SC13 Home > SC13 Schedule > SC13 Presentation - A Scalable Parallel Algorithm for Dynamic Range-Limited N-Tuple Computation in Many-Body Molecular Dynamics Simulation

SCHEDULE: NOV 16-22, 2013

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A Scalable Parallel Algorithm for Dynamic Range-Limited N-Tuple Computation in Many-Body Molecular Dynamics Simulation

SESSION: Physical Frontiers


TIME: 4:00PM - 4:30PM

SESSION CHAIR: Richard Vuduc

AUTHOR(S):Manaschai Kunaseth, Rajiv K. Kalia, Aiichiro Nakano, Ken-ichi Nomura, Priya Vashishta


Recent advancements in reactive molecular dynamics (MD) simulations based on many-body interatomic potentials necessitate efficient dynamic n-tuple computation, where a set of atomic n-tuples within a given spatial range is constructed at every time step. Here, we develop a computation-pattern algebraic framework to mathematically formulate general n-tuple computation. Based on translation/reflection-invariant properties of computation patterns within this framework, we design a shift-collapse (SC) algorithm for cell-based parallel MD. Theoretical analysis quantifies the compact n-tuple search space and small communication cost of SC-MD for arbitrary n, which are reduced to those in best pair-computation approaches (e.g. eighth-shell method) for n = 2. Benchmark tests show that SC-MD outperforms our production MD code at the finest grain, with 9.7- and 5.1-fold speedups on Intel-Xeon and BlueGene/Q clusters. SC-MD also exhibits excellent strong scalability.

Chair/Author Details:

Richard Vuduc (Chair) - Georgia Institute of Technology

Manaschai Kunaseth - University of Southern California

Rajiv K. Kalia - University of Southern California

Aiichiro Nakano - University of Southern California

Ken-ichi Nomura - University of Southern California

Priya Vashishta - University of Southern California

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The full paper can be found in the ACM Digital Library