{"id":"https://openalex.org/W2887194095","doi":"https://doi.org/10.1145/3229710.3229734","title":"Increasing Molecular Dynamics Simulations Throughput by Virtualizing Remote GPUs with rCUDA","display_name":"Increasing Molecular Dynamics Simulations Throughput by Virtualizing Remote GPUs with rCUDA","publication_year":2018,"publication_date":"2018-07-31","ids":{"openalex":"https://openalex.org/W2887194095","doi":"https://doi.org/10.1145/3229710.3229734","mag":"2887194095"},"language":"en","primary_location":{"id":"doi:10.1145/3229710.3229734","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3229710.3229734","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 47th International Conference on Parallel Processing Companion","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/A5073517799","display_name":"Javier Prades","orcid":"https://orcid.org/0000-0003-3349-2200"},"institutions":[{"id":"https://openalex.org/I60053951","display_name":"Universitat Polit\u00e8cnica de Val\u00e8ncia","ror":"https://ror.org/01460j859","country_code":"ES","type":"education","lineage":["https://openalex.org/I60053951"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Javier Prades","raw_affiliation_strings":["Universitat Polit\u00e8cnica de Val\u00e8ncia, Valencia, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universitat Polit\u00e8cnica de Val\u00e8ncia, Valencia, Spain","institution_ids":["https://openalex.org/I60053951"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054612127","display_name":"Carlos Rea\u00f1o","orcid":"https://orcid.org/0000-0001-7871-9152"},"institutions":[{"id":"https://openalex.org/I60053951","display_name":"Universitat Polit\u00e8cnica de Val\u00e8ncia","ror":"https://ror.org/01460j859","country_code":"ES","type":"education","lineage":["https://openalex.org/I60053951"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Carlos Rea\u00f1o","raw_affiliation_strings":["Universitat Polit\u00e8cnica de Val\u00e8ncia, Valencia, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universitat Polit\u00e8cnica de Val\u00e8ncia, Valencia, Spain","institution_ids":["https://openalex.org/I60053951"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050691850","display_name":"Federico Silla","orcid":"https://orcid.org/0000-0002-6435-1200"},"institutions":[{"id":"https://openalex.org/I60053951","display_name":"Universitat Polit\u00e8cnica de Val\u00e8ncia","ror":"https://ror.org/01460j859","country_code":"ES","type":"education","lineage":["https://openalex.org/I60053951"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Federico Silla","raw_affiliation_strings":["Universitat Polit\u00e8cnica de Val\u00e8ncia, Valencia, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universitat Polit\u00e8cnica de Val\u00e8ncia, Valencia, Spain","institution_ids":["https://openalex.org/I60053951"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028232016","display_name":"Baldomero Imbern\u00f3n","orcid":"https://orcid.org/0000-0002-2758-8364"},"institutions":[{"id":"https://openalex.org/I68763199","display_name":"Universidad Cat\u00f3lica de Murcia","ror":"https://ror.org/05b1rsv17","country_code":"ES","type":"education","lineage":["https://openalex.org/I68763199"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Baldomero Imbern\u00f3n","raw_affiliation_strings":["Universidad Cat\u00f3lica de Murcia (UCAM), Murcia, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universidad Cat\u00f3lica de Murcia (UCAM), Murcia, Spain","institution_ids":["https://openalex.org/I68763199"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037673215","display_name":"Horacio P\u00e9rez\u2010S\u00e1nchez","orcid":"https://orcid.org/0000-0003-4468-7898"},"institutions":[{"id":"https://openalex.org/I68763199","display_name":"Universidad Cat\u00f3lica de Murcia","ror":"https://ror.org/05b1rsv17","country_code":"ES","type":"education","lineage":["https://openalex.org/I68763199"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Horacio P\u00e9rez-S\u00e1nchez","raw_affiliation_strings":["Universidad Cat\u00f3lica de Murcia (UCAM), Murcia, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universidad Cat\u00f3lica de Murcia (UCAM), Murcia, Spain","institution_ids":["https://openalex.org/I68763199"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088468258","display_name":"Jos\u00e9 M. Cecilia","orcid":"https://orcid.org/0000-0001-5648-214X"},"institutions":[{"id":"https://openalex.org/I68763199","display_name":"Universidad Cat\u00f3lica de Murcia","ror":"https://ror.org/05b1rsv17","country_code":"ES","type":"education","lineage":["https://openalex.org/I68763199"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 M. Cecilia","raw_affiliation_strings":["Universidad Cat\u00f3lica de Murcia (UCAM), Murcia, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universidad Cat\u00f3lica de Murcia (UCAM), Murcia, Spain","institution_ids":["https://openalex.org/I68763199"]}]}],"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":3,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/T10101","display_name":"Cloud Computing and Resource Management","score":0.9959999918937683,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9933000206947327,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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":0.7877382040023804},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.6887223720550537},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.6302329897880554},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5855136513710022},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.5351454019546509},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.48989027738571167},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.48090648651123047},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.43735527992248535},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.42663252353668213},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.17527157068252563},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.16131597757339478},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.1433333158493042},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10676157474517822}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7877382040023804},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.6887223720550537},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