High speed calculation for solid molecular dynamics on vector processors

Itakura, Kenichi; Yokokawa, Mitsuo; Shimizu, Futoshi; Kimizuka, Hajime*; Kaburaki, Hideo

Joho Shori Gakkai Kenkyu Hokoku 2001-HPC-88, p.67 - 72, 2001/10

he Earth Simulator which is under development has 640 processor nodes and its peak performance is 40 Tflop/s. In this study, we have evaluated performance of solid molecular dynamics simulation on an SMP node of the Earth Simulator. In molecular dynamics simulation, each particle is influenced by all particles within a cut-off region and the representation of these pairs of particles is made by a matrix. Two matrix representations, compressed row form and jagged diagonal form, are considered for vectorization. The jagged diagonal form is better than the compressed row form in performance on a vector processor for the force calculation of every pairs, because the vector length of the former is longer than that of the latter. However, computational cost for converting the normal matrix form to the jagged diagonal form is quite expensive and the total performance in using the jagged diagonal form is low. Speedup by parallelization with the compressed row form is 2.4 to 2.7 with 8 vector processors.