The Hodgkin-Huxley (HH) neuron is one of the most biophysically-meaningful models used in computational neuroscience today. Ironically, the model's high experimental value is offset by its disproportional computational complexity. To such an extent that neuroscientists have either resorted to simpler models, losing precious neuron detail, or to using high-performance computing systems, to gain acceleration, for complex models. However, multicore/multinode CPU-based systems have proven too slow while FPGA-based ones have proven too time-consuming to (re)deploy to. Clearly, a solution that bridges user friendliness and high speedups is necessary. This paper presents flexHH, a flexible FPGA library implementing five popular, highly parameterizable variants of the HH neuron model. flexHH is the first crucial step towards making FPGA-based simulations of compute-intensive neural models available to neuroscientists without the debilitating penalty of re-engineering and re-synthesis. Through flexHH, the user can instantiate custom models and immediately take advantage of the acceleration without the mediation of an engineer, which has proven to be a major inhibitor to full adoption of FPGAs in neuroscience labs. In terms of performance, flexHH achieves speedups between 8 × - 20 × compared to sequential-C implementations, while only a small drop in real-time capabilities is observed when compared to hardcoded FPGA-based versions of the models tested. @en

IntroductionIn-silico simulations are a powerful tool in modern neuroscience for enhancing our understanding of complex brain systems at various physiological levels. To model biologically realistic and detailed systems, an ideal simulation platform must possess: (1) high performance and performance scalability, (2) flexibility, and (3) ease of use for non-technical users. However, most existing platforms and libraries do not meet all three criteria, particularly for complex models such as the Hodgkin-Huxley (HH) model or for complex neuron-connectivity modeling such as gap junctions.MethodsThis work introduces ExaFlexHH, an exascale-ready, flexible library for simulating HH models on multi-FPGA platforms. Utilizing FPGA-based Data-Flow Engines (DFEs) and the dataflow programming paradigm, ExaFlexHH addresses all three requirements. The library is also parameterizable and compliant with NeuroML, a prominent brain-description language in computational neuroscience. We demonstrate the performance scalability of the platform by implementing a highly demanding extended-Hodgkin-Huxley (eHH) model of the Inferior Olive using ExaFlexHH.ResultsModel simulation results show linear scalability for unconnected networks and near-linear scalability for networks with complex synaptic plasticity, with a 1.99 × performance increase using two FPGAs compared to a single FPGA simulation, and 7.96 × when using eight FPGAs in a scalable ring topology. Notably, our results also reveal consistent performance efficiency in GFLOPS per watt, further facilitating exascale-ready computing speeds and pushing the boundaries of future brain-simulation platforms.DiscussionThe ExaFlexHH library shows superior resource efficiency, quantified in FLOPS per hardware resources, benchmarked against other competitive FPGA-based brain simulation implementations.@en

Computational neuroscience aims to investigate and explain the behaviour and functions of neural structures, through mathematical models. Due to the models' complexity, they can only be explored through computer simulation. Modern research in this field is increasingly adopting large networks of neurons, and diverse, physiologically-detailed neuron models, based on the extended Hodgkin-Huxley (eHH) formalism. However, existing eHH simulators either support highly specific neuron models, or they provide low computational performance, making model exploration costly in time and effort. This work introduces a simulator for extended Hodgkin-Huxley neural networks, on multiprocessing platforms. This simulator supports a broad range of neuron models, while still providing high performance. Simulator performance is evaluated against varying neuron complexity parameters, network size and density, and thread-level parallelism. Results indicate performance is within existing literature for single-model eHH codes, and scales well for large CPU core counts. Ultimately, this application combines model flexibility with high performance, and can serve as a new tool in computational neuroscience.@en

Computational neuroscience aims to investigate and explain the behaviour and functions of neural structures, through mathematical models. Due to the models' complexity, they can only be explored through computer simulation. Modern research in this field is increasingly adopting large networks of neurons, and diverse, physiologically-detailed neuron models, based on the extended Hodgkin-Huxley (eHH) formalism. However, existing eHH simulators either support highly specific neuron models, or they provide low computational performance, making model exploration costly in time and effort. This work introduces a simulator for extended Hodgkin-Huxley neural networks, on multiprocessing platforms. This simulator supports a broad range of neuron models, while still providing high performance. Simulator performance is evaluated against varying neuron complexity parameters, network size and density, and thread-level parallelism. Results indicate performance is within existing literature for single-model eHH codes, and scales well for large CPU core counts. Ultimately, this application combines model flexibility with high performance, and can serve as a new tool in computational neuroscience.@en

