André Merzky

Liubov Kurafeeva, Ryan Hartung, Benjamin Carter et al.

Emerging cyber-physical systems increasingly require low-latency inference from streaming sensor data while maintaining models that reflect complex and evolving physical processes. In many domains, however, model updates depend on high-fidelity simulations and training executed on remote high-performance computing (HPC) systems under batch scheduling. This creates a fundamental mismatch between the responsiveness required at the edge and the cost, throughput, and availability of simulation-driven model updates. We present RBF (Reverse Backfill), a hybrid edge-HPC learning and inference architecture that integrates low-latency edge inference with asynchronous, simulation-driven model improvement. RBF targets simulation-bounded settings in which model updates are constrained by simulation throughput and HPC scheduling delays, and reinterprets HPC backfilling by using opportunistic computation to improve model accuracy rather than system utilization. RBF decouples inference from simulation and training by deploying lightweight surrogate models at the edge while incorporating improved models asynchronously as they become available. The architecture supports pluggable surrogate models and orchestrates computation across heterogeneous infrastructure spanning edge devices, private 5G, cloud, and HPC resources. We instantiate RBF using a real-world digital agriculture deployment that couples edge sensing with computational fluid dynamics (CFD) simulations to infer airflow patterns in a large agricultural screenhouse. Our evaluation characterizes end-to-end system behavior under realistic constraints, quantifying simulation latency, training cost, inference throughput, and the impact of delayed model updates on prediction accuracy. Results demonstrate that RBF enables continuous, low-latency inference while improving model fidelity over time despite delayed and irregular model updates.

Austin Clyde, Thomas Brettin, Alexander Partin et al.

We propose a benchmark to study surrogate model accuracy for protein-ligand docking. We share a dataset consisting of 200 million 3D complex structures and 2D structure scores across a consistent set of 13 million "in-stock" molecules over 15 receptors, or binding sites, across the SARS-CoV-2 proteome. Our work shows surrogate docking models have six orders of magnitude more throughput than standard docking protocols on the same supercomputer node types. We demonstrate the power of high-speed surrogate models by running each target against 1 billion molecules in under a day (50k predictions per GPU seconds). We showcase a workflow for docking utilizing surrogate ML models as a pre-filter. Our workflow is ten times faster at screening a library of compounds than the standard technique, with an error rate less than 0.01\% of detecting the underlying best scoring 0.1\% of compounds. Our analysis of the speedup explains that to screen more molecules under a docking paradigm, another order of magnitude speedup must come from model accuracy rather than computing speed (which, if increased, will not anymore alter our throughput to screen molecules). We believe this is strong evidence for the community to begin focusing on improving the accuracy of surrogate models to improve the ability to screen massive compound libraries 100x or even 1000x faster than current techniques.

Agastya P. Bhati, Shunzhou Wan, Dario Alfè et al.

The race to meet the challenges of the global pandemic has served as a reminder that the existing drug discovery process is expensive, inefficient and slow. There is a major bottleneck screening the vast number of potential small molecules to shortlist lead compounds for antiviral drug development. New opportunities to accelerate drug discovery lie at the interface between machine learning methods, in this case developed for linear accelerators, and physics-based methods. The two in silico methods, each have their own advantages and limitations which, interestingly, complement each other. Here, we present an innovative infrastructural development that combines both approaches to accelerate drug discovery. The scale of the potential resulting workflow is such that it is dependent on supercomputing to achieve extremely high throughput. We have demonstrated the viability of this workflow for the study of inhibitors for four COVID-19 target proteins and our ability to perform the required large-scale calculations to identify lead antiviral compounds through repurposing on a variety of supercomputers.

Vivek Balasubramanian, Shantenu Jha, Andre Merzky et al.

RADICAL-Cybertools (RCT) are a set of software systems that serve as middleware to develop efficient and effective tools for scientific computing. Specifically, RCT enable executing many-task applications at extreme scale and on a variety of computing infrastructures. RCT are building blocks, designed to work as stand-alone systems, integrated among themselves or integrated with third-party systems. RCT enables innovative science in multiple domains, including but not limited to biophysics, climate science and particle physics, consuming hundreds of millions of core hours. This paper provides an overview of RCT systems, their impact, and the architectural principles and software engineering underlying RCT

Matteo Turilli, Andre Merzky, Vivek Balasubramanian et al.

We suggest there is a need for a fresh perspective on the design and development of workflow systems and argue for a building blocks approach. We outline a description of this approach and define the properties of software building blocks. We discuss RADICAL-Cybertools as one implementation of the building blocks concept, showing how they have been designed and developed in accordance with this approach. Four case studies are presented, covering a dozen science problems. We discuss how RADICAL-Cybertools have been used to develop new workflow systems capabilities and integrated to enhance existing ones, illustrating the applicability and potential of software building blocks. In doing so, we have begun an investigation of an alternative approach to thinking about the design and implementation of workflow systems.