{"id":"https://openalex.org/W2894208163","doi":"https://doi.org/10.1177/1094342018802347","title":"Dynamic reconfiguration of noniterative scientific applications: A case study with HPG aligner","display_name":"Dynamic reconfiguration of noniterative scientific applications: A case study with HPG aligner","publication_year":2018,"publication_date":"2018-09-27","ids":{"openalex":"https://openalex.org/W2894208163","doi":"https://doi.org/10.1177/1094342018802347","mag":"2894208163"},"language":"en","primary_location":{"id":"doi:10.1177/1094342018802347","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342018802347","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/2117/345721","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006767413","display_name":"Sergio Iserte","orcid":"https://orcid.org/0000-0003-3654-7924"},"institutions":[{"id":"https://openalex.org/I10902133","display_name":"Universitat Jaume I","ror":"https://ror.org/02ws1xc11","country_code":"ES","type":"education","lineage":["https://openalex.org/I10902133"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Sergio Iserte","raw_affiliation_strings":["Department of Computer Science and Engineering, Universitat Jaume I (UJI), Castell\u00f3n de la Plana, Spain"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Universitat Jaume I (UJI), Castell\u00f3n de la Plana, Spain","institution_ids":["https://openalex.org/I10902133"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018719028","display_name":"H\u00e8ctor Mart\u00ednez","orcid":"https://orcid.org/0000-0001-5891-4479"},"institutions":[{"id":"https://openalex.org/I10902133","display_name":"Universitat Jaume I","ror":"https://ror.org/02ws1xc11","country_code":"ES","type":"education","lineage":["https://openalex.org/I10902133"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"H\u00e9ctor Mart\u00ednez","raw_affiliation_strings":["Department of Computer Science and Engineering, Universitat Jaume I (UJI), Castell\u00f3n de la Plana, Spain"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Universitat Jaume I (UJI), Castell\u00f3n de la Plana, Spain","institution_ids":["https://openalex.org/I10902133"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090675958","display_name":"Sergio Barrachina","orcid":"https://orcid.org/0000-0003-4642-7467"},"institutions":[{"id":"https://openalex.org/I10902133","display_name":"Universitat Jaume I","ror":"https://ror.org/02ws1xc11","country_code":"ES","type":"education","lineage":["https://openalex.org/I10902133"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Sergio Barrachina","raw_affiliation_strings":["Department of Computer Science and Engineering, Universitat Jaume I (UJI), Castell\u00f3n de la Plana, Spain"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Universitat Jaume I (UJI), Castell\u00f3n de la Plana, Spain","institution_ids":["https://openalex.org/I10902133"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101773656","display_name":"Maribel Castillo","orcid":"https://orcid.org/0000-0002-2826-3086"},"institutions":[{"id":"https://openalex.org/I10902133","display_name":"Universitat Jaume I","ror":"https://ror.org/02ws1xc11","country_code":"ES","type":"education","lineage":["https://openalex.org/I10902133"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Maribel Castillo","raw_affiliation_strings":["Department of Computer Science and Engineering, Universitat Jaume I (UJI), Castell\u00f3n de la Plana, Spain"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Universitat Jaume I (UJI), Castell\u00f3n de la Plana, Spain","institution_ids":["https://openalex.org/I10902133"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032916877","display_name":"Rafael Mayo","orcid":"https://orcid.org/0000-0003-1552-3069"},"institutions":[{"id":"https://openalex.org/I10902133","display_name":"Universitat Jaume I","ror":"https://ror.org/02ws1xc11","country_code":"ES","type":"education","lineage":["https://openalex.org/I10902133"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Rafael Mayo","raw_affiliation_strings":["Department of Computer Science and Engineering, Universitat Jaume I (UJI), Castell\u00f3n de la Plana, Spain"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Universitat Jaume I (UJI), Castell\u00f3n de la Plana, Spain","institution_ids":["https://openalex.org/I10902133"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000573036","display_name":"Antonio J. Pe\u00f1a","orcid":"https://orcid.org/0000-0002-3575-4617"},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Antonio J Pe\u00f1a","raw_affiliation_strings":["Barcelona