{"id":"https://openalex.org/W4224226906","doi":"https://doi.org/10.1021/acs.jcim.1c01538","title":"Performance Analysis of CP2K Code for Ab Initio Molecular Dynamics on CPUs and GPUs","display_name":"Performance Analysis of CP2K Code for Ab Initio Molecular Dynamics on CPUs and GPUs","publication_year":2022,"publication_date":"2022-04-22","ids":{"openalex":"https://openalex.org/W4224226906","doi":"https://doi.org/10.1021/acs.jcim.1c01538","pmid":"https://pubmed.ncbi.nlm.nih.gov/35451847"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.1c01538","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c01538","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5009000154","display_name":"Dewi Yokelson","orcid":"https://orcid.org/0000-0003-1453-5906"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dewi Yokelson","raw_affiliation_strings":["Applied Computer Science Division (CCS-7), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States"],"raw_orcid":"https://orcid.org/0000-0003-1453-5906","affiliations":[{"raw_affiliation_string":"Applied Computer Science Division (CCS-7), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035860179","display_name":"Nikolay V. Tkachenko","orcid":"https://orcid.org/0000-0002-7296-4293"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nikolay V. Tkachenko","raw_affiliation_strings":["Chemistry Division (C-IIAC), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States"],"raw_orcid":"https://orcid.org/0000-0002-7296-4293","affiliations":[{"raw_affiliation_string":"Chemistry Division (C-IIAC), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027394799","display_name":"Robert Robey","orcid":"https://orcid.org/0000-0001-5018-5793"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]},{"id":"https://openalex.org/I4210138427","display_name":"Computational Physics (United States)","ror":"https://ror.org/03grsxg62","country_code":"US","type":"company","lineage":["https://openalex.org/I4210138427"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Robey","raw_affiliation_strings":["Computational Physics Division (XCP-2), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Physics Division (XCP-2), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States","institution_ids":["https://openalex.org/I1343871089","https://openalex.org/I4210138427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060737716","display_name":"Ying Wai Li","orcid":"https://orcid.org/0000-0003-0124-8262"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ying Wai Li","raw_affiliation_strings":["Applied Computer Science Division (CCS-7), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Applied Computer Science Division (CCS-7), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070272149","display_name":"Pavel A. Dub","orcid":"https://orcid.org/0000-0001-9750-6603"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Pavel A. Dub","raw_affiliation_strings":["Chemistry Division (C-IIAC), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States"],"raw_orcid":"https://orcid.org/0000-0001-9750-6603","affiliations":[{"raw_affiliation_string":"Chemistry Division (C-IIAC), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States","institution_ids":["https://openalex.org/I1343871089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5070272149"],"corresponding_institution_ids":["https://openalex.org/I1343871089"],"apc_list":null,"apc_paid":null,"fwci":3.2646,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.9232287,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"62","issue":"10","first_page":"2378","last_page":"2386"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9991999864578247,"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"}},"topics":[{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9991999864578247,"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"}},{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.998199999332428,"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":0.9977999925613403,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.8440647721290588},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.8395025730133057},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8014969825744629},{"id":"https://openalex.org/keywords/xeon-phi","display_name":"Xeon Phi","score":0.7283605337142944},{"id":"https://openalex.org/keywords/xeon","display_name":"Xeon","score":0.7215673327445984},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.6280859708786011},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.5556316375732422},{"id":"https://openalex.org/keywords/central-processing-unit","display_name":"Central processing unit","score":0.5229290723800659},{"id":"https://openalex.org/keywords/scaling","display_name":"Scaling","score":0.5149974822998047},{"id":"https://openalex.org/keywords/thread","display_name":"Thread (computing)","score":0.5099049806594849},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.47265565395355225},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.4481085538864136},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3904692530632019},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.15658515691757202},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.13808667659759521},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.11935418844223022},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.11531221866607666},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10325324535369873}],"concepts":[{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.8440647721290588},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.8395025730133057},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8014969825744629},{"id":"https://openalex.org/C96972482","wikidata":"https://www.wikidata.org/wiki/Q1049168","display_name":"Xeon