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Reliable evaluations of geotechnical hazards like landslides and debris flow require accurate simulation of granular flow dynamics. Traditional numerical methods can simulate the complex behaviors of such flows that involve solid-like to fluid-like transitions, but they are computationally intractable when simulating large-scale systems. Surrogate models based on statistical or machine learning methods are a viable alternative, but they are typically empirical and rely on a confined set of parameters in evaluating associated risks. Due to their permutation-dependent learning, conventional machine learning models require an unreasonably large amount of training data for building generalizable surrogate models. We employ a graph neural network (GNN), a novel deep learning technique, to develop a GNN-based simulator (GNS) for granular flows to address these issues. Graphs represent the state of granular flows and interactions, like the exchange of energy and momentum between grains, and GNN learns the local interaction law. GNS takes the current state of the granular flow and estimates the next state using Euler explicit integration. We train GNS on a limited set of granular flow trajectories and evaluate its performance in a three-dimensional granular column collapse domain. GNS successfully reproduces the overall behaviors of column collapses with various aspect ratios that were not encountered during training. The computation speed of GNS outperforms high-fidelity numerical simulators by 300 times.