{"id":"https://openalex.org/W4398186362","doi":"https://doi.org/10.1145/3605098.3635986","title":"Applying dynamic balancing to improve the performance of MPI parallel genomics applications","display_name":"Applying dynamic balancing to improve the performance of MPI parallel genomics applications","publication_year":2024,"publication_date":"2024-04-08","ids":{"openalex":"https://openalex.org/W4398186362","doi":"https://doi.org/10.1145/3605098.3635986"},"language":"en","primary_location":{"id":"doi:10.1145/3605098.3635986","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3605098.3635986","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 39th ACM/SIGAPP Symposium on Applied Computing","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hdl.handle.net/2183/37990","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083390470","display_name":"Alejandro Fern\u00e1ndez-Fraga","orcid":"https://orcid.org/0000-0002-4193-995X"},"institutions":[{"id":"https://openalex.org/I11019714","display_name":"Universidade da Coru\u00f1a","ror":"https://ror.org/01qckj285","country_code":"ES","type":"education","lineage":["https://openalex.org/I11019714"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Alejandro Fernandez-Fraga","raw_affiliation_strings":["Universidade da Coru\u00f1a, A Coru\u00f1a, Spain"],"affiliations":[{"raw_affiliation_string":"Universidade da Coru\u00f1a, A Coru\u00f1a, Spain","institution_ids":["https://openalex.org/I11019714"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008112601","display_name":"Jorge Gonz\u00e1lez\u2010Dom\u00ednguez","orcid":"https://orcid.org/0000-0002-2602-4874"},"institutions":[{"id":"https://openalex.org/I11019714","display_name":"Universidade da Coru\u00f1a","ror":"https://ror.org/01qckj285","country_code":"ES","type":"education","lineage":["https://openalex.org/I11019714"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jorge Gonzalez-Dominguez","raw_affiliation_strings":["Universidade da Coru\u00f1a, A Coru\u00f1a, Spain"],"affiliations":[{"raw_affiliation_string":"Universidade da Coru\u00f1a, A Coru\u00f1a, Spain","institution_ids":["https://openalex.org/I11019714"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021488012","display_name":"Mar\u00eda J. Mart\u00edn","orcid":null},"institutions":[{"id":"https://openalex.org/I11019714","display_name":"Universidade da Coru\u00f1a","ror":"https://ror.org/01qckj285","country_code":"ES","type":"education","lineage":["https://openalex.org/I11019714"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Maria J. Martin","raw_affiliation_strings":["Universidade da Coru\u00f1a, A Coru\u00f1a, Spain"],"affiliations":[{"raw_affiliation_string":"Universidade da Coru\u00f1a, A Coru\u00f1a, Spain","institution_ids":["https://openalex.org/I11019714"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5083390470"],"corresponding_institution_ids":["https://openalex.org/I11019714"],"apc_list":null,"apc_paid":null,"fwci":0.539,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.70978821,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"506","last_page":"514"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.977400004863739,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.977400004863739,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9768999814987183,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9643999934196472,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/computer-science","display_name":"Computer science","score":0.8256321549415588},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7023631930351257},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.46541643142700195},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.32685911655426025}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8256321549415588},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7023631930351257},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.46541643142700195},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.32685911655426025}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3605098.3635986","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3605098.3635986","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 39th ACM/SIGAPP Symposium on Applied Computing","raw_type":"proceedings-article"},{"id":"pmh:oai:zenodo.org:12783152","is_oa":true,"landing_page_url":"https://ruc.udc.es/dspace/bitstream/2183/37990/2/FernandezFraga_Alejandro_2024_Applying_dynamic_balancing_improve_MPI.pdf","pdf_url":"https://hdl.handle.net/2183/37990","source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"SAC '24, 39th ACM/SIGAPP Symposium on Applied Computing, Avila, Spain, 8-12 April 2024","raw_type":"info:eu-repo/semantics/conferencePaper"}],"best_oa_location":{"id":"pmh:oai:zenodo.org:12783152","is_oa":true,"landing_page_url":"https://ruc.udc.es/dspace/bitstream/2183/37990/2/FernandezFraga_Alejandro_2024_Applying_dynamic_balancing_improve_MPI.pdf","pdf_url":"https://hdl.handle.net/2183/37990","source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"SAC '24, 39th ACM/SIGAPP Symposium on Applied Computing, Avila, Spain, 8-12 April 2024","raw_type":"info:eu-repo/semantics/conferencePaper"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.4699999988079071,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1218400627","display_name":null,"funder_award_id":"2019-2022","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G1496055848","display_name":null,"funder_award_id":"ED431C","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G175951205","display_name":null,"funder_award_id":"ED431C 2021/30","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G1869016439","display_name":null,"funder_award_id":"2019-2022","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G1933851018","display_name":null,"funder_award_id":"ED431G 2019/01","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G2262748287","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G230230324","display_name":null,"funder_award_id":"FEDER","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G2530961444","display_name":null,"funder_award_id":"ED431C 2021/30","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G272322064","display_name":null,"funder_award_id":"ED431G 20","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G2863773509","display_name":null,"funder_award_id":"MCIN/AEI/ 10.13039/501100011033","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G300979063","display_name":null,"funder_award_id":"10.13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3025668325","display_name":null,"funder_award_id":"RB-I00","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3412273058","display_name":null,"funder_award_id":"AEI/ 