Simulative Analysis of a Multidimensional Torus-Based Reconfigurable Cluster for Molecular Dynamics

Novo‐G#: a multidimensional torus‐based reconfigurable cluster for molecular dynamics

“…Traditionally, the router block is the bottleneck in such network architectures and much research has been carried out on optimizing on‐chip network architectures. In our previous work on Novo‐G# performance prediction , we observed that the internal bandwidth provided and latency incurred by the network architecture have the greatest effects on execution time. Distributed architectures like the ring network in scale linearly with the width and number of ports but exhibit high latency because packets may need to traverse half the length of the ring.…”

“…In order to understand the behavior of Novo‐G# at scale, we created a simulation model of Novo‐G# based on our previous research into modeling the behavior of 3D FFT on the Anton machine . VisualSim , a commercial discrete‐event simulation and modeling tool, was used because of its simple graphical interface and available library of basic blocks with which to construct models.…”

“…‡ ‡ Extension of Conference Paper: An earlier version of this work featured a conceptual design of the Novo‐G# network and a performance model based on Anton . Since that publication, an initial deployment of 32 nodes of Novo‐G# has been completed.…”

“…Finally, through simulation studies, we show that this system at scale performs better than specialized systems like Anton and outperforms established CPU-based clusters like Blue Gene/Q by an order of magnitude for the 3D FFT kernel, with greater flexibility and lower costs. ‡ Extension of Conference Paper: An earlier version of this work featured a conceptual design of the Novo-G# network and a performance model based on Anton [1]. Since that publication, an initial deployment of 32 nodes of Novo-G# has been completed.…”

“…Data cube for a 1616 16 point FFT running on a 4 4 4 system. Data distribution is shown for a single node at Cartesian coordinates(1,1,0). FFT, fast Fourier transform.…”