Accelerating Molecular Dynamic Simulation on the Cell processor and PlayStation 3

Edgar Luttmann, Daniel L. Ensign, Vishal Vaidyanathan, Mike Houston, Noam Rimon, Jeppe Øland, Guha Jayachandran, Mark Friedrichs, Vijay S. Pande. Journal of Computational Chemistry (2009)

SUMMARY. In this paper, we detail how we were able to get great speed increases for Folding@home (and actually certain molecular dynamics calculations in general) on the PS3. This is our first paper using the PS3, laying out the “how does it work,” with a follow up paper in the works describing the results obtained in FAH from PS3 clients. It is also worth noting that this paper is a collaboration between FAH team members (Luttmann, Ensign, Vaidyanathan, Houston [now at AMD], Jayachandran, Friedrichs, and Pande) with developers at Sony (Rimon and Øland and their coworkers).

ABSTRACT. Implementation of molecular dynamics (MD) calculations on novel architectures will vastly increase its power to calculate the physical properties of complex systems. Herein, we detail algorithmic advances developed to accelerate MD simulations on the Cell processor, a commodity processor found in PlayStation 3 (PS3). In particular, we discuss issues regarding memory access versus computation and the types of calculations which are best suited for streaming processors such as the Cell, focusing on implicit solvation models. We conclude with a comparison of improved performance on the PS3′s Cell processor over more traditional processors.