{"id":"https://openalex.org/W3204494816","doi":"https://doi.org/10.1145/3472456.3472517","title":"Scaling Generalized N-Body Problems, A Case Study from Genomics","display_name":"Scaling Generalized N-Body Problems, A Case Study from Genomics","publication_year":2021,"publication_date":"2021-08-09","ids":{"openalex":"https://openalex.org/W3204494816","doi":"https://doi.org/10.1145/3472456.3472517","mag":"3204494816"},"language":"en","primary_location":{"id":"doi:10.1145/3472456.3472517","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3472456.3472517","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3472456.3472517","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"50th International Conference on Parallel Processing","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/10.1145/3472456.3472517","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007110536","display_name":"Marquita Ellis","orcid":"https://orcid.org/0000-0002-4158-9101"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Marquita Ellis","raw_affiliation_strings":["The University of California at Berkeley, Lawrence Berkeley National Lab, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The University of California at Berkeley, Lawrence Berkeley National Lab, United States of America","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035719914","display_name":"Ayd\u0131n Bulu\u00e7","orcid":"https://orcid.org/0000-0001-7253-9038"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aydin Buluc","raw_affiliation_strings":["Lawrence Berkeley National Lab, The University of California at Berkeley, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lawrence Berkeley National Lab, The University of California at Berkeley, United States of America","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112630097","display_name":"Katherine Yelick","orcid":null},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Katherine Yelick","raw_affiliation_strings":["The University of California at Berkeley, Lawrence Berkeley National Lab, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The University of California at Berkeley, Lawrence Berkeley National Lab, United States of America","institution_ids":["https://openalex.org/I148283060"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5007110536"],"corresponding_institution_ids":["https://openalex.org/I148283060"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.15119567,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"9"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13126","display_name":"Scientific Research and Discoveries","score":0.9513999819755554,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T13126","display_name":"Scientific Research and Discoveries","score":0.9513999819755554,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9376999735832214,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9275000095367432,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/scaling","display_name":"Scaling","score":0.6862300038337708},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5544414520263672},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.45357856154441833},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2181238830089569},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.14683881402015686},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13096576929092407},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12367749214172363},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.10041454434394836}],"concepts":[{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.6862300038337708},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5544414520263672},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.45357856154441833},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2181238830089569},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.14683881402015686},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13096576929092407},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12367749214172363},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.10041454434394836},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3472456.3472517","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3472456.3472517","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3472456.3472517","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"50th International Conference on Parallel Processing","raw_type":"proceedings-article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt5tr1z6td","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/5tr1z6td","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1145/3472456.3472517","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3472456.3472517","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3472456.3472517","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"50th International Conference on Parallel Processing","raw_type":"proceedings-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.49000000953674316}],"awards":[{"id":"https://openalex.org/G1071216263","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320332369","funder_display_name":"National Nuclear Security Administration"},{"id":"https://openalex.org/G1286236842","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G1677143136","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320317220","funder_display_name":"National Energy Research Scientific Computing Center"},{"id":"https://openalex.org/G2503023272","display_name":null,"funder_award_id":"Contract No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G2857863752","display_name":null,"funder_award_id":"No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320338292","funder_display_name":"Lawrence Berkeley National Laboratory"},{"id":"https://openalex.org/G2900453181","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332369","funder_display_name":"National Nuclear Security Administration"},{"id":"https://openalex.org/G291699705","display_name":null,"funder_award_id":"1823034","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3083819904","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3232922872","display_name":null,"funder_award_id":"17-SC-20-SC","funder_id":"https://openalex.org/F4320332369","funder_display_name":"National Nuclear Security