{"id":"https://openalex.org/W2579859441","doi":"https://doi.org/10.1109/bibm.2016.7822595","title":"mAMBER: A CPU/MIC collaborated parallel framework for AMBER on Tianhe-2 supercomputer","display_name":"mAMBER: A CPU/MIC collaborated parallel framework for AMBER on Tianhe-2 supercomputer","publication_year":2016,"publication_date":"2016-12-01","ids":{"openalex":"https://openalex.org/W2579859441","doi":"https://doi.org/10.1109/bibm.2016.7822595","mag":"2579859441"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2016.7822595","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2016.7822595","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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/A5108008219","display_name":"Shaoliang Peng","orcid":"https://orcid.org/0000-0002-4647-2615"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shaoliang Peng","raw_affiliation_strings":["School of Computer Science, National University of Defense Technology, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, National University of Defense Technology, Changsha, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115595570","display_name":"Xiaoyu Zhang","orcid":"https://orcid.org/0000-0002-3227-5071"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoyu Zhang","raw_affiliation_strings":["School of Computer Science, National University of Defense Technology, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, National University of Defense Technology, Changsha, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101633465","display_name":"Yutong Lu","orcid":"https://orcid.org/0000-0001-5315-3375"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yutong Lu","raw_affiliation_strings":["School of Computer Science, National University of Defense Technology, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, National University of Defense Technology, Changsha, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000688713","display_name":"Xiangke Liao","orcid":"https://orcid.org/0000-0002-6125-3330"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangke Liao","raw_affiliation_strings":["School of Computer Science, National University of Defense Technology, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, National University of Defense Technology, Changsha, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100625357","display_name":"Kai Lu","orcid":"https://orcid.org/0000-0003-2284-7897"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kai Lu","raw_affiliation_strings":["School of Computer Science, National University of Defense Technology, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, National University of Defense Technology, Changsha, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101044975","display_name":"Canqun Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Canqun Yang","raw_affiliation_strings":["School of Computer Science, National University of Defense Technology, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, National University of Defense Technology, Changsha, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052226742","display_name":"Jie Liu","orcid":"https://orcid.org/0000-0002-9297-7729"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jie Liu","raw_affiliation_strings":["School of Computer Science, National University of Defense Technology, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, National University of Defense Technology, Changsha, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059083216","display_name":"Weiliang Zhu","orcid":"https://orcid.org/0000-0001-6699-5299"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weiliang Zhu","raw_affiliation_strings":["Drug Discovery and Design Center, Chinese Academy of Sciences, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Drug Discovery and Design Center, Chinese Academy of Sciences, Shanghai, China","institution_ids":["https://openalex.org/I4210112820","https://openalex.org/I19820366"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041491902","display_name":"Dong\u2010Qing Wei","orcid":"https://orcid.org/0000-0003-4200-7502"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dongqing Wei","raw_affiliation_strings":["College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanzhai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanzhai, China","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"1","issue":null,"first_page":"651","last_page":"657"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9979000091552734,"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":0.9979000091552734,"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/T11809","display_name":"Advanced NMR Techniques and