{"id":"https://openalex.org/W2295760680","doi":"https://doi.org/10.1177/1094342015585846","title":"Large-scale genome-wide association studies on a GPU cluster using a CUDA-accelerated PGAS programming model","display_name":"Large-scale genome-wide association studies on a GPU cluster using a CUDA-accelerated PGAS programming model","publication_year":2015,"publication_date":"2015-05-17","ids":{"openalex":"https://openalex.org/W2295760680","doi":"https://doi.org/10.1177/1094342015585846","mag":"2295760680"},"language":"en","primary_location":{"id":"doi:10.1177/1094342015585846","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342015585846","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/2183/20970","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008112601","display_name":"Jorge Gonz\u00e1lez\u2010Dom\u00ednguez","orcid":"https://orcid.org/0000-0002-2602-4874"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Jorge Gonz\u00e1lez-Dom\u00ednguez","raw_affiliation_strings":["Parallel and Distributed Architectures Group, Johannes Gutenberg University-Mainz, Mainz, Germany"],"affiliations":[{"raw_affiliation_string":"Parallel and Distributed Architectures Group, Johannes Gutenberg University-Mainz, Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086592721","display_name":"Jan Christian K\u00e4ssens","orcid":"https://orcid.org/0000-0001-7840-1160"},"institutions":[{"id":"https://openalex.org/I32021983","display_name":"Kiel University","ror":"https://ror.org/04v76ef78","country_code":"DE","type":"education","lineage":["https://openalex.org/I32021983"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jan Christian K\u00e4ssens","raw_affiliation_strings":["Department of Computer Science, Christian-Albrechts-University of Kiel, Kiel, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Christian-Albrechts-University of Kiel, Kiel, Germany","institution_ids":["https://openalex.org/I32021983"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003785979","display_name":"Lars Wienbrandt","orcid":"https://orcid.org/0000-0001-5685-2032"},"institutions":[{"id":"https://openalex.org/I32021983","display_name":"Kiel University","ror":"https://ror.org/04v76ef78","country_code":"DE","type":"education","lineage":["https://openalex.org/I32021983"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Lars Wienbrandt","raw_affiliation_strings":["Department of Computer Science, Christian-Albrechts-University of Kiel, Kiel, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Christian-Albrechts-University of Kiel, Kiel, Germany","institution_ids":["https://openalex.org/I32021983"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020388832","display_name":"Bertil Schmidt","orcid":"https://orcid.org/0000-0003-2597-8331"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bertil Schmidt","raw_affiliation_strings":["Parallel and Distributed Architectures Group, Johannes Gutenberg University-Mainz, Mainz, Germany"],"affiliations":[{"raw_affiliation_string":"Parallel and Distributed Architectures Group, Johannes Gutenberg University-Mainz, Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5008112601"],"corresponding_institution_ids":["https://openalex.org/I197323543"],"apc_list":null,"apc_paid":null,"fwci":2.2244,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.88985522,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"29","issue":"4","first_page":"506","last_page":"510"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11482","display_name":"RNA modifications and cancer","score":0.9814000129699707,"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":0.9812999963760376,"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/partitioned-global-address-space","display_name":"Partitioned global address space","score":0.930548906326294},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.7858836650848389},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7653103470802307},{"id":"https://openalex.org/keywords/gpu-cluster","display_name":"GPU cluster","score":0.7593435645103455},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6888378858566284},{"id":"https://openalex.org/keywords/workload","display_name":"Workload","score":0.5279668569564819},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.5130687952041626},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4717318117618561},{"id":"https://openalex.org/keywords/cluster","display_name":"Cluster (spacecraft)","score":0.4224618077278137},{"id":"https://openalex.org/keywords/epistasis","display_name":"Epistasis","score":0.41418665647506714},{"id":"https://openalex.org/keywords/programming-paradigm","display_name":"Programming paradigm","score":0.33966270089149475},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14622431993484497},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.07240813970565796},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.06305962800979614}],"concepts":[{"id":"https://openalex.org/C60832428","wikidata":"https://www.wikidata.org/wiki/Q945818","display_name":"Partitioned