{"dffb2a37e29a0efe71208a49226516a6c.niethammer":{"DOI":"10.1007/978-3-642-38750-0_1","ISBN":"978-3-642-38750-0","ISSN":"","URL":"https://doi.org/10.1007/978-3-642-38750-0_1","abstract":"Anticipating large-scale molecular dynamics simulations (MD) in nano-fluidics, we conduct performance and scalability studies of an optimized version of the code ls1 mardyn. We present our implementation requiring only 32 Bytes per molecule, which allows us to run the, to our knowledge, largest MD simulation to date. Our optimizations tailored to the Intel Sandy Bridge processor are explained, including vectorization as well as shared-memory parallelization to make use of Hyperthreading. Finally we present results for weak and strong scaling experiments on up to 146016 Cores of SuperMUC at the Leibniz Supercomputing Centre, achieving a speed-up of 133k times which corresponds to an absolute performance of 591.2 TFLOPS.","annote":"","author":[{"family":"Eckhardt","given":"Wolfgang"},{"family":"Heinecke","given":"Alexander"},{"family":"Bader","given":"Reinhold"},{"family":"Brehm","given":"Matthias"},{"family":"Hammer","given":"Nicolay"},{"family":"Huber","given":"Herbert"},{"family":"Kleinhenz","given":"Hans-Georg"},{"family":"Vrabec","given":"Jadran"},{"family":"Hasse","given":"Hans"},{"family":"Horsch","given":"Martin"},{"family":"Bernreuther","given":"Martin"},{"family":"Glass","given":"Colin W."},{"family":"Niethammer","given":"Christoph"},{"family":"Bode","given":"Arndt"},{"family":"Bungartz","given":"Hans-Joachim"}],"citation-label":"Eckhardt2013","collection-editor":[{"family":"Kunkel","given":"Julian Martin"},{"family":"Ludwig","given":"Thomas"},{"family":"Meuer","given":"Hans Werner"}],"collection-title":"","container-author":[{"family":"Kunkel","given":"Julian Martin"},{"family":"Ludwig","given":"Thomas"},{"family":"Meuer","given":"Hans Werner"}],"container-title":"Supercomputing: 28th International Supercomputing Conference, ISC 2013, Leipzig, Germany, June 16-20, 2013. Proceedings","documents":[],"edition":"","editor":[{"family":"Kunkel","given":"Julian Martin"},{"family":"Ludwig","given":"Thomas"},{"family":"Meuer","given":"Hans Werner"}],"event-date":{"date-parts":[["2013"]],"literal":"2013"},"event-place":"Berlin, Heidelberg","id":"dffb2a37e29a0efe71208a49226516a6c.niethammer","interhash":"a0dbaf1fbdff3c8d5401f74e8d6a7aad","intrahash":"dffb2a37e29a0efe71208a49226516a6","issue":"","issued":{"date-parts":[["2013"]],"literal":"2013"},"keyword":"dynamics highly molecular parallel programming scalable simulation simulations vectorization","misc":{"isbn":"978-3-642-38750-0","doi":"10.1007/978-3-642-38750-0_1"},"note":"","number":"","number-of-pages":"11","page":"1--12","page-first":"1","publisher":"Springer Berlin Heidelberg","publisher-place":"Berlin, Heidelberg","status":"","title":"591 TFLOPS Multi-trillion Particles Simulation on SuperMUC","type":"chapter","username":"c.niethammer","version":"","volume":""},"cdcc9c23758fe8aad2fd902ccc79b611c.niethammer":{"DOI":"10.1021/ct500169q","ISBN":"","ISSN":"","URL":"/brokenurl#         http://dx.doi.org/10.1021/ct500169q","abstract":"","annote":"","author":[{"family":"Niethammer","given":"Christoph"},{"family":"Becker","given":"Stefan"},{"family":"Bernreuther","given":"Martin"},{"family":"Buchholz","given":"Martin"},{"family":"Eckhardt","given":"Wolfgang"},{"family":"Heinecke","given":"Alexander"},{"family":"Werth","given":"Stephan"},{"family":"Bungartz","given":"Hans-Joachim"},{"family":"Glass","given":"Colin W."},{"family":"Hasse","given":"Hans"},{"family":"Vrabec","given":"Jadran"},{"family":"Horsch","given":"Martin"}],"citation-label":"niethammer2014mardyn","collection-editor":[],"collection-title":"","container-author":[],"container-title":"Journal of Chemical Theory and Computation","documents":[],"edition":"","editor":[],"event-date":{"date-parts":[["2014"]],"literal":"2014"},"event-place":"","id":"cdcc9c23758fe8aad2fd902ccc79b611c.niethammer","interhash":"e55164114995631b666027f82d58105e","intrahash":"cdcc9c23758fe8aad2fd902ccc79b611","issue":"10","issued":{"date-parts":[["2014"]],"literal":"2014"},"keyword":"MD hlrs myown parallel program programming simulation spmt","misc":{"doi":"10.1021/ct500169q","eprint":"http://dx.doi.org/10.1021/ct500169q"},"note":"","number":"10","number-of-pages":"9","page":"4455-4464","page-first":"4455","publisher":"","publisher-place":"","status":"","title":"ls1 mardyn: The Massively Parallel Molecular Dynamics Code for Large Systems","type":"article-journal","username":"c.niethammer","version":"","volume":"10"}}