Keith R. Bisset
Xizhou Feng
Madhav V. Marathe
ABSTRACT
Large scale realistic epidemic simulations have recently become an increasingly important application of high-performance computing. We propose a parallel algorithm, EpiFast, based on a novel interpretation of the stochastic disease propagation in a contact network. We implement it using a master-slave computation model which allows scalability on distributed memory systems.
EpiFast runs extremely fast for realistic simulations that involve: (i) large populations consisting of millions of individuals and their heterogeneous details, (ii) dynamic interactions between the disease propagation, the individual behaviors, and the exogenous interventions, as well as (iii) large number of replicated runs necessary for statistically sound estimates about the stochastic epidemic evolution. We find that EpiFast runs several magnitude faster than another comparable simulation tool while delivering similar results.
EpiFast has been tested on commodity clusters as well as SGI shared memory machines. For a fixed experiment, if given more computing resources, it scales automatically and runs faster. Finally, EpiFast has been used as the major simulation engine in real studies with rather sophisticated settings to evaluate various dynamic interventions and to provide decision support for public health policy makers.
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Index Terms
- EpiFast: a fast algorithm for large scale realistic epidemic simulations on distributed memory systems
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