Work

On-the-fly clustering for exascale molecular dynamics simulations

Year: 2024

Type: article

Abstract: Computational resources have experienced exponential growth in the last decades enabling the simulation of complex physical problems at the cost of a massive increase in data storage . This is especially true for N-body simulations now reaching billions or trillions particles in certain cases. To overcome the drawbacks of data storage on disk for post-processing purposes, on-the-fly analysis has gained momentum but still represents a challenge in both its implementation and efficiency without impacting the simulation engine performances. This work provides a new in-situ procedure for features detection in massive N-body simulations, leveraging state-of-the-art techniques from various fields. Based on a discrete-to-continuum paradigm shift, particles and their respective physical quantities are projected onto a 3D regular grid before applying image analysis algorithms to group voxels based on specific user-defined criteria. A significant extension to the hybrid parallelism of connected component analysis within the image processing community is also introduced in the present study. Traditionally operating in shared memory parallelism , this extension now incorporates both distributed and shared memory approaches. The implementation is carried out within the exaStamp classical Molecular Dynamics code, a variant of the open-source exaNBody platform [39] . This adaptation allows for the on-the-fly analysis of multi-billion atoms samples with at most a 1.3% overhead. In addition, the entire framework is benchmarked up to 32768 cores. The applicability of the present approach is demonstrated on the case of a spall fracture in a tantalum sample as well as high velocity impact of a tin droplets on a rigid surface.

Source: Computer Physics Communications

DOI: 10.1016/j.cpc.2024.109427