{"id":"https://openalex.org/W6950582601","doi":"https://doi.org/10.5281/zenodo.7839729","title":"LAMMPS optimazed for Fugaku","display_name":"LAMMPS optimazed for Fugaku","publication_year":2023,"publication_date":"2023-04-18","ids":{"openalex":"https://openalex.org/W6950582601","doi":"https://doi.org/10.5281/zenodo.7839729"},"language":"en","primary_location":{"id":"pmh:oai:zenodo.org:7839729","is_oa":true,"landing_page_url":"https://zenodo.org/record/7839729","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/other"},"type":"other","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://zenodo.org/record/7839729","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Li, Jianxiong","orcid":"https://orcid.org/0009-0004-0121-2360"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Li, Jianxiong","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0009-0004-0121-2360","affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Zhao, Tong","orcid":"https://orcid.org/0000-0002-2511-0172"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhao, Tong","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-2511-0172","affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Guo, Zhuoqiang","orcid":"https://orcid.org/0000-0001-9418-3861"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Guo, Zhuoqiang","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-9418-3861","affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Shi, Shunchen","orcid":"https://orcid.org/0000-0002-9514-129X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shi, Shunchen","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-9514-129X","affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Liu, Lijun","orcid":"https://orcid.org/0000-0002-7278-775X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Liu, Lijun","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-7278-775X","affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Tan, Guangming","orcid":"https://orcid.org/0000-0002-6361-5948"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tan, Guangming","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-6361-5948","affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Jia, Weile","orcid":"https://orcid.org/0000-0001-8539-8326"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jia, Weile","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-8539-8326","affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Yuan, Guojun","orcid":"https://orcid.org/0000-0002-4864-7677"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yuan, Guojun","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-4864-7677","affiliations":[]},{"author_position":"last","author":{"id":null,"display_name":"Wang, Zhan","orcid":"https://orcid.org/0009-0003-4274-7671"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wang, Zhan","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0009-0003-4274-7671","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":9,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":true,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/thread","display_name":"Thread (computing)","score":0.7617999911308289},{"id":"https://openalex.org/keywords/executable","display_name":"Executable","score":0.7336000204086304},{"id":"https://openalex.org/keywords/compiler","display_name":"Compiler","score":0.4602999985218048},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4514999985694885},{"id":"https://openalex.org/keywords/threading","display_name":"Threading (protein sequence)","score":0.30790001153945923},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.29339998960494995}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.826200008392334},{"id":"https://openalex.org/C138101251","wikidata":"https://www.wikidata.org/wiki/Q213092","display_name":"Thread (computing)","level":2,"score":0.7617999911308289},{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.7336000204086304},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5702000260353088},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5616000294685364},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.5385000109672546},{"id":"https://openalex.org/C169590947","wikidata":"https://www.wikidata.org/wiki/Q47506","display_name":"Compiler","level":2,"score":0.4602999985218048},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4514999985694885},{"id":"https://openalex.org/C200307862","wikidata":"https://www.wikidata.org/wiki/Q7797175","display_name":"Threading (protein sequence)","level":3,"score":0.30790001153945923},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.29339998960494995},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.2906000018119812},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.2809999883174896},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.2782000005245209},{"id":"https://openalex.org/C85687889","wikidata":"https://www.wikidata.org/wiki/Q445962","display_name":"Legacy