{"id":"https://openalex.org/W7161232799","doi":"https://doi.org/10.48550/arxiv.2605.14655","title":"Malleable Molecular Dynamics Simulations with GROMACS and DMR","display_name":"Malleable Molecular Dynamics Simulations with GROMACS and DMR","publication_year":2026,"publication_date":"2026-05-14","ids":{"openalex":"https://openalex.org/W7161232799","doi":"https://doi.org/10.48550/arxiv.2605.14655"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2605.14655","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.14655","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2605.14655","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5120624454","display_name":"Petter Sand\u00e5s","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sand\u00e5s, Petter","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136217728","display_name":"Sergio Iserte","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Iserte, Sergio","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136218171","display_name":"\u00cd\u00f1igo Ar\u00e9jula-A\u00edsa","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ar\u00e9jula-A\u00edsa, \u00cd\u00f1igo","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050108763","display_name":"Berk Hess","orcid":"https://orcid.org/0000-0002-7498-7763"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hess, Berk","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5097946716","display_name":"Antonio J. Pena","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pe\u00f1a, Antonio J.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"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/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.3231000006198883,"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"}},"topics":[{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.3231000006198883,"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/T10101","display_name":"Cloud Computing and Resource Management","score":0.225600004196167,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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":0.16779999434947968,"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/control-reconfiguration","display_name":"Control reconfiguration","score":0.7239000201225281},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4936999976634979},{"id":"https://openalex.org/keywords/queue","display_name":"Queue","score":0.47189998626708984},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.4666000008583069},{"id":"https://openalex.org/keywords/malleability","display_name":"Malleability","score":0.4251999855041504},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.41670000553131104},{"id":"https://openalex.org/keywords/middleware","display_name":"Middleware (distributed applications)","score":0.3912999927997589},{"id":"https://openalex.org/keywords/cloud-computing","display_name":"Cloud computing","score":0.36000001430511475},{"id":"https://openalex.org/keywords/protocol","display_name":"Protocol (science)","score":0.3546999990940094}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7982000112533569},{"id":"https://openalex.org/C119701452","wikidata":"https://www.wikidata.org/wiki/Q5165881","display_name":"Control reconfiguration","level":2,"score":0.7239000201225281},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.5436000227928162},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4936999976634979},{"id":"https://openalex.org/C160403385","wikidata":"https://www.wikidata.org/wiki/Q220543","display_name":"Queue","level":2,"score":0.47189998626708984},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.4666000008583069},{"id":"https://openalex.org/C100980136","wikidata":"https://www.wikidata.org/wiki/Q4668956","display_name":"Malleability","level":4,"score":0.4251999855041504},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.41670000553131104},{"id":"https://openalex.org/C169468491","wikidata":"https://www.wikidata.org/wiki/Q146923","display_name":"Middleware (distributed applications)","level":2,"score":0.3912999927997589},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3797000050544739},{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.36000001430511475},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.3546999990940094},{"id":"https://openalex.org/C16320812","wikidata":"https://www.wikidata.org/wiki/Q1812200","display_name":"Idle","level":2,"score":0.3352999985218048},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3328000009059906},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.33059999346733093},{"id":"https://openalex.org/C2780609101","wikidata":"https://www.wikidata.org/wiki/Q17156588","display_name":"Resource management (computing)","level":2,"score":0.3116999864578247},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.2948000133037567},{"id":"https://openalex.org/C22684755","wikidata":"https://www.wikidata.org/wiki/Q847526","display_name":"Queueing theory","level":2,"score":0.29249998927116394},{"id":"https://openalex.org/C159886148","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov process","level":2,"score":0.2904999852180481},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.28060001134872437},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.2791000008583069},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.2782999873161316},{"id":"https://openalex.org/C206729178","wikidata":"https://www.wikidata.org/wiki/Q2271896","display_name":"Scheduling (production processes)","level":2,"score":0.26440000534057617},{"id":"https://openalex.org/C2984822820","wikidata":"https://www.wikidata.org/wiki/Q1123036","display_name":"Processor scheduling","level":3,"score":0.26409998536109924},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.2599000036716461},{"id":"https://openalex.org/C22927095","wikidata":"https://www.wikidata.org/wiki/Q1784206","display_name":"Stateful firewall","level":3,"score":0.2549999952316284},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.2517000138759613},{"id":"https://openalex.org/C77405623","wikidata":"https://www.wikidata.org/wiki/Q598451","display_name":"System dynamics","level":2,"score":0.25130000710487366},{"id":"https://openalex.org/C29202148","wikidata":"https://www.wikidata.org/wiki/Q287260","display_name":"Resource allocation","level":2,"score":0.25040000677108765}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2605.14655","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.14655","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2605.14655","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.14655","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"sustainable_development_goals":[{"display_name":"Decent work and economic growth","score":0.4953484535217285,"id":"https://metadata.un.org/sdg/8"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Static":[0],"resource":[1],"allocations":[2],"in":[3,33],"high-performance":[4],"computing":[5],"(HPC)":[6],"lead":[7],"to":[8,55],"inefficiencies":[9],"for":[10,99],"time-varying":[11],"workloads,":[12],"causing":[13],"idle":[14],"resources,":[15],"queue":[16],"delays,":[17],"and":[18,91,96],"higher":[19],"node-hour":[20,97],"costs.":[21],"The":[22],"Dynamic":[23],"Management":[24],"of":[25],"Resources":[26],"(DMR)":[27],"middleware":[28],"enables":[29],"MPI":[30,65],"process":[31,66],"malleability":[32],"Slurm":[34],"via":[35],"a":[36,57],"simple":[37],"API":[38],"decoupled":[39],"from":[40],"scheduler":[41],"internals.":[42],"In":[43],"this":[44,79],"work,":[45],"we":[46],"integrate":[47],"DMR":[48],"into":[49],"the":[50,82],"GROMACS":[51,101],"molecular":[52],"dynamics":[53],"engine":[54],"obtain":[56],"malleable":[58],"variant":[59],"that":[60],"can":[61],"dynamically":[62],"adapt":[63],"its":[64],"count":[67],"by":[68],"combining":[69],"communication-efficiency-aware":[70],"reconfiguration":[71,93],"with":[72],"GROMACS'":[73],"native":[74],"checkpoint/restart":[75],"mechanism.":[76],"We":[77],"evaluate":[78],"design":[80],"on":[81],"MareNostrum~5":[83],"supercomputer,":[84],"comparing":[85],"dynamic":[86],"runs":[87],"against":[88],"static":[89],"executions":[90],"quantifying":[92],"overheads,":[94],"time-to-solution,":[95],"savings":[98],"bursty":[100],"workloads.":[102]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2026-05-16T00:00:00"}