{"id":"https://openalex.org/W2060201803","doi":"https://doi.org/10.1109/sc.2014.12","title":"Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation","display_name":"Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation","publication_year":2014,"publication_date":"2014-11-01","ids":{"openalex":"https://openalex.org/W2060201803","doi":"https://doi.org/10.1109/sc.2014.12","mag":"2060201803","pmid":"https://pubmed.ncbi.nlm.nih.gov/25594075"},"language":"en","primary_location":{"id":"doi:10.1109/sc.2014.12","is_oa":false,"landing_page_url":"https://doi.org/10.1109/sc.2014.12","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SC14: International Conference for High Performance Computing, Networking, Storage and Analysis","raw_type":"proceedings-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/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, USA","[University of Illinois at Urbana-Champaign,Urbana,IL]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"[University of Illinois at Urbana-Champaign,Urbana,IL]","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, USA","[University of Illinois at Urbana-Champaign,Urbana,IL]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"[University of Illinois at Urbana-Champaign,Urbana,IL]","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025115023","display_name":"Nikhil Jain","orcid":"https://orcid.org/0009-0002-1555-9125"},"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":"Nikhil Jain","raw_affiliation_strings":["University of Illinois at Urbana-Champaign, Urbana, IL, USA","[University of Illinois at Urbana-Champaign,Urbana,IL]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"[University of Illinois at Urbana-Champaign,Urbana,IL]","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, USA","[University of Illinois at Urbana-Champaign,Urbana,IL]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"[University of Illinois at Urbana-Champaign,Urbana,IL]","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","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, USA","[University of Illinois at Urbana-Champaign,Urbana,IL]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"[University of Illinois at Urbana-Champaign,Urbana,IL]","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":5.0417,"has_fulltext":false,"cited_by_count":34,"citation_normalized_percentile":{"value":0.95541727,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"2014","issue":null,"first_page":"81","last_page":"91"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.994700014591217,"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":0.994700014591217,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9753000140190125,"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/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9695000052452087,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/petascale-computing","display_name":"Petascale computing","score":0.9483639001846313},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.790452778339386},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.7519104480743408},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.6070474982261658},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.5831706523895264},{"id":"https://openalex.org/keywords/grid-network","display_name":"Grid network","score":0.5333390831947327},{"id":"https://openalex.org/keywords/ibm","display_name":"IBM","score":0.5258165597915649},{"id":"https://openalex.org/keywords/grid","display_name":"Grid","score":0.49636703729629517},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.4799802005290985},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4470658600330353},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.43701714277267456},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.41398051381111145},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.2537470757961273},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.11742785573005676}],"concepts":[{"id":"https://openalex.org/C185410017","wikidata":"https://www.wikidata.org/wiki/Q7171778","display_name":"Petascale computing","level":3,"score":0.9483639001846313},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.790452778339386},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.7519104480743408},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.6070474982261658},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.5831706523895264},{"id":"https://openalex.org/C24337046","wikidata":"https://www.wikidata.org/wiki/Q4394138","display_name":"Grid