title: SIMENGINE: a low-cost, high-performance platform for embedded biophysical simulations.
abstract: Numerical simulations of dynamical systems are an obvious application of high-performance computing. Unfortunately, this application is underutilized because many modelers lack the technical expertise and financial resources to leverage high-performance computing hardware. Additionally, few platforms exist that can enable high-performance computing with real-time guarantees for inclusion into embedded systems--a prerequisite for working with medical devices. Here we introduce simEngine, a platform for numerical simulations of dynamical systems that reduces modelers' programming effort, delivers simulation speeds 10-100 times faster than a conventional microprocessor, and targets high-performance hardware suitable for real-time and embedded applications. This platform consists of a high-level mathematical language used to describe the simulation, a compiler/resource scheduler that generates the high-performance implementation of the simulation, and the high-performance hardware target. In this paper we present an overview of the platform, including a network-attached embedded computing device utilizing field-programmable gate arrays (FPGAs) suitable for real-time, high-performance computing. We go on to describe an example model implementation to demonstrate the platform's performance and describe how future development will improve system performance.
authors: Simatra Modeling Technologies, Atlanta, Georgia 30308, USA. info@simatratechnologies.com
authors: Randall K
authors: RK
authors: Weinstein
authors: Christopher T
authors: CT
authors: Church
authors: Carl S
authors: CS
authors: Lebsack
authors: Joshua E
authors: JE
authors: Cook
authors: Michael E
authors: ME
authors: Sorensen
mesh_terms: D000465:Algorithms; D001703:Biophysics / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D003201:Computers; D003205:Computing Methodologies; D004867:Equipment Design; D008962:Models, Theoretical; D011381:Programming Languages; D012815:Signal Processing, Computer-Assisted; D012984:Software; D013997:Time Factors