{"id":"https://openalex.org/W3169244019","doi":"https://doi.org/10.1145/3447818.3460365","title":"MD-HM","display_name":"MD-HM","publication_year":2021,"publication_date":"2021-06-03","ids":{"openalex":"https://openalex.org/W3169244019","doi":"https://doi.org/10.1145/3447818.3460365","mag":"3169244019"},"language":"en","primary_location":{"id":"doi:10.1145/3447818.3460365","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3447818.3460365","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3447818.3460365","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM International Conference on Supercomputing","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3447818.3460365","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100457289","display_name":"Zhen Xie","orcid":"https://orcid.org/0000-0001-7916-8313"},"institutions":[{"id":"https://openalex.org/I156087764","display_name":"University of California, Merced","ror":"https://ror.org/00d9ah105","country_code":"US","type":"education","lineage":["https://openalex.org/I156087764"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhen Xie","raw_affiliation_strings":["University of California, Merced"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California, Merced","institution_ids":["https://openalex.org/I156087764"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102994344","display_name":"Wenqian Dong","orcid":"https://orcid.org/0000-0002-8376-6647"},"institutions":[{"id":"https://openalex.org/I156087764","display_name":"University of California, Merced","ror":"https://ror.org/00d9ah105","country_code":"US","type":"education","lineage":["https://openalex.org/I156087764"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wenqian Dong","raw_affiliation_strings":["University of California, Merced"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California, Merced","institution_ids":["https://openalex.org/I156087764"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100454211","display_name":"Jie Liu","orcid":"https://orcid.org/0000-0003-3745-7541"},"institutions":[{"id":"https://openalex.org/I156087764","display_name":"University of California, Merced","ror":"https://ror.org/00d9ah105","country_code":"US","type":"education","lineage":["https://openalex.org/I156087764"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jie Liu","raw_affiliation_strings":["University of California, Merced"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California, Merced","institution_ids":["https://openalex.org/I156087764"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037069204","display_name":"Ivy Peng","orcid":"https://orcid.org/0000-0003-4158-3583"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ivy Peng","raw_affiliation_strings":["Lawrence Livermore National Laboratory"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lawrence Livermore National Laboratory","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086147578","display_name":"Yanbao Ma","orcid":"https://orcid.org/0000-0001-9721-3333"},"institutions":[{"id":"https://openalex.org/I156087764","display_name":"University of California, Merced","ror":"https://ror.org/00d9ah105","country_code":"US","type":"education","lineage":["https://openalex.org/I156087764"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yanbao Ma","raw_affiliation_strings":["University of California, Merced"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California, Merced","institution_ids":["https://openalex.org/I156087764"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101758400","display_name":"Li Dong","orcid":"https://orcid.org/0000-0002-0509-6019"},"institutions":[{"id":"https://openalex.org/I156087764","display_name":"University of California, Merced","ror":"https://ror.org/00d9ah105","country_code":"US","type":"education","lineage":["https://openalex.org/I156087764"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dong Li","raw_affiliation_strings":["University of California, Merced"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California, Merced","institution_ids":["https://openalex.org/I156087764"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5100457289"],"corresponding_institution_ids":["https://openalex.org/I156087764"],"apc_list":null,"apc_paid":null,"fwci":3.535,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.92884527,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"215","last_page":"226"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9998999834060669,"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/T12326","display_name":"Network Packet Processing and Optimization","score":0.9937999844551086,"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/computer-science","display_name":"Computer