":[34],"spread":[35],"over":[36],"multiple":[37],"GPUs,":[38],"which":[39],"communicate":[40],"border":[41],"elements":[42],"neighbour,":[45],"using":[46,64],"circular":[48],"buffer":[49],"mechanism":[50],"that":[51],"hides":[52],"communication":[54],"overhead.":[55],"We":[56],"compared":[57],"4":[58],"pairs":[59],"human-chimpanzee":[61],"homologous":[62],"chromosomes":[63],"2":[65],"different":[66],"GPU":[67],"environments,":[68],"obtaining":[69],"performance":[71],"up":[73],"140.36":[75],"GCUPS":[76],"(Billion":[77],"cells":[79],"processed":[80],"per":[81],"second)":[82],"with":[83],"3":[84],"GPUS.":[86]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2014,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2016-06-24T00:00:00"}
