A 32x32x32, spatially distributed 3D FFT in four microseconds on Anton

Anton, a massively parallel special-purpose machine for molecular dynamics simulations, performs a 32 × 32 × 32 FFT in 3.7 microseconds and a 64 × 64 × 64 FFT in 13.3 microseconds on a configuration with 512 nodes-an order of magnitude faster than all other FFT implementations of which we are aware. Achieving this FFT performance requires a coordinated combination of computation and communication techniques that leverage Anton´s underlying hardware mechanisms. Most significantly, Anton´s communication subsystem provides over 300 gigabits per second of bandwidth per node, message latency in the hundreds of nanoseconds, and support for word-level writes and single-ended communication. In addition, Anton´s general-purpose computation system incorporates primitives that support the efficient parallelization of small 1D FFTs. Although Anton was designed specifically for molecular dynamics simulations, a number of the hardware primitives and software implementation techniques described in this paper may also be applicable to the acceleration of FFTs on general-purpose high-performance machines.