{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T17:52:51Z","timestamp":1760205171394,"version":"3.37.3"},"reference-count":50,"publisher":"Springer Science and Business Media LLC","issue":"7","license":[{"start":{"date-parts":[[2022,1,17]],"date-time":"2022-01-17T00:00:00Z","timestamp":1642377600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2022,1,17]],"date-time":"2022-01-17T00:00:00Z","timestamp":1642377600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"funder":[{"name":"Spanish Governement","award":["SEV-2015-0493"],"award-info":[{"award-number":["SEV-2015-0493"]}]},{"DOI":"10.13039\/501100006280","name":"Spanish Ministry of Science and Technology","doi-asserted-by":"crossref","award":["TIN2015-65316-P"],"award-info":[{"award-number":["TIN2015-65316-P"]}],"id":[{"id":"10.13039\/501100006280","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100002809","name":"Generalitat de Catalunya","doi-asserted-by":"publisher","award":["2017-SGR-1414"],"award-info":[{"award-number":["2017-SGR-1414"]}],"id":[{"id":"10.13039\/501100002809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European POP CoE","award":["824080"],"award-info":[{"award-number":["824080"]}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["800925","823712"],"award-info":[{"award-number":["800925","823712"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"name":"UK EPSRC for the High-End Computing Consortium","award":["EP\/R029598\/1"],"award-info":[{"award-number":["EP\/R029598\/1"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Supercomput"],"published-print":{"date-parts":[[2022,5]]},"DOI":"10.1007\/s11227-021-04214-4","type":"journal-article","created":{"date-parts":[[2022,1,17]],"date-time":"2022-01-17T00:03:47Z","timestamp":1642377827000},"page":"9184-9215","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Hybrid parallelization of molecular dynamics simulations to reduce load imbalance"],"prefix":"10.1007","volume":"78","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8448-9995","authenticated-orcid":false,"given":"Julian","family":"Morillo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maxime","family":"Vassaux","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter V.","family":"Coveney","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marta","family":"Garcia-Gasulla","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,1,17]]},"reference":[{"key":"4214_CR1","doi-asserted-by":"publisher","unstructured":"Thompson AP, Aktulga HM, Berger R, Bolintineanu DS, Michael Brown W, Crozier PS, in \u2019t Veld PJ, Kohlmeyer A, Moore SG, Nguyen TD, Shan R, Stevens M, Tranchida J, Trott C, Plimpton SJ (2021) Lammps - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Computer Physics Communications p. 108171. https:\/\/doi.org\/10.1016\/j.cpc.2021.108171. https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0010465521002836","DOI":"10.1016\/j.cpc.2021.108171"},{"issue":"1","key":"4214_CR2","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1006\/jcph.1995.1039","volume":"117","author":"S Plimpton","year":"1995","unstructured":"Plimpton S (1995) Fast parallel algorithms for short-range molecular dynamics. J Comput Phys 117(1):1\u201319","journal-title":"J Comput Phys"},{"issue":"2\u20133","key":"4214_CR3","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1016\/j.apnum.2004.08.028","volume":"52","author":"KD Devine","year":"2005","unstructured":"Devine KD, Boman EG, Heaphy RT, Hendrickson BA, Teresco JD, Faik J, Flaherty JE, Gervasio LG (2005) New challenges in dynamic load balancing. Appl Numer Math 52(2\u20133):133\u2013152","journal-title":"Appl Numer Math"},{"key":"4214_CR4","doi-asserted-by":"publisher","unstructured":"Deng Y, Peierls RF, Rivera C (2000) An Adaptive Load Balancing Method for Parallel Molecular Dynamics Simulations. Journal of Computational Physics 161(1):250\u2013263 https:\/\/doi.org\/10.1006\/jcph.2000.6501. http:\/\/www.sciencedirect.com\/science\/article\/pii\/S002199910096501X","DOI":"10.1006\/jcph.2000.6501"},{"key":"4214_CR5","unstructured":"Plimpton S, Pollock R, Stevens M (2000) Particle-mesh ewald and rrespa for parallel molecular dynamics simulations. In: Proceeding 8th SIAM Conference on Parallel Processing for Scientific Computing"},{"issue":"1","key":"4214_CR6","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1137\/S1064827598337373","volume":"22","author":"C