{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,30]],"date-time":"2024-09-30T04:26:38Z","timestamp":1727670398238},"reference-count":43,"publisher":"SAGE Publications","issue":"12","license":[{"start":{"date-parts":[[2016,11,3]],"date-time":"2016-11-03T00:00:00Z","timestamp":1478131200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["SIMULATION"],"published-print":{"date-parts":[[2016,12]]},"abstract":" Due to its unrivaled ability to predict the dynamical evolution of interacting atoms, molecular dynamics (MD) is a widely used computational method in theoretical chemistry, physics, biology, and engineering. Despite its success, MD is only capable of modeling timescales within several orders of magnitude of thermal vibrations, leaving out many important phenomena that occur at slower rates. The temperature-accelerated dynamics (TAD) method overcomes this limitation by thermally accelerating the state-to-state evolution captured by MD. Due to the algorithmically complex nature of the serial TAD procedure, implementations have yet to improve performance by parallelizing the concurrent exploration of multiple states. Here we utilize a discrete-event-based application simulator to introduce and explore a new speculatively parallel TAD (SpecTAD) method. We investigate the SpecTAD algorithm, without a full-scale implementation, by constructing an application simulator proxy (SpecTADSim). Following this method, we discover that a non-trivial relationship exists between the optimal SpecTAD parameter set and the number of CPU cores available at run-time. Furthermore, we find that a majority of the available SpecTAD boost can be achieved within an existing TAD application using relatively simple algorithm modifications. <\/jats:p>","DOI":"10.1177\/0037549716674806","type":"journal-article","created":{"date-parts":[[2016,11,3]],"date-time":"2016-11-03T02:03:44Z","timestamp":1478138624000},"page":"1065-1086","update-policy":"http:\/\/dx.doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":10,"title":["Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics"],"prefix":"10.1177","volume":"92","author":[{"given":"Richard J","family":"Zamora","sequence":"first","affiliation":[{"name":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA"}]},{"given":"Arthur F","family":"Voter","sequence":"additional","affiliation":[{"name":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA"}]},{"given":"Danny","family":"Perez","sequence":"additional","affiliation":[{"name":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA"}]},{"given":"Nandakishore","family":"Santhi","sequence":"additional","affiliation":[{"name":"Computer, Computational & Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA"}]},{"given":"Susan M","family":"Mniszewski","sequence":"additional","affiliation":[{"name":"Computer, Computational & Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA"}]},{"given":"Sunil","family":"Thulasidasan","sequence":"additional","affiliation":[{"name":"Computer, Computational & Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA"}]},{"given":"Stephan J","family":"Eidenbenz","sequence":"additional","affiliation":[{"name":"Computer, Computational & Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA"}]}],"member":"179","published-online":{"date-parts":[[2016,11,3]]},"reference":[{"key":"bibr1-0037549716674806","unstructured":"US Department of Energy Office of Science. Scientific discovery through advanced computing (SciDAC) co-design, http:\/\/science.energy.gov\/ascr\/research\/scidac\/co-design\/ (2012, accessed 19 October 2016)."},{"key":"bibr2-0037549716674806","unstructured":"US Department of Energy Office of Science. Applied mathematics research for exascale computing, http:\/\/science.energy.gov\/~\/media\/ascr\/pdf\/research\/am\/docs\/EMWGreport.pdf (2014, accessed 19 October 2016)."},{"key":"bibr3-0037549716674806","unstructured":"Advanced Simulation and Computing Program. National security applications co-design project, https:\/\/asc.llnl.gov\/codesign\/ (2012, accessed 19 October 2016)."},{"volume-title":"Proceedings of the U. S. Department of Energy exascale research conference","author":"Eidenbenz S","key":"bibr4-0037549716674806"},{"key":"bibr5-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1145\/2699715"},{"key":"bibr6-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevB.76.205439"},{"key":"bibr7-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1063\/1.3541823"},{"key":"bibr8-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1063\/1.4894391"},{"key":"bibr9-0037549716674806","first-page":"131","volume-title":"Computer simulation studies in condensed-matter physics XVIII","author":"Shim Y","year":"2007"},{"key":"bibr10-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1145\/79173.79181"},{"first-page":"145","volume-title":"Proceedings of the 6th ACM\/SPEC international conference on performance