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This research demonstrates a scalable multi-GPU framework for simulating complex 3D multicellular growth using subcellular element models, addressing the high computational costs inherent in such detailed biological modeling. By integrating an RNN-based load-balancing controller trained on differentiable surrogates, the system dynamically adjusts to evolving workload distributions caused by cell movement and division, significantly reducing global imbalance and runtime compared to static or reactive baselines. The approach effectively leverages GPU acceleration and history-aware control to optimize simulation performance for spatially and temporally evolving biological processes.
Scalable Multi-GPU Simulation of 3D Multicellular Growth with RNN-Based Workload Balancing
arXiv:2608.25890v1 Announce Type: cross Abstract: Detailed multicellular growth simulations based on subcellular element models (SEMs) can capture complex tissue development, but their element-level interactions impose substantial computational cost. This work presents a scalable multi-GPU framework for 3D multicellular growth simulation that combines GPU acceleration, spatial binning, domain decomposition, and workload-aware partitioning. Cell movement, growth, and division continuously reshape the spatial workload distribution, causing initially balanced partitions to become inefficient over time. To address this, we introduce an RNN-based load-balancing controller that observes recent per-rank execution times and partition states and learns residual corrections to a reactive boundary-adjustment rule. The controller is trained offline in a differentiable surrogate of the load-balancing loop with randomized workload dynamics, requiring no measured execution traces for training. We evaluate the framework in terms of single-GPU acceleration, multi-GPU computation scaling, controller-level load-balancing behavior, and end-to-end simulation performance, with comparisons against static partitioning, reactive load balancing, and conventional time-series prediction baselines. A representative embryonic epidermal development use case further demonstrates the type of spatially and temporally evolving workload targeted by the framework. In our evaluation, GPU acceleration with spatial binning accelerates the interaction computation by roughly three orders of magnitude over a serial CPU baseline. RNN-guided load balancing reduces the mean global imbalance from 11.3% under static partitioning to 3.5%, lowers end-to-end runtime by 9.0% relative to static partitioning, and reduces slice migration by 7.7x compared with the reactive baseline, showing that history-aware control can improve workload balance while avoiding unnecessary repartitioning.
Abstract:Detailed multicellular growth simulations based on subcellular element models (SEMs) can capture complex tissue development, but their element-level interactions impose substantial computational cost. This work presents a scalable multi-GPU framework for 3D multicellular growth simulation that combines GPU acceleration, spatial binning, domain decomposition, and workload-aware partitioning. Cell movement, growth, and division continuously reshape the spatial workload distribution, causing initially balanced partitions to become inefficient over time. To address this, we introduce an RNN-based load-balancing controller that observes recent per-rank execution times and partition states and learns residual corrections to a reactive boundary-adjustment rule. The controller is trained offline in a differentiable surrogate of the load-balancing loop with randomized workload dynamics, requiring no measured execution traces for training. We evaluate the framework in terms of single-GPU acceleration, multi-GPU computation scaling, controller-level load-balancing behavior, and end-to-end simulation performance, with comparisons against static partitioning, reactive load balancing, and conventional time-series prediction baselines. A representative embryonic epidermal development use case further demonstrates the type of spatially and temporally evolving workload targeted by the framework. In our evaluation, GPU acceleration with spatial binning accelerates the interaction computation by roughly three orders of magnitude over a serial CPU baseline. RNN-guided load balancing reduces the mean global imbalance from 11.3% under static partitioning to 3.5%, lowers end-to-end runtime by 9.0% relative to static partitioning, and reduces slice migration by 7.7x compared with the reactive baseline, showing that history-aware control can improve workload balance while avoiding unnecessary repartitioning.
10 pages, 9 figures. Currently under review for IEEE BigData 2026
Distributed, Parallel, and Cluster Computing (cs.DC); Computational Engineering, Finance, and Science (cs.CE); Machine Learning (cs.LG); Optimization and Control (math.OC)
arXiv:2608.25890 [cs.DC]
(or arXiv:2608.25890v1 [cs.DC] for this version)
https://doi.org/10.48550/arXiv.2608.25890 arXiv-issued DOI via DataCite (pending registration)
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