global address space","level":3,"score":0.930548906326294},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.7858836650848389},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7653103470802307},{"id":"https://openalex.org/C2781335571","wikidata":"https://www.wikidata.org/wiki/Q2633544","display_name":"GPU cluster","level":3,"score":0.7593435645103455},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6888378858566284},{"id":"https://openalex.org/C2778476105","wikidata":"https://www.wikidata.org/wiki/Q628539","display_name":"Workload","level":2,"score":0.5279668569564819},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.5130687952041626},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4717318117618561},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.4224618077278137},{"id":"https://openalex.org/C61727976","wikidata":"https://www.wikidata.org/wiki/Q751748","display_name":"Epistasis","level":3,"score":0.41418665647506714},{"id":"https://openalex.org/C34165917","wikidata":"https://www.wikidata.org/wiki/Q188267","display_name":"Programming paradigm","level":2,"score":0.33966270089149475},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14622431993484497},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.07240813970565796},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.06305962800979614},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1177/1094342015585846","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342015585846","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"},{"id":"pmh:oai:dnet:ruc_________::3fa4b5b868492ec3e3266b87912164a3","is_oa":true,"landing_page_url":"http://hdl.handle.net/2183/20970","pdf_url":null,"source":{"id":"https://openalex.org/S4306402641","display_name":"LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Cient\u00edficas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4383465926","host_organization_name":"LA Referencia","host_organization_lineage":["https://openalex.org/I4383465926"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:dnet:ruc_________::3fa4b5b868492ec3e3266b87912164a3","is_oa":true,"landing_page_url":"http://hdl.handle.net/2183/20970","pdf_url":null,"source":{"id":"https://openalex.org/S4306402641","display_name":"LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Cient\u00edficas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4383465926","host_organization_name":"LA Referencia","host_organization_lineage":["https://openalex.org/I4383465926"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W116308793","https://openalex.org/W1822695366","https://openalex.org/W2042680665","https://openalex.org/W2117138514","https://openalex.org/W2133695315","https://openalex.org/W2134783591"],"related_works":["https://openalex.org/W2056717482","https://openalex.org/W2166185777","https://openalex.org/W2494227547","https://openalex.org/W3004875591","https://openalex.org/W2913497647","https://openalex.org/W2295760680","https://openalex.org/W2913919777","https://openalex.org/W1673512521","https://openalex.org/W2121504627","https://openalex.org/W4285429071"],"abstract_inverted_index":{"Detecting":[0],"epistasis,":[1],"such":[2],"as":[3],"2-SNP":[4],"interactions,":[5],"in":[6,46,117],"genome-wide":[7],"association":[8],"studies":[9],"(GWAS)":[10],"is":[11,67,79,104],"an":[12],"important":[13],"but":[14],"time":[15],"consuming":[16],"operation.":[17],"Consequently,":[18],"GPUs":[19,78],"have":[20],"already":[21],"been":[22],"used":[23,68],"to":[24,34,57,106],"accelerate":[25],"these":[26],"studies,":[27],"reducing":[28],"the":[29,74,96],"runtime":[30],"for":[31,69],"moderately-sized":[32],"datasets":[33,109],"less":[35,118],"than":[36,119],"1":[37],"hour.":[38],"However,":[39],"single-GPU":[40],"approaches":[41],"cannot":[42],"perform":[43],"large-scale":[44,108],"GWAS":[45],"reasonable":[47],"time.":[48],"In":[49],"this":[50],"work":[51],"we":[52],"present":[53],"multiEpistSearch,":[54],"a":[55,88],"tool":[56],"detect":[58],"epistasis":[59],"that":[60,94],"works":[61],"on":[62],"GPU":[63],"clusters.":[64],"While":[65],"CUDA":[66],"parallelization":[70],"within":[71],"each":[72],"GPU,":[73],"workload":[75],"distribution":[76],"among":[77],"performed":[80],"with":[81,110],"Unified":[82],"Parallel":[83],"C+":[84,92],"+":[85,93],"(UPC+":[86],"+),":[87],"novel":[89],"extension":[90],"of":[91],"follows":[95],"Partitioned":[97],"Global":[98],"Address":[99],"Space":[100],"(PGAS)":[101],"model.":[102],"multiEpistSearch":[103],"able":[105],"analyze":[107],"5":[111],"million":[112],"SNPs":[113],"from":[114],"10,000":[115],"individuals":[116],"3":[120],"hours":[121],"using":[122],"24":[123],"NVIDIA":[124],"GTX":[125],"Titans.":[126]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
