{"id":"https://openalex.org/W2077364005","doi":"https://doi.org/10.1145/1854776.1854844","title":"Accelerating HMMER on GPUs by implementing hybrid data and task parallelism","display_name":"Accelerating HMMER on GPUs by implementing hybrid data and task parallelism","publication_year":2010,"publication_date":"2010-08-02","ids":{"openalex":"https://openalex.org/W2077364005","doi":"https://doi.org/10.1145/1854776.1854844","mag":"2077364005"},"language":"en","primary_location":{"id":"doi:10.1145/1854776.1854844","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1854776.1854844","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology","raw_type":"proceedings-article"},"type":"conference-paper","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/A5081065290","display_name":"Narayan Ganesan","orcid":null},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Narayan Ganesan","raw_affiliation_strings":["University of Delaware, Newark, DE"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Delaware, Newark, DE","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006814645","display_name":"Roger D. Chamberlain","orcid":"https://orcid.org/0000-0002-7207-6106"},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Roger D. Chamberlain","raw_affiliation_strings":["Washington University in St. Louis, St. Louis, MO"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Washington University in St. Louis, St. Louis, MO","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080937008","display_name":"Jeremy Buhler","orcid":"https://orcid.org/0000-0002-4159-4226"},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremy Buhler","raw_affiliation_strings":["Washington University in St. Louis, St. Louis, MO"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Washington University in St. Louis, St. Louis, MO","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078387820","display_name":"Michela Taufer","orcid":"https://orcid.org/0000-0002-0031-6377"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michela Taufer","raw_affiliation_strings":["University of Delaware, Newark, DE"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Delaware, Newark, DE","institution_ids":["https://openalex.org/I86501945"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":25,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"418","last_page":"421"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9972000122070312,"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"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9972000122070312,"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9962000250816345,"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/T10743","display_name":"Software Testing and Debugging Techniques","score":0.9934999942779541,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8872672915458679},{"id":"https://openalex.org/keywords/parallelism","display_name":"Parallelism (grammar)","score":0.8608091473579407},{"id":"https://openalex.org/keywords/data-parallelism","display_name":"Data parallelism","score":0.8169630765914917},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7571624517440796},{"id":"https://openalex.org/keywords/task-parallelism","display_name":"Task parallelism","score":0.7565591335296631},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.6443654298782349},{"id":"https://openalex.org/keywords/implicit-parallelism","display_name":"Implicit parallelism","score":0.5392429232597351},{"id":"https://openalex.org/keywords/instruction-level-parallelism","display_name":"Instruction-level parallelism","score":0.5301086902618408},{"id":"https://openalex.org/keywords/programming-paradigm","display_name":"Programming paradigm","score":0.4306226670742035},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2228025496006012}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8872672915458679},{"id":"https://openalex.org/C2781172179","wikidata":"https://www.wikidata.org/wiki/Q853109","display_name":"Parallelism (grammar)","level":2,"score":0.8608091473579407},{"id":"https://openalex.org/C61483411","wikidata":"https://www.wikidata.org/wiki/Q3124522","display_name":"Data parallelism","level":3,"score":0.8169630765914917},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7571624517440796},{"id":"https://openalex.org/C42992933","wikidata":"https://www.wikidata.org/wiki/Q691169","display_name":"Task parallelism","level":3,"score":0.7565591335296631},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.6443654298782349},{"id":"https://openalex.org/C3543717","wikidata":"https://www.wikidata.org/wiki/Q6007302","display_name":"Implicit parallelism","level":4,"score":0.5392429232597351},{"id":"https://openalex.org/C140763907","wikidata":"https://www.wikidata.org/wiki/Q2714055","display_name":"Instruction-level parallelism","level":3,"score":0.5301086902618408},{"id":"https://openalex.org/C34165917","wikidata":"https://www.wikidata.org/wiki/Q188267","display_name":"Programming paradigm","level":2,"score":0.4306226670742035},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2228025496006012},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/1854776.1854844","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1854776.1854844","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":7,"referenced_works":["https://openalex.org/W1598336441","https://openalex.org/W1964629970","https://openalex.org/W2059848742","https://openalex.org/W2074522660","https://openalex.org/W2102122585","https://openalex.org/W2133642410","https://openalex.org/W2151831732"],"related_works":["https://openalex.org/W2526302199","https://openalex.org/W2003935582","https://openalex.org/W4240606930","https://openalex.org/W2105992728","https://openalex.org/W74409296","https://openalex.org/W2950520577","https://openalex.org/W2494130044","https://openalex.org/W305742777","https://openalex.org/W3189160234","https://openalex.org/W3007272028"],"abstract_inverted_index":{"Many":[0],"biologically":[1],"motivated":[2],"problems":[3,83],"are":[4,11,41,52],"expressed":[5],"as":[6,39,68,78],"dynamic":[7],"programming":[8],"recurrences":[9],"and":[10,84],"difficult":[12],"to":[13,16,55,63,90],"parallelize":[14],"due":[15],"the":[17,48,57,75,103],"intrinsic":[18],"data":[19,69,92,108],"dependencies":[20],"in":[21],"their":[22,25],"algorithms.":[23],"Therefore":[24],"solutions":[26],"have":[27],"been":[28],"sped":[29],"up":[30],"using":[31],"task":[32],"level":[33],"parallelism":[34,66,93],"only.":[35],"Emerging":[36],"platforms":[37],"such":[38,67],"GPUs":[40],"appealing":[42],"parallel":[43],"architectures":[44],"for":[45,94],"high-performance;":[46],"at":[47],"same":[49],"time":[50],"they":[51],"a":[53,79,95,118],"motivation":[54],"rethink":[56],"algorithms":[58],"associated":[59],"with":[60],"these":[61,82],"problems,":[62],"extract":[64,91],"finer-grained":[65],"parallelism.In":[70],"this":[71],"paper,":[72],"we":[73,85],"consider":[74],"hmmersearch":[76,106],"program":[77],"representative":[80],"of":[81,122],"re-design":[86],"its":[87],"computational":[88],"algorithm":[89],"more":[96],"efficient":[97],"execution":[98],"on":[99,125],"emerging":[100],"platforms,":[101],"despite":[102],"fact":[104],"that":[105],"has":[107],"dependencies.":[109],"Our":[110],"approach":[111],"outperforms":[112],"other":[113],"existing":[114],"methods":[115],"when":[116],"searching":[117],"very":[119],"large":[120],"database":[121],"unsorted":[123],"sequences":[124],"GPUs.":[126]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
