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Molecular Dynamics is an important tool for computational biologists,chemists, and materials scientists, consuming a sizable amount ofsupercomputing resources. Many of the investigated systems contain chargedparticles, which can only be simulated accurately using a long-range solver,such as PPPM. We extend the popular LAMMPS molecular dynamics code with animplementation of PPPM particularly suitable for the second generation IntelXeon Phi. Our main target is the optimization of computational kernels by meansof vectorization, and we observe speedups in these kernels of up to 12x. Theseimprovements carry over to LAMMPS users, with overall speedups ranging between2-3x, without requiring users to retune input parameters. Furthermore, ouroptimizations make it easier for users to determine optimal input parametersfor attaining top performance.

LAMMPS' PPPM Long-Range Solver for the Second Generation Xeon Phi