Design of a Greedy Algorithm for Non-Uniform Space Partitioning across Homogeneous FPGAs in Molecular Simulation
Faezeh Sadat Mozneb, Kambiz Rahbar, Parvaneh Asghari, Parand Akhlaghi · Journal of Artificial Intelligence Applications and Innovations · 2024
Efficient partitioning of the atomic space among parallel FPGAs is crucial for accelerating molecular simulations. Existing research has primarily focused on uniform partitioning, assuming a homogeneous distribution of atoms. However, in scenarios with non-uniform atomic distributions, these approaches may lead to suboptimal performance. This study investigates the impact of non-uniform atom distributions on molecular simulation performance across parallel FPGAs. We propose a novel space partitioning scheme that optimizes the distribution of atomic space among FPGAs, taking into account the spatial heterogeneity of atoms. Our evaluation demonstrates that the proposed scheme consistently outperforms uniform partitioning in terms of simulation speed across various spatial dimensions and atom counts, particularly in scenarios with non-uniform atom distributions.