{"id":"https://openalex.org/W2030228046","doi":"https://doi.org/10.1109/iwsg.2014.12","title":"MapReduce-Based RESTMD: Enabling Large-Scale Sampling Tasks with Distributed HPC Systems","display_name":"MapReduce-Based RESTMD: Enabling Large-Scale Sampling Tasks with Distributed HPC Systems","publication_year":2014,"publication_date":"2014-06-01","ids":{"openalex":"https://openalex.org/W2030228046","doi":"https://doi.org/10.1109/iwsg.2014.12","mag":"2030228046"},"language":"en","primary_location":{"id":"doi:10.1109/iwsg.2014.12","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iwsg.2014.12","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 6th International Workshop on Science Gateways","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/A5073337564","display_name":"Praveenkumar Kondikoppa","orcid":null},"institutions":[{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Praveenkumar Kondikoppa","raw_affiliation_strings":["Louisiana State University Paul M Hebert Law Center, Baton Rouge, LA, US","[Center for Comput. & Technol., Louisiana State Univ., Baton Rouge, LA, USA]"],"affiliations":[{"raw_affiliation_string":"Louisiana State University Paul M Hebert Law Center, Baton Rouge, LA, US","institution_ids":["https://openalex.org/I121820613"]},{"raw_affiliation_string":"[Center for Comput. & Technol., Louisiana State Univ., Baton Rouge, LA, USA]","institution_ids":["https://openalex.org/I121820613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064959930","display_name":"Richard Platania","orcid":"https://orcid.org/0000-0002-2761-4729"},"institutions":[{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard Platania","raw_affiliation_strings":["Louisiana State University Paul M Hebert Law Center, Baton Rouge, LA, US","[Center for Comput. & Technol., Louisiana State Univ., Baton Rouge, LA, USA]"],"affiliations":[{"raw_affiliation_string":"Louisiana State University Paul M Hebert Law Center, Baton Rouge, LA, US","institution_ids":["https://openalex.org/I121820613"]},{"raw_affiliation_string":"[Center for Comput. & Technol., Louisiana State Univ., Baton Rouge, LA, USA]","institution_ids":["https://openalex.org/I121820613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079637252","display_name":"Seung\u2010Jong Park","orcid":"https://orcid.org/0000-0001-7821-7793"},"institutions":[{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Seung-Jong Park","raw_affiliation_strings":["Louisiana State University Paul M Hebert Law Center, Baton Rouge, LA, US","[Center for Comput. & Technol., Louisiana State Univ., Baton Rouge, LA, USA]"],"affiliations":[{"raw_affiliation_string":"Louisiana State University Paul M Hebert Law Center, Baton Rouge, LA, US","institution_ids":["https://openalex.org/I121820613"]},{"raw_affiliation_string":"[Center for Comput. & Technol., Louisiana State Univ., Baton Rouge, LA, USA]","institution_ids":["https://openalex.org/I121820613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013743403","display_name":"T. Keyes","orcid":"https://orcid.org/0000-0002-4955-3621"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tom Keyes","raw_affiliation_strings":["Boston University, Boston, MA, US","Chem. Dept., Boston Univ., Boston, MA, USA"],"affiliations":[{"raw_affiliation_string":"Boston University, Boston, MA, US","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Chem. Dept., Boston Univ., Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103208897","display_name":"Jaegil Kim","orcid":"https://orcid.org/0000-0001-8091-095X"},"institutions":[{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]},{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jaegil Kim","raw_affiliation_strings":["Boston University, Boston, MA, US","Louisiana State University Paul M Hebert Law Center, Baton Rouge, LA, US","Chem. Dept., Boston Univ., Boston, MA, USA"],"affiliations":[{"raw_affiliation_string":"Boston University, Boston, MA, US","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Louisiana State University Paul M Hebert Law Center, Baton Rouge, LA, US","institution_ids":["https://openalex.org/I121820613"]},{"raw_affiliation_string":"Chem. Dept., Boston Univ., Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009898966","display_name":"Nayong Kim","orcid":"https://orcid.org/0000-0003-3412-9956"},"institutions":[{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nayong Kim","raw_affiliation_strings":["Louisiana State University Paul M Hebert Law Center, Baton Rouge, LA, US","[Center for Comput. & Technol., Louisiana State Univ., Baton Rouge, LA, USA]"],"affiliations":[{"raw_affiliation_string":"Louisiana State University Paul M Hebert Law Center, Baton Rouge, LA, US","institution_ids":["https://openalex.org/I121820613"]},{"raw_affiliation_string":"[Center for