network","level":3,"score":0.5333390831947327},{"id":"https://openalex.org/C70388272","wikidata":"https://www.wikidata.org/wiki/Q5968558","display_name":"IBM","level":2,"score":0.5258165597915649},{"id":"https://openalex.org/C187691185","wikidata":"https://www.wikidata.org/wiki/Q2020720","display_name":"Grid","level":2,"score":0.49636703729629517},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.4799802005290985},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4470658600330353},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.43701714277267456},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.41398051381111145},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.2537470757961273},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.11742785573005676},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","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},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/sc.2014.12","is_oa":false,"landing_page_url":"https://doi.org/10.1109/sc.2014.12","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SC14: International Conference for High Performance Computing, Networking, Storage and Analysis","raw_type":"proceedings-article"},{"id":"pmid:25594075","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25594075","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":"SC ... conference proceedings. SC (Conference : Supercomputing)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.649.107","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.649.107","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/14-17/paper.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:3260630","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4292797","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309480","display_name":"Nvidia","ror":"https://ror.org/03jdj4y14"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1929976086","https://openalex.org/W1974422362","https://openalex.org/W1984853348","https://openalex.org/W1986340747","https://openalex.org/W1992432622","https://openalex.org/W2009852231","https://openalex.org/W2021064626","https://openalex.org/W2026600854","https://openalex.org/W2027926022","https://openalex.org/W2049459394","https://openalex.org/W2056879607","https://openalex.org/W2059691633","https://openalex.org/W2105885962","https://openalex.org/W2108386759","https://openalex.org/W2112769850","https://openalex.org/W2123859357","https://openalex.org/W2135269176","https://openalex.org/W2150981663","https://openalex.org/W2159497832","https://openalex.org/W2159826908","https://openalex.org/W2167173222","https://openalex.org/W2168319550","https://openalex.org/W3037896947","https://openalex.org/W3141032579","https://openalex.org/W3145412265","https://openalex.org/W4244430623","https://openalex.org/W6643760237","https://openalex.org/W6653138830","https://openalex.org/W6657282960","https://openalex.org/W6662638037","https://openalex.org/W7036137438"],"related_works":["https://openalex.org/W819935270","https://openalex.org/W4307656122","https://openalex.org/W2087210673","https://openalex.org/W4232104505","https://openalex.org/W2080435752","https://openalex.org/W164663419","https://openalex.org/W1541476310","https://openalex.org/W2060201803","https://openalex.org/W2000584869","https://openalex.org/W2135656976"],"abstract_inverted_index":{"Currently":[0],"deployed":[1],"petascale":[2],"supercomputers":[3],"typically":[4],"use":[5],"toroidal":[6,94],"network":[7,37],"topologies":[8],"in":[9],"three":[10],"or":[11,58],"more":[12],"dimensions.":[13],"While":[14],"these":[15],"networks":[16,95],"perform":[17],"well":[18],"for":[19,39,74,112,127],"topology-agnostic":[20],"codes":[21],"on":[22],"a":[23,76],"few":[24],"thousand":[25],"nodes,":[26],"leadership":[27],"machines":[28],"with":[29],"20,000":[30],"nodes":[31,57],"require":[32],"topology":[33],"awareness":[34],"to":[35,54,85,96,104],"avoid":[36],"contention":[38],"communication-intensive":[40],"codes.":[41],"Topology":[42],"adaptation":[43],"is":[44,125],"complicated":[45],"by":[46],"irregular":[47],"node":[48,107],"allocation":[49],"shapes":[50],"and":[51,89,103,123,137],"holes":[52],"due":[53],"dedicated":[55],"input/output":[56],"hardware":[59],"failure.":[60],"In":[61],"the":[62,65],"context":[63],"of":[64,80],"popular":[66],"molecular":[67],"dynamics":[68],"program":[69],"NAMD,":[70],"we":[71],"present":[72],"methods":[73],"mapping":[75],"periodic":[77],"3-D":[78,86],"grid":[79],"fixed-size":[81],"spatial":[82],"decomposition":[83],"domains":[84,111],"Cray":[87],"Gemini":[88],"5-D":[90],"IBM":[91],"Blue":[92,129],"Gene/Q":[93],"enable":[97],"hundred-million":[98],"atom":[99],"full":[100],"machine":[101],"simulations,":[102],"similarly":[105],"partition":[106],"allocations":[108],"into":[109],"compact":[110],"smaller":[113],"simulations":[114],"using":[115],"multiple-copy":[116],"algorithms.":[117],"Additional":[118],"enabling":[119],"techniques":[120],"are":[121],"discussed":[122],"performance":[124],"reported":[126],"NCSA":[128],"Waters,":[130],"ORNL":[131],"Titan,":[132],"ANL":[133],"Mira,":[134],"TACC":[135],"Stampede,":[136],"NERSC":[138],"Edison.":[139]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
