Pandemics in Silico: Scaling Agent-Based Simulations on Realistic Social Contact Networks

Joy Kitson, Ian J. Costello, Jiangzhuo Chen, Diego Jiménez, Stefan Hoops, Henning S. Mortveit, Esteban Meneses, Jae-Seung Yeom, Madhav V. Marathe, Abhinav Bhatele

Abstract: Preventing the spread of infectious diseases requires implementing interventions at various levels of government and evaluating the potential impact and efficacy of those preemptive measures. Agent-based modeling can be used for detailed studies of the spread of such diseases in the presence of possible interventions. The computational cost of modeling epidemic diffusion through large social contact networks necessitates the use of parallel algorithms and resources in order to achieve quick turnaround times. In this work, we present Loimos, a scalable parallel framework for simulating epidemic diffusion. Loimos uses a hybrid of time-stepping and discrete event simulation to model disease spread, and is implemented on top of Charm++, an asynchronous, many-task runtime that enables over-decomposition and adaptive overlap of computation and communication. We demonstrate that Loimos is able to achieve significant speedups while scaling to large core counts. In particular, Loimos is able to simulate 200 days of a COVID19 outbreak on a digital twin of California in about 42 seconds, for an average of 4.6 billion traversed edges per second (TEPS), using 4096 cores on Perlmutter at NERSC.

External IDs:dblp:conf/ipps/KitsonCCJHMMYMB25