{"id":"https://openalex.org/W2076285911","doi":"https://doi.org/10.1109/access.2013.2272434","title":"Using SST/Macro for Effective Analysis of MPI-Based Applications: Evaluating Large-Scale Genomic Sequence Search","display_name":"Using SST/Macro for Effective Analysis of MPI-Based Applications: Evaluating Large-Scale Genomic Sequence Search","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W2076285911","doi":"https://doi.org/10.1109/access.2013.2272434","mag":"2076285911"},"language":"en","primary_location":{"id":"doi:10.1109/access.2013.2272434","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2013.2272434","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/6336544/06553357.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://ieeexplore.ieee.org/ielx7/6287639/6336544/06553357.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006132411","display_name":"Damian Dechev","orcid":"https://orcid.org/0000-0002-0569-3403"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. Dechev","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL, USA","[Dept. of Electr. Eng. & Comput. Sci., Univ. of Central Florida, Orlando, FL, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL, USA","institution_ids":["https://openalex.org/I106165777"]},{"raw_affiliation_string":"[Dept. of Electr. Eng. & Comput. Sci., Univ. of Central Florida, Orlando, FL, USA]","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047054370","display_name":"Tae-Hyuk Ahn","orcid":"https://orcid.org/0000-0002-7281-9459"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tae-Hyuk Ahn","raw_affiliation_strings":["Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA","Comput. Sci. & Math. Div., Oak Ridge Nat. Lab., Oak Ridge, TN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]},{"raw_affiliation_string":"Comput. Sci. & Math. Div., Oak Ridge Nat. Lab., Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1850,"currency":"USD","value_usd":1850},"apc_paid":{"value":1850,"currency":"USD","value_usd":1850},"fwci":0.0,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.09355227,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"1","issue":null,"first_page":"428","last_page":"435"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9940000176429749,"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9940000176429749,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9886999726295471,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.9855999946594238,"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":0.8868288397789001},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.8124241828918457},{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.640835165977478},{"id":"https://openalex.org/keywords/macro","display_name":"Macro","score":0.5447701811790466},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.4922317564487457},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.4510473906993866},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.44581061601638794},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.43996915221214294},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.16622120141983032}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8868288397789001},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.8124241828918457},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.640835165977478},{"id":"https://openalex.org/C166955791","wikidata":"https://www.wikidata.org/wiki/Q629579","display_name":"Macro","level":2,"score":0.5447701811790466},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.4922317564487457},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.4510473906993866},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.44581061601638794},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.43996915221214294},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.16622120141983032},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/access.2013.2272434","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2013.2272434","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/6336544/06553357.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},{"id":"pmh:oai:stars.library.ucf.edu:scopus2010-8270","is_oa":true,"landing_page_url":"https://stars.library.ucf.edu/scopus2010/7271","pdf_url":null,"source":{"id":"https://openalex.org/S4210172555","display_name":"Journal of International Crisis and Risk Communication Research","issn_l":"2576-0017","issn":["2576-0017","2576-0025"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Scopus Export 2010-2014","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:5920477a449947998375477dcbd87c82","is_oa":true,"landing_page_url":"https://doaj.org/article/5920477a449947998375477dcbd87c82","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Access, Vol 1, Pp 428-435 (2013)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1109/access.2013.2272434","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2013.2272434","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/6336544/06553357.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320338291","display_name":"Sandia National Laboratories","ror":"https://ror.org/01apwpt12"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2076285911.pdf","grobid_xml":"https://content.openalex.org/works/W2076285911.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W95282149","https://openalex.org/W145805655","https://openalex.org/W385108639","https://openalex.org/W1480147318","https://openalex.org/W1501077214","https://openalex.org/W1522923330","https://openalex.org/W1558960195","https://openalex.org/W1566403276","https://openalex.org/W1985928578","https://openalex.org/W2005129098","https://openalex.org/W2009749659","https://openalex.org/W2026532005","https://openalex.org/W2053792124","https://openalex.org/W2078466430","https://openalex.org/W2084018711","https://openalex.org/W2105421658","https://openalex.org/W2112286591","https://openalex.org/W2113781114","https://openalex.org/W2115036455","https://openalex.org/W2116856633","https://openalex.org/W2125062675","https://openalex.org/W2134516420","https://openalex.org/W2135002184","https://openalex.org/W2137244898","https://openalex.org/W2153456949","https://openalex.org/W2156137607","https://openalex.org/W2158714788","https://openalex.org/W2162260260","https://openalex.org/W2404525716","https://openalex.org/W2559931738","https://openalex.org/W4234578858","https://openalex.org/W4236236547","https://openalex.org/W4246704440","https://openalex.org/W6603821543","https://openalex.org/W6606052223","https://openalex.org/W6628691834","https://openalex.org/W6671213136","https://openalex.org/W6676715003","https://openalex.org/W6676952826","https://openalex.org/W6713580433"],"related_works":["https://openalex.org/W2030816003","https://openalex.org/W4239992647","https://openalex.org/W2076325756","https://openalex.org/W81423522","https://openalex.org/W2150013480","https://openalex.org/W2488264085","https://openalex.org/W1509860481","https://openalex.org/W4386206750","https://openalex.org/W2049983311","https://openalex.org/W2088946561"],"abstract_inverted_index":{"Future":[0],"and":[1,10,30,49,101],"current":[2],"high-performance":[3,89],"computing":[4],"applications":[5],"will":[6,22],"have":[7],"to":[8],"change":[9],"adapt":[11],"as":[12],"node":[13],"architectures":[14],"evolve.":[15],"The":[16],"application":[17],"of":[18,32,51,54,57,75,81,85,121],"advanced":[19,67],"architecture":[20],"simulators":[21],"play":[23],"a":[24,52,58,103],"crucial":[25],"role":[26],"for":[27,45,78,95,105],"the":[28,47,73,79,119,122],"design":[29],"optimization":[31],"future":[33],"data":[34],"intensive":[35],"applications.":[36],"In":[37,109],"this":[38],"paper,":[39],"we":[40,113],"present":[41],"our":[42,76,110],"simulation-based":[43],"framework":[44,77],"analyzing":[46],"scalability":[48],"performance":[50],"number":[53],"critical":[55],"optimizations":[56],"massively":[59],"parallel":[60,90],"genomic":[61],"search":[62],"application,":[63],"mpiBLAST,":[64],"using":[65],"an":[66,93],"macroscale":[68],"simulator":[69],"(SST/macro).":[70],"We":[71],"report":[72],"use":[74],"evaluation":[80],"three":[82],"potential":[83],"improvements":[84],"mpiBLAST:":[86],"1)":[87],"enabling":[88],"output;":[91],"2)":[92],"approach":[94],"caching":[96],"database":[97,107],"fragments":[98],"in":[99],"memory;":[100],"3)":[102],"methodology":[104],"pre-distributing":[106],"segments.":[108],"experimental":[111],"setup,":[112],"performed":[114],"query":[115],"sequence":[116],"matching":[117],"on":[118],"genome":[120],"yellow":[123],"fever":[124],"mosquito,":[125],"Aedes":[126],"aegypti.":[127]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2018,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}