{"id":"https://openalex.org/W2135371742","doi":"https://doi.org/10.1109/clustr.2003.1253329","title":"A case study of parallel I/O for biological sequence search on Linux clusters","display_name":"A case study of parallel I/O for biological sequence search on Linux clusters","publication_year":2003,"publication_date":"2003-01-01","ids":{"openalex":"https://openalex.org/W2135371742","doi":"https://doi.org/10.1109/clustr.2003.1253329","mag":"2135371742"},"language":"en","primary_location":{"id":"doi:10.1109/clustr.2003.1253329","is_oa":false,"landing_page_url":"https://doi.org/10.1109/clustr.2003.1253329","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings IEEE International Conference on Cluster Computing CLUSTR-03","raw_type":"proceedings-article"},"type":"conference-paper","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/A5102214085","display_name":"Yifeng Zhu","orcid":null},"institutions":[{"id":"https://openalex.org/I114395901","display_name":"University of Nebraska\u2013Lincoln","ror":"https://ror.org/043mer456","country_code":"US","type":"education","lineage":["https://openalex.org/I114395901"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yifeng Zhu","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Nebraska, Lincoln, Lincolnshire, NE, USA","Department of Computer Science and Engineering, University of Nebraska Lincoln, NE, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Nebraska, Lincoln, Lincolnshire, NE, USA","institution_ids":["https://openalex.org/I114395901"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Nebraska Lincoln, NE, USA","institution_ids":["https://openalex.org/I114395901"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111641195","display_name":"Hong Jiang","orcid":"https://orcid.org/0000-0003-3652-6488"},"institutions":[{"id":"https://openalex.org/I114395901","display_name":"University of Nebraska\u2013Lincoln","ror":"https://ror.org/043mer456","country_code":"US","type":"education","lineage":["https://openalex.org/I114395901"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hong Jiang","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Nebraska, Lincoln, Lincolnshire, NE, USA","Department of Computer Science and Engineering, University of Nebraska Lincoln, NE, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Nebraska, Lincoln, Lincolnshire, NE, USA","institution_ids":["https://openalex.org/I114395901"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Nebraska Lincoln, NE, USA","institution_ids":["https://openalex.org/I114395901"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115589629","display_name":"Xiao Qin","orcid":null},"institutions":[{"id":"https://openalex.org/I114395901","display_name":"University of Nebraska\u2013Lincoln","ror":"https://ror.org/043mer456","country_code":"US","type":"education","lineage":["https://openalex.org/I114395901"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiao Qin","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Nebraska, Lincoln, Lincolnshire, NE, USA","Department of Computer Science and Engineering, University of Nebraska Lincoln, NE, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Nebraska, Lincoln, Lincolnshire, NE, USA","institution_ids":["https://openalex.org/I114395901"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Nebraska Lincoln, NE, USA","institution_ids":["https://openalex.org/I114395901"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071847595","display_name":"Swanson","orcid":null},"institutions":[{"id":"https://openalex.org/I114395901","display_name":"University of Nebraska\u2013Lincoln","ror":"https://ror.org/043mer456","country_code":"US","type":"education","lineage":["https://openalex.org/I114395901"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Swanson","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Nebraska, Lincoln, Lincolnshire, NE, USA","Department of Computer Science and Engineering, University of Nebraska Lincoln, NE, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Nebraska, Lincoln, Lincolnshire, NE, USA","institution_ids":["https://openalex.org/I114395901"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Nebraska Lincoln, NE, USA","institution_ids":["https://openalex.org/I114395901"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I114395901"],"apc_list":null,"apc_paid":null,"fwci":0.5246,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.69380114,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"1662","issue":null,"first_page":"308","last_page":"315"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9997000098228455,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.9997000098228455,"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/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9937000274658203,"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/T10772","display_name":"Distributed systems and fault tolerance","score":0.9884999990463257,"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":0.629483699798584},{"id":"https://openalex.org/keywords/server","display_name":"Server","score":0.612551212310791},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.516841471195221},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4999358654022217},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.47419458627700806},{"id":"https://openalex.org/keywords/file-system","display_name":"File