Computational neuroscience uses models to study the brain. The Hodgkin-Huxley (HH) model, and its extensions, is one of the most powerful, biophysically meaningful models currently used. The high experimental value of the (extended) Hodgkin-Huxley (eHH) models comes at the cost of steep computational requirements. Consequently, for larger networks, neuroscientists either opt for simpler models, losing neuro-computational features, or use high-performance computing systems. The eHH models can be efficiently implemented as a dataflow application on a FPGA-based architecture. The state-of-the-art FPGA-based implementations have proven to be time-consuming because of the long-duration synthesis requirements. We have developed flexHH, a flexible hardware library, compatible with a widely used neuron-model description format, implementing five FPGA-accelerated and parameterizable variants of eHH models (standard HH with optional extensions: custom ion-gates, gap junctions, and/or multiple cell compartments). Therefore, flexHH is a crucial step towards high-flexibility and high-performance FPGA-based simulations, eschewing the penalty of re-engineering and re-synthesis, dismissing the need for an engineer. In terms of performance, flexHH achieves a speedup of 1,065x against NEURON, the simulator standard in computational neuroscience, and speedups between 8x-20x against sequential C. Furthermore, flexHH is faster per simulation step compared to other HPC technologies, provides 65% or better performance density (in FLOPS/LUT) compared to related works, and only shows a marginal performance drop in real-time simulations.@en

Computational neuroscience uses models to study the brain. The Hodgkin-Huxley (HH) model, and its extensions, is one of the most powerful, biophysically meaningful models currently used. The high experimental value of the (extended) Hodgkin-Huxley (eHH) models comes at the cost of steep computational requirements. Consequently, for larger networks, neuroscientists either opt for simpler models, losing neuro-computational features, or use high-performance computing systems. The eHH models can be efficiently implemented as a dataflow application on a FPGA-based architecture. The state-of-the-art FPGA-based implementations have proven to be time-consuming because of the long-duration synthesis requirements. We have developed flexHH, a flexible hardware library, compatible with a widely used neuron-model description format, implementing five FPGA-accelerated and parameterizable variants of eHH models (standard HH with optional extensions: custom ion-gates, gap junctions, and/or multiple cell compartments). Therefore, flexHH is a crucial step towards high-flexibility and high-performance FPGA-based simulations, eschewing the penalty of re-engineering and re-synthesis, dismissing the need for an engineer. In terms of performance, flexHH achieves a speedup of 1,065x against NEURON, the simulator standard in computational neuroscience, and speedups between 8x-20x against sequential C. Furthermore, flexHH is faster per simulation step compared to other HPC technologies, provides 65% or better performance density (in FLOPS/LUT) compared to related works, and only shows a marginal performance drop in real-time simulations.@en

Computational neuroscience uses models to study the brain. The Hodgkin-Huxley (HH) model, and its extensions, is one of the most powerful, biophysically meaningful models currently used. The high experimental value of the (extended) Hodgkin-Huxley (eHH) models comes at the cost of steep computational requirements. Consequently, for larger networks, neuroscientists either opt for simpler models, losing neuro-computational features, or use high-performance computing systems. The eHH models can be efficiently implemented as a dataflow application on a FPGA-based architecture. The state-of-the-art FPGA-based implementations have proven to be time-consuming because of the long-duration synthesis requirements. We have developed flexHH, a flexible hardware library, compatible with a widely used neuron-model description format, implementing five FPGA-accelerated and parameterizable variants of eHH models (standard HH with optional extensions: custom ion-gates, gap junctions, and/or multiple cell compartments). Therefore, flexHH is a crucial step towards high-flexibility and high-performance FPGA-based simulations, eschewing the penalty of re-engineering and re-synthesis, dismissing the need for an engineer. In terms of performance, flexHH achieves a speedup of 1,065x against NEURON, the simulator standard in computational neuroscience, and speedups between 8x-20x against sequential C. Furthermore, flexHH is faster per simulation step compared to other HPC technologies, provides 65% or better performance density (in FLOPS/LUT) compared to related works, and only shows a marginal performance drop in real-time simulations.@en

