{"id":"https://openalex.org/W2026600854","doi":"https://doi.org/10.1145/2063384.2063466","title":"Enabling and scaling biomolecular simulations of 100 million atoms on petascale machines with a multicore-optimized message-driven runtime","display_name":"Enabling and scaling biomolecular simulations of 100 million atoms on petascale machines with a multicore-optimized message-driven runtime","publication_year":2011,"publication_date":"2011-11-08","ids":{"openalex":"https://openalex.org/W2026600854","doi":"https://doi.org/10.1145/2063384.2063466","mag":"2026600854"},"language":"en","primary_location":{"id":"doi:10.1145/2063384.2063466","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2063384.2063466","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis","raw_type":"proceedings-article"},"type":"article","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/A5101833824","display_name":"Chao Mei","orcid":"https://orcid.org/0000-0002-3948-8897"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chao Mei","raw_affiliation_strings":["University of Illinois at Urbana-Champaign, Urbana, IL","Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Illinois at Urbana-Champaign, Urbana, IL","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100945967","display_name":"Yanhua Sun","orcid":null},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yanhua Sun","raw_affiliation_strings":["University of Illinois at Urbana-Champaign, Urbana, IL","Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Illinois at Urbana-Champaign, Urbana, IL","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109069612","display_name":"Gengbin Zheng","orcid":null},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gengbin Zheng","raw_affiliation_strings":["University of Illinois at Urbana-Champaign, Urbana, IL","Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Illinois at Urbana-Champaign, Urbana, IL","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088710224","display_name":"Eric J. Bohm","orcid":null},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric J. Bohm","raw_affiliation_strings":["University of Illinois at Urbana-Champaign, Urbana, IL","Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Illinois at Urbana-Champaign, Urbana, IL","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051465480","display_name":"Laxmikant V. Kal\u00e9","orcid":"https://orcid.org/0000-0001-9673-8445"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Laxmikant V. Kale","raw_affiliation_strings":["University of Illinois at Urbana-Champaign, Urbana, IL","Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Illinois at Urbana-Champaign, Urbana, IL","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056552672","display_name":"J. C. Phillips","orcid":"https://orcid.org/0000-0002-2296-3591"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James C. Phillips","raw_affiliation_strings":["University of Illinois at Urbana-Champaign, Urbana, IL","Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Illinois at Urbana-Champaign, Urbana, IL","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110274015","display_name":"Chris Harrison","orcid":null},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chris Harrison","raw_affiliation_strings":["University of Illinois at Urbana-Champaign, Urbana, IL","Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Illinois at Urbana-Champaign, Urbana, IL","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":3.3266,"has_fulltext":false,"cited_by_count":48,"citation_normalized_percentile":{"value":0.92801272,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"11"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9962000250816345,"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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9962000250816345,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9937999844551086,"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/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9897000193595886,"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/petascale-computing","display_name":"Petascale computing","score":0.978689968585968},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8597445487976074},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6661208271980286},{"id":"https://openalex.org/keywords/memory-footprint","display_name":"Memory footprint","score":0.6447881460189819},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.6126867532730103},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.5932340025901794},{"id":"https://openalex.org/keywords/oak-ridge-national-laboratory","display_name":"Oak Ridge National Laboratory","score":0.5877726078033447},{"id":"https://openalex.org/keywords/asynchronous-communication","display_name":"Asynchronous communication","score":0.5202696919441223},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.4993577003479004},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.4920586943626404},{"id":"https://openalex.org/keywords/scaling","display_name":"Scaling","score":0.4716317653656006},{"id":"https://openalex.org/keywords/upgrade","display_name":"Upgrade","score":0.4440465271472931},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4163277745246887},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3855217397212982},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.08697676658630371}],"concepts":[{"id":"https://openalex.org/C185410017","wikidata":"https://www.wikidata.org/wiki/Q7171778","display_name":"Petascale computing","level":3,"score":0.978689968585968},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8597445487976074},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6661208271980286},{"id":"https://openalex.org/C74912251","wikidata":"https://www.wikidata.org/wiki/Q6815727","display_name":"Memory