{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,3]],"date-time":"2025-05-03T14:44:51Z","timestamp":1746283491347,"version":"3.38.0"},"reference-count":6,"publisher":"SAGE Publications","issue":"4","license":[{"start":{"date-parts":[[2015,5,17]],"date-time":"2015-05-17T00:00:00Z","timestamp":1431820800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["The International Journal of High Performance Computing Applications"],"published-print":{"date-parts":[[2015,11]]},"abstract":"<jats:p> Detecting epistasis, such as 2-SNP interactions, in genome-wide association studies (GWAS) is an important but time consuming operation. Consequently, GPUs have already been used to accelerate these studies, reducing the runtime for moderately-sized datasets to less than 1 hour. However, single-GPU approaches cannot perform large-scale GWAS in reasonable time. In this work we present multiEpistSearch, a tool to detect epistasis that works on GPU clusters. While CUDA is used for parallelization within each GPU, the workload distribution among GPUs is performed with Unified Parallel C+ + (UPC+ +), a novel extension of C+ + that follows the Partitioned Global Address Space (PGAS) model. multiEpistSearch is able to analyze large-scale datasets with 5 million SNPs from 10,000 individuals in less than 3 hours using 24 NVIDIA GTX Titans. <\/jats:p>","DOI":"10.1177\/1094342015585846","type":"journal-article","created":{"date-parts":[[2015,5,19]],"date-time":"2015-05-19T00:01:07Z","timestamp":1431993667000},"page":"506-510","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":12,"title":["Large-scale genome-wide association studies on a GPU cluster using a CUDA-accelerated PGAS programming model"],"prefix":"10.1177","volume":"29","author":[{"given":"Jorge","family":"Gonz\u00e1lez-Dom\u00ednguez","sequence":"first","affiliation":[{"name":"Parallel and Distributed Architectures Group, Johannes Gutenberg University-Mainz, Mainz, Germany"}]},{"given":"Jan Christian","family":"K\u00e4ssens","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Christian-Albrechts-University of Kiel, Kiel, Germany"}]},{"given":"Lars","family":"Wienbrandt","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Christian-Albrechts-University of Kiel, Kiel, Germany"}]},{"given":"Bertil","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Parallel and Distributed Architectures Group, Johannes Gutenberg University-Mainz, Mainz, Germany"}]}],"member":"179","published-online":{"date-parts":[[2015,5,17]]},"reference":[{"key":"bibr1-1094342015585846","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-09873-9_57"},{"key":"bibr2-1094342015585846","doi-asserted-by":"publisher","DOI":"10.1109\/CLUSTER.2014.6968770"},{"key":"bibr3-1094342015585846","doi-asserted-by":"publisher","DOI":"10.1038\/nature05911"},{"key":"bibr4-1094342015585846","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2010.07.021"},{"key":"bibr5-1094342015585846","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr114"},{"key":"bibr6-1094342015585846","doi-asserted-by":"publisher","DOI":"10.1109\/IPDPS.2014.115"}],"container-title":["The International Journal of High Performance Computing Applications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1177\/1094342015585846","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/full-xml\/10.1177\/1094342015585846","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1177\/1094342015585846","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T17:18:02Z","timestamp":1740849482000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/10.1177\/1094342015585846"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,5,17]]},"references-count":6,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2015,11]]}},"alternative-id":["10.1177\/1094342015585846"],"URL":"https:\/\/doi.org\/10.1177\/1094342015585846","relation":{},"ISSN":["1094-3420","1741-2846"],"issn-type":[{"type":"print","value":"1094-3420"},{"type":"electronic","value":"1741-2846"}],"subject":[],"published":{"date-parts":[[2015,5,17]]}}}