Performance and Energy Evaluation of CoMD on Intel Xeon Phi Co-processors

Abstract

Molecular dynamics simulations are used extensively in science and engineering. Co-Design Molecular Dynamics (CoMD) is a proxy application that reflects the workload characteristics of production molecular dynamics software. In particular, CoMD is computationally intensive with 90+% of execution time spent to calculate inter-atomic force potentials. Hence, this application is an ideal candidate for acceleration with the Intel Xeon Phi because it has high theoretical computational performance with low energy consumption. In this work, the kernel computing Embedded Atom model (EAM) forces is adapted to utilize the Intel Xeon Phi acceleration. Performance and energy are measured in the experiments that vary thread affinity, thread count, problem size, node count, and the number of Xeon Phi's per node. Dynamic voltage and frequency scaling (DVFS) is used to reduce host-side power draw during Xeon Phi accelerated phases of the application. Test results are compared against the original (host-only) implementation that uses multithreading, and energy savings as high as 30% are observed.