Walshaw","year":"2000","unstructured":"Walshaw C, Cross M (2000) Mesh partitioning: a multilevel balancing and refinement algorithm. SIAM J Sci Comput 22(1):63\u201380","journal-title":"SIAM J Sci Comput"},{"issue":"1","key":"4214_CR7","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1137\/S1064827595287997","volume":"20","author":"G Karypis","year":"1998","unstructured":"Karypis G, Kumar V (1998) A fast and high quality multilevel scheme for partitioning irregular graphs. SIAM J Sci Comput 20(1):359\u2013392","journal-title":"SIAM J Sci Comput"},{"key":"4214_CR8","doi-asserted-by":"crossref","unstructured":"Harlacher DF, Klimach H, Roller S, Siebert C, Wolf F (2012). Dynamic load balancing for unstructured meshes on space-filling curves. In: 2012 IEEE 26th international parallel and distributed processing symposium workshops & PhD forum, pp 1661\u20131669. IEEE (2012)","DOI":"10.1109\/IPDPSW.2012.207"},{"key":"4214_CR9","doi-asserted-by":"crossref","unstructured":"Schloegel K, Karypis G, Kumar V (2000) A unified algorithm for load-balancing adaptive scientific simulations. In: SC\u201900: Proceedings of the 2000 ACM\/IEEE Conference on Supercomputing, pp 59\u201359. IEEE (2000)","DOI":"10.1109\/SC.2000.10035"},{"key":"4214_CR10","unstructured":"LAMMPS balance command. https:\/\/docs.lammps.org\/balance.html. [Online; accessed 03-November-2021]"},{"key":"4214_CR11","unstructured":"LAMMPS fix balance command. https:\/\/docs.lammps.org\/fix_balance.html. [Online; accessed 03-November-2021]"},{"key":"4214_CR12","doi-asserted-by":"crossref","unstructured":"Huang C, Lawlor O, Kale LV (2003) Adaptive mpi. In: international workshop on languages and compilers for parallel computing, pp. 306\u2013322. Springer","DOI":"10.1007\/978-3-540-24644-2_20"},{"key":"4214_CR13","doi-asserted-by":"crossref","unstructured":"Acun B, Gupta A, Jain N, Langer A, Menon H, Mikida E, Ni X, Robson M, Sun Y, Totoni E et al (2014) Parallel programming with migratable objects: Charm++ in practice. In: SC\u201914: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, pp 647\u2013658. IEEE","DOI":"10.1109\/SC.2014.58"},{"key":"4214_CR14","unstructured":"Adaptive MPI - Using Existing MPI Codes with AMPI. https:\/\/charm.readthedocs.io\/en\/latest\/ampi\/03-using.html. [Online; accessed 04-November-2021]"},{"key":"4214_CR15","doi-asserted-by":"crossref","unstructured":"Etinski M, Corbalan J, Labarta J, Valero M, Veidenbaum A (2009). Power-aware load balancing of large scale mpi applications. In: 2009 IEEE international symposium on parallel & distributed processing, pp 1\u20138. IEEE","DOI":"10.1109\/IPDPS.2009.5160973"},{"key":"4214_CR16","doi-asserted-by":"crossref","unstructured":"Garcia M, Corbalan J, Labarta, J (2009) LeWI: A Runtime Balancing Algorithm for Nested Parallelism. In: Proceedings of the International Conference on Parallel Processing (ICPP09)","DOI":"10.1109\/ICPP.2009.56"},{"issue":"1","key":"4214_CR17","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1177\/1094342019842919","volume":"34","author":"M Garcia-Gasulla","year":"2020","unstructured":"Garcia-Gasulla M, Mantovani F, Josep-Fabrego M, Eguzkitza B, Houzeaux G (2020) Runtime mechanisms to survive new hpc architectures: a use case in human respiratory simulations. Int J High Performance Comput Appl 34(1):42\u201356","journal-title":"Int J High Performance Comput Appl"},{"key":"4214_CR18","doi-asserted-by":"crossref","unstructured":"Rabenseifner R, Hager G, Jost G (2009) Hybrid mpi\/openmp parallel programming on clusters of multi-core smp nodes. In: 2009 17th Euromicro International Conference on Parallel, Distributed and Network-Based Processing, pp 427\u2013436. IEEE","DOI":"10.1109\/PDP.2009.43"},{"issue":"1","key":"4214_CR19","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1177\/1094342003017001005","volume":"17","author":"R Rabenseifner","year":"2003","unstructured":"Rabenseifner R, Wellein G (2003) Communication and optimization aspects of parallel programming models on hybrid architectures. Int J High Performance Comput Appl 17(1):49\u201362","journal-title":"Int J High Performance Comput Appl"},{"key":"4214_CR20","doi-asserted-by":"publisher","unstructured":"Berger R, Kloss C, Kohlmeyer A, Pirker S (2015) Hybrid parallelization of the LIGGGHTS open-source DEM code. Powder Technology 278:234\u2013247 