Comput. & Technol., Louisiana State Univ., Baton Rouge, LA, USA]","institution_ids":["https://openalex.org/I121820613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100615688","display_name":"Joo-Hyun Kim","orcid":"https://orcid.org/0000-0003-2123-7093"},"institutions":[{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]},{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joohyun Kim","raw_affiliation_strings":["Boston University, Boston, MA, US","Louisiana State University Paul M Hebert Law Center, Baton Rouge, LA, US","[Center for Comput. & Technol., Louisiana State Univ., Baton Rouge, LA, USA]"],"affiliations":[{"raw_affiliation_string":"Boston University, Boston, MA, US","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Louisiana State University Paul M Hebert Law Center, Baton Rouge, LA, US","institution_ids":["https://openalex.org/I121820613"]},{"raw_affiliation_string":"[Center for Comput. & Technol., Louisiana State Univ., Baton Rouge, LA, USA]","institution_ids":["https://openalex.org/I121820613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102784918","display_name":"Shuju Bai","orcid":"https://orcid.org/0000-0002-6277-3362"},"institutions":[{"id":"https://openalex.org/I145610796","display_name":"Southern University and Agricultural and Mechanical College","ror":"https://ror.org/04r3m2882","country_code":"US","type":"education","lineage":["https://openalex.org/I145610796"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shuju Bai","raw_affiliation_strings":["Southern University and Agricultural and Mechanical College, Baton Rouge, LA, US","Dept. of Comput. Sci., Southern Univ., Baton Rouge, LA, USA"],"affiliations":[{"raw_affiliation_string":"Southern University and Agricultural and Mechanical College, Baton Rouge, LA, US","institution_ids":["https://openalex.org/I145610796"]},{"raw_affiliation_string":"Dept. of Comput. Sci., Southern Univ., Baton Rouge, LA, USA","institution_ids":["https://openalex.org/I145610796"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5073337564"],"corresponding_institution_ids":["https://openalex.org/I121820613"],"apc_list":null,"apc_paid":null,"fwci":0.7035,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.70179036,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"22","issue":null,"first_page":"30","last_page":"35"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10064","display_name":"Complex Network Analysis Techniques","score":0.9902999997138977,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10064","display_name":"Complex Network Analysis Techniques","score":0.9902999997138977,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9847000241279602,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9843999743461609,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8334190249443054},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.7314384579658508},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.592832088470459},{"id":"https://openalex.org/keywords/replica","display_name":"Replica","score":0.5615189075469971},{"id":"https://openalex.org/keywords/cloud-computing","display_name":"Cloud computing","score":0.5441476106643677},{"id":"https://openalex.org/keywords/data-intensive-computing","display_name":"Data-intensive computing","score":0.46853959560394287},{"id":"https://openalex.org/keywords/computer-cluster","display_name":"Computer cluster","score":0.4670853614807129},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4620785713195801},{"id":"https://openalex.org/keywords/cluster","display_name":"Cluster (spacecraft)","score":0.437486469745636},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.4337727427482605},{"id":"https://openalex.org/keywords/big-data","display_name":"Big data","score":0.43055811524391174},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2091732621192932},{"id":"https://openalex.org/keywords/grid-computing","display_name":"Grid computing","score":0.12704342603683472}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8334190249443054},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.7314384579658508},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.592832088470459},{"id":"https://openalex.org/C2775937380","wikidata":"https://www.wikidata.org/wiki/Q1232589","display_name":"Replica","level":2,"score":0.5615189075469971},{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.5441476106643677},{"id":"https://openalex.org/C76831024","wikidata":"https://www.wikidata.org/wiki/Q5227096","display_name":"Data-intensive computing","level":4,"score":0.46853959560394287},{"id":"https://openalex.org/C29140674","wikidata":"https://www.wikidata.org/wiki/Q206637","display_name":"Computer