HPC on FPGA clouds: 3D FFTs and implications for molecular dynamics

The architecture of the Microsoft Catapult II cloud places the accelerator (FPGA) as a bump-in-the-wire on the way to the network and thus promises a dramatic reduction in latency as layers of hardware and software are avoided. We demonstrate this capability with an implementation of the 3D FFT. Next we examine phased application elasticity, i.e., the use of a reduced set of nodes for some phases of an HPC application. We find that, for the FFT phase within Molecular Dynamics, such contraction is beneficial with a 13%–14% performance improvement. Turning to MD, we show how this elasticity can be integrated into the existing data transformation to hide its communication overhead and increase the performance benefit to 16%–29%.