Molecular dynamics proxy applications for optimizing performance of simulations under extreme conditions
Exascale performance of scientific application is a prominent goal for the scientific community and computer hardware vendors. As a result, several proxy applications for the widely used scientific codes have been developed with the purpose of testing performance, memory and power consumption issues associated with simulations at the exascale. Co-MD is a proxy application for classical Molecular Dynamics (MD) codes based on the (SPaSM) Los Alamos code. This work comprises two different but related computational aspects: performance evaluation and optimization of Co-MD (Co-Design Molecular Dynamics) for different computer architectures/execution models, and direct application of SPaSM (Scalable Parallel Short-range Molecular Dynamics) to the study of material strength employing large-scale MD simulations. Co-MD had been implemented in different computer architectures. An OpenCL implementation of Co-MD was developed starting from the MPI version, which included optimized interatomic force evaluation kernels and atom neighbor lists to eliminate exhaustive searches within 27 neighbor cells. Co-MD supports Lennard-Jones (LJ) pair-potential and Embedded Atom Method (EAM) many-body potentials for evaluating the atomic interactions. The embedded atom method is widely used in high performance computing MD simulations since it can deliver accurate results at a low computational cost. Generally, EAM potentials are in tabular format and the access pattern of these tables is random. Performance of EAM force evaluation kernels was studied by developing routines that simulate a multi-component system within Co-MD. Large-Scale molecular dynamics (MD) simulations utilizing the Los Alamos SPaSM code were carried out to investigate the strength of materials subjected to high strain rate of deformation under quasi-isentropic compression (QIC). Defective copper and tantalum crystals were chosen as prototypes due to the large body of experimental data on these systems. The atomic interactions were modelled employing (EAM) potentials. Quasi-isentropic uniaxial compression is achieved by incorporating a strain rate function in the positions and velocities equations of motion, which makes possible to quantify plastic work with temperature changes. In this new formalism the change in internal energy is exactly equal to the work done in compression. We examined the deformation mechanisms and material strength for strain rates in the 10 9 -10 12 s ranges for both Cu and Ta defective crystals. We find that the strain rate dependence of the flow stress in this strain rate regime follows a power law with an exponent close to 0.45 for Tantalum and 0.49 for Copper. Dislocations analysis was also performed on the compressed samples using DXA-CAT, which identifies different types of the dislocations and length of them. The relation between temperature change and the final dislocation density was analysed as a way of studying the mobility of the dislocations.
Abeywardhana, Jayalath Abeywardhana Mudiyanselage Madawa, "Molecular dynamics proxy applications for optimizing performance of simulations under extreme conditions" (2016). ETD Collection for University of Texas, El Paso. AAI10118808.