Supercomputing Center (BSC), Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center (BSC), Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5006767413"],"corresponding_institution_ids":["https://openalex.org/I10902133"],"apc_list":null,"apc_paid":null,"fwci":0.7798,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.76313266,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"33","issue":"5","first_page":"804","last_page":"816"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9990000128746033,"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"}},"topics":[{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9990000128746033,"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/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9966999888420105,"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/T10772","display_name":"Distributed systems and fault tolerance","score":0.9904999732971191,"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":0.8302550315856934},{"id":"https://openalex.org/keywords/control-reconfiguration","display_name":"Control reconfiguration","score":0.7981471419334412},{"id":"https://openalex.org/keywords/workload","display_name":"Workload","score":0.6691268682479858},{"id":"https://openalex.org/keywords/malleability","display_name":"Malleability","score":0.6494507193565369},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.5846424698829651},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.5774478912353516},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.517463743686676},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.49236738681793213},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3435612916946411},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.2698177695274353},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.12138417363166809}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8302550315856934},{"id":"https://openalex.org/C119701452","wikidata":"https://www.wikidata.org/wiki/Q5165881","display_name":"Control reconfiguration","level":2,"score":0.7981471419334412},{"id":"https://openalex.org/C2778476105","wikidata":"https://www.wikidata.org/wiki/Q628539","display_name":"Workload","level":2,"score":0.6691268682479858},{"id":"https://openalex.org/C100980136","wikidata":"https://www.wikidata.org/wiki/Q4668956","display_name":"Malleability","level":4,"score":0.6494507193565369},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.5846424698829651},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.5774478912353516},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.517463743686676},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.49236738681793213},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3435612916946411},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.2698177695274353},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.12138417363166809},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"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/C93974786","wikidata":"https://www.wikidata.org/wiki/Q1589480","display_name":"Ciphertext","level":3,"score":0.0},{"id":"https://openalex.org/C148730421","wikidata":"https://www.wikidata.org/wiki/Q141090","display_name":"Encryption","level":2,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1177/1094342018802347","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342018802347","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"},{"id":"pmh:oai:repositori.uji.es:10234/178287","is_oa":false,"landing_page_url":"http://hdl.handle.net/10234/178287","pdf_url":null,"source":{"id":"https://openalex.org/S4306400303","display_name":"Repositori UJI (Universitat Jaume I)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I10902133","host_organization_name":"Universitat Jaume I","host_organization_lineage":["https://openalex.org/I10902133"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:upcommons.upc.edu:2117/345721","is_oa":true,"landing_page_url":"http://hdl.handle.net/2117/345721","pdf_url":null,"source":{"id":"https://openalex.org/S4377196262","display_name":"UPCommons institutional repository (Universitat Polit\u00e8cnica de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9617848","host_organization_name":"Universitat Polit\u00e8cnica de Catalunya","host_organization_lineage":["https://openalex.org/I9617848"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:upcommons.upc.edu:2117/345721","is_oa":true,"landing_page_url":"http://hdl.handle.net/2117/345721","pdf_url":null,"source":{"id":"https://openalex.org/S4377196262","display_name":"UPCommons