cluster","level":2,"score":0.4670853614807129},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4620785713195801},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.437486469745636},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.4337727427482605},{"id":"https://openalex.org/C75684735","wikidata":"https://www.wikidata.org/wiki/Q858810","display_name":"Big data","level":2,"score":0.43055811524391174},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2091732621192932},{"id":"https://openalex.org/C70429105","wikidata":"https://www.wikidata.org/wiki/Q249999","display_name":"Grid computing","level":3,"score":0.12704342603683472},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C187691185","wikidata":"https://www.wikidata.org/wiki/Q2020720","display_name":"Grid","level":2,"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/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/iwsg.2014.12","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iwsg.2014.12","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 6th International Workshop on Science Gateways","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6200000047683716,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1483061211","https://openalex.org/W1565709818","https://openalex.org/W1975222035","https://openalex.org/W1985824186","https://openalex.org/W1993883578","https://openalex.org/W2000363949","https://openalex.org/W2010058829","https://openalex.org/W2020851807","https://openalex.org/W2028680274","https://openalex.org/W2050453808","https://openalex.org/W2060150991","https://openalex.org/W2064704940","https://openalex.org/W2090113173","https://openalex.org/W2106798647","https://openalex.org/W2110745592","https://openalex.org/W2117443107","https://openalex.org/W2119180969","https://openalex.org/W2122465391","https://openalex.org/W2319389150","https://openalex.org/W6633901960"],"related_works":["https://openalex.org/W2525033434","https://openalex.org/W4280533024","https://openalex.org/W4300992253","https://openalex.org/W1942762218","https://openalex.org/W1985270856","https://openalex.org/W1541308303","https://openalex.org/W3101274117","https://openalex.org/W4298207756","https://openalex.org/W1966875563","https://openalex.org/W1943333326"],"abstract_inverted_index":{"A":[0],"novel":[1],"implementation":[2,26,64,80],"of":[3,65,102,112,133,141,150,156,158,182,195,198],"Replica":[4],"Exchange":[5],"Statistical":[6],"Temperature":[7],"Molecular":[8],"Dynamics":[9],"(RESTMD),":[10],"belonging":[11],"to":[12,164],"a":[13,54,62,89,154,192],"generalized":[14],"ensemble":[15],"method":[16],"and":[17,91,129,179],"also":[18],"known":[19],"as":[20,75,77],"parallel":[21],"tempering,":[22],"is":[23,61,202],"presented.":[24],"Our":[25,58],"employs":[27],"the":[28,69,78,83,100,110,113,139,180,196],"MapReduce":[29],"(MR)-based":[30],"iterative":[31],"framework":[32,115],"for":[33,48,99,146,171,184],"launching":[34],"RESTMD":[35,79,142,189],"over":[36,130,174],"high":[37],"performance":[38,111],"computing":[39,176],"(HPC)":[40],"clusters":[41],"including":[42],"our":[43],"test":[44],"bed":[45],"system,":[46],"Cyber-infrastructure":[47],"Reconfigurable":[49],"Optical":[50],"Networks":[51],"(CRON)":[52],"simulating":[53],"network-connected":[55],"distributed":[56,93,175],"system.":[57],"main":[59],"contribution":[60],"new":[63],"STMD":[66],"plugged":[67],"into":[68],"well-known":[70],"CHARMM":[71],"molecular":[72],"dynamics":[73],"package":[74],"well":[76],"powered":[81],"by":[82,206,213],"Hadoop":[84,103,183],"that":[85,125],"scales":[86],"out":[87],"in":[88,127,153,210],"cluster":[90],"across":[92],"systems":[94,124,163],"effectively.":[95],"To":[96],"address":[97],"challenges":[98,152],"use":[101,140,181],"MapReduce,":[104],"we":[105],"examined":[106],"contributing":[107],"factors":[108],"on":[109],"proposed":[114],"with":[116,121,138,168],"various":[117],"runtime":[118],"analysis":[119],"experiments":[120],"two":[122],"biological":[123],"differ":[126],"size":[128],"different":[131],"types":[132],"HPC":[134],"resources.":[135],"Many":[136],"advantages":[137],"suggest":[143],"its":[144,169],"effectiveness":[145],"enhanced":[147],"sampling,":[148],"one":[149],"grand":[151],"variety":[155],"areas":[157],"studies":[159],"ranging":[160],"from":[161],"chemical":[162],"statistical":[165],"inference.":[166],"Lastly,":[167],"support":[170],"scale-across":[172],"capacity":[173],"infrastructure":[177],"(DCI)":[178],"coarse-grained":[185],"task-level":[186],"parallelism,":[187],"MapReduce-based":[188],"represents":[190],"truly":[191],"good":[193],"example":[194],"next-generation":[197],"applications":[199],"whose":[200],"provision":[201],"increasingly":[203],"becoming":[204],"demanded":[205],"science":[207],"gateway":[208],"projects,":[209],"particular,":[211],"backed":[212],"IaaS":[214],"clouds.":[215]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
