Preventing and controlling outbreaks of infectious diseases such as pandemic influenza is a top public health priority. EpiSimdemics is an implementation of a scalable parallel algorithm to simulate the spread of cont...
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ISBN:
(纸本)9780769546766
Preventing and controlling outbreaks of infectious diseases such as pandemic influenza is a top public health priority. EpiSimdemics is an implementation of a scalable parallel algorithm to simulate the spread of contagion, including disease, fear and information, in large (10(8) individuals), realistic social contact networks using individual-based models. It also has a rich language for describing public policy and agent behavior. We describe CharmSimdemics and evaluate its performance on national scale populations. Charm++ is a machine independent parallel programming system, providing high-level mechanisms and strategies to facilitate the task of developing highly complex parallel applications. Our design includes mapping of application entities to tasks, leveraging the efficient and scalable communication, synchronization and load balancing strategies of Charm++. Our experimental results on a 768 core system show that the Charm++ version achieves up to a 4-fold increase in performance when compared to the MPI version.
Here we present the ENteric Immunity Simulator (ENISI), a modeling system for the inflammatory and regulatory immune pathways triggered by microbe-immune cell interactions in the gut. With ENISI, immunologists and inf...
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ISBN:
(纸本)9780769546759
Here we present the ENteric Immunity Simulator (ENISI), a modeling system for the inflammatory and regulatory immune pathways triggered by microbe-immune cell interactions in the gut. With ENISI, immunologists and infectious disease experts can test and generate hypotheses for enteric disease pathology and propose interventions through experimental infection of an in silico gut. ENISI is an agent based simulator, in which individual cells move through the simulated tissues, and engage in context-dependent interactions with the other cells with which they are in contact. The scale of ENISI is unprecedented in this domain, with the ability to simulate 10 7 cells for 250 simulated days on 576 cores in one and a half hours, with the potential to scale to even larger hardware and problem sizes. In this paper we describe the ENISI simulator for modeling mucosal immune responses to gastrointestinal pathogens. We then demonstrate the utility of ENISI by recreating an experimental infection of a mouse with Helicobacter pylori 26695. The results identify specific processes by which bacterial virulence factors do and do not contribute to pathogenesis associated with H. pylori strain 26695. These modeling results inform general intervention strategies by indicating immunomodulatory mechanisms such as those used in inflammatory bowel disease may be more appropriate therapeutically than directly targeting specific microbial populations through vaccination or by using antimicrobials.
Mathematical models with fractional-order differential operators are computationally expensive due to the non-local nature of these operators. In this work, we construct and investigate parallel solvers for problems d...
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Mathematical models with fractional-order differential operators are computationally expensive due to the non-local nature of these operators. In this work, we construct and investigate parallel solvers for problems described by fractional powers of elliptic operators, like fractional diffusion. Three state-of-the-art approaches are used to transform the non-local fractional-order differential problem into local partial differential equation problems formulated in a space of higher dimension. Numerical schemes and parallel algorithms are developed for all three approaches. The resulting parallel algorithms have very different properties. We investigate the weak and strong scalability of the developed parallel algorithms and compare their parallel performance.
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