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

Motivation: Agent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulation platforms do not always take full advantage of modern hardware and often have a field-specific software design. Results: We present a novel simulation platform called BioDynaMo that alleviates both of these problems. BioDynaMo features a modular and high-performance simulation engine. We demonstrate that BioDynaMo can be used to simulate use cases in: neuroscience, oncology and epidemiology. For each use case, we validate our findings with experimental data or an analytical solution. Our performance results show that BioDynaMo performs up to three orders of magnitude faster than the state-of-the-art baselines. This improvement makes it feasible to simulate each use case with one billion agents on a single server, showcasing the potential BioDynaMo has for computational biology research.

The increased availability of High-Performance Computing resources can enable data scientists to deploy and evaluate data-driven approaches, notably in the field of deep learning, at a rapid pace. As deep neural networks become more complex and are ingesting increasingly larger datasets, it becomes unpractical to perform the training phase on single machine instances due to memory constraints, and extremely long training time. Rather than scaling up, scaling out the computing resources is a productive approach to improve performance. The paradigm of data parallelism allows us to split the training dataset into manageable chunks that can be processed in parallel. In this work, we evaluate the scaling performance of training a 3D generative adversarial network (GAN) on an IBM POWER8 cluster, equipped with 12 NVIDIA P100 GPUs. The full training duration of the GAN, including evaluation, is reduced from 20 h and 16 min on a single GPU, to 2 h and 14 min on all 12 GPUs. We achieve a scaling efficiency of 98.9% when scaling from 1 to 12 GPUs, taking only the training process into consideration.