Detailed brain modeling has been presenting significant challenges to the world of high-performance computing (HPC), posing computational problems that can benefit from modern hardware-acceleration technologies. We explore the capacity of GPUs for simulating large-scale neuronal networks based on the Adaptive Exponential neuron-model, which is widely used in the neuroscientific community. Our GPU-powered simulator acts as a benchmark to evaluate the strengths and limitations of modern GPUs, as well as to explore their scaling properties when simulating large neural networks. This work presents an optimized GPU implementation that outperforms a reference multicore implementation by 50x, whereas utilizing a dual-GPU configuration can deliver a speedup of 90x for networks of 20,000 fully interconnected AdEx neurons.

Brain modeling has been receiving significant attention over the years, both for its neuroscientific potential and for its challenges in the context of high-performance computing. The development of physiologically plausible neuron models comes at the cost of increased complexity. In this work, we have selected a highly computationally demanding model of the Inferior-Olivary Nucleus (InfOli) based on the Hodgkin-Huxley (HH) neuron model. This brain region, functionally coupled with the cerebellum, is of vital importance for motor skills and time-sensitive cognitive functions. The computing fabric of choice is an Intel Xeon/Xeon Phi system, which is a typical node of modern computing infrastructure. The target application is parallelized with various combinations of MPI and OpenMP and performance is measured on the target platform. The different implementations are compared and the best one is chosen. Further optimization of this implementation is presented in detail. Its behaviour is then examined when scaling up to neuron populations representative of realistic, human Inferior-Olivary neuronal networks. The evaluation's results highlight the importance of examining a network's size and density before choosing the best platform for its simulation. All the parallelization and vectorization options presented in the current paper are available on a public repository for further examination.

In-vivo and in-vitro experiments are routinely used in neuroscience to unravel brain functionality. Although they are a powerful experimentation tool, they are also time-consuming and, often, restrictive. Computational neuroscience attempts to solve this by using biologically-plausible and biophysically-meaningful neuron models, most prominent among which are the conductance-based models. Their computational complexity calls for accelerator-based computing to mount large-scale or real-time neuroscientific experiments. In this paper, we analyze and draw conclusions on the class of conductance models by using a representative modeling application of the inferior olive (InfOli), an important part of the olivocerebellar brain circuit. We conduct an extensive profiling session to identify the computational and data-transfer requirements of the application under various realistic use cases. The application is, then, ported onto two acceleration nodes, an Intel Xeon Phi and a Maxeler Vectis Data Flow Engine (DFE). We evaluate the performance scalability and resource requirements of the InfOli application on the two target platforms. The analysis of InfOli, which is a real-life neuroscientific application, can serve as a useful guide for porting a wide range of similar workloads on platforms like the Xeon Phi or the Maxeler DFEs. As accelerators are increasingly populating High-Performance Computing (HPC) infrastructure, the current paper provides useful insight on how to optimally use such nodes to run complex and relevant neuron modeling workloads.