Applications","score":0.9876999855041504,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9782000184059143,"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/supercomputer","display_name":"Supercomputer","score":0.9264867305755615},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7847001552581787},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7516043186187744},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.7054779529571533},{"id":"https://openalex.org/keywords/acceleration","display_name":"Acceleration","score":0.6614256501197815},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.6226462125778198},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.5931161642074585},{"id":"https://openalex.org/keywords/popularity","display_name":"Popularity","score":0.4754497706890106},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.4678289294242859},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.43962258100509644},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.14481249451637268},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1418699324131012},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.11987349390983582}],"concepts":[{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.9264867305755615},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7847001552581787},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7516043186187744},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.7054779529571533},{"id":"https://openalex.org/C117896860","wikidata":"https://www.wikidata.org/wiki/Q11376","display_name":"Acceleration","level":2,"score":0.6614256501197815},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.6226462125778198},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.5931161642074585},{"id":"https://openalex.org/C2780586970","wikidata":"https://www.wikidata.org/wiki/Q1357284","display_name":"Popularity","level":2,"score":0.4754497706890106},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4678289294242859},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.43962258100509644},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.14481249451637268},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1418699324131012},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.11987349390983582},{"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/C77805123","wikidata":"https://www.wikidata.org/wiki/Q161272","display_name":"Social psychology","level":1,"score":0.0},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2016.7822595","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2016.7822595","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.7200000286102295,"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1966078827","https://openalex.org/W1976203248","https://openalex.org/W2004822259","https://openalex.org/W2027053193","https://openalex.org/W2057054012","https://openalex.org/W2082586732","https://openalex.org/W2103325328","https://openalex.org/W2111946172","https://openalex.org/W2118233996","https://openalex.org/W2120385681","https://openalex.org/W2124745044","https://openalex.org/W2132262459","https://openalex.org/W2150981663","https://openalex.org/W2159010139","https://openalex.org/W2313116527","https://openalex.org/W2794630033","https://openalex.org/W3010525046","https://openalex.org/W3022388728","https://openalex.org/W4211202817"],"related_works":["https://openalex.org/W2368605798","https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W2146343568","https://openalex.org/W98480971","https://openalex.org/W2150291671","https://openalex.org/W2013643406","https://openalex.org/W1582436825","https://openalex.org/W1996803181","https://openalex.org/W2979588510"],"abstract_inverted_index":{"Molecular":[0],"dynamics":[1],"(MD)":[2],"is":[3,55,108],"a":[4,94,120],"computer":[5],"simulation":[6,31],"method":[7],"of":[8,12,57,71,79,106,138,148],"studying":[9],"physical":[10],"movements":[11],"atoms":[13,80],"and":[14,28,38,44,128],"molecules":[15],"that":[16],"provide":[17],"detailed":[18],"microscopic":[19],"sampling":[20],"on":[21,100,111,119],"molecular":[22],"scale.":[23,47],"With":[24],"the":[25,58,69,135,145,153],"continuous":[26],"efforts":[27],"improvements,":[29],"MD":[30,66,73],"gained":[32],"popularity":[33],"in":[34,81],"materials":[35],"science,":[36],"biochemistry":[37],"biophysics":[39],"with":[40,51,77,152],"various":[41],"application":[42],"areas":[43],"expanding":[45],"data":[46],"Assisted":[48],"Model":[49],"Building":[50],"Energy":[52],"Refinement":[53],"(AMBER)":[54],"one":[56],"most":[59],"widely":[60],"used":[61],"software":[62],"packages":[63],"for":[64,75,98],"conducting":[65],"simulations.":[67],"However,":[68],"speed":[70],"AMBER":[72,99,107],"simulations":[74],"system":[76],"millions":[78],"microsecond":[82],"scale":[83],"still":[84],"need":[85],"to":[86],"be":[87],"improved.":[88],"In":[89],"this":[90],"paper,":[91],"we":[92,143],"propose":[93],"parallel":[95,104,118,126,132,139],"acceleration":[96,140],"strategy":[97,141],"Tianhe-2":[101],"supercomputer.":[102],"The":[103],"optimization":[105,127],"carried":[109],"out":[110],"three":[112,136],"different":[113],"levels:":[114],"fine":[115],"grained":[116],"OpenMP":[117],"single":[121],"MIC,":[122],"single-node":[123],"CPU/MIC":[124],"collaborated":[125,131],"multi-node":[129],"multi-MIC":[130],"acceleration.":[133],"By":[134],"levels":[137],"above,":[142],"achieved":[144],"highest":[146],"speedup":[147],"25-33":[149],"times":[150],"compared":[151],"original":[154],"program.":[155],"Source":[156],"Code:":[157],"https://github.com/tianhe2/mAMBER.":[158]},"counts_by_year":[{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}