{"id":"https://openalex.org/W2786530904","doi":"https://doi.org/10.1145/3144779.3169109","title":"MerBench","display_name":"MerBench","publication_year":2017,"publication_date":"2017-11-12","ids":{"openalex":"https://openalex.org/W2786530904","doi":"https://doi.org/10.1145/3144779.3169109","mag":"2786530904"},"language":"en","primary_location":{"id":"doi:10.1145/3144779.3169109","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3144779.3169109","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Second Annual PGAS Applications Workshop","raw_type":"proceedings-article"},"type":"article","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/A5057664789","display_name":"Evangelos Georganas","orcid":null},"institutions":[{"id":"https://openalex.org/I1343180700","display_name":"Intel (United States)","ror":"https://ror.org/01ek73717","country_code":"US","type":"company","lineage":["https://openalex.org/I1343180700"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Evangelos Georganas","raw_affiliation_strings":["Parallel Computing Lab, Intel Corp"],"affiliations":[{"raw_affiliation_string":"Parallel Computing Lab, Intel Corp","institution_ids":["https://openalex.org/I1343180700"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007110536","display_name":"Marquita Ellis","orcid":"https://orcid.org/0000-0002-4158-9101"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]},{"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":"Marquita Ellis","raw_affiliation_strings":["EECS Department, University of California, Berkeley, USA and Computational Research Division, Lawrence Berkeley National Laboratory, USA"],"affiliations":[{"raw_affiliation_string":"EECS Department, University of California, Berkeley, USA and Computational Research Division, Lawrence Berkeley National Laboratory, USA","institution_ids":["https://openalex.org/I148283060","https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082270383","display_name":"Rob Egan","orcid":"https://orcid.org/0000-0001-7080-7801"},"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"]},{"id":"https://openalex.org/I196679689","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rob Egan","raw_affiliation_strings":["Joint Genome Institute, Lawrence Berkeley National Laboratory, USA"],"affiliations":[{"raw_affiliation_string":"Joint Genome Institute, Lawrence Berkeley National Laboratory, USA","institution_ids":["https://openalex.org/I196679689","https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016671058","display_name":"Steven Hofmeyr","orcid":"https://orcid.org/0000-0002-3299-472X"},"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":"Steven Hofmeyr","raw_affiliation_strings":["Computational Research Division, Lawrence Berkeley National Laboratory, USA"],"affiliations":[{"raw_affiliation_string":"Computational Research Division, Lawrence Berkeley National Laboratory, USA","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/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]},{"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 Bulu\u00e7","raw_affiliation_strings":["EECS Department, University of California, Berkeley, USA and Computational Research Division, Lawrence Berkeley National Laboratory, USA"],"affiliations":[{"raw_affiliation_string":"EECS Department, University of California, Berkeley, USA and Computational Research Division, Lawrence Berkeley National Laboratory, USA","institution_ids":["https://openalex.org/I148283060","https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000643884","display_name":"Brandon Cook","orcid":"https://orcid.org/0000-0002-4203-4079"},"institutions":[{"id":"https://openalex.org/I4210151627","display_name":"National Energy Research Scientific Computing Center","ror":"https://ror.org/05v3mvq14","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521","https://openalex.org/I4210151627"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brandon Cook","raw_affiliation_strings":["National Energy Research Scientific Computing Center, USA"],"affiliations":[{"raw_affiliation_string":"National Energy Research Scientific Computing Center, USA","institution_ids":["https://openalex.org/I4210151627"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110759506","display_name":"Leonid Oliker","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":"Leonid Oliker","raw_affiliation_strings":["Computational Research Division, Lawrence Berkeley National Laboratory, USA"],"affiliations":[{"raw_affiliation_string":"Computational Research Division, Lawrence Berkeley National Laboratory, USA","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091741596","display_name":"Katherine Yelick","orcid":"https://orcid.org/0000-0003-0957-701X"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]},{"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":["EECS Department, University of California, Berkeley, USA and Computational Research Division, Lawrence Berkeley National Laboratory, USA"],"affiliations":[{"raw_affiliation_string":"EECS Department, University of California, Berkeley, USA and Computational Research Division, Lawrence Berkeley National Laboratory, USA","institution_ids":["https://openalex.org/I148283060","https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5057664789"],"corresponding_institution_ids":["https://openalex.org/I1343180700"],"apc_list":null,"apc_paid":null,"fwci":0.7801,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.80468765,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T11269","display_name":"Algorithms