footprint","level":2,"score":0.6447881460189819},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.6126867532730103},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.5932340025901794},{"id":"https://openalex.org/C2775907726","wikidata":"https://www.wikidata.org/wiki/Q714439","display_name":"Oak Ridge National Laboratory","level":2,"score":0.5877726078033447},{"id":"https://openalex.org/C151319957","wikidata":"https://www.wikidata.org/wiki/Q752739","display_name":"Asynchronous communication","level":2,"score":0.5202696919441223},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.4993577003479004},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.4920586943626404},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.4716317653656006},{"id":"https://openalex.org/C2780615140","wikidata":"https://www.wikidata.org/wiki/Q920419","display_name":"Upgrade","level":2,"score":0.4440465271472931},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4163277745246887},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3855217397212982},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08697676658630371},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"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/C185544564","wikidata":"https://www.wikidata.org/wiki/Q81197","display_name":"Nuclear physics","level":1,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/2063384.2063466","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2063384.2063466","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.646.5711","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.646.5711","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://charm.cs.illinois.edu/newPapers/11-17/paper.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1736987090","display_name":null,"funder_award_id":"PHS 5 P41 RR05969-04","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4495649530","display_name":null,"funder_award_id":"OCI-0725070","funder_id":"https://openalex.org/F4320337377","funder_display_name":"Office of Advanced Cyberinfrastructure"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332222","display_name":"University of Illinois at Urbana-Champaign","ror":"https://ror.org/047426m28"},{"id":"https://openalex.org/F4320337377","display_name":"Office of Advanced Cyberinfrastructure","ror":"https://ror.org/04nh1dc89"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1603470798","https://openalex.org/W1963882433","https://openalex.org/W1965351873","https://openalex.org/W1966078827","https://openalex.org/W1980670496","https://openalex.org/W2029464737","https://openalex.org/W2029667189","https://openalex.org/W2049492770","https://openalex.org/W2051212021","https://openalex.org/W2056879607","https://openalex.org/W2074727733","https://openalex.org/W2110338379","https://openalex.org/W2118233996","https://openalex.org/W2124451342","https://openalex.org/W2136985651","https://openalex.org/W2141514639","https://openalex.org/W2145285934","https://openalex.org/W2150981663","https://openalex.org/W2153228625","https://openalex.org/W2159817808","https://openalex.org/W2161412129","https://openalex.org/W2163059351","https://openalex.org/W2166734474","https://openalex.org/W6641021676"],"related_works":["https://openalex.org/W2021702679","https://openalex.org/W3038449658","https://openalex.org/W1582746211","https://openalex.org/W3129378740","https://openalex.org/W2607572736","https://openalex.org/W2266027327","https://openalex.org/W2278366184","https://openalex.org/W1486544172","https://openalex.org/W4206324154","https://openalex.org/W1978931242"],"abstract_inverted_index":{"A":[0,53],"100-million-atom":[1],"biomolecular":[2],"simulation":[3],"with":[4,111],"NAMD":[5,95],"is":[6,57,90,136],"one":[7],"of":[8,142],"the":[9,13,51,68,80,83,97,143],"three":[10],"benchmarks":[11],"for":[12,129],"NSF-funded":[14],"sustainable":[15],"petascale":[16,25],"machine.":[17],"Simulating":[18],"this":[19,42],"large":[20,33],"molecular":[21],"system":[22],"on":[23,139],"a":[24,130],"machine":[26],"presents":[27],"great":[28],"challenges,":[29],"including":[30],"handling":[31],"I/O,":[32],"memory":[34],"footprint":[35],"and":[36,82,112],"getting":[37],"good":[38],"strong-scaling":[39],"results.":[40],"In":[41],"paper,":[43],"we":[44],"present":[45],"parallel":[46,119],"I/O":[47],"techniques":[48,76],"to":[49,59,77,93,96],"enable":[50],"simulation.":[52],"new":[54],"SMP":[55,85],"model":[56],"designed":[58],"efficiently":[60],"utilize":[61],"ubiquitous":[62],"wide":[63],"multicore":[64],"clusters":[65],"by":[66],"extending":[67],"Charm++":[69],"asynchronous":[70],"message-driven":[71],"runtime.":[72,86],"We":[73],"exploit":[74],"node-aware":[75],"optimize":[78],"both":[79,110],"application":[81],"underlying":[84],"Hierarchical":[87],"load":[88],"balancing":[89],"further":[91],"exploited":[92],"scale":[94],"full":[98,115],"Jaguar":[99],"PF":[100],"Cray":[101],"XT5":[102],"(224,076":[103],"cores)":[104,123],"at":[105,124,147],"Oak":[106],"Ridge":[107],"National":[108,149],"Laboratory,":[109],"without":[113],"PME":[114],"electrostatics,":[116],"achieving":[117],"93%":[118],"efficiency":[120],"(vs":[121],"6720":[122],"9":[125],"ms":[126],"per":[127],"step":[128],"simple":[131],"cutoff":[132],"calculation.":[133],"Excellent":[134],"scaling":[135],"also":[137],"obtained":[138],"65,536":[140],"cores":[141],"Intrepid":[144],"Blue":[145],"Gene/P":[146],"Argonne":[148],"Laboratory.":[150]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":9}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}