Phi","level":2,"score":0.7283605337142944},{"id":"https://openalex.org/C145108525","wikidata":"https://www.wikidata.org/wiki/Q656154","display_name":"Xeon","level":2,"score":0.7215673327445984},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.6280859708786011},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.5556316375732422},{"id":"https://openalex.org/C49154492","wikidata":"https://www.wikidata.org/wiki/Q5300","display_name":"Central processing unit","level":2,"score":0.5229290723800659},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.5149974822998047},{"id":"https://openalex.org/C138101251","wikidata":"https://www.wikidata.org/wiki/Q213092","display_name":"Thread (computing)","level":2,"score":0.5099049806594849},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.47265565395355225},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.4481085538864136},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3904692530632019},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.15658515691757202},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.13808667659759521},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.11935418844223022},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.11531221866607666},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10325324535369873},{"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/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.1c01538","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c01538","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:35451847","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35451847","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8299999833106995,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G8420571625","display_name":null,"funder_award_id":"20210087DR","funder_id":"https://openalex.org/F4320337547","funder_display_name":"Laboratory Directed Research and Development"}],"funders":[{"id":"https://openalex.org/F4320337547","display_name":"Laboratory Directed Research and Development","ror":"https://ror.org/01e41cf67"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W63372954","https://openalex.org/W1974755878","https://openalex.org/W1982952953","https://openalex.org/W1988888548","https://openalex.org/W1989060947","https://openalex.org/W1991794210","https://openalex.org/W2000770615","https://openalex.org/W2003949305","https://openalex.org/W2007395042","https://openalex.org/W2014166972","https://openalex.org/W2017196167","https://openalex.org/W2023271753","https://openalex.org/W2026172453","https://openalex.org/W2030976617","https://openalex.org/W2069538140","https://openalex.org/W2074466695","https://openalex.org/W2074974429","https://openalex.org/W2079105963","https://openalex.org/W2086957099","https://openalex.org/W2092157292","https://openalex.org/W2096070062","https://openalex.org/W2120145199","https://openalex.org/W2146411229","https://openalex.org/W2148678374","https://openalex.org/W2150871235","https://openalex.org/W2230728100","https://openalex.org/W2474780748","https://openalex.org/W2736099364","https://openalex.org/W2922522932","https://openalex.org/W2984305089","https://openalex.org/W2999783700","https://openalex.org/W3020638658","https://openalex.org/W3027308092","https://openalex.org/W3093552440","https://openalex.org/W3101252710","https://openalex.org/W3104098743","https://openalex.org/W3174052312","https://openalex.org/W4229666556","https://openalex.org/W4394664034","https://openalex.org/W6835938151"],"related_works":["https://openalex.org/W2100952904","https://openalex.org/W1507301366","https://openalex.org/W2613115449","https://openalex.org/W4312275919","https://openalex.org/W2614685449","https://openalex.org/W3199219623","https://openalex.org/W4224226906","https://openalex.org/W2170268965","https://openalex.org/W4311833893","https://openalex.org/W4313406770"],"abstract_inverted_index":{"Using":[0],"a":[1,138,167],"realistic":[2],"molecular":[3,13,62],"catalyst":[4],"system,":[5],"we":[6],"conduct":[7],"scaling":[8,121],"studies":[9],"of":[10,55,118],"ab":[11],"initio":[12],"dynamics":[14,63],"simulations":[15,112],"using":[16],"the":[17,56,108,119,129,155,171],"popular":[18],"CP2K":[19],"code":[20],"on":[21,137],"both":[22],"Intel":[23],"Xeon":[24],"CPU":[25,68],"and":[26,42],"NVIDIA":[27,144],"V100":[28,145],"GPU":[29,164],"architectures.":[30],"Additional":[31],"performance":[32,51],"improvements":[33],"were":[34,47,70],"gained":[35],"by":[36],"finding":[37],"more":[38,117,134],"optimal":[39],"process":[40],"placement":[41],"affinity":[43],"settings.":[44],"Statistical":[45],"methods":[46],"employed":[48],"to":[49,123,132,154],"understand":[50],"changes":[52],"in":[53,58],"spite":[54],"variability":[57],"runtime":[59],"for":[60,67,107,147],"each":[61,84],"timestep.":[64],"Ideal":[65],"conditions":[66],"runs":[69,165],"found":[71],"when":[72,104],"running":[73],"at":[74,114],"least":[75],"four":[76],"MPI":[77],"ranks":[78],"per":[79,99],"node,":[80],"bound":[81],"evenly":[82],"across":[83,175],"socket.":[85],"This":[86],"study":[87],"also":[88],"showed":[89,166],"that":[90],"fully":[91],"utilizing":[92],"processing":[93],"cores,":[94],"with":[95,142],"one":[96],"OpenMP":[97],"thread":[98],"core,":[100],"performed":[101],"better":[102],"than":[103],"reserving":[105],"cores":[106],"system.":[109],"The":[110],"CPU-only":[111,160,177],"scaled":[113],"70%":[115],"or":[116],"ideal":[120],"up":[122],"10":[124],"compute":[125],"nodes,":[126],"after":[127],"which":[128],"returns":[130],"began":[131],"diminish":[133],"quickly.":[135],"Simulations":[136],"single":[139,157],"40-core":[140],"node":[141,159],"two":[143],"GPUs":[146],"acceleration":[148],"achieved":[149,174],"over":[150,170],"3.7\u00d7":[151],"speedup":[152,169],"compared":[153],"fastest":[156,172],"36-core":[158],"version.":[161],"These":[162],"same":[163],"13%":[168],"time":[173],"five":[176],"nodes.":[178]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2}],"updated_date":"2026-05-13T08:25:38.343686","created_date":"2025-10-10T00:00:00"}