institutional repository (Universitat Polit\u00e8cnica de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9617848","host_organization_name":"Universitat Polit\u00e8cnica de Catalunya","host_organization_lineage":["https://openalex.org/I9617848"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/8","display_name":"Decent work and economic growth","score":0.44999998807907104}],"awards":[{"id":"https://openalex.org/G7702789587","display_name":null,"funder_award_id":"TIN2014-53495-R","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"}],"funders":[{"id":"https://openalex.org/F4320321837","display_name":"Ministerio de Econom\u00eda y Competitividad","ror":"https://ror.org/034900433"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1528246556","https://openalex.org/W1539774972","https://openalex.org/W1585314083","https://openalex.org/W1596936080","https://openalex.org/W1733137719","https://openalex.org/W1975904117","https://openalex.org/W2025495823","https://openalex.org/W2096173343","https://openalex.org/W2134971118","https://openalex.org/W2141930780","https://openalex.org/W2209677773","https://openalex.org/W2277827603","https://openalex.org/W2532284696","https://openalex.org/W2752303704","https://openalex.org/W2884290932","https://openalex.org/W3100792311","https://openalex.org/W4214585270","https://openalex.org/W4241355993"],"related_works":["https://openalex.org/W2065857835","https://openalex.org/W1981002473","https://openalex.org/W2357657342","https://openalex.org/W4240042177","https://openalex.org/W2153432761","https://openalex.org/W3029108995","https://openalex.org/W2152623100","https://openalex.org/W2074221157","https://openalex.org/W4214878056","https://openalex.org/W4309152918"],"abstract_inverted_index":{"Several":[0],"studies":[1],"have":[2],"proved":[3],"the":[4,11,45,49,54,67,70,118,129,143,148,187,203,219,228],"benefits":[5,204],"of":[6,13,25,32,38,53,76,121,146,156,175,197,205,218],"job":[7,95],"malleability,":[8],"that":[9],"is,":[10],"capacity":[12],"an":[14,107,165,176,215],"application":[15,178],"to":[16,20,62,91,132,151,179,193,227],"adapt":[17],"its":[18],"parallelism":[19],"a":[21,39,80,153,159,180,239],"dynamically":[22],"changing":[23],"number":[24],"allocated":[26],"processors.":[27],"The":[28],"most":[29],"remarkable":[30],"advantages":[31],"executing":[33],"malleable":[34,94,134,154,181,200,220,236],"jobs":[35,223],"as":[36],"part":[37],"high":[40],"performance":[41],"computer":[42],"workload":[43],"are":[44,98,102],"throughput":[46,241],"increase":[47],"and":[48,78,201],"more":[50],"efficient":[51],"utilization":[52],"underlying":[55],"resources.":[56],"Malleability":[57],"has":[58],"been":[59],"mostly":[60],"applied":[61],"iterative":[63],"applications":[64,89,100,198],"where":[65],"all":[66,87],"processes":[68],"execute":[69],"same":[71],"operations":[72],"over":[73],"different":[74],"sets":[75],"data":[77],"with":[79],"balanced":[81],"per":[82,109],"process":[83,110],"load.":[84],"Unfortunately,":[85],"not":[86],"scientific":[88,99],"adhere":[90],"this":[92,139,172,195,206],"process-level":[93],"structure.":[96],"There":[97],"which":[101],"either":[103],"noniterative":[104,161],"or":[105],"present":[106],"irregular":[108,166],"load":[111],"distribution.":[112],"Unlike":[113],"many":[114],"other":[115],"reconfiguration":[116],"tools,":[117],"Dynamic":[119],"Management":[120],"Resources":[122],"Application":[123],"Programming":[124],"Interface":[125],"(DMR":[126],"API)":[127],"provides":[128],"necessary":[130],"flexibility":[131],"make":[133],"these":[135],"out-of-target":[136,177],"applications.":[137],"In":[138],"article,":[140],"we":[141,183],"study":[142],"particular":[144],"case":[145],"using":[147],"DMR":[149,188],"API":[150,189],"generate":[152],"version":[155],"HPG":[157,221,230,234],"aligner,":[158],"distributed-memory":[160],"genomic":[162],"sequencer":[163],"featuring":[164],"communication":[167],"pattern":[168],"among":[169],"processes.":[170],"Through":[171],"first":[173],"conversion":[174,207],"job,":[182],"both":[184],"illustrate":[185],"how":[186],"may":[190],"be":[191],"used":[192],"convert":[194],"type":[196],"into":[199],"test":[202],"in":[208],"production":[209],"clusters.":[210],"Our":[211],"experimental":[212],"results":[213],"reveal":[214],"important":[216],"reduction":[217],"aligner":[222,231,235],"completion":[224],"time":[225],"compared":[226],"original":[229],"version.":[232],"Furthermore,":[233],"workloads":[237],"achieve":[238],"greater":[240],"than":[242],"their":[243],"fixed":[244],"counterparts.":[245]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}
