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Parallel and Distributed Processing Symposium, International (2008)
Miami, FL, USA
Apr. 14, 2008 to Apr. 18, 2008
ISBN: 978-1-4244-1693-6
pp: 1-7
Jeffrey S. Vetter , Computer Science and Mathematics Division, Oak Ridge National Laboratory, TN 37831, USA
Hong Ong , Computer Science and Mathematics Division, Oak Ridge National Laboratory, TN 37831, USA
Sadaf R. Alam , Computer Science and Mathematics Division, Oak Ridge National Laboratory, TN 37831, USA
Pratul K. Agarwal , Computer Science and Mathematics Division, Oak Ridge National Laboratory, TN 37831, USA
Scott S. Hampton , Computer Science and Mathematics Division, Oak Ridge National Laboratory, TN 37831, USA
ABSTRACT
Processing nodes of the Cray XT and IBM Blue Gene Massively Parallel Processing (MPP) systems are composed of multiple execution units, sharing memory and network subsystems. These multicore processors offer greater computational power, but may be hindered by resource contention. In order to understand and avoid such situations, we investigate the impact of resource contention on three scalable molecular dynamics suites: AMBER (PMEMD module), LAMMPS, and NAMD. The results reveal the factors that can inhibit scaling and performance efficiency on emerging multicore processors.
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CITATION
Jeffrey S. Vetter, Hong Ong, Sadaf R. Alam, Pratul K. Agarwal, Scott S. Hampton, "Impact of multicores on large-scale molecular dynamics simulations", Parallel and Distributed Processing Symposium, International, vol. 00, no. , pp. 1-7, 2008, doi:10.1109/IPDPS.2008.4536181
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