Overcoming the Scalability Challenges of Epidemic Simulations on Blue Waters

Modeling dynamical systems represents an important application class covering a wide range of disciplines including but not limited to biology, chemistry, finance, national security, and health care. Such applications typically involve large-scale, irregular graph processing, which makes them difficult to scale due to the evolutionary nature of their workload, irregular communication and load imbalance. EpiSimdemics is such an application simulating epidemic diffusion in extremely large and realistic social contact networks. It implements a graph-based system that captures dynamics among co-evolving entities. This paper presents an implementation of EpiSimdemics in Charm++ that enables future research by social, biological and computational scientists at unprecedented data and system scales. We present new methods for application-specific processing of graph data and demonstrate the effectiveness of these methods on a Cray XE6, specifically NCSA’s Blue Waters system.

@inproceedings{yeom:ipdps2014,
  author = {Yeom, Jae-Seung and Bhatele, Abhinav and Bisset, Keith R. and Bohm, Eric and Gupta, Abhishek and Kale, Laxmikant V. and Marathe, Madhav and Nikolopoulos, Dimitrios S. and Schulz, Martin and Wesolowski, Lukasz},
  title = {Overcoming the Scalability Challenges of Epidemic Simulations on Blue Waters},
  booktitle = {Proceedings of the IEEE International Parallel \& Distributed Processing Symposium},
  series = {IPDPS '14},
  year = {2014},
  month = may,
  publisher = {IEEE Computer Society},
}