{"id":"https://openalex.org/W4283735536","doi":"https://doi.org/10.26434/chemrxiv-2022-2951t","title":"ARMer: A Python Library for Adaptive Resource Allocation in High-Throughput Workflow","display_name":"ARMer: A Python Library for Adaptive Resource Allocation in High-Throughput Workflow","publication_year":2022,"publication_date":"2022-06-30","ids":{"openalex":"https://openalex.org/W4283735536","doi":"https://doi.org/10.26434/chemrxiv-2022-2951t"},"language":"en","primary_location":{"id":"doi:10.26434/chemrxiv-2022-2951t","doi":"https://doi.org/10.26434/chemrxiv-2022-2951t","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv-2022-2951t","pdf_url":"https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bcce5ee60d983c2df1f9e1/original/ar-mer-a-python-library-for-adaptive-resource-allocation-in-high-throughput-workflow.pdf","source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bcce5ee60d983c2df1f9e1/original/ar-mer-a-python-library-for-adaptive-resource-allocation-in-high-throughput-workflow.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059001674","display_name":"Qianzhen Shao","orcid":"https://orcid.org/0000-0002-7787-0966","observed_orcids":["https://orcid.org/0000-0002-7787-0966"]},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qianzhen Shao","raw_affiliation_strings":["Vanderbilt University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt University","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055785990","display_name":"Zhongyue John Yang","orcid":"https://orcid.org/0000-0003-0395-6617","observed_orcids":["https://orcid.org/0000-0003-0395-6617"]},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhongyue Yang","raw_affiliation_strings":["Vanderbilt University"],"raw_orcid":"https://orcid.org/0000-0003-0395-6617","affiliations":[{"raw_affiliation_string":"Vanderbilt University","institution_ids":["https://openalex.org/I200719446"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I200719446"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.5346999764442444,"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"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.5346999764442444,"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"}},{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.3515999913215637,"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/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.08340000361204147,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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/adaptive-resource-allocation","display_name":"adaptive resource allocation","score":0.9929999709129333},{"id":"https://openalex.org/keywords/high-throughput-workflow","display_name":"high-throughput workflow","score":0.7540000081062317},{"id":"https://openalex.org/keywords/hpc-clusters","display_name":"HPC clusters","score":0.49000000953674316},{"id":"https://openalex.org/keywords/enzyme-modeling","display_name":"enzyme modeling","score":0.7910000085830688},{"id":"https://openalex.org/keywords/fluoroacetate-dehalogenase","display_name":"fluoroacetate dehalogenase","score":0.9940000176429749},{"id":"https://openalex.org/keywords/molecular-dynamics-simulation","display_name":"molecular dynamics simulation","score":0.6639999747276306},{"id":"https://openalex.org/keywords/quantum-chemical-calculations","display_name":"quantum chemical calculations","score":0.7820000052452087}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8484911322593689},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8184311389923096},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7138767242431641},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.6037563681602478},{"id":"https://openalex.org/C29202148","wikidata":"https://www.wikidata.org/wiki/Q287260","display_name":"Resource allocation","level":2,"score":0.49329107999801636},{"id":"https://openalex.org/C140824633","wikidata":"https://www.wikidata.org/wiki/Q2808660","display_name":"Workflow management system","level":3,"score":0.4733177125453949},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.46782511472702026},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.4471403658390045},{"id":"https://openalex.org/C19612761","wikidata":"https://www.wikidata.org/wiki/Q8034836","display_name":"Workflow technology","level":3,"score":0.44101086258888245},{"id":"https://openalex.org/C206729178","wikidata":"https://www.wikidata.org/wiki/Q2271896","display_name":"Scheduling (production