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Stream-AI-MD: streaming AI-driven adaptive molecular simulations for heterogeneous computing platforms

Authors:

Alexander Brace,

Vishal Subbiah,

Austin R. Clyde,

Venkatram Vishwanath,

Arvind RamanathanAuthors Info & Claims

PASC '21: Proceedings of the Platform for Advanced Scientific Computing Conference

Article No.: 6, Pages 1 - 13

https://doi.org/10.1145/3468267.3470578

Published: 26 August 2021 Publication History

Abstract

Emerging hardware tailored for artificial intelligence (AI) and machine learning (ML) methods provide novel means to couple them with traditional high performance computing (HPC) workflows involving molecular dynamics (MD) simulations. We propose Stream-AI-MD, a novel instance of applying deep learning methods to drive adaptive MD simulation campaigns in a streaming manner. We leverage the ability to run ensemble MD simulations on GPU clusters, while the data from atomistic MD simulations are streamed continuously to AI/ML approaches to guide the conformational search in a biophysically meaningful manner on a wafer-scale AI accelerator. We demonstrate the efficacy of Stream-AI-MD simulations for two scientific use-cases: (1) folding a small prototypical protein, namely ββα-fold (BBA) FSD-EY and (2) understanding protein-protein interaction (PPI) within the SARS-CoV-2 proteome between two proteins, nsp16 and nsp10. We show that Stream-AI-MD simulations can improve time-to-solution by ~50X for BBA protein folding. Further, we also discuss performance trade-offs involved in implementing AI-coupled HPC workflows on heterogeneous computing architectures.

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Stream-AI-MD: streaming AI-driven adaptive molecular simulations for heterogeneous computing platforms

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cover image ACM Conferences

PASC '21: Proceedings of the Platform for Advanced Scientific Computing Conference

July 2021

186 pages

ISBN:9781450385633

DOI:10.1145/3468267

Conference Chair:
Timothy Robinson
ETH Zurich / CSCS

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Published: 26 August 2021

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DOE U.S. Department of Energy

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PASC '21

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PASC '21: Platform for Advanced Scientific Computing Conference

July 5 - 9, 2021

Geneva, Switzerland

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PASC '21 Paper Acceptance Rate 17 of 33 submissions, 52%;

Overall Acceptance Rate 109 of 221 submissions, 49%

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