{"id":"https://openalex.org/W2083792262","doi":"https://doi.org/10.1145/1345206.1345262","title":"Semantics-based distributed I/O for mpiBLAST","display_name":"Semantics-based distributed I/O for mpiBLAST","publication_year":2008,"publication_date":"2008-02-20","ids":{"openalex":"https://openalex.org/W2083792262","doi":"https://doi.org/10.1145/1345206.1345262","mag":"2083792262"},"language":"en","primary_location":{"id":"doi:10.1145/1345206.1345262","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1345206.1345262","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 13th ACM SIGPLAN Symposium on Principles and practice of parallel programming","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/A5050531633","display_name":"Pavan Balaji","orcid":null},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Pavan Balaji","raw_affiliation_strings":["Argonne National Laboratory, Argonne, IL, USA",", Argonne National Laboratory, Argonne, IL, USA"],"affiliations":[{"raw_affiliation_string":"Argonne National Laboratory, Argonne, IL, USA","institution_ids":["https://openalex.org/I1282105669"]},{"raw_affiliation_string":", Argonne National Laboratory, Argonne, IL, USA","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058539554","display_name":"Wu-chun Feng","orcid":"https://orcid.org/0000-0002-6015-0727"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wu-chun Feng","raw_affiliation_strings":["Virginia Tech, Blacksburg, VA, USA","Virginia Tech, , Blacksburg, VA, USA"],"affiliations":[{"raw_affiliation_string":"Virginia Tech, Blacksburg, VA, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Virginia Tech, , Blacksburg, VA, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024547145","display_name":"Jeremy Archuleta","orcid":null},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremy Archuleta","raw_affiliation_strings":["Virginia Tech, Blacksburg, VA, USA","Virginia Tech, , Blacksburg, VA, USA"],"affiliations":[{"raw_affiliation_string":"Virginia Tech, Blacksburg, VA, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Virginia Tech, , Blacksburg, VA, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103124804","display_name":"Heshan Lin","orcid":"https://orcid.org/0000-0003-0825-6169"},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Heshan Lin","raw_affiliation_strings":["North Carolina State University, Raleigh, NC, USA"],"affiliations":[{"raw_affiliation_string":"North Carolina State University, Raleigh, NC, USA","institution_ids":["https://openalex.org/I137902535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068373159","display_name":"Rajkumar Kettimuthu","orcid":"https://orcid.org/0000-0002-0046-9883"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rajkumar Kettimuthu","raw_affiliation_strings":["Argonne National Laboratory, Argonne, IL, USA",", Argonne National Laboratory, Argonne, IL, USA"],"affiliations":[{"raw_affiliation_string":"Argonne National Laboratory, Argonne, IL, USA","institution_ids":["https://openalex.org/I1282105669"]},{"raw_affiliation_string":", Argonne National Laboratory, Argonne, IL, USA","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014920685","display_name":"Rajeev Thakur","orcid":"https://orcid.org/0000-0002-5532-3048"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rajeev Thakur","raw_affiliation_strings":["Argonne National Laboratory, Argonne, IL, USA",", Argonne National Laboratory, Argonne, IL, USA"],"affiliations":[{"raw_affiliation_string":"Argonne National Laboratory, Argonne, IL, USA","institution_ids":["https://openalex.org/I1282105669"]},{"raw_affiliation_string":", Argonne National Laboratory, Argonne, IL, USA","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083800790","display_name":"Xiaosong Ma","orcid":"https://orcid.org/0000-0003-1261-2496"},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaosong Ma","raw_affiliation_strings":["North Carolina State University, Raleigh, NC, USA"],"affiliations":[{"raw_affiliation_string":"North Carolina State University, Raleigh, NC, USA","institution_ids":["https://openalex.org/I137902535"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5050531633"],"corresponding_institution_ids":["https://openalex.org/I1282105669"],"apc_list":null,"apc_paid":null,"fwci":1.0773,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.76205735,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"293","last_page":"294"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9955000281333923,"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":0.9955000281333923,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9886000156402588,"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":0.9837999939918518,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.8812034130096436},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8781909942626953},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.8111450672149658},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.6238818764686584},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5546144247055054},{"id":"https://openalex.org/keywords/distributed-database","display_name":"Distributed