Paper Citing NAMD - Abstract
Kunaseth, Manaschai; Kalia, Rajiv K.; Nakano, Aiichiro; Nomura, Ken-ichi; Vashishta, Priya
A Scalable Parallel Algorithm for Dynamic Range-Limited n-Tuple Computation in Many-Body Molecular Dynamics Simulation
2013 INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS (SC), DOI:10.1145/2503210.2503235, 2013
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.
