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.