BMapper: A Scalable and Efficient Framework for Brain Simulations Acceleration on Supercomputers

Brain simulation is an inherently highly parallel and time-sensitive task, requiring the simulation of billions of neurons and their interactions within just a few milliseconds. With the growing availability of brain data from biological research, more realistic and detailed simulations are becoming feasible. However, this also poses unprecedented challenges for parallel computing due to the extreme sparsity and heterogeneity of the emerging workloads. Efficient deployment of such workloads on modern HPC systems is critical to overcoming these challenges. We propose BMapper, a deployment framework that enables efficient parallel execution of brain simulations on supercomputers. BMapper comprises three synergistic components: BPartitioning, which introduces a novel multi-dimensional hybrid partitioning strategy to balance workloads across GPUs and reduce inter-GPU spike traffic; BPlacement, which applies deterministic spectral partitioning to minimize inter-server communication; and BRelaying, which identifies lightly loaded GPUs to assist the top-k heavily loaded ones by relaying spike traffic. These components work together to balance loads and minimize communication overhead, enabling high-speed simulation of large-scale brain models. BMapper has been deployed to simulate up to 10 billion neurons on a 1000-GPU supercomputer, achieving 25.15%-47.48% faster execution than state-of-the-art methods.