{"id":"https://openalex.org/W2946594008","doi":"https://doi.org/10.2312/ceig.20181149","title":"A Prototype of a Scalable Multi-GPU Molecular Dynamics Simulator for Large Molecular Systems","display_name":"A Prototype of a Scalable Multi-GPU Molecular Dynamics Simulator for Large Molecular Systems","publication_year":2018,"publication_date":"2018-01-01","ids":{"openalex":"https://openalex.org/W2946594008","doi":"https://doi.org/10.2312/ceig.20181149","mag":"2946594008"},"language":"en","primary_location":{"id":"pmh:oai:dsp.tecnalia.com:11556/7953","is_oa":false,"landing_page_url":"https://hdl.handle.net/11556/7953","pdf_url":null,"source":{"id":"https://openalex.org/S4306402037","display_name":"TECNALIA Publications (Fundaci\u00f3n TECNALIA Research & Innovation)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210113430","host_organization_name":"Tecnalia","host_organization_lineage":["https://openalex.org/I4210113430"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"conference output"},"type":"article","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.2312/ceig.20181149","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058262404","display_name":"Gonzalo Nicolas-Barreales","orcid":"https://orcid.org/0000-0002-4600-4950"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Nicolas-Barreales, Gonzalo","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075415441","display_name":"Marcos Novalbos","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Novalbos, Marcos","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071183334","display_name":"Miguel \u00c1. Otaduy","orcid":"https://orcid.org/0000-0002-3880-7622"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Otaduy, Miguel \u00c1ngel","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5003817684","display_name":"Alberto S\u00e1nchez","orcid":"https://orcid.org/0000-0002-5382-6805"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"S\u00e1nchez, Alberto","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5058262404"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0985,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.42665911,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":93},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9451000094413757,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9451000094413757,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10913","display_name":"Molecular Junctions and Nanostructures","score":0.9117000102996826,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7003489136695862},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6828594207763672},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5961188673973083},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.33669114112854004},{"id":"https://openalex.org/keywords/simulation","display_name":"Simulation","score":0.32515066862106323},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.13111191987991333},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.10804644227027893}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7003489136695862},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6828594207763672},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5961188673973083},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.33669114112854004},{"id":"https://openalex.org/C44154836","wikidata":"https://www.wikidata.org/wiki/Q45045","display_name":"Simulation","level":1,"score":0.32515066862106323},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.13111191987991333},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.10804644227027893},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:dsp.tecnalia.com:11556/7953","is_oa":false,"landing_page_url":"https://hdl.handle.net/11556/7953","pdf_url":null,"source":{"id":"https://openalex.org/S4306402037","display_name":"TECNALIA Publications (Fundaci\u00f3n TECNALIA Research & Innovation)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210113430","host_organization_name":"Tecnalia","host_organization_lineage":["https://openalex.org/I4210113430"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"conference output"},{"id":"doi:10.2312/ceig.20181149","is_oa":true,"landing_page_url":"https://doi.org/10.2312/ceig.20181149","pdf_url":null,"source":{"id":"https://openalex.org/S7407052899","display_name":"Eurographics","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.2312/ceig.20181149","is_oa":true,"landing_page_url":"https://doi.org/10.2312/ceig.20181149","pdf_url":null,"source":{"id":"https://openalex.org/S7407052899","display_name":"Eurographics","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.5899999737739563}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2966853054","https://openalex.org/W2966817554","https://openalex.org/W1530120815","https://openalex.org/W2898468574","https://openalex.org/W2159497832","https://openalex.org/W2805209071","https://openalex.org/W3117040269","https://openalex.org/W2142847852","https://openalex.org/W2134368403","https://openalex.org/W2027095034","https://openalex.org/W2326489325","https://openalex.org/W1985755689","https://openalex.org/W2168500301","https://openalex.org/W1537420279","https://openalex.org/W1983788987","https://openalex.org/W2312533264","https://openalex.org/W1588517684","https://openalex.org/W2000636639","https://openalex.org/W769579609","https://openalex.org/W2295985723"],"abstract_inverted_index":{"Parallel":[0],"architectures,":[1,29,50],"in":[2,15,37,73],"the":[3,16,55,81,162,165,171,175],"form":[4],"of":[5,18,27,57,95,115,127,151],"multi-core":[6],"or":[7,101],"multiple":[8,96],"computers,":[9],"have":[10,30,178],"produced":[11],"a":[12,44,74,89,124,149,152,185],"major":[13],"impact":[14],"field":[17],"information":[19],"technology.":[20],"GPU":[21,163],"devices,":[22],"as":[23,51,164],"an":[24,139],"extreme":[25],"example":[26],"parallel":[28,39,180],"been":[31],"adapted":[32],"to":[33,84,118,137,147,173,183],"enable":[34],"generic":[35],"computation":[36,56,116],"massively":[38],"architectures.":[40],"Molecular":[41],"dynamics":[42,87,107,154],"is":[43,88],"problem":[45],"that":[46,69,121],"fits":[47],"perfectly":[48],"such":[49],"it":[52],"relies":[53],"on":[54],"many":[58],"similar":[59],"interactions":[60],"between":[61],"atoms.":[62],"Moreover,":[63],"large":[64,157],"molecular":[65,86,106,153,158],"systems":[66],"require":[67],"resources":[68],"exceed":[70],"those":[71],"available":[72],"single":[75],"computer,":[76],"even":[77,113],"multi-GPU":[78,91,133],"computers.":[79],"Therefore,":[80],"ideal":[82],"architecture":[83],"simulate":[85],"distributed":[90,132],"cluster,":[92],"which":[93],"consists":[94],"interconnected":[97],"computers":[98],"with":[99],"one":[100],"more":[102],"GPUs":[103],"each.":[104],"A":[105],"simulation":[108],"usually":[109],"needs":[110],"days,":[111],"and":[112,141],"weeks":[114],"time":[117],"produce":[119],"results":[120],"represent":[122],"only":[123,170],"few":[125],"microseconds":[126],"atom":[128],"interactions.":[129],"In":[130],"contrast,":[131],"clusters":[134],"allows":[135],"us":[136],"develop":[138,148,184],"efficient":[140],"scalable":[142,187],"simulator.":[143],"This":[144],"paper":[145],"aims":[146],"prototype":[150],"simulator":[155],"for":[156],"systems.":[159],"It":[160],"uses":[161],"main":[166],"computing":[167],"device,":[168],"using":[169],"CPU":[172],"control":[174],"workflow.":[176],"We":[177],"implemented":[179],"processing":[181],"techniques":[182],"fully":[186],"system.":[188]},"counts_by_year":[{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-17T09:09:15.849793","created_date":"2025-10-10T00:00:00"}