system","score":0.43531301617622375},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.34086477756500244},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.31775182485580444},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07947427034378052}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.629483699798584},{"id":"https://openalex.org/C93996380","wikidata":"https://www.wikidata.org/wiki/Q44127","display_name":"Server","level":2,"score":0.612551212310791},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.516841471195221},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4999358654022217},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.47419458627700806},{"id":"https://openalex.org/C2780940931","wikidata":"https://www.wikidata.org/wiki/Q174989","display_name":"File system","level":2,"score":0.43531301617622375},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.34086477756500244},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.31775182485580444},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07947427034378052},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/clustr.2003.1253329","is_oa":false,"landing_page_url":"https://doi.org/10.1109/clustr.2003.1253329","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings IEEE International Conference on Cluster Computing CLUSTR-03","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310264","display_name":"University of Nebraska-Lincoln","ror":"https://ror.org/043mer456"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W145805655","https://openalex.org/W222729537","https://openalex.org/W1494199733","https://openalex.org/W1544970479","https://openalex.org/W1932879197","https://openalex.org/W2055043387","https://openalex.org/W2064254674","https://openalex.org/W2103016487","https://openalex.org/W2106212727","https://openalex.org/W2110298485","https://openalex.org/W2112360329","https://openalex.org/W2119633387","https://openalex.org/W2124326353","https://openalex.org/W2125269836","https://openalex.org/W2128718501","https://openalex.org/W2131610641","https://openalex.org/W2155371682","https://openalex.org/W2158714788","https://openalex.org/W2161849269","https://openalex.org/W2163534300","https://openalex.org/W2166064431","https://openalex.org/W2167477013","https://openalex.org/W2168507922","https://openalex.org/W4236236547","https://openalex.org/W6606052223","https://openalex.org/W6608843790","https://openalex.org/W6629433741","https://openalex.org/W6632681596","https://openalex.org/W6640257369","https://openalex.org/W6676560735","https://openalex.org/W6676605874","https://openalex.org/W6678701932","https://openalex.org/W6679091526","https://openalex.org/W6684172860"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W2745001401","https://openalex.org/W4321353415","https://openalex.org/W2130974462","https://openalex.org/W972276598","https://openalex.org/W4246352526","https://openalex.org/W2086519370","https://openalex.org/W2028665553","https://openalex.org/W2087343574","https://openalex.org/W2535915176"],"abstract_inverted_index":{"In":[0],"this":[1,81,109],"paper":[2],"we":[3],"analyze":[4],"the":[5,41,45,58,66,69,77,97,119,124,139,143,157,173,176,180,194],"I/O":[6,86,140,152],"access":[7,25],"patterns":[8],"of":[9,68,79,99,121,130,159,175],"a":[10,112,166,201],"widely-used":[11],"biological":[12],"sequence":[13],"search":[14],"tool":[15,47,110,178],"and":[16,33,132,179,189],"implement":[17],"two":[18,42,70,100],"variations":[19,43,71],"that":[20,40,64,129],"employ":[21],"parallel-I/O":[22],"for":[23],"data":[24,146],"based":[26,182,196],"on":[27,145,183,197],"PVFS":[28,184],"(Parallel":[29],"Virtual":[30],"File":[31],"System)":[32],"CEFT-PVFS":[34,106,198],"(cost-effective":[35],"fault-tolerant":[36],"PVFS).":[37],"Experiments":[38],"show":[39],"outperform":[44],"original":[46,177],"when":[48,74,142],"equal":[49],"or":[50],"even":[51],"fewer":[52],"storage":[53],"devices":[54],"are":[55],"used":[56],"in":[57,92,105,165],"former.":[59],"It":[60],"is":[61,148],"also":[62],"found":[63],"although":[65],"performance":[67,82,102,126,141,174,203],"improves":[72],"consistently":[73],"initially":[75],"increasing":[76],"number":[78],"servers,":[80],"gain":[83],"from":[84],"parallel":[85],"becomes":[87],"insignificant":[88],"with":[89],"further":[90],"increase":[91],"server":[93,160],"number.":[94],"We":[95],"examine":[96],"effectiveness":[98],"read":[101,125],"optimization":[103],"techniques":[104],"by":[107,162,185],"using":[108],"as":[111],"benchmark.":[113],"Performance":[114],"results":[115],"indicate:":[116],"(1)":[117],"doubling":[118],"degree":[120],"parallelism":[122],"boosts":[123],"to":[127,156,171,187],"approach":[128],"PVFS;":[131],"(2)":[133],"skipping":[134],"hot-spots":[135],"can":[136],"substantially":[137],"improve":[138],"load":[144],"servers":[147],"highly":[149],"imbalanced.":[150],"The":[151],"resource":[153],"contention":[154],"due":[155],"sharing":[158],"nodes":[161],"multiple":[163],"applications":[164],"cluster":[167],"has":[168],"been":[169],"shown":[170],"degrade":[172],"variation":[181,195],"up":[186],"10":[188],"21":[190],"folds,":[191],"respectively;":[192],"whereas,":[193],"only":[199],"suffered":[200],"two-fold":[202],"degradation.":[204]},"counts_by_year":[],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