and Data Compression","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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":0.9976999759674072,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.9945999979972839,"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/computer-science","display_name":"Computer science","score":0.8158484101295471},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7774519920349121},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7505313158035278},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.7204166650772095},{"id":"https://openalex.org/keywords/partitioned-global-address-space","display_name":"Partitioned global address space","score":0.540747880935669},{"id":"https://openalex.org/keywords/scaling","display_name":"Scaling","score":0.5230287313461304},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.47516152262687683},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.44875675439834595},{"id":"https://openalex.org/keywords/theory-of-computation","display_name":"Theory of computation","score":0.4307171404361725},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.41478031873703003},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.3547336459159851},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.22052156925201416},{"id":"https://openalex.org/keywords/programming-paradigm","display_name":"Programming paradigm","score":0.22020602226257324},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14042928814888},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07866904139518738}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8158484101295471},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7774519920349121},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7505313158035278},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.7204166650772095},{"id":"https://openalex.org/C60832428","wikidata":"https://www.wikidata.org/wiki/Q945818","display_name":"Partitioned global address space","level":3,"score":0.540747880935669},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.5230287313461304},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.47516152262687683},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.44875675439834595},{"id":"https://openalex.org/C24858836","wikidata":"https://www.wikidata.org/wiki/Q844718","display_name":"Theory of computation","level":2,"score":0.4307171404361725},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.41478031873703003},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.3547336459159851},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.22052156925201416},{"id":"https://openalex.org/C34165917","wikidata":"https://www.wikidata.org/wiki/Q188267","display_name":"Programming paradigm","level":2,"score":0.22020602226257324},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14042928814888},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07866904139518738},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3144779.3169109","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3144779.3169109","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Second Annual PGAS Applications Workshop","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":8,"referenced_works":["https://openalex.org/W297888808","https://openalex.org/W1538125091","https://openalex.org/W1989437487","https://openalex.org/W1993544900","https://openalex.org/W2005202728","https://openalex.org/W2087064593","https://openalex.org/W2135342109","https://openalex.org/W2739560434"],"related_works":["https://openalex.org/W2494227547","https://openalex.org/W2133695315","https://openalex.org/W4236792535","https://openalex.org/W2052234289","https://openalex.org/W2072270916","https://openalex.org/W1786600822","https://openalex.org/W2912015630","https://openalex.org/W3150557277","https://openalex.org/W2171525159","https://openalex.org/W2766886462"],"abstract_inverted_index":{"De":[0],"novo":[1],"genome":[2,77],"assembly":[3],"is":[4,41],"one":[5],"of":[6,61,69,93,114],"the":[7,66,70,97,111,115],"most":[8],"important":[9,24],"and":[10,21,29,40,48,100],"challenging":[11],"computational":[12],"problems":[13],"in":[14],"modern":[15],"genomics;":[16],"further,":[17],"it":[18,34],"shares":[19],"algorithms":[20,72],"communication":[22,67],"patterns":[23,68],"to":[25,84,86,109],"other":[26],"graph":[27],"analytic":[28],"irregular":[30],"applications.":[31],"Unlike":[32],"simulations,":[33],"has":[35,81],"no":[36],"floating":[37],"point":[38],"arithmetic":[39],"dominated":[42],"by":[43],"small":[44],"memory":[45],"transactions":[46],"within":[47],"between":[49],"computing":[50],"nodes.":[51],"In":[52],"this":[53],"work,":[54],"we":[55],"introduce":[56],"MerBench,":[57],"a":[58,75],"compact":[59],"set":[60],"PGAS":[62],"benchmarks":[63],"that":[64,80],"capture":[65],"parallel":[71,76],"throughout":[73],"HipMer,":[74],"assembler":[78],"pipeline":[79],"been":[82],"shown":[83],"scale":[85],"massive":[87],"concurrencies.":[88],"We":[89],"also":[90],"present":[91],"results":[92,105],"these":[94,103],"microbenchmarks":[95],"on":[96],"Edison":[98],"supercomputer":[99],"illustrate":[101],"how":[102],"empirical":[104],"can":[106],"be":[107],"used":[108],"assess":[110],"scaling":[112],"behavior":[113],"pipeline.":[116]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2018-02-23T00:00:00"}
