{"id":"https://openalex.org/W2913519563","doi":"https://doi.org/10.1109/bibm.2018.8621415","title":"Mmalloc: A Dynamic Memory Management on Many-core Coprocessor for the Acceleration of Storage-intensive Bioinformatics Application","display_name":"Mmalloc: A Dynamic Memory Management on Many-core Coprocessor for the Acceleration of Storage-intensive Bioinformatics Application","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2913519563","doi":"https://doi.org/10.1109/bibm.2018.8621415","mag":"2913519563"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2018.8621415","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621415","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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/A5110920014","display_name":"Zihao Wang","orcid":"https://orcid.org/0000-0002-6994-2309"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zihao Wang","raw_affiliation_strings":["High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101985755","display_name":"Mingzhe Zhang","orcid":"https://orcid.org/0000-0002-6440-7550"},"institutions":[{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mingzhe Zhang","raw_affiliation_strings":["High-Throughput Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"High-Throughput Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075095992","display_name":"Jingrong Zhang","orcid":"https://orcid.org/0000-0002-7829-7348"},"institutions":[{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jingrong Zhang","raw_affiliation_strings":["High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003979715","display_name":"Rui Yan","orcid":"https://orcid.org/0000-0002-1336-1740"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rui Yan","raw_affiliation_strings":["High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058683397","display_name":"Xiaohua Wan","orcid":"https://orcid.org/0000-0002-9340-878X"},"institutions":[{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaohua Wan","raw_affiliation_strings":["High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100766031","display_name":"Zhiyong Liu","orcid":"https://orcid.org/0000-0001-8257-4347"},"institutions":[{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhiyong Liu","raw_affiliation_strings":["High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100731978","display_name":"Fa Zhang","orcid":"https://orcid.org/0000-0002-2081-9369"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fa Zhang","raw_affiliation_strings":["High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101906222","display_name":"Xuefeng Cui","orcid":"https://orcid.org/0000-0002-8816-3482"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuefeng Cui","raw_affiliation_strings":["Institute for Interdisciplinary Information Sciences (IIIS) Tsinghua University"],"affiliations":[{"raw_affiliation_string":"Institute for Interdisciplinary Information Sciences (IIIS) Tsinghua University","institution_ids":["https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5110920014"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210090176"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.17726919,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"771","last_page":"774"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9901999831199646,"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"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9901999831199646,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9868999719619751,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.9800000190734863,"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":0.8537601828575134},{"id":"https://openalex.org/keywords/coprocessor","display_name":"Coprocessor","score":0.8222556114196777},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5697322487831116},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5611424446105957},{"id":"https://openalex.org/keywords/allocator","display_name":"Allocator","score":0.5019426345825195},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.4800885319709778},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.4708264172077179},{"id":"https://openalex.org/keywords/heap","display_name":"Heap (data structure)","score":0.4641749858856201},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.43216660618782043},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.4024173617362976},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.36363542079925537}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8537601828575134},{"id":"https://openalex.org/C86111242","wikidata":"https://www.wikidata.org/wiki/Q859595","display_name":"Coprocessor","level":2,"score":0.8222556114196777},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5697322487831116},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5611424446105957},{"id":"https://openalex.org/C162262903","wikidata":"https://www.wikidata.org/wiki/Q343527","display_name":"Allocator","level":2,"score":0.5019426345825195},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.4800885319709778},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.4708264172077179},{"id":"https://openalex.org/C134757568","wikidata":"https://www.wikidata.org/wiki/Q274089","display_name":"Heap (data structure)","level":2,"score":0.4641749858856201},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.43216660618782043},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.4024173617362976},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.36363542079925537},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2018.8621415","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621415","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W433717059","https://openalex.org/W1988437413","https://openalex.org/W2013062050","https://openalex.org/W2095680943","https://openalex.org/W2096041635","https://openalex.org/W2104234755","https://openalex.org/W2128274900","https://openalex.org/W2432427150","https://openalex.org/W2573785130","https://openalex.org/W2579859441","https://openalex.org/W4230708893","https://openalex.org/W4394666350","https://openalex.org/W6674561012"],"related_works":["https://openalex.org/W2291943064","https://openalex.org/W2920417665","https://openalex.org/W4379518516","https://openalex.org/W3033802101","https://openalex.org/W2766468145","https://openalex.org/W92825922","https://openalex.org/W3104774169","https://openalex.org/W2486766535","https://openalex.org/W2209727271","https://openalex.org/W2953153984"],"abstract_inverted_index":{"In":[0],"the":[1,52,87,92,101,106,121,126,130,134,139,160,168],"past":[2],"decades,":[3],"many":[4],"applications":[5,25],"in":[6,55],"bioinformatics":[7],"have":[8,35],"achieved":[9],"great":[10],"success":[11],"by":[12],"extracting":[13],"useful":[14],"information":[15,128],"from":[16,129],"huge":[17],"amounts":[18],"of":[19,51,141],"data.":[20,143],"However,":[21],"when":[22],"some":[23],"storage-intensive":[24,80],"like":[26,165],"BWA-MEM":[27,147],"ported":[28],"to":[29,31,90,104,119,137],"coprocessors":[30],"accelerate,":[32],"they":[33],"often":[34],"memory":[36,47],"bottleneck":[37],"that":[38,78,150],"severely":[39],"limits":[40],"program":[41],"performance":[42],"and":[43,57,74,97,110,156],"scalability.":[44],"While":[45],"dynamic":[46],"allocation":[48],"is":[49,86],"one":[50],"important":[53],"topics":[54],"CPU":[56,164],"GPU,":[58],"there":[59],"has":[60,152],"been":[61],"relatively":[62],"little":[63],"work":[64],"on":[65,82,146,167],"many-core":[66,83,169],"coprocessors.":[67],"This":[68],"paper":[69],"introduces":[70],"Mmalloc,":[71],"a":[72,114,153],"fast":[73],"highly":[75],"scalable":[76],"allocator":[77,89,162],"accelerates":[79],"application":[81],"coprocessor.":[84,170],"Mmalloc":[85,99,112,151],"first":[88],"consider":[91],"different":[93],"architecture":[94],"between":[95],"MIC":[96],"CPU.":[98],"removes":[100],"global":[102],"heap":[103],"reduce":[105],"long-distance":[107],"on-chip":[108],"coherent":[109],"communication.":[111],"uses":[113],"binary":[115],"sort":[116],"interval":[117],"tree":[118],"manage":[120],"memory.":[122],"We":[123],"also":[124],"separate":[125],"header":[127],"data":[131],"area":[132],"using":[133],"logical":[135],"structure":[136],"keep":[138],"locality":[140],"processed":[142],"Our":[144],"results":[145],"benchmarks":[148],"demonstrate":[149],"better":[154],"speedup":[155],"scalability":[157],"comparing":[158],"with":[159],"state-of-the-art":[161],"for":[163],"Hoard":[166]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
