{"id":"https://openalex.org/W2064496884","doi":"https://doi.org/10.1145/2541228.2555311","title":"GPU code generation for ODE-based applications with phased shared-data access patterns","display_name":"GPU code generation for ODE-based applications with phased shared-data access patterns","publication_year":2013,"publication_date":"2013-12-01","ids":{"openalex":"https://openalex.org/W2064496884","doi":"https://doi.org/10.1145/2541228.2555311","mag":"2064496884"},"language":"en","primary_location":{"id":"doi:10.1145/2541228.2555311","is_oa":true,"landing_page_url":"https://doi.org/10.1145/2541228.2555311","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/2541228.2555311","source":{"id":"https://openalex.org/S26056741","display_name":"ACM Transactions on Architecture and Code Optimization","issn_l":"1544-3566","issn":["1544-3566","1544-3973"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Architecture and Code Optimization","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://dl.acm.org/doi/pdf/10.1145/2541228.2555311","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054042334","display_name":"Andrei Hagiescu","orcid":null},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Andrei Hagiescu","raw_affiliation_strings":["National University of Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National University of Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043819328","display_name":"Bing Liu","orcid":"https://orcid.org/0000-0002-7257-2441"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bing Liu","raw_affiliation_strings":["Carnegie Mellon University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Carnegie Mellon University","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072433592","display_name":"Ravishankar Ramanathan","orcid":"https://orcid.org/0000-0003-1119-8721"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"R. Ramanathan","raw_affiliation_strings":["National University of Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National University of Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070784871","display_name":"Sucheendra K. Palaniappan","orcid":"https://orcid.org/0000-0002-2829-2311"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Sucheendra K. Palaniappan","raw_affiliation_strings":["National University of Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National University of Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079257435","display_name":"Zheng Cui","orcid":"https://orcid.org/0000-0002-3837-7407"},"institutions":[{"id":"https://openalex.org/I4210108443","display_name":"Advanced Digital Sciences Center","ror":"https://ror.org/01xaqx887","country_code":"SG","type":"facility","lineage":["https://openalex.org/I4210108443"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Zheng Cui","raw_affiliation_strings":["Advanced Digital Science Centre, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Advanced Digital Science Centre, Singapore","institution_ids":["https://openalex.org/I4210108443"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080776779","display_name":"Bipasa Chattopadhyay","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bipasa Chattopadhyay","raw_affiliation_strings":["University of North Carolina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of North Carolina","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111462984","display_name":"P. S. Thiagarajan","orcid":"https://orcid.org/0009-0007-6469-9243"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"P. S. Thiagarajan","raw_affiliation_strings":["National University of Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National University of Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023989495","display_name":"Weng\u2010Fai Wong","orcid":"https://orcid.org/0000-0002-4281-2053"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Weng-Fai Wong","raw_affiliation_strings":["National University of Singapore, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.295,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.61694859,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"10","issue":"4","first_page":"1","last_page":"19"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9991000294685364,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9991000294685364,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9926999807357788,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9787999987602234,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8395729660987854},{"id":"https://openalex.org/keywords/code-generation","display_name":"Code generation","score":0.7148629426956177},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5549418330192566},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5450324416160583},{"id":"https://openalex.org/keywords/ode","display_name":"Ode","score":0.49878931045532227},{"id":"https://openalex.org/keywords/data-parallelism","display_name":"Data parallelism","score":0.49006855487823486},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.448834627866745},{"id":"https://openalex.org/keywords/von-neumann-architecture","display_name":"Von Neumann architecture","score":0.4380784332752228},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.43185606598854065},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.43018031120300293},{"id":"https://openalex.org/keywords/porting","display_name":"Porting","score":0.4199657440185547},{"id":"https://openalex.org/keywords/shared-memory","display_name":"Shared memory","score":0.41054001450538635},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.40478360652923584},{"id":"https://openalex.org/keywords/parallelism","display_name":"Parallelism (grammar)","score":0.3114432394504547},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.1398320198059082}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8395729660987854},{"id":"https://openalex.org/C133162039","wikidata":"https://www.wikidata.org/wiki/Q1061077","display_name":"Code generation","level":3,"score":0.7148629426956177},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5549418330192566},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5450324416160583},{"id":"https://openalex.org/C34862557","wikidata":"https://www.wikidata.org/wiki/Q178985","display_name":"Ode","level":2,"score":0.49878931045532227},{"id":"https://openalex.org/C61483411","wikidata":"https://www.wikidata.org/wiki/Q3124522","display_name":"Data parallelism","level":3,"score":0.49006855487823486},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.448834627866745},{"id":"https://openalex.org/C80469333","wikidata":"https://www.wikidata.org/wiki/Q189088","display_name":"Von