code","level":3,"score":0.2660999894142151},{"id":"https://openalex.org/C197129107","wikidata":"https://www.wikidata.org/wiki/Q1921621","display_name":"Merge (version control)","level":2,"score":0.26019999384880066},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.2549999952316284}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:zenodo.org:7839729","is_oa":true,"landing_page_url":"https://zenodo.org/record/7839729","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/other"},{"id":"doi:10.5281/zenodo.7839729","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.7839729","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:zenodo.org:7839729","is_oa":true,"landing_page_url":"https://zenodo.org/record/7839729","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/other"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"In":[0,383],"this":[1],"paper,":[2,138,292,367],"we":[3,24,56,183,210,218,310,387],"implemented":[4],"an":[5],"efficient":[6],"coarse-grained":[7],"and":[8,17,67,92,107,139,157,182,189,235,248,284,321,343,348,364,394,404],"fine-grained":[9],"peer-to-peer":[10],"neighbor":[11],"communication":[12,15,117,187],"to":[13,28,96,111,131,192,232,298,341,401],"reduce":[14,29],"time":[16,378,406],"improve":[18],"parallel":[19],"efficiency":[20],"for":[21,345],"LAMMPS.":[22,411],"Additionally,":[23],"use":[25],"pre-registered":[26],"address":[27],"buffer":[30],"overhead.":[31],"The":[32,41,50,126,174,279,325,333,376],"above":[33,127,374],"contributions":[34],"are":[35,129,168,263],"all":[36],"in":[37,136,147,165,170,206,266,290,331,365],"our":[38,77,137,144,207],"optimized":[39,78,145],"code.":[40],"experimental":[42,54,163],"results":[43,164],"of":[44,84,201,246,256,272,314,360,407,410],"the":[45,53,81,122,132,140,148,162,166,171,178,186,193,198,202,212,220,225,233,243,257,291,315,349,353,358,366,370,373,384,402,405],"paper":[46,167],"can":[47,294],"be":[48,230,295,339],"reproduced.":[49],"following":[51],"is":[52,63,75,142,177,197,276,329,352,369,379],"code":[55,83,146],"provide:":[57],"opt:":[58],"p2p":[59,87,102],"pattern":[60,88,103,120],"with":[61,64,89,98,104,113,121],"utofu":[62,65,90,105,123],"interface":[66,91,106],"6":[68,99],"TNIs":[69],"using":[70,118],"thread":[71,95,110,194,203],"pool.":[72,195],"And":[73],"it":[74,368],"also":[76,143,169,338],"code.<br>":[79],"ref:":[80],"original":[82],"LAMMPS.<br>":[85],"6tni_p2p:":[86],"a":[93,108,154,158],"single":[94,109],"communicate":[97,112],"TNIs.<br>":[100,115],"4tni_p2p:":[101],"4":[114],"utofu_3stage:":[116],"3-stage":[119],"interface.":[124],"<br>":[125,236,304,308],"projects":[128],"corresponding":[130,172],"five":[133],"step-by-step":[134],"experiments":[135],"opt":[141,213,216],"scaling":[149,346],"experiment.":[150],"Each":[151],"project":[152],"has":[153],"compile":[155,219],"script":[156,280,307],"run":[159],"script.":[160,303],"Besides,":[161],"project.":[173],"software":[175],"architecture":[176],"same":[179,354,371],"as":[180,260,355,372],"LAMMPS":[181,269],"mainly":[184,388],"changed":[185],"part":[188],"switched":[190],"OpenMP":[191],"Below":[196],"compilation":[199],"process":[200,351],"pool":[204],"version":[205],"paper:":[208],"First,":[209],"enter":[211,254],"folder:":[214],"cd":[215,319],"Then":[217,253,309],"project:":[221],"./compile.sh":[222],"After":[223],"compiling,":[224],"executable":[226],"file":[227,271,328],"lmp_threadpool":[228],"will":[229,337],"copied":[231,340],"BIN_threadpool_lj":[234,320],"BIN_threadpool_eam":[237],"folders.":[238],"These":[239],"two":[240,391],"folders":[241],"have":[242],"input":[244,270],"files":[245,265],"Lennard-Jones":[247,273],"embedded-atom":[249],"method":[250],"potentials":[251],"respectively.":[252],"one":[255,313],"folders,":[258],"such":[259],"BIN_threadpool_lj.":[261,267],"There":[262],"three":[264],"in.threadpool.lj:":[268],"potential,":[274],"default":[275],"60k":[277],"atoms.":[278],"provides":[281],"60k,":[282],"1.7M":[283],"5M":[285],"atomic":[286],"scales":[287],"that":[288],"appear":[289],"which":[293],"selected":[296],"according":[297],"requirements.<br>":[299],"lmp_threadpool.pjsub:":[300],"Fugaku":[301],"job":[302],"run.sh:":[305,323],"execution":[306,334,377],"go":[311],"into":[312],"potential":[316],"evaluation":[317],"folders:":[318],"execute":[322],"./run.sh":[324],"generated":[326],"log":[327,385],"stored":[330],"output/output\\_result/output.xxxxxxxx/0/1/stdout.1.0.<br>":[332],"file,":[335,386],"lmp_threadpool,":[336],"BIN_scaling_test_lj":[342],"BIN_scaling_test_eam":[344],"evaluation,":[347],"test":[350,359],"above.<br>":[356],"For":[357],"6tni_p2p,":[361],"4tni_p2p,":[362],"utofu_3stage":[363],"process.":[375],"within":[380],"2":[381],"minutes.":[382],"focus":[389],"on":[390],"indicators:":[392],"performance":[393,403],"mpi":[395],"task":[396],"timing":[397],"breakdown.":[398],"They":[399],"correspond":[400],"different":[408],"stages":[409]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