science","score":0.8490504622459412},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.7885502576828003},{"id":"https://openalex.org/keywords/memoization","display_name":"Memoization","score":0.7410030364990234},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6882683038711548},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.6236349940299988},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.41247791051864624},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.23997756838798523},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.11947986483573914}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8490504622459412},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.7885502576828003},{"id":"https://openalex.org/C79516417","wikidata":"https://www.wikidata.org/wiki/Q1376168","display_name":"Memoization","level":4,"score":0.7410030364990234},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6882683038711548},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.6236349940299988},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.41247791051864624},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.23997756838798523},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.11947986483573914},{"id":"https://openalex.org/C42560504","wikidata":"https://www.wikidata.org/wiki/Q15419395","display_name":"Top-down parsing","level":3,"score":0.0},{"id":"https://openalex.org/C53893814","wikidata":"https://www.wikidata.org/wiki/Q7378909","display_name":"Rule-based machine translation","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3447818.3460365","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3447818.3460365","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3447818.3460365","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM International Conference on Supercomputing","raw_type":"proceedings-article"},{"id":"pmh:oai:osti.gov:1830494","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1830494","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null}],"best_oa_location":{"id":"doi:10.1145/3447818.3460365","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3447818.3460365","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3447818.3460365","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM International Conference on Supercomputing","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1308124067","display_name":null,"funder_award_id":"1718194","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2459876197","display_name":"CSR: Small: Collaborative Research: Exploring Portable Data Placement on Massively Parallel Platforms with Heterogeneous Memory Architectures","funder_award_id":"1617967","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4248083046","display_name":null,"funder_award_id":"No. DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G765874931","display_name":null,"funder_award_id":"No. DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320338286","funder_display_name":"Lawrence Livermore National Laboratory"},{"id":"https://openalex.org/G7806955302","display_name":null,"funder_award_id":"DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7968365520","display_name":null,"funder_award_id":"CCF-1553645","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8374966015","display_name":null,"funder_award_id":"AC52-07NA27344","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G8434336419","display_name":"CAREER: Application-centric, Reliable and Efficient High Performance Computing","funder_award_id":"1553645","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G991281326","display_name":null,"funder_award_id":"AC52-07NA27344","funder_id":"https://openalex.org/F4320338286","funder_display_name":"Lawrence Livermore National Laboratory"}],"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/F4320333031","display_name":"University of California Merced","ror":"https://ror.org/00d9ah105"},{"id":"https://openalex.org/F4320338286","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3169244019.pdf","grobid_xml":"https://content.openalex.org/works/W3169244019.grobid-xml"},"referenced_works_count":87,"referenced_works":["https://openalex.org/W1526967281","https://openalex.org/W1639305476","https://openalex.org/W1801766752","https://openalex.org/W1965067299","https://openalex.org/W1973396301","https://openalex.org/W1974196001","https://openalex.org/W1975734016","https://openalex.org/W1978159078","https://openalex.org/W1986423389","https://openalex.org/W1990537115","https://openalex.org/W1993765343","https://openalex.org/W1996174326","https://openalex.org/W2000197341","https://openalex.org/W2020498246","https://openalex.org/W2029059028","https://openalex.org/W2030980866","https://openalex.org/W2031264859