https:\/\/doi.org\/10.1016\/j.powtec.2015.03.019. https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0032591015002144","DOI":"10.1016\/j.powtec.2015.03.019"},{"key":"4214_CR21","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1007\/s11227-013-0915-x","volume":"66","author":"M Kunaseth","year":"2013","unstructured":"Kunaseth M, Richards D, Glosli J, Kalia R, Nakano A, Vashishta P (2013) Analysis of scalable data-privatization threading algorithms for hybrid mpi\/openmp parallelization of molecular dynamics. J Supercomput 66:406\u2013430. https:\/\/doi.org\/10.1007\/s11227-013-0915-x","journal-title":"J Supercomput"},{"key":"4214_CR22","doi-asserted-by":"publisher","unstructured":"Jung J, Mori T, Sugita Y (2014) Midpoint cell method for hybrid (mpi+openmp) parallelization of molecular dynamics simulations. J Comput Chem. 35(14):1064\u20131072 https:\/\/doi.org\/10.1002\/jcc.23591. https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1002\/jcc.23591","DOI":"10.1002\/jcc.23591"},{"key":"4214_CR23","doi-asserted-by":"publisher","unstructured":"Pal A, Agarwala A, Raha S, Bhattacharya B (2014) Performance metrics in a hybrid mpi-openmp based molecular dynamics simulation with short-range interactions. J Parallel Distribut Comput. 74(3):2203\u20132214 https:\/\/doi.org\/10.1016\/j.jpdc.2013.12.008. https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0743731513002505","DOI":"10.1016\/j.jpdc.2013.12.008"},{"key":"4214_CR24","unstructured":"OpenMP. https:\/\/www.openmp.org\/. [Online; accessed 03-November-2021]"},{"key":"4214_CR25","unstructured":"NAMD Scalable Molecular Dynamics. https:\/\/www.ks.uiuc.edu\/Research\/namd\/. [Online; accessed 04-November-2021]"},{"key":"4214_CR26","unstructured":"GROMACS. https:\/\/www.gromacs.org\/. [Online; accessed 04-November-2021]"},{"key":"4214_CR27","unstructured":"LAMMPS documentation, OpenMP section. https:\/\/docs.lammps.org\/Speed_omp.html. [Online; accessed 04-October-2021]"},{"key":"4214_CR28","unstructured":"POP (Performance Optimisation and Productivity, A Centre of Excellence in HPC. Patterns, Loop iterations manually distributed. https:\/\/co-design.pop-coe.eu\/patterns\/loop-manual-distribution.html. [Online; accessed 04-October-2021]"},{"key":"4214_CR29","unstructured":"LAMMPS website. https:\/\/www.lammps.org\/. [Online; accessed 08-November-2021]"},{"key":"4214_CR30","unstructured":"Official LAMMPS website, benchmark section: Billion-atom LJ benchmarks. https:\/\/www.lammps.org\/bench.html#billionl. [Online; accessed 29-September-2021]"},{"key":"4214_CR31","unstructured":"Rhodopsin protein benchmark. https:\/\/www.lammps.org\/bench.html#rhodo. [Online; accessed 08-November-2021]"},{"key":"4214_CR32","unstructured":"Granular chute flow benchmark. https:\/\/www.lammps.org\/bench.html#chute. [Online; accessed 08-November-2021]"},{"key":"4214_CR33","unstructured":"Polymer chain melt benchmark. https:\/\/www.lammps.org\/bench.html#chain. [Online; accessed 08-November-2021]"},{"key":"4214_CR34","unstructured":"EAM metallic solid benchmark. https:\/\/www.lammps.org\/bench.html#eam. [Online; accessed 08-November-2021]"},{"key":"4214_CR35","unstructured":"Lennard-Jones liquid benchmark. https:\/\/www.lammps.org\/bench.html#lj. [Online; accessed 08-November-2021]"},{"key":"4214_CR36","doi-asserted-by":"publisher","unstructured":"Vassaux M, Sinclair RC, Richardson RA, Suter JL, Coveney PV (2019) The role of graphene in enhancing the material properties of thermosetting polymers. Adv Theor Simulations. 2(5):1800168 https:\/\/doi.org\/10.1002\/adts.201800168. https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1002\/adts.201800168","DOI":"10.1002\/adts.201800168"},{"key":"4214_CR37","doi-asserted-by":"publisher","unstructured":"Suter JL, Sinclair RC, Coveney PV (2020) Principles governing control of aggregation and dispersion of graphene and graphene oxide in polymer melts. Adv Mater. 