On-the-fly clustering for exascale molecular dynamics simulations.

For the weak scaling results, we maintain a constant load per core. As we increase the number of cores, we also increase the number of atoms, targeting approximately 160,000 atoms per core. Although the scalability of our existing system is not ideal, the scalability of the molecular dynamics is nearly perfect, indicating that communication is not a significant issue.

In our analysis, while the performance is not as strong, the bottleneck we identified—reducing the information from a single molecular interaction—is manageable. Our primary objective is to conduct an analysis that does not excessively increase computation time. We must ensure that the time required for analysis does not exceed that of a single step of molecular dynamics. The accompanying slide presents the ratio of analysis time to one step of dynamics.