engineering","author":"Didona D","key":"bibr11-0037549716674806"},{"first-page":"238","volume-title":"2015 IEEE 17th International Conference on High Performance Computing and Communications, 2015 IEEE 12th International Conference on Embedded Software and Systems and 2015 IEEE 7th International Symposium on Cyberspace Safety and Security","author":"Anger E","key":"bibr12-0037549716674806"},{"first-page":"35","volume-title":"Proceedings of the first annual ACM SIGMM conference on multimedia systems","author":"Barker SK","key":"bibr13-0037549716674806"},{"key":"bibr14-0037549716674806","doi-asserted-by":"publisher","DOI":"10.2172\/1170619"},{"first-page":"405","volume-title":"Proceedings of the 29th ACM international conference on supercomputing","author":"Lee S","key":"bibr15-0037549716674806"},{"key":"bibr16-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-chembioeng-080615-033608"},{"key":"bibr17-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1063\/1.481576"},{"key":"bibr18-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1063\/1.1449865"},{"key":"bibr19-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevB.66.205404"},{"key":"bibr20-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1063\/1.480097"},{"key":"bibr21-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511816581"},{"key":"bibr22-0037549716674806","doi-asserted-by":"publisher","DOI":"10.3390\/ijms10125135"},{"volume-title":"A handbook of computational chemistry: A practical guide to chemical structure and energy calculations","year":"1985","author":"Clark T.","key":"bibr23-0037549716674806"},{"volume-title":"Dynamics of proteins and nucleic acids","year":"1988","author":"McCammon JA","key":"bibr24-0037549716674806"},{"key":"bibr25-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.matsci.32.112601.141541"},{"key":"bibr26-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1016\/S1574-1400(09)00504-0"},{"key":"bibr27-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1126\/science.1183723"},{"key":"bibr28-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.106.126101"},{"key":"bibr29-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1016\/j.commatsci.2014.12.011"},{"volume-title":"Computer simulation of liquids","year":"1989","author":"Allen MP","key":"bibr30-0037549716674806"},{"key":"bibr31-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1016\/0022-3697(57)90059-8"},{"key":"bibr32-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1063\/1.1329672"},{"key":"bibr33-0037549716674806","unstructured":"Santhi N. Simian just in time parallel discrete event simulation engine. Technical Report, Los Alamos National Laboratory, NM, 2015."},{"volume-title":"Proceedings of the 2015 winter simulation conference","author":"Chapuis G","key":"bibr34-0037549716674806"},{"volume-title":"Proceedings of the 2015 winter simulation conference","author":"Park EJ","key":"bibr35-0037549716674806"},{"volume-title":"Proceedings of the 2015 winter simulation conference","author":"Santhi N","key":"bibr36-0037549716674806"},{"key":"bibr37-0037549716674806","unstructured":"Kroc L, Eidenbenz S, Ramaswamy V. Simcore. Technical Report 07-0590, Los Alamos National Laboratory, Los Alamos, NM, 2007."},{"volume-title":"Simcore tutorial","year":"2010","author":"Mniszewski SM.","key":"bibr38-0037549716674806"},{"first-page":"188","volume-title":"4th international conference on simulation and modeling methodologies, technologies and applications","author":"Thulasidasan S","key":"bibr39-0037549716674806"},{"key":"bibr40-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcp.2010.12.030"},{"key":"bibr41-0037549716674806","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevB.29.6443"},{"key":"bibr42-0037549716674806","first-page":"77","volume-title":"Intermetallic compounds","author":"Voter AF.","year":"1994"},{"first-page":"214","volume-title":"31st annual technical symposium, International Society for Optics and Photonics","author":"Voter AF","key":"bibr43-0037549716674806"}],"container-title":["SIMULATION"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1177\/0037549716674806","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/full-xml\/10.1177\/0037549716674806","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1177\/0037549716674806","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,29]],"date-time":"2024-09-29T23:31:21Z","timestamp":1727652681000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/10.1177\/0037549716674806"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,11,3]]},"references-count":43,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2016,12]]}},"alternative-id":["10.1177\/0037549716674806"],"URL":"https:\/\/doi.org\/10.1177\/0037549716674806","relation":{},"ISSN":["0037-5497","1741-3133"],"issn-type":[{"type":"print","value":"0037-5497"},{"type":"electronic","value":"1741-3133"}],"subject":[],"published":{"date-parts":[[2016,11,3]]}}}