{"id":"https://openalex.org/W2381704803","doi":"https://doi.org/10.3233/978-1-61499-621-7-63","title":"Execution Performance Analysis of the ABySS Genome Sequence Assembler using Scalasca on the K Computer","display_name":"Execution Performance Analysis of the ABySS Genome Sequence Assembler using Scalasca on the K Computer","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2381704803","doi":"https://doi.org/10.3233/978-1-61499-621-7-63","mag":"2381704803"},"language":"en","primary_location":{"id":"doi:10.3233/978-1-61499-621-7-63","is_oa":false,"landing_page_url":"https://doi.org/10.3233/978-1-61499-621-7-63","pdf_url":null,"source":{"id":"https://openalex.org/S4210175178","display_name":"Advances in parallel computing","issn_l":"0927-5452","issn":["0927-5452","1879-808X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Parallel Computing","raw_type":"book-chapter"},"type":"book-chapter","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/A5064845161","display_name":"Itaru Kitayama","orcid":"https://orcid.org/0000-0002-5753-341X"},"institutions":[{"id":"https://openalex.org/I2800939219","display_name":"RIKEN Center for Brain Science","ror":"https://ror.org/04j1n1c04","country_code":"JP","type":"facility","lineage":["https://openalex.org/I2800939219","https://openalex.org/I4210110652"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Kitayama Itaru","raw_affiliation_strings":["RIKEN Center for Brain Science, Wako, Japan"],"affiliations":[{"raw_affiliation_string":"RIKEN Center for Brain Science, Wako, Japan","institution_ids":["https://openalex.org/I2800939219"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006096182","display_name":"Brian J. N. Wylie","orcid":"https://orcid.org/0000-0003-2770-2443"},"institutions":[{"id":"https://openalex.org/I171892758","display_name":"Forschungszentrum J\u00fclich","ror":"https://ror.org/02nv7yv05","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I171892758"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Wylie Brian J.N.","raw_affiliation_strings":["Forschungszentrum J\u00fclich, J\u00fclich, Germany"],"affiliations":[{"raw_affiliation_string":"Forschungszentrum J\u00fclich, J\u00fclich, Germany","institution_ids":["https://openalex.org/I171892758"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087364915","display_name":"Toshiyuki Maeda","orcid":"https://orcid.org/0000-0002-1689-4833"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Maeda Toshiyuki","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5064845161"],"corresponding_institution_ids":["https://openalex.org/I2800939219"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.02401511,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9932000041007996,"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":0.9932000041007996,"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":0.9480999708175659,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9244999885559082,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6221728324890137},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5257198214530945},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.44767534732818604},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.42787009477615356},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38249391317367554},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3659033179283142},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2512109875679016},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19284525513648987},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10074996948242188}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6221728324890137},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5257198214530945},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.44767534732818604},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.42787009477615356},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38249391317367554},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3659033179283142},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2512109875679016},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19284525513648987},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10074996948242188},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.3233/978-1-61499-621-7-63","is_oa":false,"landing_page_url":"https://doi.org/10.3233/978-1-61499-621-7-63","pdf_url":null,"source":{"id":"https://openalex.org/S4210175178","display_name":"Advances in parallel computing","issn_l":"0927-5452","issn":["0927-5452","1879-808X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Parallel Computing","raw_type":"book-chapter"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":5,"referenced_works":["https://openalex.org/W1545880915","https://openalex.org/W1549907467","https://openalex.org/W1631513913","https://openalex.org/W2154503441","https://openalex.org/W2891375331"],"related_works":["https://openalex.org/W2721624558","https://openalex.org/W2166654698","https://openalex.org/W2115140794","https://openalex.org/W2112284452","https://openalex.org/W2041120224","https://openalex.org/W2767590279","https://openalex.org/W1504320321","https://openalex.org/W2067902980","https://openalex.org/W2766401759","https://openalex.org/W3134563641"],"abstract_inverted_index":{"Performance":[0],"analysis":[1],"of":[2,58,61,92,119],"the":[3,11,56,114,120],"ABySS":[4],"genome":[5],"sequence":[6],"assembler":[7],"(ABYSS-P)":[8],"executing":[9],"on":[10,113],"K":[12,121],"computer":[13],"with":[14,40,109],"up":[15],"to":[16,28,52],"8192":[17],"compute":[18,32,44,117],"nodes":[19,33,118],"is":[20],"described":[21],"which":[22],"identified":[23],"issues":[24],"that":[25,76],"limited":[26],"scalability":[27,107],"less":[29],"than":[30],"1024":[31],"and":[34,71,86,96,106],"required":[35],"prohibitive":[36],"message":[37],"buffer":[38],"memory":[39],"16384":[41],"or":[42],"more":[43],"nodes.":[45],"The":[46],"open-source":[47],"Scalasca":[48],"toolset":[49],"was":[50],"employed":[51],"analyse":[53],"executions,":[54],"revealing":[55],"impact":[57],"massive":[59],"amounts":[60],"MPI":[62,83],"point-to-point":[63],"communication":[64,94],"used":[65],"particularly":[66],"for":[67,99],"master/worker":[68],"process":[69],"coordination,":[70],"inefficient":[72],"parallel":[73,100],"file":[74,101],"operations":[75,95],"manifest":[77],"as":[78],"waiting":[79],"time":[80],"at":[81],"later":[82],"collective":[84,93],"synchronisations":[85],"communications.":[87],"Initial":[88],"remediation":[89],"via":[90],"use":[91],"alternate":[97],"strategies":[98],"handling":[102],"show":[103],"large":[104],"performance":[105],"improvements,":[108],"partial":[110],"executions":[111],"validated":[112],"full":[115],"82,944":[116],"computer.":[122]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}
