ITR: Asynchronous Execution for Scalable Simulation of Cell Physiology

University Of California-San Diego, La Jolla CA

Investigators

Abstract

This project will develop algorithms, run time support, and software infrastructure for scalable biological modeling will be developed, based on MCell, a general Monte Carlo simulator of cellular microphysiology, and Tarragon, a run-time environment for optimized asynchronous parallel computing. This project matches the underlying asynchronous dynamics of Monte Carlo simulations to a corresponding model of execution and the ability to alter scheduling accordingly. Thus, the outcome will be novel programming methodology and a run-time library for large-scale biological simulations, and, more generally, increased knowledge about software techniques in support of scheduling and latency-tolerant formulation.