Computational neuroscience uses models to study the brain. The Hodgkin-Huxley (HH) model, and its extensions, is one of the most powerful, biophysically meaningful models currently used. The high experimental value of the (extended) Hodgkin-Huxley (eHH) models comes at the cost of steep computational requirements. Consequently, for larger networks, neuroscientists either opt for simpler models, losing neuro-computational features, or use high-performance computing systems. The eHH models can be efficiently implemented as a dataflow application on a FPGA-based architecture. The state-of-the-art FPGA-based implementations have proven to be time-consuming because of the long-duration synthesis requirements. We have developed flexHH, a flexible hardware library, compatible with a widely used neuron-model description format, implementing five FPGA-accelerated and parameterizable variants of eHH models (standard HH with optional extensions: custom ion-gates, gap junctions, and/or multiple cell compartments). Therefore, flexHH is a crucial step towards high-flexibility and high-performance FPGA-based simulations, eschewing the penalty of re-engineering and re-synthesis, dismissing the need for an engineer. In terms of performance, flexHH achieves a speedup of 1,065x against NEURON, the simulator standard in computational neuroscience, and speedups between 8x-20x against sequential C. Furthermore, flexHH is faster per simulation step compared to other HPC technologies, provides 65% or better performance density (in FLOPS/LUT) compared to related works, and only shows a marginal performance drop in real-time simulations.@en

Computational neuroscience uses models to study the brain. The Hodgkin-Huxley (HH) model, and its extensions, is one of the most powerful, biophysically meaningful models currently used. The high experimental value of the (extended) Hodgkin-Huxley (eHH) models comes at the cost of steep computational requirements. Consequently, for larger networks, neuroscientists either opt for simpler models, losing neuro-computational features, or use high-performance computing systems. The eHH models can be efficiently implemented as a dataflow application on a FPGA-based architecture. The state-of-the-art FPGA-based implementations have proven to be time-consuming because of the long-duration synthesis requirements. We have developed flexHH, a flexible hardware library, compatible with a widely used neuron-model description format, implementing five FPGA-accelerated and parameterizable variants of eHH models (standard HH with optional extensions: custom ion-gates, gap junctions, and/or multiple cell compartments). Therefore, flexHH is a crucial step towards high-flexibility and high-performance FPGA-based simulations, eschewing the penalty of re-engineering and re-synthesis, dismissing the need for an engineer. In terms of performance, flexHH achieves a speedup of 1,065x against NEURON, the simulator standard in computational neuroscience, and speedups between 8x-20x against sequential C. Furthermore, flexHH is faster per simulation step compared to other HPC technologies, provides 65% or better performance density (in FLOPS/LUT) compared to related works, and only shows a marginal performance drop in real-time simulations.@en

Computational neuroscience uses models to study the brain. The Hodgkin-Huxley (HH) model, and its extensions, is one of the most powerful, biophysically meaningful models currently used. The high experimental value of the (extended) Hodgkin-Huxley (eHH) models comes at the cost of steep computational requirements. Consequently, for larger networks, neuroscientists either opt for simpler models, losing neuro-computational features, or use high-performance computing systems. The eHH models can be efficiently implemented as a dataflow application on a FPGA-based architecture. The state-of-the-art FPGA-based implementations have proven to be time-consuming because of the long-duration synthesis requirements. We have developed flexHH, a flexible hardware library, compatible with a widely used neuron-model description format, implementing five FPGA-accelerated and parameterizable variants of eHH models (standard HH with optional extensions: custom ion-gates, gap junctions, and/or multiple cell compartments). Therefore, flexHH is a crucial step towards high-flexibility and high-performance FPGA-based simulations, eschewing the penalty of re-engineering and re-synthesis, dismissing the need for an engineer. In terms of performance, flexHH achieves a speedup of 1,065x against NEURON, the simulator standard in computational neuroscience, and speedups between 8x-20x against sequential C. Furthermore, flexHH is faster per simulation step compared to other HPC technologies, provides 65% or better performance density (in FLOPS/LUT) compared to related works, and only shows a marginal performance drop in real-time simulations.@en

Ordinary Differential Equations (ODEs) are widely used in many high-performance computing applications. However, contemporary processors generally provide limited throughput for these kinds of calculations. A high-performance hardware accelerator has been developed for speeding-up the solution of ODEs. The hardware accelerator has been developed both for single and double floating-point precision types and a design-space exploration has been performed in terms of performance and hardware resources. The hardware accelerator has been mapped to an FPGA board and connected through PCIe to a typical processor. The performance evaluation shows that the proposed scheme can achieve up to 14x speedup compared to a reference, single-core CPU solution.@en