processes)","level":2,"score":0.4164489805698395},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.32653751969337463},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.30157655477523804},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.24110442399978638},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.13402968645095825},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.26434/chemrxiv-2022-2951t","doi":"https://doi.org/10.26434/chemrxiv-2022-2951t","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv-2022-2951t","pdf_url":"https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bcce5ee60d983c2df1f9e1/original/ar-mer-a-python-library-for-adaptive-resource-allocation-in-high-throughput-workflow.pdf","source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.26434/chemrxiv-2022-2951t","doi":"https://doi.org/10.26434/chemrxiv-2022-2951t","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv-2022-2951t","pdf_url":"https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bcce5ee60d983c2df1f9e1/original/ar-mer-a-python-library-for-adaptive-resource-allocation-in-high-throughput-workflow.pdf","source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320338008","display_name":"Vanderbilt Institute of Chemical Biology, School of Medicine, Vanderbilt University","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4283735536.pdf","grobid_xml":"https://content.openalex.org/works/W4283735536.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W248108529","https://openalex.org/W2039350725","https://openalex.org/W2043701535","https://openalex.org/W2064719117","https://openalex.org/W2124426289","https://openalex.org/W2132525235","https://openalex.org/W2138085558","https://openalex.org/W2162653998","https://openalex.org/W2296686360","https://openalex.org/W2468618868","https://openalex.org/W2560598712","https://openalex.org/W2576153484","https://openalex.org/W2886156228","https://openalex.org/W2895843105","https://openalex.org/W2902677469","https://openalex.org/W2940242941","https://openalex.org/W2949941039","https://openalex.org/W2973087556","https://openalex.org/W2981554790","https://openalex.org/W3012320417","https://openalex.org/W3043464017","https://openalex.org/W3125427056","https://openalex.org/W3162160000","https://openalex.org/W4200453578","https://openalex.org/W4205328756","https://openalex.org/W4214865324","https://openalex.org/W4220661692","https://openalex.org/W4220669883","https://openalex.org/W4221041249","https://openalex.org/W4226280369","https://openalex.org/W4233253307","https://openalex.org/W4235515687","https://openalex.org/W4246447715","https://openalex.org/W4251596815","https://openalex.org/W4252222576"],"related_works":["https://openalex.org/W4394865781","https://openalex.org/W4386585077","https://openalex.org/W7221581172","https://openalex.org/W7102584127","https://openalex.org/W4400409869","https://openalex.org/W3213987511","https://openalex.org/W7140256349","https://openalex.org/W3198232371","https://openalex.org/W7131622171","https://openalex.org/W2784407602"],"abstract_inverted_index":{"High-throughput":[0],"modeling":[1,48,83],"requires":[2],"allocation":[3,33,111],"of":[4,7,24,45,70,84,127,149],"different":[5],"types":[6],"computing":[8,18,38,77],"resources":[9,39,78],"(e.g.,":[10],"GPU/CPU)":[11],"for":[12,75,119,162],"various":[13],"computational":[14,151],"sub-tasks":[15],"in":[16,50,129,153,166],"high-performance":[17],"(HPC)":[19],"clusters.":[20],"To":[21],"enhance":[22],"efficiency":[23],"resource":[25,32,64,110],"consumption,":[26],"here":[27],"we":[28,72],"developed":[29],"an":[30],"adaptive":[31,63],"strategy":[34,56],"to":[35,108,135],"dynamically":[36],"request":[37],"based":[40],"on":[41],"the":[42,51,55,80,122,125,130,167],"specific":[43],"need":[44],"a":[46,58,68,154],"certain":[47],"sub-task":[49],"workflow.":[52,168],"We":[53],"implemented":[54],"as":[57],"new":[59],"Python":[60],"library,":[61],"i.e.,":[62],"manager":[65],"(ARMer).":[66],"As":[67],"proof":[69],"concept,":[71],"employed":[73],"ARMer":[74,128,145],"allocating":[76],"during":[79,121],"high-throughput":[81],"enzyme":[82],"fluoroacetate":[85],"dehalogenase":[86],"using":[87],"EnzyHTP.":[88],"The":[89],"workflow":[90,131],"involves":[91],"four":[92],"sequential":[93],"sub-tasks,":[94],"including:":[95],"mutant":[96],"generation,":[97],"molecular":[98],"dynamics":[99],"simulation,":[100],"quantum":[101],"mechanical":[102],"calculation,":[103],"and":[104,115,139,157],"data":[105],"analysis.":[106],"Compared":[107],"fixed":[109],"where":[112],"both":[113],"CPU":[114,137],"GPU":[116,141],"are":[117],"on-call":[118],"use":[120,126],"entire":[123],"workflow,":[124],"can":[132],"save":[133],"up":[134],"87%":[136],"hours":[138],"14%":[140],"hours.":[142],"In":[143],"addition,":[144],"allows":[146],"parallel":[147],"submission":[148],"multiple":[150],"jobs":[152],"job":[155],"array":[156],"provides":[158],"customized":[159],"environment":[160],"settings":[161],"each":[163],"software":[164],"used":[165]},"counts_by_year":[],"updated_date":"2026-10-08T09:06:37.294493","created_date":"2022-07-01T00:00:00"}
