High-Performance and Scalable Agent-Based Simulation with BioDynaMo
We’d like to congratulate Lukas Breitwieser and co-authors Ahmad Hesam, Fons Rademakers, Juan Gómez Luna, Onur Mutlu on receiving the Best Artifact Award at PPoPP 2023 for BioDynaMo, a flexible and high-performance agent based simulation engine.
Abstract:
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, BioDynaMo.
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.
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.
Artifact Evaluation at PPoPP23:
The PPoPP 2023 Artifact Evaluation Committee (AEC) received 24 submissions in total, from the 31 accepted papers. The AEC awarded the Available badge (green) for 22 submissions, the Functional badge (pink) for 8 submissions, the Reusable badge (red) for 13 submissions, and the Reproduced badge (blue) for 17 submissions (with the Functional and Reusable badges being mutually exclusive). All 24 submissions were marked as accepted artifacts, receiving at least one badge.
Biodynamo was officially evaluated as available, reusable and reproducible.
To read more about artifact review and badging, click here
Finally, the AEC nominated 5 artifacts for the Best Artifact Award, with BioDynaMo selected as the best artifact.
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