.6302329897880554},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5855136513710022},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.5351454019546509},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.48989027738571167},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.48090648651123047},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.43735527992248535},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.42663252353668213},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.17527157068252563},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.16131597757339478},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.1433333158493042},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10676157474517822},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","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/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3229710.3229734","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3229710.3229734","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 47th International Conference on Parallel Processing Companion","raw_type":"proceedings-article"},{"id":"pmh:oai:pure.qub.ac.uk/portal:publications/f9287466-a481-4dd8-a193-842d31727fd8","is_oa":false,"landing_page_url":"https://pure.qub.ac.uk/en/publications/f9287466-a481-4dd8-a193-842d31727fd8","pdf_url":null,"source":{"id":"https://openalex.org/S4306402319","display_name":"Research Portal (Queen's University Belfast)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I126231945","host_organization_name":"Queen's University Belfast","host_organization_lineage":["https://openalex.org/I126231945"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Prades , J , Rea\u00f1o , C , Silla , F , Imbern\u00f3n , B , P\u00e9rez S\u00e1nchez , H &amp; Cecilia , J M 2018 , Increasing Molecular Dynamics Simulations Throughput by Virtualizing Remote GPUs with rCUDA . in Proceedings of the 47th International Conference on Parallel Processing Companion (ICPP '18 ) . Association for Computing Machinery . https://doi.org/10.1145/3229710.3229734","raw_type":"contributionToPeriodical"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6646869981","display_name":null,"funder_award_id":"PROMETEO/2017/077","funder_id":"https://openalex.org/F4320321864","funder_display_name":"Generalitat Valenciana"}],"funders":[{"id":"https://openalex.org/F4320321864","display_name":"Generalitat Valenciana","ror":"https://ror.org/0097mvx21"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1512801428","https://openalex.org/W1596936080","https://openalex.org/W1908931110","https://openalex.org/W1966078827","https://openalex.org/W1986240377","https://openalex.org/W2004181813","https://openalex.org/W2016047921","https://openalex.org/W2022595490","https://openalex.org/W2033528237","https://openalex.org/W2075460992","https://openalex.org/W2118233996","https://openalex.org/W2140239055","https://openalex.org/W2150981663","https://openalex.org/W2160544821","https://openalex.org/W2318998108","https://openalex.org/W2400913246","https://openalex.org/W2489700861","https://openalex.org/W2600072887","https://openalex.org/W2795186145"],"related_works":["https://openalex.org/W3062287","https://openalex.org/W2384867379","https://openalex.org/W3189307731","https://openalex.org/W1582436825","https://openalex.org/W2949962288","https://openalex.org/W2364686214","https://openalex.org/W1428699136","https://openalex.org/W1998560227","https://openalex.org/W1996803181","https://openalex.org/W2979588510"],"abstract_inverted_index":{"The":[0,140],"full-understanding":[1],"of":[2,5,13,19,46,52,104,118,150,201,235],"the":[3,9,17,43,55,81,92,101,112,128,138,164,198,206,214,233,244],"dynamics":[4,33],"molecular":[6],"systems":[7],"at":[8,178],"atomic":[10],"scale":[11],"is":[12,35,62,74,182],"great":[14],"relevance":[15],"in":[16,69,91,107,152],"fields":[18],"chemistry":[20],"physics,":[21],"materials":[22],"science":[23],"and":[24,94,97,99,120,225],"drug":[25,108],"discovery":[26,109],"just":[27],"to":[28,65,110,196,220,243],"name":[29],"a":[30,36,115,121,169,179,194,218,238,250],"few.":[31],"Molecular":[32],"(MD)":[34],"widely":[37],"used":[38],"computer":[39],"tool":[40,219],"for":[41],"simulating":[42],"dynamical":[44],"behavior":[45],"molecules":[47],"by":[48,59,77,86,146,204],"solving":[49],"Newton's":[50],"equations":[51],"motion.":[53],"However,":[54,163],"computational":[56,154],"horsepower":[57],"required":[58,85,106],"MD":[60,88,176,202],"simulations":[61,105,151,203],"too":[63],"high":[64,102],"obtain":[66],"conclusive":[67],"results":[68,230],"real":[70],"world":[71],"scenarios.":[72],"This":[73],"mainly":[75],"motivated":[76],"two":[78],"factors:":[79],"(1)":[80],"long":[82],"execution":[83],"time":[84],"each":[87,161],"simulation":[89],"(usually":[90],"nanosecond":[93],"microsecond":[95],"scale,":[96],"beyond)":[98],"(2)":[100],"number":[103],"study":[111],"interactions":[113],"between":[114],"large":[116,148,153],"library":[117],"compounds":[119],"given":[122],"protein":[123],"target.":[124],"To":[125],"deal":[126],"with":[127],"former,":[129],"Graphics":[130],"Processing":[131],"Units":[132],"(GPUs)":[133],"have":[134],"come":[135],"up":[136],"into":[137,184],"scene.":[139],"latter":[141],"has":[142],"been":[143],"traditionally":[144],"approached":[145],"launching":[147],"amounts":[149],"clusters":[155],"that":[156,172,232],"may":[157],"contain":[158],"GPUs":[159,165,222],"on":[160],"node.":[162],"are":[166],"targeted":[167],"as":[168,217],"single":[170],"node":[171],"only":[173],"runs":[174],"one":[175],"instance":[177],"time,":[180],"which":[181],"translated":[183],"low":[185],"GPU":[186,207],"occupancy":[187,208],"ratios.":[188],"In":[189],"this":[190],"paper,":[191],"we":[192],"design":[193],"strategy":[195],"increase":[197],"overall":[199],"throughput":[200],"increasing":[205],"through":[209],"virtualized":[210],"GPUs.":[211],"We":[212],"use":[213,234],"rCUDA":[215,236],"middleware":[216],"decouple":[221],"from":[223],"CPUs,":[224],"thus":[226],"enabling":[227],"time-sharing.":[228],"Our":[229],"show":[231],"obtains":[237],"2x":[239],"speed-up":[240],"factor":[241],"compared":[242],"CUDA":[245],"counterpart":[246],"version":[247],"while":[248],"requiring":[249],"similar":[251],"power":[252],"budget.":[253]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":2}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
