Modern neuroscience employs in silico experimentation on ever-increasing and more detailed neural networks. The high modeling detail goes hand in hand with the need for high model reproducibility, reusability and transparency. Besides, the size of the models and the long timescales under study mandate the use of a simulation system with high computational performance, so as to provide an acceptable time to result. In this work, we present EDEN (Extensible Dynamics Engine for Networks), a new general-purpose, NeuroML-based neural simulator that achieves both high model flexibility and high computational performance, through an innovative model-analysis and code-generation technique. The simulator runs NeuroML-v2 models directly, eliminating the need for users to learn yet another simulator-specific, model-specification language. EDEN's functional correctness and computational performance were assessed through NeuroML models available on the NeuroML-DB and Open Source Brain model repositories. In qualitative experiments, the results produced by EDEN were verified against the established NEURON simulator, for a wide range of models. At the same time, computational-performance benchmarks reveal that EDEN runs from one to nearly two orders-of-magnitude faster than NEURON on a typical desktop computer, and does so without additional effort from the user. Finally, and without added user effort, EDEN has been built from scratch to scale seamlessly over multiple CPUs and across computer clusters, when available.@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.

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Mathematical models with varying degrees of complexity have been proposed and simulated in an attempt to represent the intricate mechanisms of the human neuron. One of the most biochemically realistic and analytical models, based on the Hodgkin–Huxley (HH) model, has been selected for study in this paper. In order to satisfy the model's computational demands, we present a simulator implemented on Intel Xeon Phi Knights Landing manycore processors. This high-performance platform features an x86-based architecture, allowing our implementation to be portable to other common manycore processing machines. This is reinforced by the fact that Phi adopts the popular OpenMP and MPI programming models. The simulator performance is evaluated when calculating neuronal networks of varying sizes, density and network connectivity maps. The evaluation leads to an analysis of the neuronal synaptic patterns and their impact on performance when tackling this type of workload on a multinode system. It will be shown that the simulator can calculate 100 ms of simulated brain activity for up to 2 millions of biophysically-accurate neurons and 2 billion neuronal synapses within one minute of execution time. This level of performance renders the application an efficient solution for large-scale detailed model simulation.

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Emerging cloud applications like machine learning, AI, big data analytics and scientific computing require highperformance computing systems that can sustain the increased amount of data processing without consuming excessive power. To this end, many cloud operators have started deploying hardware accelerators, like GPUs and FPGAs, to increase the performance of computationally intensive tasks. However, increased performance, comes at a higher cost of increased programming complexity for utilizing these accelerators. VINEYARD has developed a versatile framework that allows the seamless deployment and utilization of heterogeneous accelerators in the cloud without increasing the programming complexity while offering the flexibility of software packages. This paper presents the main components that have been developed in the VINEYARD framework and focuses on BrainFrame, the neurocomputing case that demonstrates the new framework's value. BrainFrame not only accelerates neuronal simulations but also has an architecture that allows easy access to neuroscientists, hiding the system complexity, and enabling a modular integration of new accelerated simulators.

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Brain modeling has been presenting significant challenges to the world of high-performance computing (HPC) over the years. The field of computational neuroscience has been developing a demand for physiologically plausible neuron models, that feature increased complexity and thus, require greater computational power. We explore Intel’s newest generation of Xeon Phi computing platforms, named Knights Landing (KNL), as a way to match the need for processing power and as an upgrade over the previous generation of Xeon Phi models, the Knights Corner (KNC). Our neuron simulator of choice features a Hodgkin-Huxley-based (HH) model which has been ported on both generations of Xeon Phi platforms and aggressively draws on both platforms’ computational assets. The application uses the OpenMP interface for efficient parallelization and the Xeon Phi’s vectorization buffers for Single-Instruction Multiple Data (SIMD) processing. In this study we offer insight into the efficiency with which the application utilizes the assets of the two Xeon Phi generations and we evaluate the merits of utilizing the KNL over its predecessor. In our case, an out-of-the-box transition on Knights Landing, offers on average 2.4x speed up while consuming 48% less energy than KNC.

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Objective. The advent of high-performance computing (HPC) in recent years has led to its increasing use in brain studies through computational models. The scale and complexity of such models are constantly increasing, leading to challenging computational requirements. Even though modern HPC platforms can often deal with such challenges, the vast diversity of the modeling field does not permit for a homogeneous acceleration platform to effectively address the complete array of modeling requirements. Approach. In this paper we propose and build BrainFrame, a heterogeneous acceleration platform that incorporates three distinct acceleration technologies, an Intel Xeon-Phi CPU, a NVidia GP-GPU and a Maxeler Dataflow Engine. The PyNN software framework is also integrated into the platform. As a challenging proof of concept, we analyze the performance of BrainFrame on different experiment instances of a state-of-the-art neuron model, representing the inferior-olivary nucleus using a biophysically-meaningful, extended Hodgkin-Huxley representation. The model instances take into account not only the neuronal-network dimensions but also different network-connectivity densities, which can drastically affect the workload's performance characteristics. Main results. The combined use of different HPC technologies demonstrates that BrainFrame is better able to cope with the modeling diversity encountered in realistic experiments while at the same time running on significantly lower energy budgets. Our performance analysis clearly shows that the model directly affects performance and all three technologies are required to cope with all the model use cases. Significance. The BrainFrame framework is designed to transparently configure and select the appropriate back-end accelerator technology for use per simulation run. The PyNN integration provides a familiar bridge to the vast number of models already available. Additionally, it gives a clear roadmap for extending the platform support beyond the proof of concept, with improved usability and directly useful features to the computational-neuroscience community, paving the way for wider adoption.

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