32(36):2003213 https:\/\/doi.org\/10.1002\/adma.202003213. https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1002\/adma.202003213","DOI":"10.1002\/adma.202003213"},{"key":"4214_CR38","unstructured":"Barcelona Supercomputing Center: Extrae. https:\/\/tools.bsc.es\/extrae. [Online; accessed 03-November-2021]"},{"issue":"8","key":"4214_CR39","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1016\/j.parco.2013.05.004","volume":"39","author":"H Servat","year":"2013","unstructured":"Servat H et al (2013) Framework for a productive performance optimization. Parallel Comput 39(8):336\u2013353","journal-title":"Parallel Comput"},{"key":"4214_CR40","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1007\/978-3-642-11261-4_11","volume-title":"Tools for High Performance Computing 2009","author":"D Terpstra","year":"2010","unstructured":"Terpstra D, Jagode H, You H, Dongarra J (2010) Collecting performance data with papi-c. In: M\u00fcller MS, Resch MM, Schulz A, Nagel WE (eds) Tools for High Performance Computing 2009. Springer, Berlin, pp 157\u2013173"},{"key":"4214_CR41","unstructured":"Barcelona Supercomputing Center: Paraver. https:\/\/tools.bsc.es\/paraver. [Online; accessed 03-November-2021]"},{"key":"4214_CR42","unstructured":"Pillet V, Labarta J, Cortes T, Girona S (1995) Paraver: A tool to visualize and analyze parallel code. In: Proceedings of WoTUG-18: Transputer and Occam Developments, 44, pp 17\u201331"},{"key":"4214_CR43","doi-asserted-by":"crossref","unstructured":"Wagner M, Mohr S, Gim\u00e9nez J, Labarta J (2017) A structured approach to performance analysis. In: International Workshop on Parallel Tools for High Performance Computing, pp 1\u201315. Springer","DOI":"10.1007\/978-3-030-11987-4_1"},{"key":"4214_CR44","doi-asserted-by":"crossref","unstructured":"Banchelli F, Peiro K, Querol A, Ramirez-Gargallo G, Ramirez-Miranda G, Vinyals J, Vizcaino P, Garcia-Gasulla M, Mantovani F (2020) Performance study of hpc applications on an arm-based cluster using a generic efficiency model. In: 2020 28th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP), pp 167\u2013174. IEEE","DOI":"10.1109\/PDP50117.2020.00032"},{"issue":"1\u20132","key":"4214_CR45","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1080\/08927028708080929","volume":"1","author":"D Fincham","year":"1987","unstructured":"Fincham D (1987) Parallel computers and molecular simulation. Mol Simul 1(1\u20132):1\u201345. https:\/\/doi.org\/10.1080\/08927028708080929","journal-title":"Mol Simul"},{"key":"4214_CR46","doi-asserted-by":"publisher","unstructured":"Smith W (1991) Molecular dynamics on hypercube parallel computers. Comput Phys Commun. 62(2):229\u2013248 https:\/\/doi.org\/10.1016\/0010-4655(91)90097-5. http:\/\/www.sciencedirect.com\/science\/article\/pii\/0010465591900975","DOI":"10.1016\/0010-4655(91)90097-5"},{"issue":"3","key":"4214_CR47","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1002\/(SICI)1096-987X","volume":"17","author":"S Plimpton","year":"1996","unstructured":"Plimpton S, Hendrickson B (1996) A new parallel method for molecular dynamics simulation of macromolecular systems. J Comput Chem 17(3):326\u2013337. https:\/\/doi.org\/10.1002\/(SICI)1096-987X","journal-title":"J Comput Chem"},{"key":"4214_CR48","doi-asserted-by":"publisher","unstructured":"Rabenseifner R, Hager G, Jost G (2009) Hybrid mpi\/openmp parallel programming on clusters of multi-core smp nodes. In: 2009 17th Euromicro International Conference on Parallel, Distributed and Network-Based Processing, pp 427\u2013436. https:\/\/doi.org\/10.1109\/PDP.2009.43","DOI":"10.1109\/PDP.2009.43"},{"key":"4214_CR49","unstructured":"LAMMPS release 20 Nov 2019. https:\/\/github.com\/lammps\/lammps\/releases\/tag\/patch_20Nov2019. [Online; accessed 08-November-2021]"},{"key":"4214_CR50","unstructured":"Marenostrum4. https:\/\/www.bsc.es\/marenostrum\/marenostrum. [Online; accessed 03-November-2021]"}],"container-title":["The Journal of Supercomputing"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11227-021-04214-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11227-021-04214-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11227-021-04214-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,19]],"date-time":"2022-04-19T15:15:06Z","timestamp":1650381306000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s11227-021-04214-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,1,17]]},"references-count":50,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2022,5]]}},"alternative-id":["4214"],"URL":"https:\/\/doi.org\/10.1007\/s11227-021-04214-4","relation":{},"ISSN":["0920-8542","1573-0484"],"issn-type":[{"type":"print","value":"0920-8542"},{"type":"electronic","value":"1573-0484"}],"subject":[],"published":{"date-parts":[[2022,1,17]]},"assertion":[{"value":"13 November 2021","order":1,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 January 2022","order":2,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}]}}