10.13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3429648993","display_name":null,"funder_award_id":"PID202","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3480869486","display_name":null,"funder_award_id":"13039","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3694284866","display_name":null,"funder_award_id":"ED431C","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G3876637791","display_name":null,"funder_award_id":"ED431G","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G410571670","display_name":null,"funder_award_id":"10.13039/501100011033","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G4126322094","display_name":null,"funder_award_id":"01100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G451917667","display_name":null,"funder_award_id":"13039/501100011033","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G4718490797","display_name":null,"funder_award_id":"MCIN/AEI/ 10.13039/501100011033","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G4816244515","display_name":null,"funder_award_id":"FEDER","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G4912030886","display_name":null,"funder_award_id":"2019-2022","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G5080475149","display_name":null,"funder_award_id":"10.13039","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G5967599077","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G6056837937","display_name":null,"funder_award_id":"PID2019-104184RB-I00","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G661330594","display_name":null,"funder_award_id":"00110","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G6685425346","display_name":null,"funder_award_id":"0011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G7224627388","display_name":null,"funder_award_id":"ED431","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G7252005220","display_name":null,"funder_award_id":"PID2022-136435NB-I00","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G726424357","display_name":null,"funder_award_id":"ED431G 2019/01","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G7266728691","display_name":null,"funder_award_id":"13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G7834025948","display_name":null,"funder_award_id":"FPU21/03408","funder_id":"https://openalex.org/F7296444849","funder_display_name":"Ministerio de Universidades"},{"id":"https://openalex.org/G801766868","display_name":null,"funder_award_id":"ED431G 2019/0","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G8260616629","display_name":null,"funder_award_id":"011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G8570012161","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G8638682022","display_name":null,"funder_award_id":"10.13039/50110001103","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G8684520763","display_name":null,"funder_award_id":"PID2019","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G8909017353","display_name":null,"funder_award_id":"MCIN/AEI/ 10.13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"}],"funders":[{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320326655","display_name":"Xunta de Galicia","ror":"https://ror.org/0181xnw06"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320335598","display_name":"Agencia Estatal de Investigaci\u00f3n","ror":null},{"id":"https://openalex.org/F7296444849","display_name":"Ministerio de Universidades","ror":"https://ror.org/03zcny908"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4398186362.pdf","grobid_xml":"https://content.openalex.org/works/W4398186362.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W2008420899","https://openalex.org/W2049907774","https://openalex.org/W2135904340","https://openalex.org/W2157380828","https://openalex.org/W2165101781","https://openalex.org/W2184365323","https://openalex.org/W2274792685","https://openalex.org/W2583619517","https://openalex.org/W2763932798","https://openalex.org/W2898366320","https://openalex.org/W2912857220","https://openalex.org/W2927518284","https://openalex.org/W2971083208","https://openalex.org/W2998011509","https://openalex.org/W4312610881"],"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/W2382290278","https://openalex.org/W4395014643"],"abstract_inverted_index":{"Genomics":[0],"applications":[1,64],"are":[2],"becoming":[3],"more":[4,6],"and":[5,53,114,166,182],"important":[7],"in":[8,160],"the":[9,22,29,46,60,74,80,110,115,122,140,150,154,157,179,187],"field":[10],"of":[11,25,35,48,62,89,142,153],"bioinformatics,":[12],"as":[13,129],"they":[14],"allow":[15],"researchers":[16],"to":[17,69,76,108,118,133,174],"extract":[18],"meaningful":[19],"information":[20],"from":[21],"huge":[23],"amount":[24],"data":[26,37,75],"generated":[27],"by":[28,72],"new":[30,151],"sequencing":[31],"technologies.":[32],"The":[33,125],"analysis":[34],"these":[36,63],"is":[38,57,85,127,172],"a":[39,86,97,130,193,197],"very":[40],"time":[41],"consuming":[42],"task":[43],"and,":[44],"therefore,":[45],"use":[47],"High":[49],"Performance":[50],"Computing":[51],"(HPC)":[52],"parallel":[54,70,137,189],"processing":[55,192],"techniques":[56],"essential.":[58],"Although":[59],"structure":[61],"can":[65],"be":[66,77],"easily":[67],"adapted":[68],"systems":[71],"distributing":[73],"processed":[78],"among":[79,112],"available":[81],"processors,":[82],"load":[83,99],"imbalance":[84],"usual":[87],"cause":[88],"performance":[90,165],"degradation.":[91],"In":[92],"this":[93],"paper":[94],"we":[95],"propose":[96],"dynamic":[98],"balancing":[100],"method":[101],"based":[102],"on":[103,196],"MPI":[104],"RMA":[105],"one-sided":[106],"communications":[107,119],"minimize":[109],"synchronization":[111],"processes":[113],"overhead":[116],"due":[117],"while":[120],"improving":[121],"workload":[123],"balance.":[124],"strategy":[126],"applied,":[128],"case":[131],"study,":[132],"ParRADMeth,":[134],"an":[135],"MPI/OpenMP":[136],"application":[138],"for":[139],"identification":[141],"Differential":[143],"Methylated":[144],"Regions":[145],"(DMRs).":[146],"Results":[147],"show":[148],"that":[149],"version":[152,181,190],"tool":[155],"outperforms":[156],"previous":[158,188],"one":[159,203],"all":[161],"cases,":[162],"achieving":[163],"high":[164],"scalability.":[167],"For":[168],"example,":[169],"our":[170],"approach":[171],"up":[173],"243":[175],"times":[176,184],"faster":[177,185],"than":[178,186],"sequential":[180],"1.74":[183],"when":[191],"real":[194],"dataset":[195],"cluster":[198],"with":[199,204],"8":[200],"nodes,":[201],"each":[202],"32":[205],"CPU":[206],"cores.":[207]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