database","score":0.46573296189308167},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4191974401473999},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4105411767959595},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.30957767367362976},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.26336178183555603}],"concepts":[{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.8812034130096436},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8781909942626953},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.8111450672149658},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.6238818764686584},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5546144247055054},{"id":"https://openalex.org/C70061542","wikidata":"https://www.wikidata.org/wiki/Q989016","display_name":"Distributed database","level":2,"score":0.46573296189308167},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4191974401473999},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4105411767959595},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.30957767367362976},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.26336178183555603}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/1345206.1345262","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1345206.1345262","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 13th ACM SIGPLAN Symposium on Principles and practice of parallel programming","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":3,"referenced_works":["https://openalex.org/W145805655","https://openalex.org/W2125062675","https://openalex.org/W2130022432"],"related_works":["https://openalex.org/W2392768766","https://openalex.org/W2058118494","https://openalex.org/W2382021449","https://openalex.org/W2095118173","https://openalex.org/W2104269053","https://openalex.org/W2106424170","https://openalex.org/W1985426483","https://openalex.org/W2501188010","https://openalex.org/W4299935056","https://openalex.org/W3091099154"],"abstract_inverted_index":{"BLAST":[0,19],"is":[1,12],"a":[2,13,46,67,84],"widely":[3],"used":[4],"software":[5],"toolkit":[6],"for":[7,69,109],"genomic":[8],"sequence":[9],"search.":[10],"mpiBLAST":[11,49,187],"freely":[14],"available,":[15],"open-source":[16],"parallelization":[17],"of":[18,35,123],"that":[20,93],"uses":[21,94],"database":[22],"segmentation":[23],"to":[24,29,45,53,98,128,142,149,158,166,174,181],"allow":[25],"different":[26],"worker":[27,113],"processes":[28,114],"search":[30],"(in":[31],"parallel)":[32],"unique":[33],"segments":[34],"the":[36,40,126,129,131,134,140,147,150,159,168,175],"database.":[37],"After":[38],"searching,":[39],"workers":[41,132],"write":[42,146,172],"their":[43],"output":[44,127,135,170],"filesystem.":[47,151,176],"While":[48],"has":[50],"been":[51],"shown":[52],"achieve":[54],"high":[55],"performance":[56,104],"in":[57,72,105],"clusters":[58],"with":[59],"fast":[60],"local":[61],"filesystems,":[62],"its":[63],"I/O":[64,76,100,118,152,183],"processing":[65],"remains":[66],"concern":[68],"scalability,":[70],"especially":[71],"systems":[73],"having":[74],"limited":[75],"capabilities":[77],"such":[78],"as":[79,189,191],"distributed":[80,106],"filesystems":[81],"spread":[82],"across":[83],"wide-area":[85],"network.":[86],"Thus,":[87],"we":[88],"present":[89],"ParaMEDIC---a":[90],"novel":[91],"environment":[92],"application-specific":[95],"semantic":[96,137],"information":[97],"compress":[99],"data":[101],"and":[102,117,145,171],"improve":[103],"environments.":[107],"Specifically,":[108],"mpiBLAST,":[110],"ParaMEDIC":[111,180],"partitions":[112],"into":[115],"compute":[116],"workers.":[119],"Compute":[120],"workers,":[121,153],"instead":[122],"directly":[124],"writing":[125],"filesystem,":[130],"process":[133,163],"using":[136],"knowledge":[138],"about":[139],"application":[141],"generate":[143],"metadata":[144,148,165],"which":[154],"physically":[155],"reside":[156],"closer":[157],"actual":[160,169],"storage,":[161],"then":[162],"this":[164],"re-create":[167],"it":[173],"This":[177],"approach":[178],"allows":[179],"reduce":[182],"time,":[184],"thus":[185],"accelerating":[186],"by":[188],"much":[190],"25-fold.":[192]},"counts_by_year":[{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
