In molecular dynamics (MD) simulations, calculations of potentials and their derivatives by coordinate, i.e., forces, in a pairwise additive manner such as the Lennard–Jones interactions and a short-range part of the Coulombic interactions form the main part of arithmetic operations. It is essential to achieve high thread-level parallelization efficiency of these pairwise additive calculations of potentials and forces to use current supercomputers with many-core architectures effectively. In this paper, we propose four new thread-level parallelization algorithms for the pairwise additive potential and force calculations. We implement the four codes in a MD calculation code based on the fast multipole method. Performance benchmarks were taken on the FX100 supercomputer and Intel Xeon Phi coprocessor. The code succeeds in achieving high thread-level parallelization efficiency with 32 threads on the FX100 and up to 60 threads on the Xeon Phi.
CITATION STYLE
Andoh, Y., Suzuki, S., Ohshima, S., Sakashita, T., Ogino, M., Katagiri, T., … Okazaki, S. (2018). A thread-level parallelization of pairwise additive potential and force calculations suitable for current many-core architectures. Journal of Supercomputing, 74(6), 2449–2469. https://doi.org/10.1007/s11227-018-2272-2
Mendeley helps you to discover research relevant for your work.