arXiv:2608.25890cs.DCcs.CE2026-08

用RNN动态调整多GPU模拟中的负载,让细胞生长模拟更快更稳。

Scalable Multi-GPU Simulation of 3D Multicellular Growth with RNN-Based Workload Balancing

论文配图:Scalable Multi-GPU Simulation of 3D Multicellular Growth with RNN-Based Workload Balancing
图 1 · 摘自论文原文
  • 用RNN分析各GPU执行情况,自动修正分区边界以平衡负载。
  • 相比静态划分,整体不平衡率从11.3%降到3.5%,运行快9%。
  • 适合需要长时间、空间动态变化的生物组织发育模拟场景。

基于亚细胞单元模型(SEMs)的精细多细胞生长模拟能捕捉复杂组织发育过程,但其单元级交互带来巨大计算开销。本文提出一种可扩展的多GPU框架,结合GPU加速、空间分箱、域分解与负载感知分区。细胞运动、生长和分裂持续改变空间负载分布,使初始均衡的分区随时间变得低效。为此,引入基于RNN的负载平衡控制器,通过观察近期各节点执行时间和分区状态,学习对反应式边界调整规则的残差修正。控制器在具有随机负载动态的可微代理环境中离线训练,无需实测执行轨迹。评估涵盖单卡加速、多卡扩展性、控制器行为及端到端性能,对比静态划分、反应式负载均衡与传统时序预测基线。一个代表性胚胎表皮发育案例展示了该框架针对的空间-时间动态负载特性。结果表明,结合空间分箱的GPU加速使交互计算比串行CPU基准提升约三个数量级;RNN引导的负载平衡将平均全局不平衡率从静态划分的11.3%降至3.5%,端到端运行时间减少9.0%,切片迁移次数降低7.7倍,证明历史感知控制可在避免过度重分区的同时提升负载均衡性。

原文摘要 · Abstract (English)

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.

多细胞模拟RNN负载均衡多GPU加速生物发育建模

Thank you to arXiv for use of its open access interoperability. PaperDance 不是 arXiv 官方产品;中文卡片由大模型生成,请以原文为准。