Workshops Archive

DDStore: Distributed Data Store for Scalable Training of Graph Neural Networks on Large Atomistic Modeling Datasets

Workshop: Workshop on Machine Learning with Graphs in High Performance Computing Environments

Authors: Jong Youl Choi (Oak Ridge National Laboratory (ORNL)); Massimiliano Lupo Pasini, Pei Zhang, Kshitij Mehta, and Frank Liu (Oak Ridge National Laboratory); and Jonghyun Bae and Khaled Ibrahim (Lawrence Berkeley National Laboratory (LBNL))

Abstract: Graph neural networks (GNNs) are a class of Deep Learning models used in designing atomistic materials for effective screening of large chemical spaces. To ensure robust prediction, GNN models must be trained on large volumes of atomistic modeling data on leadership class supercomputing facilities. Even with the advent of modern architectures that consist of multiple storage layers that include node-local NVMe devices in addition to device memory for caching large datasets, extreme-scale model training faces I/O challenges at scale.

We present DDStore, an in-memory distributed data store designed for GNN training on large-scale graph data. DDStore provides a hierarchical, distributed, data caching technique that combines data chunking, replication, low-latency random access, and high throughput communication. DDStore achieves near-linear scaling for training a GNN model using up to 1000 GPUs on the Summit and Perlmutter supercomputers, and reaches up to a 6.15x reduction in GNN training time compared to state-of-the-art methodologies.

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