Impact of multicores on large-scale molecular dynamics simulations

SR Alam and PK Agarwal and SS Hampton and H Ong and JS Vetter, 2008 IEEE INTERNATIONAL SYMPOSIUM ON PARALLEL & DISTRIBUTED PROCESSING, VOLS 1-8, 544-550 (2008).

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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