Past Event: Babuška Forum

High-Performance & Automatic Computing -- Fast & portable code for complex molecular dynamics simulations

Paolo Bientinesi and Markus Hoehnerbach, Aachen Institute for Advanced Study in Computational Engineering Science, Aachen, Germany

Abstract

With the increase in complexity and heterogeneity of computing architectures, it is especially challenging and time consuming to devise algorithms that exploit the available computational power. Typically, scientific computing practitioners either invest in months-long cycles of software development --favoring computer efficiency at the expense of productivity and portability-- or resort to high-level languages --in favor of productivity, but entirely disregarding computer performance--. The High-Performance and Automatic Computing group aims to bridge the disconnect between application experts and computing architectures by providing tools that enable both productivity and performance. In this talk, we first give a short overview of our activities in the domanins of linear algebra and tensor operations, and then dive into the specific case of molecular dynamics (MD), an extremely popular technique to simulate the evolution of large systems of particles. We present a domain specific compiler that takes as input the mathematical description of the law that regulates how the particles attract each other, and returns optimized code. While code generation from an abstract representation of the target problem is a common technique for the solution of PDEs (e.g., the Fenics project), it is still largely unexplored in MD. We discuss different optimizations, both with respect to performance and portability, demonstrating efficiency on par to what achieved by human experts.