","https://openalex.org/W2036640156","https://openalex.org/W2038177296","https://openalex.org/W2041902442","https://openalex.org/W2045194442","https://openalex.org/W2048621586","https://openalex.org/W2049076931","https://openalex.org/W2055755574","https://openalex.org/W2063384380","https://openalex.org/W2065963893","https://openalex.org/W2068739275","https://openalex.org/W2070991879","https://openalex.org/W2072570762","https://openalex.org/W2072627547","https://openalex.org/W2082144555","https://openalex.org/W2082912027","https://openalex.org/W2086209713","https://openalex.org/W2088311074","https://openalex.org/W2089479778","https://openalex.org/W2093221728","https://openalex.org/W2107892091","https://openalex.org/W2114239896","https://openalex.org/W2115550977","https://openalex.org/W2123366448","https://openalex.org/W2159498975","https://openalex.org/W2161522487","https://openalex.org/W2161694911","https://openalex.org/W2162006472","https://openalex.org/W2166051062","https://openalex.org/W2294552621","https://openalex.org/W2338063762","https://openalex.org/W2487018225","https://openalex.org/W2514808252","https://openalex.org/W2560356169","https://openalex.org/W2576352453","https://openalex.org/W2583648466","https://openalex.org/W2590565640","https://openalex.org/W2625392185","https://openalex.org/W2766455145","https://openalex.org/W2767918720","https://openalex.org/W2769084511","https://openalex.org/W2807205576","https://openalex.org/W2808435167","https://openalex.org/W2902981860","https://openalex.org/W2903504144","https://openalex.org/W2911001665","https://openalex.org/W2921153466","https://openalex.org/W2949223833","https://openalex.org/W2950713841","https://openalex.org/W2951973024","https://openalex.org/W2952598959","https://openalex.org/W2952777853","https://openalex.org/W2968671528","https://openalex.org/W2980084320","https://openalex.org/W2987081155","https://openalex.org/W2995037337","https://openalex.org/W3080489857","https://openalex.org/W3097202158","https://openalex.org/W3098393085","https://openalex.org/W3100446627","https://openalex.org/W3103902563","https://openalex.org/W3104005636","https://openalex.org/W3130134189","https://openalex.org/W3131379896","https://openalex.org/W3157025177","https://openalex.org/W3157864729","https://openalex.org/W3159461405","https://openalex.org/W4229614829","https://openalex.org/W4239872375","https://openalex.org/W4254455346","https://openalex.org/W6600680261"],"related_works":["https://openalex.org/W2317245370","https://openalex.org/W4249323025","https://openalex.org/W198851386","https://openalex.org/W1980160788","https://openalex.org/W2030310580","https://openalex.org/W947442053","https://openalex.org/W2148915962","https://openalex.org/W4313433561","https://openalex.org/W2283866686","https://openalex.org/W2948365806"],"abstract_inverted_index":{"Molecular":[0],"dynamics":[1],"(MD)":[2],"simulation":[3,61,93,104,152],"is":[4],"a":[5,18,68,90,115,119,131],"fundamental":[6],"method":[7,20],"for":[8,41,58,96],"modeling":[9],"ensembles":[10],"of":[11,25,158],"particles.":[12],"In":[13,35],"this":[14],"paper,":[15],"we":[16,37,144],"introduce":[17,88],"new":[19,132],"to":[21,44,78,123,135],"improve":[22,45],"the":[23,29,49,59,83,97,103,127,149,162],"performance":[24,47,80],"MD":[26,46,60,92,142],"by":[27,48],"leveraging":[28],"emerging":[30],"TB-scale":[31],"big":[32,84,98,165],"memory":[33,39,85,99,166],"system.":[34,86,100,167],"particular,":[36],"trade":[38],"capacity":[40],"computation":[42,110,125],"capability":[43],"lookup":[50],"table-based":[51],"memoization":[52,56],"technique.":[53],"The":[54],"traditional":[55],"technique":[57],"uses":[62,130],"relatively":[63],"small":[64],"DRAM,":[65],"bases":[66],"on":[67,118,161],"suboptimal":[69],"data":[70],"structure,":[71],"and":[72,108],"replaces":[73,109],"pair-wise":[74],"computation,":[75],"which":[76],"leads":[77],"limited":[79],"benefit":[81],"in":[82,111,126],"We":[87],"MD-HM,":[89],"memoization-based":[91],"framework":[94,153],"customized":[95],"MD-HM":[101,129,147],"partitions":[102],"field":[105],"into":[106],"subgrids,":[107],"each":[112],"subgrid":[113],"as":[114],"whole":[116],"based":[117,160],"lightweight":[120],"pattern-match":[121],"algorithm":[122],"recognize":[124],"subgrid.":[128],"two-phase":[133],"LSM-tree":[134],"optimize":[136],"read/write":[137],"performance.":[138],"Evaluating":[139],"with":[140,154],"nine":[141],"simulations,":[143],"show":[145],"that":[146],"outperforms":[148],"state-of-the-art":[150],"LAMMPS":[151],"an":[155],"average":[156],"speedup":[157],"7.6x":[159],"Intel":[163],"Optane-based":[164]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":5}],"updated_date":"2026-06-05T09:01:59.212387","created_date":"2021-06-22T00:00:00"}