{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,25]],"date-time":"2026-01-25T05:54:21Z","timestamp":1769320461354,"version":"3.49.0"},"reference-count":29,"publisher":"SAGE Publications","issue":"5","license":[{"start":{"date-parts":[[2019,1,6]],"date-time":"2019-01-06T00:00:00Z","timestamp":1546732800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"funder":[{"name":"Task-based load balancing and auto-tuning in particle simulations","award":["01IH16008"],"award-info":[{"award-number":["01IH16008"]}]}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["The International Journal of High Performance Computing Applications"],"published-print":{"date-parts":[[2019,9]]},"abstract":"<jats:p> Significant improvements are presented for the molecular dynamics code ls1 mardyn \u2014 a linked cell-based code for simulating a large number of small, rigid molecules with application areas in chemical engineering. The changes consist of a redesign of the SIMD vectorization via wrappers, MPI improvements and a software redesign to allow memory-efficient execution with the production trunk to increase portability and extensibility. Two novel, memory-efficient OpenMP schemes for the linked cell-based force calculation are presented, which are able to retain Newton\u2019s third law optimization. Comparisons to well-optimized Verlet list-based codes, such as LAMMPS and GROMACS, demonstrate the viability of the linked cell-based approach. The present version of ls1 mardyn is used to run simulations on entire supercomputers, maximizing the number of sampled atoms. Compared to the preceding version of ls1 mardyn on the entire set of 9216 nodes of SuperMUC, Phase 1, 27% more atoms are simulated. Weak scaling performance is increased by up to 40% and strong scaling performance by up to more than 220%. On Hazel Hen, strong scaling efficiency of up to 81% and 189 billion molecule updates per second is attained, when scaling from 8 to 7168 nodes. Moreover, a total of 20 trillion atoms is simulated at up to 88% weak scaling efficiency running at up to 1.33 PFLOPS. This represents a fivefold increase in terms of the number of atoms simulated to date. <\/jats:p>","DOI":"10.1177\/1094342018819741","type":"journal-article","created":{"date-parts":[[2019,1,7]],"date-time":"2019-01-07T05:35:55Z","timestamp":1546839355000},"page":"838-854","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":57,"title":["TweTriS: Twenty trillion-atom simulation"],"prefix":"10.1177","volume":"33","author":[{"given":"Nikola","family":"Tchipev","sequence":"first","affiliation":[{"name":"Department of Informatics, Technical University of Munich, Garching, Germany"}]},{"given":"Steffen","family":"Seckler","sequence":"additional","affiliation":[{"name":"Department of Informatics, Technical University of Munich, Garching, Germany"}]},{"given":"Matthias","family":"Heinen","sequence":"additional","affiliation":[{"name":"Thermodynamics and Process Engineering, Technical University Berlin, Berlin, Germany"}]},{"given":"Jadran","family":"Vrabec","sequence":"additional","affiliation":[{"name":"Thermodynamics and Process Engineering, Technical University Berlin, Berlin, Germany"}]},{"given":"Fabio","family":"Gratl","sequence":"additional","affiliation":[{"name":"Department of Informatics, Technical University of Munich, Garching, Germany"}]},{"given":"Martin","family":"Horsch","sequence":"additional","affiliation":[{"name":"Engineering Department, American University of Iraq, Sulaimani (AUIS), Sulaimani, Iraq"},{"name":"Scientific Computing Department, STFC Daresbury Laboratory, Warrington, UK"}]},{"given":"Martin","family":"Bernreuther","sequence":"additional","affiliation":[{"name":"High Performance Computing Center Stuttgart (HLRS), Stuttgart, Germany"}]},{"given":"Colin W","family":"Glass","sequence":"additional","affiliation":[{"name":"Mechanical Engineering, Helmut Schmidt University, Hamburg, Germany"}]},{"given":"Christoph","family":"Niethammer","sequence":"additional","affiliation":[{"name":"High Performance Computing Center Stuttgart (HLRS), Stuttgart, Germany"}]},{"given":"Nicolay","family":"Hammer","sequence":"additional","affiliation":[{"name":"Leibniz Supercomputing Centre, Garching, Germany"}]},{"given":"Bernd","family":"Krischok","sequence":"additional","affiliation":[{"name":"High Performance Computing Center Stuttgart (HLRS), Stuttgart, Germany"}]},{"given":"Michael","family":"Resch","sequence":"additional","affiliation":[{"name":"High Performance Computing Center Stuttgart (HLRS), Stuttgart, Germany"},{"name":"Institute for High-Performance Computing, University of Stuttgart, Stuttgart, Germany"}]},{"given":"Dieter","family":"Kranzlm\u00fcller","sequence":"additional","affiliation":[{"name":"Leibniz Supercomputing Centre, Garching, Germany"}]},{"given":"Hans","family":"Hasse","sequence":"additional","affiliation":[{"name":"Laboratory of Engineering Thermodynamics (LTD), TU Kaiserslautern, Kaiserslautern, Germany"}]},{"given":"Hans-Joachim","family":"Bungartz","sequence":"additional","affiliation":[{"name":"Department of Informatics, Technical University of Munich, Garching, Germany"},{"name":"Leibniz Supercomputing Centre, Garching, Germany"}]},{"given":"Philipp","family":"Neumann","sequence":"additional","affiliation":[{"name":"Department of Informatics, Universit\u00e4t Hamburg, Hamburg, Germany"}]}],"member":"179","published-online":{"date-parts":[[2019,1,6]]},"reference":[{"key":"bibr1-1094342018819741","doi-asserted-by":"publisher","DOI":"10.1063\/1.2121687"},{"key":"bibr2-1094342018819741","doi-asserted-by":"publisher","DOI":"10.1016\/j.softx.2015.06.001"},{"key":"bibr3-1094342018819741","volume-title":"Computer Simulation of Liquids","author":"Allen M","year":"1989"},{"key":"bibr4-1094342018819741","doi-asserted-by":"publisher","DOI":"10.1080\/00268977300102101"},{"key":"bibr5-1094342018819741","doi-asserted-by":"publisher","DOI":"10.1016\/j.cpc.2010.12.021"},{"key":"bibr6-1094342018819741","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-biophys-042910-155245"},{"key":"bibr7-1094342018819741","doi-asserted-by":"publisher","DOI":"10.1039\/C5CP03415A"},{"key":"bibr8-1094342018819741","unstructured":"Eckhardt W (2014) Efficient HPC Implementations for Large-Scale Molecular Simulation in Process Engineering. 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