High-Performance and Scalable Agent-Based Simulation with BioDynaMo
Agent-based modeling plays an essential role in gaining insights into biology, sociology, economics, and other fields. However, many existing agent-based simulation platforms are not suitable for large-scale studies due to the low performance of the underlying simulation engines. To overcome this limitation, we present a novel high-performance simulation engine.
We identify three key challenges for which we present the following solutions. First, to maximize parallelization, we present an optimized grid to search for neighbors and parallelize the merging of thread-local results. Second, we reduce the memory access latency with a NUMA-aware agent iterator, agent sorting with a space-filling curve, and a custom heap memory allocator. Third, we present a mechanism to omit the collision force calculation under certain conditions.
Our evaluation shows an order of magnitude improvement over Biocellion, three orders of magnitude speedup over Cortex3D and NetLogo, and the ability to simulate 1.72 billion agents on a single server.
Supplementary Materials, including instructions to reproduce the results, are available at: https://doi.org/10.5281/zenodo.6463816
Mon 27 FebDisplayed time zone: Eastern Time (US & Canada) change
15:40 - 17:00 | Session 3: PracticeMain Conference at Montreal 4 Chair(s): I-Ting Angelina Lee Washington University in St. Louis, USA | ||
15:40 20mTalk | A Scalable Hybrid Total FETI Method for Massively Parallel FEM Simulations Main Conference Kehao Lin Hangzhou Dianzi University, Chunbao Zhou Computer Network Information Center, Chinese Academy of Sciences, Yan Zeng Hangzhou Dianzi University, Ningming Nie Computer Network Information Center, Chinese Academy of Sciences, Jue Wang Computer Network Information Center, Chinese Academy of Sciences, Shigang Li Beijing University of Posts and Telecommunications, Yangde Feng Computer Network Information Center, Chinese Academy of Sciences, Yangang Wang Computer Network Information Center, Chinese Academy of Sciences, Kehan Yao Hangzhou Dianzi University, Tiechui Yao Computer Network Information Center, Chinese Academy of Sciences, Jilin Zhang Hangzhou Dianzi University, Jian Wan Hangzhou Dianzi University | ||
16:00 20mTalk | Lifetime-based Optimization for Simulating Quantum Circuits on a New Sunway Supercomputer Main Conference Yaojian Chen Tsinghua University, Yong Liu National Supercomputer center in wuxi, Xinmin Shi Information Engineering University, Jiawei Song National Supercomputer center in wuxi, Xin Liu National Supercomputer center in wuxi, Lin Gan Tsinghua University, Chu Guo Information Engineering University, Haohuan Fu Tsinghua University, Jie Gao National Research Centre of Parallel Engineering and Technology, Dexun Chen National Supercomputer center in wuxi, Guangwen Yang Tsinghua University | ||
16:20 20mTalk | High-Performance Filters for GPUs Main Conference Hunter James McCoy University of Utah, Steven Hofmeyr Lawrence Berkeley National Laboratory, Katherine Yelick University of California at Berkeley & Lawrence Berkeley National Lab, Prashant Pandey University of Utah | ||
16:40 20mTalk | High-Performance and Scalable Agent-Based Simulation with BioDynaMo Main Conference Lukas Breitwieser European Organization for Nuclear Research (CERN), ETH Zurich, Ahmad Hesam Delft University of Technology, Fons Rademakers European Organization for Nuclear Research (CERN), Juan Gómez Luna ETH Zurich, Onur Mutlu ETH Zurich Pre-print Media Attached | ||