The International Conference for High Performance Computing, Networking, Storage and Analysis
A High Performance C++ Generic Benchmark for Computational Epidemiology.
Authors: Aniket Pugaonkar (Virginia Polytechnic Institute and State University), Sandeep Gupta (Virginia Polytechnic Institute and State University), Keith R. Bisset (Virginia Polytechnic Institute and State University), Madhav V. Marathe (Virginia Polytechnic Institute and State University)
Abstract: We design a benchmark consisting of several kernels which capture the essential compute, communication, and, data access patterns of high performance contagion-diffusion simulations used in computational networked epidemiology. The goal is to (a) derive alternative implementations for computing the contagion by combining different implementation of the kernels, and (b) evaluate which combination of implementation, run-time, and hardware is most effective in running large scale contagion diffusion simulations.
Our proposed benchmark is designed using C++ generic programming primitives and lifting sequential strategies for parallel computations. Together these lead to a succinct description of the benchmark and significant code re-use when deriving strategies for new hardware. These aspects are crucial for an effective benchmark because the potential combination of hardware and runtimes are growing rapidly thereby making infeasible to write optimized strategy for the complete contagion diffusion from ground up for each compute system.