Administration"},{"id":"https://openalex.org/G3944918260","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4501827968","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4565140552","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G498139845","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G5076365615","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320317220","funder_display_name":"National Energy Research Scientific Computing Center"},{"id":"https://openalex.org/G5296923526","display_name":null,"funder_award_id":"Contract No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320317220","funder_display_name":"National Energy Research Scientific Computing Center"},{"id":"https://openalex.org/G542631466","display_name":null,"funder_award_id":"No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6348972864","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G654302390","display_name":null,"funder_award_id":"Contract No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320338292","funder_display_name":"Lawrence Berkeley National Laboratory"},{"id":"https://openalex.org/G6558272803","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6859237865","display_name":null,"funder_award_id":"17-SC-20-SC","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7233692708","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7354628648","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320338292","funder_display_name":"Lawrence Berkeley National Laboratory"},{"id":"https://openalex.org/G7672463193","display_name":null,"funder_award_id":"No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G805243471","display_name":null,"funder_award_id":"Contract No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G8253304997","display_name":null,"funder_award_id":"17-SC-20-SC","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G8306346728","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320338292","funder_display_name":"Lawrence Berkeley National Laboratory"},{"id":"https://openalex.org/G969889393","display_name":null,"funder_award_id":"DE-AC02-","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"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/F4320317220","display_name":"National Energy Research Scientific Computing Center","ror":"https://ror.org/05v3mvq14"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320332369","display_name":"National Nuclear Security Administration","ror":"https://ror.org/03sk1we31"},{"id":"https://openalex.org/F4320338292","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3204494816.pdf","grobid_xml":"https://content.openalex.org/works/W3204494816.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W344138311","https://openalex.org/W1490600648","https://openalex.org/W1579534339","https://openalex.org/W2055043387","https://openalex.org/W2055666215","https://openalex.org/W2066236912","https://openalex.org/W2074231493","https://openalex.org/W2075996757","https://openalex.org/W2087064593","https://openalex.org/W2137759177","https://openalex.org/W2146558186","https://openalex.org/W2196186329","https://openalex.org/W2485161901","https://openalex.org/W2574582689","https://openalex.org/W2739560434","https://openalex.org/W2755804176","https://openalex.org/W2789843538","https://openalex.org/W2896801938","https://openalex.org/W2913135575","https://openalex.org/W2950954328","https://openalex.org/W2963585318","https://openalex.org/W2998804949","https://openalex.org/W3006553333","https://openalex.org/W3122567528","https://openalex.org/W3216997764","https://openalex.org/W4230799834","https://openalex.org/W4289464760","https://openalex.org/W6772958074"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W4402327032","https://openalex.org/W2382290278"],"abstract_inverted_index":{"This":[0],"work":[1],"examines":[2],"a":[3,11,85,96],"data-intensive":[4,202],"irregular":[5,157,203],"application":[6,178],"from":[7,115,128],"genomics":[8,213],"that":[9,208],"represents":[10],"type":[12,200],"of":[13,18,22,40,71,80,112,136,155,164,191,201],"Generalized":[14],"N-Body":[15,52],"problems,":[16,53],"one":[17,116],"the":[19,23,60,64,72,78,81,107,125,152,156,162,187,192],"\u201cseven":[20],"giants\u201d":[21],"NRC":[24],"Big":[25],"Data":[26],"motifs.":[27],"In":[28],"this":[29,199],"problem,":[30],"computations":[31],"(genome":[32],"alignments)":[33],"are":[34],"performed":[35],"on":[36,68,120],"sparse":[37],"data-dependent":[38],"pairs":[39],"inputs,":[41],"with":[42,140],"variable":[43,47],"cost":[44],"computation":[45,158],"and":[46,63,94,110,159,161,176,194,205],"datum":[48],"sizes.":[49],"Unlike":[50],"simulation-based":[51],"there":[54],"is":[55],"no":[56],"inherent":[57],"locality":[58],"in":[59,92,103,173,212,216],"pairwise":[61],"interactions,":[62],"interaction":[65],"sparsity":[66],"depends":[67],"particular":[69],"parameters":[70],"input,":[73],"which":[74],"can":[75,209],"also":[76],"affect":[77],"quality":[79],"output.":[82],"We":[83,105],"build-on":[84],"pre-existing":[86],"bulk-synchronous":[87],"implementation,":[88],"using":[89,100],"collective":[90],"communication":[91],"MPI,":[93],"implement":[95],"new":[97],"asynchronous":[98,167],"one,":[99],"cross-node":[101],"RPCs":[102],"UPC++.":[104],"establish":[106],"intranode":[108],"comparability":[109],"efficiency":[111],"both,":[113],"scaling":[114,198],"to":[117,131],"all":[118],"core(s)":[119],"node.":[121],"Then":[122],"we":[123,150],"evaluate":[124],"multinode":[126],"scalability":[127],"1":[129],"node":[130],"512":[132],"nodes":[133],"(32,768":[134],"cores)":[135],"NERSC\u2019s":[137],"Cray":[138],"XC40":[139],"Intel":[141],"Xeon":[142],"Phi":[143],"\u201cKnight\u2019s":[144],"Landing\u201d":[145],"nodes.":[146],"With":[147],"real":[148],"workloads,":[149],"examine":[151],"load":[153],"balance":[154],"communication,":[160],"costs":[163],"many":[165],"small":[166],"messages":[168],"versus":[169],"few":[170],"large-aggregated":[171],"messages,":[172],"both":[174,182],"latency":[175],"overall":[177],"memory":[179],"footprint.":[180],"While":[181],"implementations":[183],"demonstrate":[184],"good":[185],"scaling,":[186],"study":[188],"reveals":[189],"some":[190],"programming":[193],"architectural":[195],"challenges":[196],"for":[197,218],"application,":[204],"contributes":[206],"code":[207],"be":[210],"used":[211],"pipelines":[214],"or":[215],"benchmarking":[217],"data":[219],"analytics":[220],"more":[221],"broadly.":[222]},"counts_by_year":[],"updated_date":"2026-05-04T08:30:34.212998","created_date":"2025-10-10T00:00:00"}