Neumann architecture","level":2,"score":0.4380784332752228},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.43185606598854065},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.43018031120300293},{"id":"https://openalex.org/C106251023","wikidata":"https://www.wikidata.org/wiki/Q851989","display_name":"Porting","level":3,"score":0.4199657440185547},{"id":"https://openalex.org/C133875982","wikidata":"https://www.wikidata.org/wiki/Q764810","display_name":"Shared memory","level":2,"score":0.41054001450538635},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.40478360652923584},{"id":"https://openalex.org/C2781172179","wikidata":"https://www.wikidata.org/wiki/Q853109","display_name":"Parallelism (grammar)","level":2,"score":0.3114432394504547},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.1398320198059082},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C124952713","wikidata":"https://www.wikidata.org/wiki/Q8242","display_name":"Literature","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2541228.2555311","is_oa":true,"landing_page_url":"https://doi.org/10.1145/2541228.2555311","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/2541228.2555311","source":{"id":"https://openalex.org/S26056741","display_name":"ACM Transactions on Architecture and Code Optimization","issn_l":"1544-3566","issn":["1544-3566","1544-3973"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Architecture and Code Optimization","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1145/2541228.2555311","is_oa":true,"landing_page_url":"https://doi.org/10.1145/2541228.2555311","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/2541228.2555311","source":{"id":"https://openalex.org/S26056741","display_name":"ACM Transactions on Architecture and Code Optimization","issn_l":"1544-3566","issn":["1544-3566","1544-3973"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Architecture and Code Optimization","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2064496884.pdf","grobid_xml":"https://content.openalex.org/works/W2064496884.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W114565888","https://openalex.org/W135306462","https://openalex.org/W1491178396","https://openalex.org/W1511986666","https://openalex.org/W1985911638","https://openalex.org/W1992851788","https://openalex.org/W2000335122","https://openalex.org/W2000564108","https://openalex.org/W2011277199","https://openalex.org/W2012986637","https://openalex.org/W2018270886","https://openalex.org/W2067971887","https://openalex.org/W2095595785","https://openalex.org/W2095890830","https://openalex.org/W2096842188","https://openalex.org/W2098426571","https://openalex.org/W2103937660","https://openalex.org/W2104009155","https://openalex.org/W2105437542","https://openalex.org/W2106629284","https://openalex.org/W2108157916","https://openalex.org/W2110575115","https://openalex.org/W2117228145","https://openalex.org/W2119304316","https://openalex.org/W2130336316","https://openalex.org/W2140375692","https://openalex.org/W2143784594","https://openalex.org/W2148153323","https://openalex.org/W2167334577","https://openalex.org/W2295862081","https://openalex.org/W3203568064","https://openalex.org/W4250981202"],"related_works":["https://openalex.org/W2356602486","https://openalex.org/W2351992668","https://openalex.org/W2324828474","https://openalex.org/W2374315191","https://openalex.org/W2391207559","https://openalex.org/W2384715785","https://openalex.org/W1994175142","https://openalex.org/W2192640005","https://openalex.org/W129777037","https://openalex.org/W2502778687"],"abstract_inverted_index":{"We":[0,79],"present":[1],"a":[2,17,89,99,113,131,164,167],"novel":[3],"code":[4,85,212],"generation":[5,15,86,213],"scheme":[6,61,214,232],"for":[7,188,196],"GPUs.":[8],"Its":[9],"key":[10],"feature":[11],"is":[12],"the":[13,28,33,40,43,48,64,81,106,128,136,150,171,184,194,197,210],"platform-aware":[14],"of":[16,20,42,47,51,67,83,97,105,108,115,130,138,153,156,163,170,243],"heterogeneous":[18],"pool":[19],"threads.":[21],"This":[22,94],"exposes":[23],"more":[24],"data-sharing":[25],"opportunities":[26],"among":[27],"concurrent":[29],"threads":[30],"and":[31,147,173],"reduces":[32],"memory":[34,68],"requirements":[35],"that":[36,75,209],"would":[37],"otherwise":[38],"exceed":[39],"capacity":[41],"on-chip":[44],"memory.":[45],"Instead":[46],"conventional":[49],"strategy":[50,87],"focusing":[52],"on":[53,63,88,221],"exposing":[54],"as":[55,58,112,191,193],"much":[56],"parallelism":[57],"possible,":[59],"our":[60,84,231],"leverages":[62],"phased":[65],"nature":[66],"access":[69],"patterns":[70],"found":[71],"in":[72,158,181],"many":[73,126],"applications":[74,240],"exhibit":[76],"massive":[77],"parallelism.":[78],"demonstrate":[80],"effectiveness":[82],"computational":[90],"systems":[91,242],"biology":[92],"application.":[93],"application":[95],"consists":[96],"computing":[98,189],"Dynamic":[100],"Bayesian":[101],"Network":[102],"(DBN)":[103],"approximation":[104,121],"dynamics":[107],"signalling":[109,224],"pathways":[110,225],"described":[111],"system":[114],"Ordinary":[116],"Differential":[117],"Equations":[118],"(ODEs).":[119],"The":[120,176],"algorithm":[122],"involves":[123],"(i)":[124],"sampling":[125],"(of":[127],"order":[129],"few":[132],"million)":[133],"times":[134],"from":[135],"set":[137,155],"initial":[139],"states,":[140],"(ii)":[141],"generating":[142],"trajectories":[143,157,177],"through":[144],"numerical":[145],"integration,":[146],"(iii)":[148],"storing":[149],"statistical":[151],"properties":[152],"this":[154],"Conditional":[159],"Probability":[160],"Tables":[161],"(CPTs)":[162],"DBN":[165],"via":[166],"prespecified":[168],"discretization":[169],"time":[172],"value":[174],"domains.":[175],"can":[178],"be":[179,203,234],"computed":[180],"parallel.":[182],"However,":[183],"intermediate":[185],"data":[186],"needed":[187],"them,":[190],"well":[192],"entries":[195],"CPTs,":[198],"are":[199],"too":[200],"large":[201],"to":[202,236],"stored":[204],"locally.":[205],"Our":[206],"experiments":[207],"show":[208],"proposed":[211],"scales":[215],"well,":[216],"achieving":[217],"significant":[218],"performance":[219],"improvements":[220],"three":[222],"realistic":[223],"models.":[226],"These":[227],"results":[228],"suggest":[229],"how":[230],"could":[233],"extended":[235],"deal":[237],"with":[238],"other":[239],"involving":[241],"ODEs.":[244]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
