RAPTOR: Ravenous Throughput Computing

TL;DR

RAPTOR is a high-throughput task execution system on HPC platforms that significantly advances computational drug discovery by enabling large-scale virtual screening with unprecedented speed and efficiency.

Contribution

It introduces RAPTOR, a novel HPC task overlay that achieves higher throughput and resource utilization for heterogeneous tasks, supporting large-scale virtual screening for COVID-19 drug discovery.

Findings

Achieved 144 million docking hits per hour.

Screened approximately 10^11 ligands.

Delivered twice the throughput of previous methods.

Abstract

We describe the design, implementation and performance of the RADICAL-Pilot task overlay (RAPTOR). RAPTOR enables the execution of heterogeneous tasks -- i.e., functions and executables with arbitrary duration -- on HPC platforms, providing high throughput and high resource utilization. RAPTOR supports the high throughput virtual screening requirements of DOE's National Virtual Biotechnology Laboratory effort to find therapeutic solutions for COVID-19. RAPTOR has been used on $>8000$ compute nodes to sustain 144M/hour docking hits, and to screen $\sim$10$^{11}$ ligands. To the best of our knowledge, both the throughput rate and aggregated number of executed tasks are a factor of two greater than previously reported in literature. RAPTOR represents important progress towards improvement of computational drug discovery, in terms of size of libraries screened, and for the possibility of generating training data fast enough to serve the last generation of docking surrogate models.