학술논문

Scaling the Leading Accuracy of Deep Equivariant Models to Biomolecular Simulations of Realistic Size
Document Type
Conference
Source
SC23: International Conference for High Performance Computing, Networking, Storage and Analysis High Performance Computing, Networking, Storage and Analysis, SC23: International Conference for. :1-12 Nov, 2023
Subject
Communication, Networking and Broadcast Technologies
Computing and Processing
Proteins
Analytical models
Computational modeling
Biological system modeling
Scalability
High performance computing
Neural networks
Language
ISSN
2167-4337
Abstract
This work brings the leading accuracy, sample efficiency, and robustness of deep equivariant neural networks to the extreme computational scale. This is achieved through a combination of innovative model architecture, massive parallelization, and models and implementations optimized for efficient GPU utilization. The resulting Allegro architecture bridges the accuracy-speed tradeoff of atomistic simulations and enables description of dynamics in structures of unprecedented complexity at quantum fidelity. To illustrate the scalability of Allegro, we perform nanoseconds-long stable simulations of protein dynamics and scale up to a 44-million atom structure of a complete, all-atom, explicitly solvated HIV capsid on the Perlmutter supercomputer. We demonstrate excellent strong scaling up to 100 million atoms and 70% weak scaling to 5120 A100 GPUs.